2012 Citations

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Authors & Works cited in this section (citations below):

Banavar, Jayanth & A. Maritan. “Life on earth: the role of proteins
Bardone, Emanuele. Seeking Chances: From Biased Rationality to Distributed Cognition
Barrett, Louise. Beyond the Brain: How Body and Environment Shape Animal and Human
Bateson, Patrick & Gluckman. Plasticity, Robustness, Development and Evolution
Bejan, Adrian & J.P. Zane. Design in Nature: How the Constructal Law Governs Evolution
Berthoz, Alain. “The Human Brain ‘Projects’ upon the World, Simplifying Principles and Rules
Bonner, John Tyler. Why Size Matters: From Bacteria
Boyd, Robert & P. Richerson. “Culture and the evolution of human cooperation.
Brussow, Harald. “The not so universal tree of life or the place of viruses in the living world
Calcott, Brett & K. Sterelny, Eds. 2011. The Major Transitions In Evolution Revisited
Calcott, Brett. “Alternative Patterns of Explanation for Major Transitions
Camazine, S., et al. Self-Organization in Biological Systems
Chapura, Mitch. “Scale, causality, complexity and emergence: rethinking scale’s ontological
Cloke, Paul & R. Johnston. “Deconstructing Human Geography’s Binaries.
Coen, Enrico. Cells to civilizations: The Principles of Change that Shape Life
Conrad, Michael. “The geometry of evolution.
Cornish-Bowden, Athel. The Pursuit of Perfection: Aspects of Biochemical Evolution
Costantini, Marcello et al. “Where does an object trigger an action?
Davidovich, Chen, et al. “The evolving ribosome: from non-coded peptide
Davies, Paul Sheldon. Norms of Nature: Naturalism and the Nature of Functions
Davies, Paul. “Fitness and the cosmic environment
Davis, T., M. Riley, Shockley & Cummins-Sebree. “Perceiving affordances for joint actions.
De Rosnay, Joel. The Symbiotic Man: A New Understanding of the Organization of Life
Deacon, Terrence. Incomplete Nature: How Mind Emerged from Matter
Denton, Michael. “Protein-based life and protein folds
Diettrich, Olaf. “The biological boundary conditions for our classical physical world view
Drack, Manfred & O. Wolkenhauer. “System approaches of Weiss and Bertalanffy
Dubreuil, Benoit. Human Evolution and The Origins of Hierarchies: The State of Nature
Dunn, Rob. The Wild Life of Our Bodies: Predators, Parasites,
Egbert, M., X. Barandiaran & E. Di Paolo. “Behavioral Metabolution: The Adaptive
Egel, Richard. “Integrative Perspectives: In Quest of a Coherent Framework for Origins
Elder-Vass, Dave. “Luhmann and Emergentism: Competing Paradigms for Social Systems
Fagot-Largeault, Anne. “Anthropological Physiology: von Uexkuell, Portmann, Buytendijk
Foley, Robert & C. Gamble. “The ecology of social transitions in human evolution.”
Fox Keller, Evelyn. “Ecosystems, Organisms, and Machines.”
Gardner, Andy & K. Foster. “The Evolution and Ecology of Cooperation – History
Gergen, Kenneth. Relational Being: Beyond Self and Community.
Gontier, Nathalie. “Universal symbiogenesis: An alternative to universal selectionist accounts
Gontier, Nathalie. “Introduction to evolutionary epistemology, language and culture
Goodman, Nelson. “Words, Works, Worlds.”
Gross, Matthias. Ignorance and Surprise: Science, Society, and Ecological
Guzman, Marcelo. “Abiotic Photosynthesis: From Prebiotic Chemistry to Metabolism.
Harold, Franklin. The Way of the Cell: Molecules, Organisms and the Order of Life
Heinze, Juergen. “Social Plasticity: Ecology, Genetics, and the Structure of Ant Societies
Hermann, Heinz. From Biology to Sociopolitics: Conceptual Continuity in Complex
Hoffmann, Peter. Life’s Ratchet: How Molecular Machines
Hoffmeyer, Jesper. “Biology is Immature Biosemiotics.
Hordijk, Wim, Hein & Steel. “Autocatalytic Sets and the Origin of Life
Huang, Sui. “The molecular and mathematical basis of Waddington’s epigenetic landscape
Hutchins, Edwin & Hazlehurst. “How to invent a shared lexicon: the emergence
Ingold, Tim. “Against Human Nature.”
Ingold, Tim. “Point, Line and Counterpoint: From Environment to Fluid Space
Ingold, Tim. The Perception of the Environment: Essays in livelihood, dwelling and skill
Isbell, Lynne. The Fruit, the Tree, and the Serpent: Why We See So Well
Ivanitskii, G.R. “21st century: what is life from the perspective of physics?”
Jackson, Ross. Occupy World Street: A Global Roadmap for Radical Economic
Kendon, Adam. “Language’s matrix.”
Klitgord, N. & D. Segre. “Ecosystems biology of microbial metabolism
Knoblich, G. & Sebanz. “Evolving intentions for social interaction: from entrainment to joint
Koonin, Eugene. “The Origin at 150: is a new evolutionary synthesis in sight?
Korb, Judith. “The Ecology of Social Evolution in Termites
Kull, Kalevi, Deacon, Emmeche, Hoffmeyer & Stjernfelt. “Theses on Biosemiotics:
Laland, Kevin & M. O’Brien. “Niche Construction Theory and Archaeology.”
Laland, Kevin, J. Odling-Smee & S. Gilbert. “EvoDevo and Niche Construction: Building
Lane, Nick. Life Ascending: The Ten Great Inventions
Lane, Nick. Power, Sex, Suicide: Mitochondria
Lee, Richard. “The Modern World-System: Its Structures, Its Geoculture, Its Crisis and
Levins, Richard. Quoted in Hahlweg, K. 1989. “A systems view of evolution and evolutionary
Lewontin, Richard. The Triple Helix: Gene, Organism, and Environment
Logan, Robert. “The extended mind model of the origin of language and culture
Lyon, Pamela. “To Be or Not To Be: Where is Self-Preservation in Evolutionary Theory?
Malafouris, Lambros. “The brain-artefact interface (BAI): a challenge for archaeology
Marsh, Kerry et al. “Toward a radically embodied, embedded social
McGhee, George. Convergent Evolution: Limited Forms Most Beautiful
Melendez-Hevia, E. et al. “From prebiotic chemistry to cellular metabolism
Minelli, Alessandro. 2009. Perspectives in Animal Phylogeny & Evolution.
Mirolli, Marco & D. Parisi. “Language as a Cognitive Tool
Miyamoto, Yuri, Nisbett & Masuda. “Culture and the Physical Environment
Moore, Bruce. “The evolution of learning.”
Morowitz, H., V. Srinivasan & E. Smith. “Ligand Field Theory and the Origin of Life
Morris, Simon Conway. “The predictability of evolution: glimpses into a post-Darwinian world
Morris, Simon C. “Tuning in the frequencies of life.
Mulkidjanian, Armen. “Energetics of the First Life.”
Mulkidjanian, A & M. Galperin. “Physico-Chemical and Evolutionary Constraints
Nagel, Thomas. Mind and Cosmos: Why the Materialist Neo-Darwinian Conception
Nisbett, R., Peng, Choi & Norenzayan. “Culture and Systems of Thought: Holistic Versus
Nolfi, Stefano. “Behaviour as a Complex Adaptive System:
Odling-Smee, F. John, Kevin Laland & Marcus Feldman. Niche Construction: The Neglected
Odling-Smee, John & K. Laland. “Cultural niche construction: evolution’s cradle of language.”
Paperin, Greg, Green & Sadedin. “Dual-phase evolution in complex adaptive systems.
Pascal, Robert & Boiteau. “Energy flows, metabolism and translation.
Pattee, Howard & K. Kull. “Between Physics and Semiotics.
Pearl, Judea. Causality: Models, Reasoning, and Inference
Peterson, Townsend et al. Ecological Niches and Geographic Distributions
Pezzulo, G. & H. Dindo. 2011. “What should I do next? Using shared representations
Piersma, Theunis & van Gils. The Flexible Phenotype: A Body-Centred Integration
Prien, Bernd, J. Skudlarek & S. Stolte. “The Role of Declarations in the Construction of Social
Pross, Addy. What is Life? How Chemistry Becomes Biology.
Putnam, Hilary. “Is There Still Anything to Say about Reality and Truth?”
Ragir, Sonia & S. Savage-Rumbaugh. “Playing with meaning: normative function and structure
Rainey, Paul & BH. Kerr. “Conflicts among Levels of Selection as Fuel for the Evolution
Ramirez-Goicoechea, Eugenia. “Cognition, evolution, and sociality
Rawls, Anne W. Epistemology and Practice: Durkheim’s The Elementary Forms of Religious
Rayner, Alan. Degrees of Freedom: Living in Dynamic Boundaries
Robbins, Paul. “Political Ecology: A Critical Introduction
Rosslenbroich, Bernd. “Outline of a concept for organismic systems
Sapp, Jan. “On the Origin of Symbiosis.
Sassen, Saskia. Territory, Authority, Rights: From Medieval to Global Assemblages
Searle, John. “The Basic Reality and the Human Reality.”
Simpson, Carl. “How Many Levels Are There?
Smil, Vaclav. The Earth’s Biosphere: Evolution, Dynamics, and Change
Smith, Eric & H. Morowitz. “Framing the question of fine-tuning for intermediary metabolism
Smolin, Lee. The Life of the Cosmos
Srinivasan, V. & H. Morowitz. “What is an autotroph?
Stallins, J. Anthony. “Scale, causality, and the new organism-environment interaction.
Steels, Luc. “Is sociality a crucial prerequisite for the emergence of language?”
Sterelny, Kim. “Evolvability Reconsidered
Sterelny, Kim. The Evolved Apprentice: How Evolution Made Humans Unique
Stout, Dietrich & T. Chaminade. “Making Tools and Making Sense
Strohman, Richard. “Epigenesis and Complexity: The coming Kuhnian revolution in biology.”
Tennie, Claudio, Call & Tomasello. “Ratcheting up the ratchet: on the evolution of cumulative
Thompson, Travis. “Relations among functional systems in behavior analysis
Thompson, John. The Geographic Mosaic of Coevolution.
Trewavas, Anthony. “Aspects of Plant Intelligence: Convergence and Evolution
Turner, J. Scott. The Tinkerer’s Accomplice: How Design Emerges from Life Itself
Van Leeuwen, Evert. “Method, Discourse, and the Act of Knowing.”
Von Uexkuell, Jakob. 1934. Streifzuege durch die Umwelten von Tieren und Menschen
Vrijenhoek, Robert. “Genetics and Evolution of Deep-Sea Chemosynthetic Bacteria
Wennekes, Paul et al. “The Neutral–Niche Debate: A Philosophical
Whiten, Andrew & D. Erdal. “The human socio-cognitive niche and its evolutionary origins.”
Whiten, A., R. Hinde, K. Laland C. Stringer. 2011. “Introduction: Culture evolves.”
Wiens, John. “The niche, biogeography and species interactions.
Williams, R.J.P. “Chemical advances in evolution by and changes in use of space during time.
Williams, R.J.P. & J.J.R. Frausto da Silva. The Chemistry of Evolution: The Development of
Woese, Carl. “A New Biology for a New Century.”
Woese, C. & Goldenfeld. “How the Microbial World Saved Evolution from the Scylla
Wuketits, F.M. “Evolutionary epistemology: A challenge to science and philosophy
Wynn, Thomas, et al. “‘An Ape’s View of the Oldowan’ Revisited.
Yoon, EY, G. Humphreys & MJ Riddoch. “The Paired-Object Affordance Effect.
Zaeef, Abdul Salam. My Life with the Taliban.
Zednik, Carlos. “The Nature of Dynamical Explanation.

Citations collected in 2012 (works listed above):


“Since the Discourse, philosophy has fallen into the bondage of scientific treatises, and no one seems able to tell whether or not there lies a truth behind the scientific fabric we have made of the world. This pessimistic view of the influence of Descartes’s philosophy is most clearly expressed when Jaspers speaks of Descartes:

‘In him one can see the origin and beginning of what will later be the enduring enemy of philosophizing, even in that place where one seeks his own truth. Descartes is a historical fate, in the sense that everyone who philosophizes has to decide about himself in the unavoidable appropriation of Descartes, through the manner in which he appropriates him.’”
Van Leeuwen, Evert. “Method, Discourse, and the Act of Knowing.” Pp. 224-241. From Essays on the Philosophy and Science of Rene Descartes. 1993. Oxford University Press. P.224. Subquote is from Jaspers, Karl. Descartes und die Philosophie. 1956. Berlin. P. 102.


“The triple-inheritance version of human gene-culture coevolution differs from the earlier dual-inheritance versions in several respects. Two of the inheritance systems ..., genetic and cultural inheritance, are the same ... Now, however genetic inheritance is directed by natural selection stemming from every kind of niche construction, and not just cultural niche construction.” Odling-Smee, F. John, Kevin Laland & Marcus Feldman. Niche Construction: The Neglected Process in Evolution. Princeton University Press. 2003. P. 252.


“Ecological inheritance is explicitly directed by niche construction, and it potentially includes human artifacts. It follows that human cultural inheritance may influence human genetic inheritance in two ways instead of one: first, directly, by influencing differential survival and reproduction, as already assumed by sociobiology, human behavioral ecology, and evolutionary psychology, and second, indirectly, by contributing to cultural niche construction, and thence to a human ecological inheritance that includes culturally modified natural selection pressures.” Odling-Smee, F. John, Kevin Laland & Marcus Feldman. Niche Construction: The Neglected Process in Evolution. Princeton University Press. 2003. P. 252.


“The kind of scientific realism we have inherited from the seventeenth century has not lost all its prestige even yet, but it has saddled us with a disastrous picture of the world. It is high time we looked for a different picture.” Putnam, Hilary. “Is There Still Anything to Say about Reality and Truth?” Pp. 11-28. From McCormick, Peter. 1996. Starmaking: Realism, Anti-Realism, and Irrealism. MIT Press. P. 15.


“The problem, in a nutshell, is that thought itself has come to be treated more and more as a ‘projection’ by the philosophy that traces its pedigree to the seventeenth century. The reason is clear: we have not succeeded in giving the theory that thought is just a primitive property of a mysterious ‘substance,’ mind, any content.” Putnam, Hilary. “Is There Still Anything to Say about Reality and Truth?” Pp. 11-28. From McCormick, Peter. 1996. Starmaking: Realism, Anti-Realism, and Irrealism. MIT Press. P. 19.


“Modern Objectivism has simply become Materialism. And the central problem for Materialism is ‘explaining the emergence of mind’.” Putnam, Hilary. “Is There Still Anything to Say about Reality and Truth?” Pp. 11-28. From McCormick, Peter. 1996. Starmaking: Realism, Anti-Realism, and Irrealism. MIT Press. P. 20.


“The overwhelming case against perception without conception, the pure given, absolute immediacy, the innocent eye, substance as substratum, has been so fully and frequently set forth–by Berkeley, Kant, Cassirer, Gombrich, Bruner, and many others–as to need no restatement here. Talk of unstructured content or an unconceptualized given or a substratum without properties is self-defeating; for the talk imposes structure, conceptualizes, ascribes properties.” Goodman, Nelson. “Words, Works, Worlds.” Pp. 61-77. From McCormick, Peter. 1996. Starmaking: Realism, Anti-Realism, and Irrealism. MIT Press. Pp. 64-5.


“Whereas classical evolutionary theory sees the organism as the key that has to fit into the environment’s lock, both ecological developmental biology and niche construction see interactions between them. Niche construction emphasizes the ability of the organism to alter its environment; eco-devo emphasizes the ability of the environment to alter the developing organism.” Laland, Kevin, J. Odling-Smee & S. Gilbert. “EvoDevo and Niche Construction: Building Bridges.” 2008. Pp. 549-566. Journal of Experimental Zoology (Mol Dev Evol) 310B:549-566. P. 550.


“A subset of EvoDevo has given rise to ecological developmental biology, which stresses the roles of developmental plasticity in evolution, especially in the formation, preservation, and prevention of novelty. The focus is the ability of the developing organism to sense cues from its environment and to modify its development to become more fit in a particular habitat.” Laland, Kevin, J. Odling-Smee & S. Gilbert. “EvoDevo and Niche Construction: Building Bridges.” 2008. Pp. 549-566. Journal of Experimental Zoology (Mol Dev Evol) 310B:549-566. P. 549.


“From the niche-construction perspective, with its emphasis on reciprocal causation, evolutionary change is not solely explained by changed selection, but also requires consideration of what causes these changes in selection pressures–and often the answer is the earlier niche construction of ancestral populations. Accordingly, the niche-construction perspective explicitly recognizes an additional process to natural selection, which could potentially be the source of directionality in evolutionary responses, namely the organism itself, and the changes it brings about in its selective environment. This means that, in addition to chance and natural selection, there is a third explicitly recognized source of evolutionary innovation, which occurs when gene-informed, directed, nonrandom, yet novel, acts of niche construction bring about consistent chances in environments.

“If individuals select or manufacture a novel environment, they and their descendants will be exposed to novel selection and novel developmental conditions.” Laland, Kevin, J. Odling-Smee & S. Gilbert. “EvoDevo and Niche Construction: Building Bridges.” 2008. Pp. 549-566. Journal of Experimental Zoology (Mol Dev Evol) 310B:549-566. Pp. 560-1.


“The conceptual leap that niche construction theorists embrace is to regard niche construction as an evolutionary process in its own right. In other words, niche construction is viewed as an initiator of evolutionary change rather than merely the end product of earlier selection.” Laland, Kevin & M. O’Brien. “Niche Construction Theory and Archaeology.” 2010. Journal of Archaeological Method and Theory. 17:303-322. Pp. 304-5.


“However, Jones and his collaborators point out that many species of ecosystem engineers can regulate energy flows, mass flows, and trophic patterns in ecosystems to generate an ‘engineering web’–a mosaic of connectivity comprising the engineering interactions of diverse species, which regulates ecosystem functioning in conjunction with the well-studied webs of trophic interactions.” Laland, Kevin & M. O’Brien. “Niche Construction Theory and Archaeology.” 2010. Journal of Archaeological Method and Theory. 17:303-322. P. 306. Reference is to Jones, C. G., Lawton, G. & Shachak, M. 1994. “Organisms as ecosystem engineers.” Oikos. 69, 373-386.


“Niche construction may be inceptive or counteractive and may occur through perturbation of the environment or through relocation in space.” Laland, Kevin & M. O’Brien. “Niche Construction Theory and Archaeology.” 2010. Journal of Archaeological Method and Theory. 17:303-322. P. 307.


“The argument that human cultural niche construction has been a co-director of recent human evolution is essentially the conclusion reached by the geneticists analyzing the human genome, who observe that many genes subject to recent selective sweeps are responses to cultural activities.” Laland, Kevin & M. O’Brien. “Niche Construction Theory and Archaeology.” 2010. Journal of Archaeological Method and Theory. 17:303-322. P. 308.


“They [Laland, Odling-Smee, & Feldman] concluded that, because cultural processes typically operate faster than natural selection, cultural niche construction probably has more profound consequences than gene-based niche construction.” Laland, Kevin & M. O’Brien. “Niche Construction Theory and Archaeology.” 2010. Journal of Archaeological Method and Theory. 17:303-322. P. 310. Reference is to Laland, K, Odling-Smee, F & M. Feldman. “Cultural niche construction and human evolution.” 2001. Journal of Evolutionary Biology. 14: 22-33.


“... rather than slipping into the assumption that the external environment (e.g., climate change) triggers an evolutionary or cultural response, NCT [niche construction theory] enthusiasts are from the outset inclined to consider those additional hypotheses stressing self-constructed (and other organism-constructed) conditions that instigate change. In this respect, NCT can be viewed as more in accord with the perspective of most archaeologists, who are highly attuned to the active agency of their subjects, than standard evolutionary theory.” Laland, Kevin & M. O’Brien. “Niche Construction Theory and Archaeology.” 2010. Journal of Archaeological Method and Theory. 17:303-322. P. 312.


“Many counteractive niche-constructing behaviors regulate the environment in such a way as to buffer against particular natural selection pressures.” Laland, Kevin & M. O’Brien. “Niche Construction Theory and Archaeology.” 2010. Journal of Archaeological Method and Theory. 17:303-322. P. 313.


“First, it [niche construction theory] offers a broad, biologically and culturally informed conceptual framework suited to the human sciences–one that recognizes the active agency of humans as part causes of their own development, history, and evolution. Second, it recognizes niche construction as an evolutionary process and ecological inheritance as a second general legacy that organisms inherit from their ancestors, thereby providing researchers with additional explanatory mechanisms. Such mechanisms are particularly relevant to archaeologists, given that human niche construction is frequently a manifestation of acquired characters and human ecological inheritance includes a rich material culture.” Laland, Kevin & M. O’Brien. “Niche Construction Theory and Archaeology.” 2010. Journal of Archaeological Method and Theory. 17:303-322. P. 318.


“Our agent-based models of language games are beginning to show how symbol-based communication systems with properties similar to human natural languages can arise and be culturally transmitted. But a crucial assumption we had to make in all these models so far is that the agents are ‘ultrasocial’ instead of Darwinian. Sociality here means that agents are programed to cooperate fully in order to make their verbal interactions a success.” Steels, Luc. “Is sociality a crucial prerequisite for the emergence of language?” Pp. 36-57. From Botha, Rudolf & C. Knight. 2009. The Prehistory of Language. Oxford University Press. P. 37.


“Joint attention means (i) that speaker and hearer have a sufficiently shared context so that the possible meanings of an utterance are highly constrained, (ii) that they are engaged in a shared cooperative activity so that both can gauge whether their communication was successful or not, and (iii) that they have the means to correct miscommunication by additional dialog or by motor behaviors such as pointing.” Steels, Luc. “Is sociality a crucial prerequisite for the emergence of language?” Pp. 36-57. From Botha, Rudolf & C. Knight. 2009. The Prehistory of Language. Oxford University Press. P. 50.


“One thing is sure: that sociality is a crucial prerequisite for language and that language in turn must have helped maintain sociality in our species.” Steels, Luc. “Is sociality a crucial prerequisite for the emergence of language?” Pp. 36-57. From Botha, Rudolf & C. Knight. 2009. The Prehistory of Language. Oxford University Press. P. 57.


“There is one kind of niche construction that we have not yet explicitly considered, ‘social niche construction.’ The social niche is the subset of natural selection pressures in an evolutionary niche that stem from interactions with other organisms in their social groups. It constitutes the resources (e.g. food), services (e.g. grooming), and other outputs (e.g. threats) provided by organisms for each other. It also includes all the ways in which individual organisms can actively defend themselves, compete with, form alliances with, cooperate, exploit, or manipulate, other organisms, and by doing so modify some of the natural selection pressures they encounter in their niche.” Odling-Smee, John & K. Laland. “Cultural niche construction: evolution’s cradle of language.” Pp. 99-121. From Botha, Rudolf & C. Knight. 2009. The Prehistory of Language. Oxford University Press. Pp. 106-7.


“It concerns the construction of communication links and networks in social groups, without which adaptive group living is probably impossible. We call it communicative niche construction. In general, communicative niche construction depends on the ability of organisms to convey meaningful information to and from each other through their bodies, products, or activities.” Odling-Smee, John & K. Laland. “Cultural niche construction: evolution’s cradle of language.” Pp. 99-121. From Botha, Rudolf & C. Knight. 2009. The Prehistory of Language. Oxford University Press. P. 108.


“The organization of animal societies, and their communication networks, can be transmitted across multiple generations of a population as an ecological inheritance. Thus, it is possible for communicative niche construction to modify one or more natural selection pressures in populations of social organisms repeatedly and consistently, and thereby to affect their evolution in a directional manner. If that happens, communication fully qualifies as another kind of niche construction.” Odling-Smee, John & K. Laland. “Cultural niche construction: evolution’s cradle of language.” Pp. 99-121. From Botha, Rudolf & C. Knight. 2009. The Prehistory of Language. Oxford University Press. P. 109.


“Humans transmit more learned information across generations than any other species. Conversely, animals typically depend primarily on horizontal transmissions based on simple forms of social learning. A comparative perspective thus implies that the earliest forms of social transmission were probably horizontal, and that the lineage leading to Homo sapiens has been selected for increasing reliance on vertical and oblique cultural transmission. The theoretical analyses of the evolution of culture, described above, imply that a shift towards increased transgenerational cultural transmission reflects a greater constancy in the environment over time. Such a shift is difficult to reconcile with culture being favored by variation in an autonomous external environment because there is no evidence to suggest that environments have become more constant over the last few million years, but rather the opposite, and if they had, other protocultural species would also be expected to show more transgenerational transmission than they do. Richerson and Boyd have suggested that independent (e.g. climatic) sources of environmental variation are the primary selection pressures favoring the human capacity for cultural transmission, but these vary on entirely the wrong scale.

“To us, a more compelling hypothesis is that our ancestors constructed the environmental conditions that favored hominid reliance on culture, building niches in which it paid them to transmit more information to their offspring. The more an organism controls and regulates its environment, and the environment of its offspring, the greater should be the advantage of transmitting cultural information across generations. For example, by tracking the movements of migrating or dispersing prey, populations of hominids increase the chances that a specific food source will be available in their environments, that the same tools used for hunting will be needed, and that the skin, bones, and other materials from these animals will be at hand to use in the manufacture of additional tools. Such activities create the kind of stable social environment in which related technologies, such as food preparation or skin processing methods, would be advantageous from one generation to the next, with methods repeatedly socially transmitted across generations. Once started, cultural niche construction may become an autocatalytic process, with greater culturally generated environmental regulation leading to increasing homogeneity of the social environment as experienced by old and young, favoring further transgenerational cultural transmission.” Odling-Smee, John & K. Laland. “Cultural niche construction: evolution’s cradle of language.” Pp. 99-121. From Botha, Rudolf & C. Knight. 2009. The Prehistory of Language. Oxford University Press. Pp. 118-9.


“The response of a player redefines and/or limits another’s intent; thus, the shared semantic understandings of objects, actions, and/or gestures that signal, query, or motivate the next move emerge as a function of this interaction. Co-constructed intentions are inherently shared, and salient gestures, sounds, and ‘incipient acts’ evoke the meaning of moves that have been played into existence. Because play actions, movements, and gestures are often without their ‘real world’ consequences or instrumental functions, these salient acts can become free to ‘stand for’ or re-present their meaning in non-play contexts. In social play as in language, participants negotiate hierarchically ordered moves and exchanges that can be modified and rearranged through repetitive actions and shared goals into normative, rule-governed behavior. We propose that these dialogic structural and normative functions make social play a proper model for understanding the emergence of language, as a negotiated, self-organizing system rather than a system of communication limited to modern human societies.” Ragir, Sonia & S. Savage-Rumbaugh. “Playing with meaning: normative function and structure in play.” Pp. 122-141. From Botha, Rudolf & C. Knight. 2009. The Prehistory of Language. Oxford University Press. P. 122.


“Play is one of many forms of negotiated, self-organizing, dynamic systems that emerge during ontogeny. This fundamentally communicative activity dominates the developmental phase of performance-dependent neural and muscular specialization in animal and human young and participates in the structuring of neural networks, modularization of function, and cognitive specialization. Form and meaning are co-constructed in play, and they serve in public systems of representation and not simply as signs of emotional states over which the individual has no control. Ape social play and perhaps all social play is first and foremost a negotiation about what is possible, what is permitted, and how to do it effectively with others. The normative and reflexive qualities of social play suggest that play has not only a proximal autoletic function but also the distal effect of generating a neural substrate that support the shared fields of behavioral and social understanding necessary for complex communication.” Ragir, Sonia & S. Savage-Rumbaugh. “Playing with meaning: normative function and structure in play.” Pp. 122-141. From Botha, Rudolf & C. Knight. 2009. The Prehistory of Language. Oxford University Press. P. 140.


“The theoretical frameworks of computationalism and connectionism are often construed as a search for cognitive mechanisms, the specific structures and processes from which cognitive phenomena arise. In contrast, the framework of dynamicism is generally understood to be a search for principles or laws–mathematical regularities that govern the way cognitive phenomena unfold over time. In recent philosophical discourse, this difference between traditional and dynamical cognitive science has been framed as a difference in scientific explanation: whereas computationalist and connectionist explanations are mechanistic explanations, dynamical explanations take the form of covering-law explanations.” Zednik, Carlos. “The Nature of Dynamical Explanation.” 2011. Philosophy of Science. Vol 78, No. 2. Pp. 238-263. P. 238.


“Kelso’s explanation of bimanual coordination is not in fact representative of dynamical explanation in general, and many dynamical explanations actually resemble mechanistic explanations rather than covering-law explanations.” Zednik, Carlos. “The Nature of Dynamical Explanation.” 2011. Philosophy of Science. Vol 78, No. 2. Pp. 238-263. P. 245. Reference is to Kelso, J. 1995. Dynamic Patterns: The Self-Organization of Brain and Behavior. MIT Press.

“Thelen et al. and Beer each offer a dynamical explanation of a (minimally) cognitive phenomenon. In each case, the explanation proceeds by identifying the component parts and operations of a mechanism and by showing how the organized activity of these parts and operations produces the phenomenon being explained.” Zednik, Carlos. “The Nature of Dynamical Explanation.” 2011. Philosophy of Science. Vol 78, No. 2. Pp. 238-263. P. 255. References are: Thelen, E., G. Schoener, C. Scheier & L. Smith. 2001. “The Dynamics of Embodiment: A Field Theory of Infant Perservative Reaching.” Behavioral and Brain Sciences. 24:1-34. Beer, R. 2003. “The Dynamics of Active Categorical Perception in an Evolved Model Agent.” Adaptive Behavior. 11 (4): 209-43.


“Coupling is a technical term that applies whenever two or more dynamical systems mutually influence one another’s change over time. In the philosophical literature, such mutual influence is more commonly known as continuous reciprocal causation.” Zednik, Carlos. “The Nature of Dynamical Explanation.” 2011. Philosophy of Science. Vol 78, No. 2. Pp. 238-263. P. 258.


“The moral of the story is that the tools and concepts of dynamical systems theory can be used to describe mechanisms that exhibit continuous reciprocal causation. Although important questions do remain about the degree to which Beer’s methods will scale up to larger and increasingly realistic systems in which continuous reciprocal causation is increasingly prevalent. Beer’s analysis shows that continuous reciprocal causation does not necessarily preclude mechanistic explanation.” Zednik, Carlos. “The Nature of Dynamical Explanation.” 2011. Philosophy of Science. Vol 78, No. 2. Pp. 238-263. P. 260. Reference is to Beer, R. 2003. “The Dynamics of Active Categorical Perception in an Evolved Model Agent.” Adaptive Behavior. 11 (4): 209-43.


“... those dynamicist researchers who seek to provide mechanistic explanations rather than covering-law explanations may be steering toward reconciliation with proponents of representationalism. By describing cognitive mechanisms rather than principles or laws, these researchers describe structures that are amenable to what Chemero and Silberstein have called representation hunting–characterizing the components of a mechanism as representation producers and representation consumers and understanding their operations in terms of the transfer and manipulation of information.” Zednik, Carlos. “The Nature of Dynamical Explanation.” 2011. Philosophy of Science. Vol 78, No. 2. Pp. 238-263. P. 261. Reference is to Chemero, A. & M. Silberstein. 2008. “After the Philosophy of Mind: Replacing Scholasticism with Science.” Philosophy of Science. 75: 1-27.


“Culture, broadly conceived as all that individuals learn from others that endures to generate customs and traditions, shapes vast swathes of human lives. Cumulative cultural achievements, from technology to social institutions, have allowed our species to invade and exploit virtually every region of the planet. Accordingly, this special capacity for culture is often thought to represent a qualitative distinction between our species and the rest of nature, and our relative independence from the Darwinian forces that shape the natural world.” Whiten, A., R. Hinde, K. Laland C. Stringer. 2011. “Introduction: Culture evolves.” Philosophical Transactions of the Royal Society: B. 366, 938-48. P. 938.


“Our understanding of the cumulative cultural achievements of the Stone Age has been transformed over the last dozen years or so by the integrated exploitation of a diverse range of evidential sources, often depending on extremely careful, painstaking and effortful work. These sources include (i) the primary one of archaeology, which in this period has established much earlier dates than known before, both for the emergence of lithic tool-making and for skilled knapping; (ii) inferences drawn by highly skilled re-creation by scientists of knapping techniques that produce the kinds of artefacts recovered; (iii) linked observations of knapping and other techniques used by peoples such as the Irian Jaya, who preserved a complex lithic tool culture; and (iv) the careful refitting of recovered sets of flakes to their cores, allowing the retro-construction of the knapping sequences used by their makers. Here Stout builds on these combined sources to generate a systematic analysis of the complexity of manufacturing techniques, tentatively concluding from this that through the whole Stone Age (extending beyond the Acheulian to later, more sophisticated achievements such as the Levallois), there has been an approximately exponential increase in quantifiable complexity of techniques.

“Intriguingly, such progress appears remarkably lacking in the Oldowan. The above-listed sources of evidence applied to the oldest known Oldowan artefacts show their manufacture to have relied on a good appreciation of fracture processes in stone-working, which exceeded that apparent in the efforts of great apes who have knapped sharp flakes in recent experimental contexts. Over the next approximately 1 Myr, Oldowan artefacts showed little if any progress beyond this–indeed, later ones often appear less sophisticated.

“However, Oldowan knapping itself may plausibly have represented a cumulative step built on the prior use of stone tools for butchery, which recent evidence dates back to about 3.4 Ma.” Whiten, A., R. Hinde, K. Laland C. Stringer. 2011. “Introduction: Culture evolves.” Philosophical Transactions of the Royal Society: B. 366, 938-48. Pp. 942-3. Reference is to Stout, D. 2011. “Stone toolmaking and the evolution of human culture and cognition.” Philosophical Transactions of the Royal Society: B. 366, 1050-1059.


“Each of the last four phases, from around 120 Ka on, is marked by accelerating cultural achievements (echoing the analysis of Stout referring to even earlier times) and greater diversity.” Whiten, A., R. Hinde, K. Laland C. Stringer. 2011. “Introduction: Culture evolves.” Philosophical Transactions of the Royal Society: B. 366, 938-48. P. 944. References are from Foley, R. & M. Mirazon Lahr. 2011. “The evolution of the diversity of cultures.” Philosophical Transactions of the Royal Society: B. 366, 1080-89 and from Stout, D. 2011. “Stone toolmaking and the evolution of human culture and cognition.” Philosophical Transactions of the Royal Society: B. 366, 1050-1059.


“... cultural change can occur through ‘cultural selection’ (for example, people select the most efficient axes) and/or ‘natural selection’ in the conventional sense (the reproductive success of the best axe makers promotes the evolution of those axes).” Whiten, A., R. Hinde, K. Laland C. Stringer. 2011. “Introduction: Culture evolves.” Philosophical Transactions of the Royal Society: B. 366, 938-48. P. 944.


“The critic wishes a word, ‘Are you trying to say that nothing exists until there is some kind of relationship? There is no physical world, no mountains, trees, a sun, and so on? This just seems absurd.’ In reply, this is not precisely what is being proposed here. We should not conclude that ‘nothing exists’ before the moment of co-action. Whatever exists simply exists. However, in the process of co-action whatever there is takes shape as something for us. It comes to be ‘mountains,’ trees,’ and ‘sun’ in terms of the way we live.” Gergen, Kenneth. Relational Being: Beyond Self and Community. 2009. Oxford University Press. P. 37.


“As I converse with you, my utterances are candidates for meaning. However, these candidates are not my possession, but the byproducts of a relational history. Without this history of constraint, I would have nothing to say. At the same time, provided we share in a tradition of conversation, my utterances and actions carry a pre-figuring potential. That is, they indicate a domain of what is possible for you to say and do.” Gergen, Kenneth. Relational Being: Beyond Self and Community. 2009. Oxford University Press. P. 40.


“Why are deontic powers so important? They are the glue that holds human society together. What is the power of the glue? The answer is that to the extent that people recognize the validity of Status Functions, they recognize them as having a deontic status, and for that reason, they recognize them as giving reasons for action which are independent of their immediate inclinations. I will abbreviate this idea by saying that Status Functions provide desire independent reasons for action.” Searle, John. “The Basic Reality and the Human Reality.” Pp. 19-44. Franken, Dirk, A. Karakus & J. Michel, Eds. John R. Searle: Thinking about the Real World. 2010. Ontos Verlaag. P. 36.


“Institutional facts = Status Functions –> deontic powers –> desire-independent reasons for action –> possible motivations for action.

“In plain English, all and only institutional facts are Status Functions, Status Functions contain deontic powers, and deontic powers, where their validity is recognized, provide desire-independent reasons for action, and these in turn provide possible motivations for actions.” Searle, John. “The Basic Reality and the Human Reality.” Pp. 19-44. Franken, Dirk, A. Karakus & J. Michel, Eds. John R. Searle: Thinking about the Real World. 2010. Ontos Verlaag. P. 37.


“Ethics is essentially concerned with desire-independent reasons for action.” Searle, John. “The Basic Reality and the Human Reality.” Pp. 19-44. Franken, Dirk, A. Karakus & J. Michel, Eds. John R. Searle: Thinking about the Real World. 2010. Ontos Verlaag. P. 39.


“What we want to deny, however, is that what happens can be called a speech act. A speech act or, to be more precise, an illocutionary act is something that can be performed by a single speaker or a group of speakers, simply by uttering linguistic expressions with the appropriate meaning-intentions. To perform Searle’s ‘maneuver’, on the other hand, speakers have to get all the others to accept their speech acts as well. So, what speakers have to do goes far beyond performing an illocutionary act.

“Searle says that he wants ‘to introduce a very strong theoretical claim’ in his new book: ‘All institutional facts [...] are created by speech acts of a type that 1975 I baptized as ‘Declaration.’‘ But if we are right and the ‘maneuver’ Searle describes cannot be understood as a speech act at all, there is no strong theoretical claim any more, at least none that goes beyond what is said in The Construction of Social Reality. If we are right, Searle is entitled only to the claim: ‘All institutional facts [...] are created by [a maneuver with certain analogies to] speech acts of a type that 1975 I baptized as “Declaration.’‘

“Moreover, the analogy to declarations suffers from the fact that one of the relata of the two directions of fit is not the same in both cases. On the one hand individual people represent an institutional fact with the word-to-world direction of fit. On the other hand, it is the collective of all people in the community representing the institutional fact that creates it. In this case, the direction of fit is not between the institutional fact and an intention of an individual, but between the institutional fact and a collection of intentions.” Prien, Bernd, J. Skudlarek & S. Stolte. “The Role of Declarations in the Construction of Social Reality.” Pp. 163-171. Franken, Dirk, A. Karakus & J. Michel, Eds. John R. Searle: Thinking about the Real World. 2010. Ontos Verlaag. P. 169.


“Multicellularity has evolved many times along the history of eukaryotes and, apparently, even in geologically recent times. For example, starting from unicellular ancestors the green algae have recently given rise to the multicellular Volvox lineage within the last 75 million years.

“Arguably, multicellularity evolves easily, provided that cell-adhesion molecules are available, but the eventual long-term stability of a multicellular organism depends on the balance between the benefits eventually obtained by the individual cells being part of a multicellular assemblage and the decrease in individual fitness associated with the same condition. In fact, cooperation among cells will easily benefit the group, but can be costly to the individual cooperating cells....”

“... the persistence of cell-to-cell competition helps to explain several key features of metazoan organization, including the origin of tissues, sexuality, cuticles, and others. Common to all these evolutionary events is cell-cell signalling, which can be regarded as a mechanism that allows one cell to gain control of the intracellular signalling of another cell. Terminal differentiation of cells can thus be interpreted as a result of metabolic control under the influence of successful neighbouring cells.” Minelli, Alessandro. 2009. Perspectives in Animal Phylogeny & Evolution. Oxford University Press. P. 19.


“Selection will easily favour cells or cell lineages producing mutants able to manipulate environmental conditions, for example by opening within a multicellular assemblage new channels through which materials can circulate (a kind of primitive angiogenesis). In this model, developmental mechanisms evolve because of the immediate metabolic advantage they may produce, not because of any morphogenetic effect eventually deriving by the operation of the same mechanisms in future generations, something we all too often assume when reconstructing the ‘origins’ of some feature in modern animals.” Minelli, Alessandro. 2009. Perspectives in Animal Phylogeny & Evolution. Oxford University Press. P. 20.


“The evolutionary step from the unicellular condition of the flagellate-grade ancestors of metazoans to the multicellular condition of the latter involved extensive loss of genes.” Minelli, Alessandro. 2009. Perspectives in Animal Phylogeny & Evolution. Oxford University Press. P. 23.


“... fossil evidence, and molecular evidence all largely concur to confirm metazoan monophyly.” Minelli, Alessandro. 2009. Perspectives in Animal Phylogeny & Evolution. Oxford University Press. P. 30.


“The issue of individuality–that is, of what actually defines the spatiotemporal boundaries and the historical continuity of an individual–emerges time and again in the analysis of living beings, at different structural levels. In zoology, the most obvious grey area is multinucleate units without cytoplasmic boundaries, whereas morphological (junctions) and functional (electrical coupling, exchange of molecules) ties between neighbouring epithelial cells are less permissive than the links provided by the plasmodesmata in plant cells, to the extent that in plants the very notion of cells is sometimes disputed.” Minelli, Alessandro. 2009. Perspectives in Animal Phylogeny & Evolution. Oxford University Press. P. 113.


“Thus, rather than taking the cell, typologically, as a standard unit of morphological organization, it seems advisable to regard it as a unit of function, integrating a complex network of local dynamics, whose independence as a distinct module of form, is not always granted, as the widespread occurrence of syncytia amply demonstrates.” Minelli, Alessandro. 2009. Perspectives in Animal Phylogeny & Evolution. Oxford University Press. P. 113.


“In 1934, Studnicka proposed a terminology that attempted to combine origin and organization of these multinucleate structures, using ‘symplasma’ for multinucleate systems whose cytoplasmic continuity results from incomplete cytokinesis but which otherwise remain independent, ‘syncytia’ for multinucleated structures whose cytoplasm is not organized around centrioles, and ‘plasmodia’ for multinucleated tissues formed by fusion of separate cells or by division of nuclei in a growing cell. Irrespective of the merits of those distinctions, current literature has increasingly adopted the term ‘syncytium’ for all these structures.” Minelli, Alessandro. 2009. Perspectives in Animal Phylogeny & Evolution. Oxford University Press. P. 113.


“Syncytial structures are present virtually everywhere that is, in the most diverse body parts of the most different animal groups. Syncytia are known, in fact, from groups as diverse as Silicea, Placozoa, Cnidaria, Acoela, Gastrotricha, Syndermata, Gnathostomulida, Rhabditophora, Nematoda, Arthropoda, Echinodermata, and Chordata. Clearly, this condition has been obtained independently a great many times.” Minelli, Alessandro. 2009. Perspectives in Animal Phylogeny & Evolution. Oxford University Press. P. 114.


“A lot of effort was devoted for a while in the search for what (say, the expression of a particular gene, or a particular metabolic condition) might turn a ‘normal’ Dictyostelium amoeba into the founder of a multicellular group. But it was eventually realized that no founder cell may actual exist. Rather, aggregation starts wherever two amoebae touch, and this happens simply because they were close enough to have a better chance of one to be hit by the chemical signal produced by the other. That is, no founder, no project.” Minelli, Alessandro. 2009. Perspectives in Animal Phylogeny & Evolution. Oxford University Press. P. 138.


“It has been suggested that multicellular organisms passed through a pre-Mendelian phase where context-dependent properties of self-organization were much more important than the canalization or determination of processes derived from gene expression, as generally happens in today’s multicellular organisms. According to this hypothesis, the morphological features of the earliest multicellulars were mainly the outcome of epigenetic processes.” Minelli, Alessandro. 2009. Perspectives in Animal Phylogeny & Evolution. Oxford University Press. Pp. 138-9. Reference is to Newman, S. “The pre-Mendelian, pre-Darwinian world: shifting relations between genetic and epigenetic mechanisms in early multicellular evolution.” 2005. Journal of Biosciences. 30: 75-85.


“It has been poignantly remarked that even cells devoid of a nucleus, as are mammalian red blood cells, can still regulate their behaviour as a function of their environmental context.” Minelli, Alessandro. 2009. Perspectives in Animal Phylogeny & Evolution. Oxford University Press. P. 139.


“... the progression of a given developmental stage to one with very different organization is likely to be accompanied by a dramatic shift in the profile of the genes that are expressed. This has been shown by Arbeitman et al in their longitudinal analysis of the expression of 4028 genes during the embryonic and post-embryonic development of Drosophila. For some 80% of these genes, the lowest level of expression during the whole span of the fly’s development is at least four times lower than the highest level of expression of the same gene. The embryonic segment of the life cycle was the most eventful, in terms of transcription, as three-quarters of the studied genes were expressed then, and for two-thirds of these the level of expression changed significantly during embryonic life. But the beginning of post-embryonic life did not correspond to the beginning of a transcriptionally stable period, as the level of expression of a total of 445 genes changed during larval life, 646 during the pupal stage, and more than 100 during the first 5 days of adult life. Thus, a complex life cycle is based on a subtly orchestrated pattern of gene expression, in which dramatic switches occur.” Minelli, Alessandro. 2009. Perspectives in Animal Phylogeny & Evolution. Oxford University Press. P. 154. Reference is to Arbeitman, M., E. Furlong, & F, Imam. 2002. “Gene expression during the life cycle of Drosophila melanogaster.” Science. 297: 2270-2275.


“It may thus be useful to revisit Anderson’s concept of ‘hybrid habitat’, introduced (in botany) to describe the environmental conditions where a population is likely to maintain an unusually elevated variation such as deriving from recent hybridization. Similarly, I think that of the environmental scenarios proposed as the theatre of singularly active evolutionary change, those pointing to the ‘creative’ nature of transitional or ecotonal environments are the most plausible, in principle at least. Those environments are more likely to support the existence of organisms that simultaneously present alternative ways to survive, such as terrestrial as well as aquatic respiration, a peculiarity which can be exploited sequentially during an animal’s life, as in dragonflies and frogs, as long as these animals remain in the transitional environments, but can also eventually be fixed in the condition opposite to the original one.” Minelli, Alessandro. 2009. Perspectives in Animal Phylogeny & Evolution. Oxford University Press. P. 232. Reference is to Anderson, E. 1948. “Hybridization of the habitat.” Evolution 2: 1-9.


“Nowadays, cell differentiation is a typical example of a biological process dependent on strictly controlled and spatiotemporally restricted gene expression, but this is arguably an acquired condition, probably preceded by a stage when alternative phenotypes within a multicellular organism were just variants within an environmentally inducible polyphenism.... In this scenario, what is new in the multicellular organisms is the evolution of cell-cell interactions that allow the coexistence of alternative phenotypes, while the production of the latter, as such, was already manifested by their unicellular precursors.” Minelli, Alessandro. 2009. Perspectives in Animal Phylogeny & Evolution. Oxford University Press. P. 238.


“In short for Darwin and his many followers, the evolution of species in nature was also an evolution out of it, in so far as it progressively liberated the mind from the promptings of innate disposition. Ever since, Western science has cleaved strongly to the view that humans differ from other animals in degree rather than kind. Darwin, it is said, finally showed us that the idea of an absolute Rubicon separating the human species from the rest of the animal kingdom is a myth. He did not, however, dispense with the dichotomy between reason and nature, or between intelligence and instinct; rather his whole argument was couched in terms of it.” Ingold, Tim. 2006. “Against Human Nature.” Pp. 259-281. From Gontier, Nathalie, J.P. Van Bendegem & D. Aerts, Editors. Evolutionary Epistemology, Language and Culture: A Non-Adaptationist, Systems Theoretical Approach. Springer. Pp. 264-5.


“Darwin’s commitment, in The Descent of Man, to an imperialist doctrine of progress according to which the morally and intellectually well-endowed are bound to supplant their inferiors, not only ran counter to the whole argument of The Origin of Species, but was also deeply racist. Whereas in the Origin Darwin had shown that the mechanism of natural selection always operates in such a way as to make species better adapted to their particular environmental conditions of life, in the Descent he argued that it would inevitably bring about absolute advance along a single, universal scale–from the lowest of animals to the highest of men–regardless of environmental conditions, leading from instinct to intelligence, and reaching its ultimate conclusion in modern European civilisation. And in bringing the rise of science and civilisation within the compass of the same evolutionary process that had made humans out of apes, and apes out of creatures lower in the scale, Darwin was forced to attribute what he saw as the ascendancy of reason to hereditary endowment. For the theory to work, there had to be significant differences in such endowment between ‘tribes’ or ‘nations’–or between what we might today call populations....

“We now recognise that the brains of hunter-gatherers are just as good, and just as capable of handling complex and sophisticated ideas, as the brains of Western scientists and philosophers....

“What was self-evident to Darwin and most of his contemporaries–namely that human populations differed in their innate intellectual capacities on a scale from the primitive to the civilised–is no longer acceptable today.” Ingold, Tim. 2006. “Against Human Nature.” Pp. 259-281. From Gontier, Nathalie, J.P. Van Bendegem & D. Aerts, Editors. Evolutionary Epistemology, Language and Culture: A Non-Adaptationist, Systems Theoretical Approach. Springer. Pp. 266-7.


“But this [Universal Declaration of Human Rights, Article 1, “All human beings are endowed with reason and conscience.”] left the Darwinians with a problem on their hands. How was the doctrine of evolutionary continuity to be reconciled with the new-found commitment to universal human rights? If all humans are alike in their possession of reason and moral conscience–if, in other words, all humans are the kinds of beings who, according to Western juridical precepts, can exercise rights and responsibilities–then they must differ in kind from all other beings which cannot. And somewhere along the line, our ancestors must have made a breakthrough from one condition to the other, from nature to humanity.

“Faced with this problem, there was only one way for modern science to go—that is, back to the 18th century. Indeed the majority of contemporary commentators on human evolution appear to be vigorously, if unwittingly, reproducing the 18th century paradigm in all its essentials. One process, of evolution, leads from our ape-like ancestors to human beings that are recognisably of the same kind as ourselves; another process, of culture or history, leads from humanity’s primitive past to modern science and civilisation. Taken together, these two axes of change–the one evolutionary, the other historical–establish by their intersection a unique point of origin, without precedent in the evolution of life, at which our ancestors are deemed to have crossed the threshold of true humanity and to have embarked on the course of history.” Ingold, Tim. 2006. “Against Human Nature.” Pp. 259-281. From Gontier, Nathalie, J.P. Van Bendegem & D. Aerts, Editors. Evolutionary Epistemology, Language and Culture: A Non-Adaptationist, Systems Theoretical Approach. Springer. P. 268.


“Following this line of argument, so far as their evolved capacities are concerned there should be little or nothing to distinguish today’s scientists and engineers from the hunter-gatherers of 50,000 or even 100,000 years ago. What makes them different, apparently, is a separate process of history, or what many have taken to calling cultural (as opposed to biological) evolution.” Ingold, Tim. 2006. “Against Human Nature.” Pp. 259-281. From Gontier, Nathalie, J.P. Van Bendegem & D. Aerts, Editors. Evolutionary Epistemology, Language and Culture: A Non-Adaptationist, Systems Theoretical Approach. Springer. P. 269.


“Short of reverting to the racially stratified scenario of Darwin, with its populations of more or less well-endowed men, the only way in which humans can be made to appear different in degree, not kind, from their evolutionary antecedents is by attributing the movement of history to a process of culture that differs in kind, not degree, from the process of biological evolution!” Ingold, Tim. 2006. “Against Human Nature.” Pp. 259-281. From Gontier, Nathalie, J.P. Van Bendegem & D. Aerts, Editors. Evolutionary Epistemology, Language and Culture: A Non-Adaptationist, Systems Theoretical Approach. Springer. P. 270.


“The search for absolute, defining attributes of common humanity does indeed seem a hopeless endeavour, since whatever attribute you choose, there will bound to be some creature born of man and woman in which it is lacking. Remember that for modern biology, reconstructed along Darwinian lines, the criterion for species membership is genealogical. Basically, this means that you are a human being if your parents are. If it is human nature to walk on two feet, what of the congenitally crippled? Is he not human? If it is human nature to communicate by means of language, what of the child who is deaf and dumb? Is she not human? If it is human nature to join in forms of social life based on a mutual awareness of self and other, what of those individuals who suffer from autism? Are they not human?

“The argument can be turned around the other way as well. Whatever attribute you choose, there is a possibility that some creature of non-human ancestry may turn out to possess it–if not now, then at some time in the future. The way a species evolves is not predictable in advance. It is perfectly possible that the descendants of chimpanzees, a million years hence, will have developed a fully linguistic capability and be walking on two feet. They have already been shown to be capable of such things up to a point, as well as of other things once thought distinctively human, like making tools. Would they then have become human? In genealogical terms that is an impossibility, yet if it is human nature to walk and talk, then these chimpanzees of the future would have to count as human too.

“I have shown that the contemporary appeal to universal human nature, in the name of evolutionary biology, is a defensive reaction to the legacy of racist science left by Darwin’s account of the evolution of the moral and intellectual faculties in The Descent of Man. But it is an appeal fraught with contradictions. While insisting on the continuity of the evolutionary process, it also reinstates the twin distinctions between biology and culture, and between evolution and history, setting an upper limit to the world of nature that humans alone appear to have breached. More than that, it asserts that human nature is fixed and universal while attributing its evolution to a theory–of variation under natural selection–that only works because the individuals of a species are endlessly variable. That is why evolutionists find themselves in the curious position of having to admit that whereas in the non-human world, biology is the source of all variability and difference, in the human world it is what makes everyone the same!” Ingold, Tim. 2006. “Against Human Nature.” Pp. 259-281. From Gontier, Nathalie, J.P. Van Bendegem & D. Aerts, Editors. Evolutionary Epistemology, Language and Culture: A Non-Adaptationist, Systems Theoretical Approach. Springer. Pp. 277-8.


“Probably the most widely applicable mechanism for generating indirect fitness benefits for cooperation is population viscosity, or limited dispersal, leading to genetic structuring of populations. This means that even indiscriminate altruistic behavior incurring a personal cost and providing a benefit to neighboring individuals could enhance the actor’s inclusive fitness because those neighbors are on average closely related kin.” Gardner, Andy & K. Foster. “The Evolution and Ecology of Cooperation – History and Concepts.” Pp. 1-36. From Korb, Judith & J. Heinze, Editors. Ecology of Social Evolution. 2008. Springer. P. 17.


“Nevertheless, considerations of kin structure and genes alone are often not sufficient to explain the social phenotype and its inter- and intraspecific variation. In fact, many features of insect societies appear to be remarkably robust against variation in genetic colony structure. For example, whether worker reproduction occurs or not appears to be much less influenced by relatedness than predicted by theory and several recent studies have documented sex ratio specializations without the expected underlying variability in relatedness asymmetries.

“Instead, variation in environmental factors, such as climate, resource availability, the occurrence of competitors, predators, or parasites, etc., appears to be as influential as variation of genetic composition at least for some features of the insect society. The importance of ecology in social evolution is clearly emphasized by factors b and c in Hamilton’s rule, i.e., the benefits and costs of helping, and numerous researchers have investigated ecological influences on the social phenotype. However, the magnitude of environmental constraints is often difficult to measure and many hypotheses about the interrelations of the social phenotype and the environment are therefore not strongly supported by empirical data.” Heinze, Juergen. “Social Plasticity: Ecology, Genetics, and the Structure of Ant Societies.” Pp. 129-150. From Korb, Judith & J. Heinze, Editors. Ecology of Social Evolution. 2008. Springer. Pp. 130-1.


“This increase in dispersal as sexuals makes adaptive sense for log dwelling termites like C. secundus because as the log diminishes, so too does the probability they will be able to reproduce in the natal colony before the wood runs out. A central component of this response is the termites’ impressive ability to detect changes in the size of their log and so predict colony longevity. In C. secundus the loss of wood from the log occurs gradually by the termites own consumption of the wood but also suddenly when cyclones or heavy thunderstorms fragment their trees. Correspondingly, the termites cannot rely on extended excavations to measure wood availability. Instead, the termites continually sense the amount of wood from the vibrations generated during wood gnawing. These vibrations constitute reliable and fast cues of food availability. This predictable variation in food availability/colony longevity probably selects for the flexible development of workers in OP termites [One-piece termites “live in their food and spend their entire colony life in a single piece of wood that serves as both food source and shelter”]. This situation contrasts with the MP termites [Multiple-pieces type termites which “live in a well-defined nest that is more or less separated from the foraging grounds”] that leave their nest to exploit resources. They reduce the long-term food variability but experience short-term variation in food supply that lacks predictable cues allowing a plastic developmental response.” Korb, Judith. “The Ecology of Social Evolution in Termites.” Pp. 151-174. From Korb, Judith & J. Heinze, Editors. Ecology of Social Evolution. 2008. Springer. Pp. 157-8, 152.


“Accordingly, two prerequisites, which birds and mammals usually lack, are necessary for the transition to eusocialiity: (a) a high fecundity and (b) large numbers of offspring that can stay at the nest and are not ‘forced’ to leave because there is no competition at the nest for food. Under most conditions, offspring are selected to disperse from the nest to avoid competition among siblings. Two mechanisms can overrule this: a high abundance of food at the nest that lasts reasonably long (i.e., for at least two generations that can co-exist) and/or high ecological constraints which make dispersal difficult. The latter is commonly included in many models on the evolution of sociality, while the former is often only implicitly assumed. The comparison with termites, therefore, suggests that the general lack of eusociality in vertebrates might be because they can only achieve small families due to their low fecundity and the difficulty to have enough food to overcome local resource competition for more than two generations to coexist as individuals are large and rather long-lived compared to their food source. Thus, the finally limiting trait accounting for the rarity of eusociality in birds and mammals would be their body size. Correspondingly, the only groups in which eusociality occurs are rodents, which are comparatively small mammals with a short generation time, high fecundity and long-lasting food sources.” Korb, Judith. “The Ecology of Social Evolution in Termites.” Pp. 151-174. From Korb, Judith & J. Heinze, Editors. Ecology of Social Evolution. 2008. Springer. P. 167.


“In a curious sense the study of the organisms is really a study of the shape of the environmental space, the organisms themselves being nothing but the passive medium through which we see the shape of the external world. They are the iron filings of the environmental field. Most evolutionary biologists would reject such a description of their science and would insist that it is the organisms themselves that are the primary objects of interest–yet the structure of adaptive explanation of traits points in the opposite direction.”

“Adaptive explanations have both a forward and a backward form. In the forward form, usually invoked for extant species, a problem for the organism is described on the basis of knowledge of or supposition about what is important to the organism. Then some anatomical, physiological, or behavioral feature of the species is proposed as the organism’s solution to the problem. The backward form, usually used for extinct species known from fossil material, starts with a trait as a solution and searches for the problem that it has solved.” Lewontin, Richard. The Triple Helix: Gene, Organism, and Environment. 2000. Harvard University Press. Pp. 44-5.


“But the claim that the environment of an organism is causally independent of the organism, and that changes in the environment are autonomous and independent of changes in the species itself, is clearly wrong. It is bad biology, and every ecologist and evolutionary biologist knows that it is bad biology. The metaphor of adaptation, while once an important heuristic for building evolutionary theory, is now an impediment to a real understanding of the evolutionary process and needs to be replaced by another. Although all metaphors are dangerous, the actual process of evolution seems best captured by the process of construction.

“Just as there can be no organism without an environment, so there can be no environment without an organism.” Lewontin, Richard. The Triple Helix: Gene, Organism, and Environment. 2000. Harvard University Press. P. 48.


“An environment is something that surrounds or encircles, but for there to be a surrounding there must be something at the center to be surrounded. The environment of an organism is the penumbra of external conditions that are relevant to it because it has effective interactions with those aspects of the outer world.” Lewontin, Richard. The Triple Helix: Gene, Organism, and Environment. 2000. Harvard University Press. Pp. 48-9.


“The concept of an empty ecological niche cannot be made concrete. There is a non-countable infinity of ways in which the physical world can be put together to describe an ecological niche, nearly all of which would seem absurd or arbitrary because we have never seen an organism occupying such a niche.” Lewontin, Richard. The Triple Helix: Gene, Organism, and Environment. 2000. Harvard University Press. P. 49.


“It is, in general, not possible to understand the geographical and temporal distribution of species if the environment is characterized as a property of the physical region, rather than of the space defined by the activities of the organism itself.” Lewontin, Richard. The Triple Helix: Gene, Organism, and Environment. 2000. Harvard University Press. P. 53.


“The microclimate near the soil surface is quite different from that between two lower leaves of a maize plant, which is again quite different from the microclimate for leaves near the growing top of the plants. The zones change as the plant grows taller and as the leaves grow longer and touch the leaves of neighboring plants. These microclimatic variations play an extremely important role in growth and production because it is the intensity of solar radiation and the carbon dioxide concentration at the surface of the leaves that determine the rate of photosynthesis and thus the growth rate and productivity of the maize plant. So the rate of growth determines the microenvironment, which determines the rate of growth.

“Not only the rate of growth but the exact morphological pattern of leaves is an important variable. The spacing of leaves along the stem and their position around the stem, the shape of each leaf, its angle of repose against the stem, the hairiness of its surface determine how much light, moisture, and carbon dioxide reach the leaves and how rapidly oxygen produced by photosynthesis is carried away. And all of these affect the plant in a way that is characteristic of the pattern of development.

“The practical consequence of all this complexity is seen in the science of plant engineering. In an attempt to increase the productivity of crops, plant engineers make detailed measurements of microclimate around the plant and then redesign the pattern of leaves to increase the light falling on the photosynthetic surfaces and the available carbon dioxide. But when these redesigned plants, produced by selective breeding, are tested it turns out that the microclimatic conditions for which they were designed have now changed as a consequence of the new design. So the process must be carried out again, and again the redesign changes the conditions. The plant engineers are chasing not only a moving target but a target whose motion is impelled by their own activities. As we will see, this process is a model for a more realistic understanding of evolution by natural selection.” Lewontin, Richard. The Triple Helix: Gene, Organism, and Environment. 2000. Harvard University Press. Pp. 56-7.


“The notion that organisms are chasing a moving target during their evolution has a wide currency. In 1973, Leigh Van Valen pointed out a seeming paradox in evolutionary theory. If organisms are constantly adapting to the outer world, then as evolution goes on species should be better and better able to survive the rigors of the environment and so they should endure for longer and longer periods. But when Van Valen examined the fossil record he found that the time between first appearance and disappearance of forms has not grown longer over evolutionary time. His conclusion was that the environment is constantly changing so that adaptation to yesterday’s environment does not improve the chance of survival tomorrow. He called this the ‘Red Queen Hypothesis’ after the chess queen in Through the Looking Glass who found that she had to keep running just to stay in the same place because the ground was moving under her feet. The Red Queen, however, is not the same as a constructionist view of the organism and its environment. Even if the external world is changing in ways that are completely independent of the organisms, organisms will still have to run to keep up. The constructionist view is that the world is changing because the organisms are changing. The Red Queen’s running only makes the problem worse.” Lewontin, Richard. The Triple Helix: Gene, Organism, and Environment. 2000. Harvard University Press. Pp. 57-8. Reference is to Van Valen, L. “A new evolutionary law.” 1973. Evolutionary Theory 1: 1-30.


“The common external phenomena of the physical and biotic world pass through a transforming filter created by the peculiar biology of each species, and it is the output of this transformation that reaches the organism and is relevant to it. Plato’s metaphor of the cave is appropriate here. Whatever the autonomous processes of the outer world may be, they cannot be perceived by the organism. Its life is determined by the shadows on the wall, passed through a transforming medium of its own creation.” Lewontin, Richard. The Triple Helix: Gene, Organism, and Environment. 2000. Harvard University Press. P. 64.


“The growing environmentalist movement to prevent alterations in the natural world that will be, at best, unpleasant and, at worst, catastrophic for human existence cannot proceed rationally under the false slogan ‘Save the Environment.’ ‘The environment’ does not exist to be saved. The world inhabited by living organisms is constantly being changed and reconstructed by the activities of all of those organisms, not just by human activity.” Lewontin, Richard. The Triple Helix: Gene, Organism, and Environment. 2000. Harvard University Press. Pp. 67-8.


“Part of the success of naive reductionism and simplistic analysis comes from the opportunistic nature of scientific work. Scientists pursue precisely those problems that yield to their methods, like a medieval army that besieges cities for a period, subduing those whose defenses are weak, but leaving behind, still unconquered, islands of resistance.” Lewontin, Richard. The Triple Helix: Gene, Organism, and Environment. 2000. Harvard University Press. Pp. 72-3.


“What developmental genetics has done is to substitute a question that it can answer for one that it cannot, but without an explicit acknowledgment of the switch.” Lewontin, Richard. The Triple Helix: Gene, Organism, and Environment. 2000. Harvard University Press. P. 75.


“A consequence of the intermediate size and internal heterogeneity of living organisms is that they are the nexus of a very large number of weakly determining forces.” Lewontin, Richard. The Triple Helix: Gene, Organism, and Environment. 2000. Harvard University Press. P. 92.


“An organism’s life consists of constant mid-course corrections.” Lewontin, Richard. The Triple Helix: Gene, Organism, and Environment. 2000. Harvard University Press. P. 93.


“The meaning of words does not lie in their possible referential relation to the world, but in their use [referring to (the later) Wittgenstein’s understanding of language]. What matters is, how these words are being put to use, by members of the same community that partake in different language games. Therefore, language has a social function; it enables social relations between members of the same community that make use of the same language. Meaning, therefore, also is explained as being intersubjective, excluding all possible forms of a private (inner, non- or, pre-linguistic)-language: meaning and language hence are externalized and are supposed to be part of a community.”

“The concept meaning is, therefore, introduced for the first time, and this notion is distinguished from truth.” Gontier, Nathalie. “Introduction to evolutionary epistemology, language and culture.” Pp. 1-29. From Gontier, Nathalie, J.P. Van Bendegem & D. Aerts, Editors. Evolutionary Epistemology, Language and Culture: A Non-Adaptationist, Systems Theoretical Approach. 2006. Springer. P. 5.


“In short, evolutionary epistemology is an epistemological system which is based upon the conjecture that cognitive activities are a product of evolution and selection and that, vice versa, evolution itself is a cognition and knowledge process.” Wuketits, F.M. “Evolutionary epistemology: A challenge to science and philosophy.” Pp. 1-33. From Wuketits, F (ed.). Concepts and approaches in evolutionary epistemology. 1984. D. Reidel Publishing. P. 2. Quoted in Gontier, Nathalie. “Introduction to evolutionary epistemology, language and culture.” Pp. 1-29. From Gontier, Nathalie, J.P. Van Bendegem & D. Aerts, Editors. Evolutionary Epistemology, Language and Culture: A Non-Adaptationist, Systems Theoretical Approach. 2006. Springer. P. 9.


“Organisms (a) select their environment, (b) actively modify their environment by their own activity, (c) define their environment in terms of relevant variables, (d) create new environments for other organisms, (e) transform the physical nature of an environment input as their effects percolate through the developmental network, (f) determine by their movements and physiological activity the effective statistical pattern of environment, and (g) adapt to the environmental pattern that is partly of their own creation. Further, each part of the organism is ‘environment’ to the other parts. The conclusion of (d), (f) and (g) that organisms adapt to and create statistical patterns of environment finally suggests that the utilization of resources by populations not only uses up ecological opportunities but also create new ones: The variability in resource level may itself behave as a resource .... The traditional separation of the world into organism and environment as mutually exclusive classes ... leaves us with the task of then connecting them. A more dialectical approach emphasizes the mutual interpenetration of organism and environment.” Levins, Richard. Quoted in Hahlweg, K. 1989. “A systems view of evolution and evolutionary epistemology.” From Hahlweg, K. & C. Hooker, (eds). Issues in evolutionary epistemology. Pp. 45-78. SUNY Press. Then quoted in Gontier, Nathalie. “Introduction to evolutionary epistemology, language and culture.” Pp. 1-29. From Gontier, Nathalie, J.P. Van Bendegem & D. Aerts, Editors. Evolutionary Epistemology, Language and Culture: A Non-Adaptationist, Systems Theoretical Approach. 2006. Springer. P. 15.


“So, basically, until recently only two positions could be taken up by an anthropologist, interested in culture: an emic position or an etic position which correlate, respectively, with an insider and outsider position....”

“A third position to take has been developed recently, by Bourdieu and Pinxten, called the praxiological position.”

“It aims at combining the objectivist and the subjectivist approach: the external knowledge of ‘the other’ is internalized by the researcher and the introspective knowledge of the researcher is externalized into the subject of research at the same time. The dialectic between both movements allows for a full understanding of cultural phenomena.”

“Now here is where evolutionary epistemology fits in. This is because of the fact that we need to look at biological, neurological and cognitive learning theories in order to understand how external knowledge is internalized and how introspective knowledge is externalized.” Gontier, Nathalie. “Introduction to evolutionary epistemology, language and culture.” Pp. 1-29. From Gontier, Nathalie, J.P. Van Bendegem & D. Aerts, Editors. Evolutionary Epistemology, Language and Culture: A Non-Adaptationist, Systems Theoretical Approach. 2006. Springer. Pp. 18-9. Subquote is from Pinxten, R. When the day breaks: Essays in anthropology and philosophy. 1997. Peter Lang, Europaeischer Verlag der Wissenschaften. P. 68.


“As mentioned above, the Modern Synthesis focuses on two steps: the sex cells, where genes possibly are passed on from one generation to the next, and possible random mutations that occur within these genes. Hence the popular idea put forward by Neo-Darwinians that animals pass on their genes from one generation to the next.”

“This is not true: animals do not pass on their genes from one generation to the next, they pass on their sex cells (that contain genes) from one generation to the next, and here a horizontal element is involved: namely, two members of the same species, of the opposite sexes, mate and if all goes well a sperm cell penetrates an egg cell, resulting in the formation of a cell with diploid chromosomes.” Gontier, Nathalie. “Evolutionary epistemology and the origin and evolution of language: Taking symbiogenesis seriously.” Pp. 195-226. From Gontier, Nathalie, J.P. Van Bendegem & D. Aerts, Editors. Evolutionary Epistemology, Language and Culture: A Non-Adaptationist, Systems Theoretical Approach. 2006. Springer. P. 200.


“This crucial horizontal step is taken for granted and even ignored by Neo-Darwinian theory, because of their focus on genes. Every mating process, however, is a crucial horizontal (temporary merging) process of the parents, and every fertilization is a permanent merging and recombining of different cells that contain (mostly already existing) genes.” Gontier, Nathalie. “Evolutionary epistemology and the origin and evolution of language: Taking symbiogenesis seriously.” Pp. 195-226. From Gontier, Nathalie, J.P. Van Bendegem & D. Aerts, Editors. Evolutionary Epistemology, Language and Culture: A Non-Adaptationist, Systems Theoretical Approach. 2006. Springer. P. 201.


“Essentialist thinking is always about distinguishing the accidental from the essential. De Saussure for example developed his three laws. These state that the primary concern of linguistics is about coming to terms with the following three dichotomous relations within language: (a) the relation between lexicon and grammar; (b) the relation between form and meaning and (c) the relation between langue and parole. These dichotomous relations indeed are instruments to distinguish the accidental from the essential and hence are used to discover the core of ‘the’ language.” Gontier, Nathalie. “Evolutionary epistemology and the origin and evolution of language: Taking symbiogenesis seriously.” Pp. 195-226. From Gontier, Nathalie, J.P. Van Bendegem & D. Aerts, Editors. Evolutionary Epistemology, Language and Culture: A Non-Adaptationist, Systems Theoretical Approach. 2006. Springer. Pp. 206-7.


“Since all languages are different manifestations of one language, all languages are uniform, meaning that there is no directionality to language change. If there were directionality, language(s) would evolve and there would be ‘lesser’ and ‘more’ languages, but the essential, reified, ideal, universal language is, once evolved, evolutionless.” Gontier, Nathalie. “Evolutionary epistemology and the origin and evolution of language: Taking symbiogenesis seriously.” Pp. 195-226. From Gontier, Nathalie, J.P. Van Bendegem & D. Aerts, Editors. Evolutionary Epistemology, Language and Culture: A Non-Adaptationist, Systems Theoretical Approach. 2006. Springer. P. 207.


“The universal symbiogenetic process can be implemented in the study of language evolution in at least three ways: in the study of language variation; language genes and within the study of conceptual blending.” Gontier, Nathalie. “Evolutionary epistemology and the origin and evolution of language: Taking symbiogenesis seriously.” Pp. 195-226. From Gontier, Nathalie, J.P. Van Bendegem & D. Aerts, Editors. Evolutionary Epistemology, Language and Culture: A Non-Adaptationist, Systems Theoretical Approach. 2006. Springer. Pp. 216-7.


“The mechanisms at the base of language variation, however, can get comprehended as a form of horizontal evolution; just as bacteria can exchange genetic material freely within one generation, so languages can exchange grammatical structures, vowels, phonological elements freely. Languages, therefore, show more resemblance to bacterial types than to rigid species.” Gontier, Nathalie. “Evolutionary epistemology and the origin and evolution of language: Taking symbiogenesis seriously.” Pp. 195-226. From Gontier, Nathalie, J.P. Van Bendegem & D. Aerts, Editors. Evolutionary Epistemology, Language and Culture: A Non-Adaptationist, Systems Theoretical Approach. 2006. Springer. P. 218.


“However, conceptual blending can also be understood as a form of symbiogenesis, so therefore, I have redefined conceptual blending just to show how symbiotic this view really is: Conceptual blending is the combining of two or more conceptual frames that results in a new conceptual frame with meaning not seen in the different components.”

“It is important to note that in this definition, the components themselves are not static, unchangeable entities.” Gontier, Nathalie. “Evolutionary epistemology and the origin and evolution of language: Taking symbiogenesis seriously.” Pp. 195-226. From Gontier, Nathalie, J.P. Van Bendegem & D. Aerts, Editors. Evolutionary Epistemology, Language and Culture: A Non-Adaptationist, Systems Theoretical Approach. 2006. Springer. P. 222. Reference is to conceptual blending per Fauconnier, G. & M. Turner. The Way We Think: Conceptual Blending and the Mind’s Hidden Complexities. 2002. Basic Books.


“It is an old understanding in evolutionary sciences that our cognitive phenotype evolves in similar ways as the organic phenotype does.” Diettrich, Olaf. “The biological boundary conditions for our classical physical world view.” Pp. 67-93. From Gontier, Nathalie, J.P. Van Bendegem & D. Aerts, Editors. Evolutionary Epistemology, Language and Culture: A Non-Adaptationist, Systems Theoretical Approach. 2006. Springer. P. 67.


“But trial and error is a little bit too simple an explanation for complex matters such as the organic or the cognitive phenotype. First of all, the environment is not that dominant as people usually think. The selection pressure which a certain habitat will exert on an organism living there does not only depend on the structure of the habitat. It depends on the structure of the organism itself as well. Horses and snakes, for example, though they may have developed in exactly the same physical environment, have entirely different organs of locomotion which have no structural element in common. And, accordingly, entirely different will be the selective pressure they have to meet. Horses have to improve the elasticity of their limbs and the strength of their muscles. Snakes have to improve the surface friction of their skin.” Diettrich, Olaf. “The biological boundary conditions for our classical physical world view.” Pp. 67-93. From Gontier, Nathalie, J.P. Van Bendegem & D. Aerts, Editors. Evolutionary Epistemology, Language and Culture: A Non-Adaptationist, Systems Theoretical Approach. 2006. Springer. P. 68.


“Objects are defined by their properties and properties are defined as invariants of measuring operators. So, objects too are defined by means of operators. As we can neither measure a property nor act upon the object in question without the preceding application of defining operations (i.e. defining the properties which characterise the object in question), we can conclude that all we see and do is a matter of interaction between three different kinds of operators: defining, measuring and acting operators. In other words, what a perception is going to tell us, or what an acting will bring about depends on how the object perceived is defined.” Diettrich, Olaf. “The biological boundary conditions for our classical physical world view.” Pp. 67-93. From Gontier, Nathalie, J.P. Van Bendegem & D. Aerts, Editors. Evolutionary Epistemology, Language and Culture: A Non-Adaptationist, Systems Theoretical Approach. 2006. Springer. Pp. 69-70.


“The evolution of notated language has lessons that can help us understand the origin and emergence of speech. In a study of notated language the effects of the phonetic alphabet and literacy on the development of deductive logic, abstract science, codified law, and monotheism were revealed. We showed that these five developments, which emerged between the Tigris-Euphrates Rivers and the Aegean Sea between 2000 and 500 BC, formed an autocatalytic set of ideas that supported each other’s development. The alphabet not only served as a convenient way to notate speech it also taught the lessons of analysis (breaking up words into their basic phonemes), coding (writing), decoding (reading) and classification (alphabetization).

“From this work emerged the notion that language is both a medium of communication and an informatics tool since the structure of a language influences the way in which people organize information and develop ideas. This work led to the hypothesis that speech, writing, math, science, computing and the Internet represented six independent languages each with its own unique semantics and syntax. It was shown that these six forms of language formed an evolutionary chain of languages with each new language emerging from the previous forms of language as a bifurcation to a new level of order a la Prigogine in response to an information overload that the previous set of languages could not handle.” Logan, Robert. “The extended mind model of the origin of language and culture.” Pp. 149-167. From Gontier, Nathalie, J.P. Van Bendegem & D. Aerts, Editors. Evolutionary Epistemology, Language and Culture: A Non-Adaptationist, Systems Theoretical Approach. 2006. Springer. Pp. 149-150. References are: McLuhan, M. & R. Logan. 1977. “Alphabet, mother of invention.” Etcetera 34: 373-383. Logan, R. 1995. The fifth language: Learning a living in the computer age. Stoddart Publishing.


“My earlier work with the evolution of notated language was based on the premise that a new form of language evolved in response to the chaos resulting from the information overload associated with the previous forms of language. In light of this we should anticipate that the origin of speech was also due to a response to chaos and information overload.” Logan, Robert. “The extended mind model of the origin of language and culture.” Pp. 149-167. From Gontier, Nathalie, J.P. Van Bendegem & D. Aerts, Editors. Evolutionary Epistemology, Language and Culture: A Non-Adaptationist, Systems Theoretical Approach. 2006. Springer. P. 150.


“When the complexity of hominid life became so great that perception and learned reactions to perceptions alone could not provide enough requisite variety to model or regulate the challenges of day to day life a new level of order emerged based on concepts. Percepts arise from our impressions of the external world that we apprehend with our senses and are mediated by neural networks in our brains. Concepts, on the other hand, are abstract ideas that result from the generalization of particular examples. Concepts allow one to deal with things that are remote in both the space and time dimension. If our first words were concepts then language allowed us to represent things that are remote is both space and time and, hence, provide language with what Hockett defines as displacement.” Logan, Robert. “The extended mind model of the origin of language and culture.” Pp. 149-167. From Gontier, Nathalie, J.P. Van Bendegem & D. Aerts, Editors. Evolutionary Epistemology, Language and Culture: A Non-Adaptationist, Systems Theoretical Approach. 2006. Springer. P. 151. Reference is to Hockett, C. 1960. “The origin of speech.” Scientific American. 203: 88-111.


“Assuming that language is both a form of communication and an information processing system it is conjectured that the emergence of speech represented the actual transition from percept-based thought to concept-based thought. The spoken word, as we shall see, is the actual medium or mechanism by which concepts are expressed or represented.” Logan, Robert. “The extended mind model of the origin of language and culture.” Pp. 149-167. From Gontier, Nathalie, J.P. Van Bendegem & D. Aerts, Editors. Evolutionary Epistemology, Language and Culture: A Non-Adaptationist, Systems Theoretical Approach. 2006. Springer. P. 152.


“The use of a word transforms the brain from one state to another and replaces a set of percepts with a concept. A word is a srange attractor for all the percepts associated with the concept represented by that word. A word, therefore, packs a great deal of experience into a single utterance or sign. Millions of percepts of a linguistic community are boiled down by the language to a single word acting as a concept and a strange attractor for all those percepts.” Logan, Robert. “The extended mind model of the origin of language and culture.” Pp. 149-167. From Gontier, Nathalie, J.P. Van Bendegem & D. Aerts, Editors. Evolutionary Epistemology, Language and Culture: A Non-Adaptationist, Systems Theoretical Approach. 2006. Springer. P. 153.


“Human beings as person can be thought of as co-ontogenetic creatures that organize their lives and are mutually constituted with and by other persons with whom they relate in multiple ways and roles.” Ramirez-Goicoechea, Eugenia. “Cognition, evolution, and sociality.” Pp. 283-312. From Gontier, Nathalie, J.P. Van Bendegem & D. Aerts, Editors. Evolutionary Epistemology, Language and Culture: A Non-Adaptationist, Systems Theoretical Approach. 2006. Springer. P. 285.


“Two processes that are lived experientially together may share some common neural paths. Short-sighted people hear better with their glasses on and people hear better when they can see people’s faces or their lips moving (not because they know lip reading!), in what has been called the McGurk effect.” Ramirez-Goicoechea, Eugenia. “Cognition, evolution, and sociality.” Pp. 283-312. From Gontier, Nathalie, J.P. Van Bendegem & D. Aerts, Editors. Evolutionary Epistemology, Language and Culture: A Non-Adaptationist, Systems Theoretical Approach. 2006. Springer. P. 287.


“What J. Bruner called the scaffolded world we live in, full of reifications and social artefacts, constitutes the scenario for children to build up their own way into a selected environment, the frameworks they will explore for meaning and (more or less) coherence, in a never-ending process of reworking the legacy of their elders and the choices–within constraints–of their generation-mates.

“Caregivers bring forth and structure children’s abilities thanks to: (1) the dialogy of care-giver/child relationships; (2) body language, indirect communication, and emotional saliency; (3) infant direct speech (IDS, babytalk, motherese), exploratory talk, proper speech styles, and appropriate commentaries to the situation; (4) alternate participation as in turn-taking; (5) guided, educated attention; and (6) anticipatory cognitive and emotional stimulation as in inter-mental developmental zone where children learn to become inter-thinkers.

“Caregivers socialize providing the focus, the clues, the saliency, the format and dynamic repetitive and standardized structures from which the child will creatively build a shared world of his/her own. The education of attention funds shared rules about ways, contexts, and relevance, of what goes without saying, of what we trust our world to be about and of which we have intuitive, self-evident knowledge.” Ramirez-Goicoechea, Eugenia. “Cognition, evolution, and sociality.” Pp. 283-312. From Gontier, Nathalie, J.P. Van Bendegem & D. Aerts, Editors. Evolutionary Epistemology, Language and Culture: A Non-Adaptationist, Systems Theoretical Approach. 2006. Springer. Pp. 293-4. Reference is to Bruner, Jerome. 1983. Child’s Talk: learning to use the language. Oxford Univ. Press.


“But emotions are important in decision making because they point towards saliency, relevance, value, purposes, communication and directionality for action. Emotions and feelings tell us about how things go in the world for us and for others. Emotions are like an ‘information holding system’, reverberating loops that keep information active for further mental purposes. They allow us to concentrate attention and energy on certain aspects of the situation so we can hierarchically organize and reorganize it. Emotional deprivation and depression have been reported as having consequences in nexploratory activity, social intelligence, and inability to envisage mental tasks from a whole perspective. The attribution of emotional and intentional states, as part of a theory of mind and social cognition has been decisivie during hominization.” Ramirez-Goicoechea, Eugenia. “Cognition, evolution, and sociality.” Pp. 283-312. From Gontier, Nathalie, J.P. Van Bendegem & D. Aerts, Editors. Evolutionary Epistemology, Language and Culture: A Non-Adaptationist, Systems Theoretical Approach. 2006. Springer. Pp. 297-8. Subquote is from D’Andrade, R. 1981. “The cultural part of cognition.” Cognitive Science 5: 179-195.


“Motivated knowledgeable human practices become objectified by means of rutinization/ritualization, typification and institutionalization, that introduce new dynamics and emergencies [emergences?] within the system. Through this externalization, knowledge becomes objectified, communicable, structured, knowable for others to evaluate, discuss, agree upon, and rework. Objectifications could be understood as attractors that orient, direct, and capture human activity in its gravitational space, in its fluxes and exchanges as well as in its more consolidated and structured forms.

“The externalized reification processes were started by hominids through their social relationship, embedded in environmental selection/appropriation/transformation (i.e. object production, technology), language, ritual enactments–including body work. Externalization allowed for a new kind of recursivity that may have sped up both cross-modality and especialization as seen in the exponential cognitive and social complexity of homo sapiens sapiens.

“Devices that were selected, biosocially created, exaptated [exapted?], thanks to sociobiological cognitive abilities became self-organized and relatively autonomous as new attractors that catalyzed some of these very same capacities, giving them new strength and new direction. Once in motion, as in Tomasello’s ratchet effect, or Vico’s history in spiral, there is no way back.” Ramirez-Goicoechea, Eugenia. “Cognition, evolution, and sociality.” Pp. 283-312. From Gontier, Nathalie, J.P. Van Bendegem & D. Aerts, Editors. Evolutionary Epistemology, Language and Culture: A Non-Adaptationist, Systems Theoretical Approach. 2006. Springer. P. 300.


“It is the function of religious practice in establishing essential shared sentiments and ideas that Durkheim argues is a necessary foundation for social life, not religious beliefs.” Rawls, Anne W. Epistemology and Practice: Durkheim’s The Elementary Forms of Religious Life. 2004. Cambridge University Press. P. 3.


“Durkheim argued in The Division of Labor, that a sense of unity and well-being based on shared belief, while it is comforting to group members, ultimately threatens the security and solidarity of an advanced division of labor because it leads inevitably to exclusive groupings within the larger collective.”

“In arguing that religion played an essential role in establishing a shared knowledge base, Durkheim was rejecting existing approaches to the problem of knowledge, replacing explanations that began with the individual with his own socially based argument that knowledge is created by the shared experience of enacted practices.” Rawls, Anne W. Epistemology and Practice: Durkheim’s The Elementary Forms of Religious Life. 2004. Cambridge University Press. P. 3.


“Durkheim’s epistemology argument, articulated in the central chapters of The Elementary Forms, locates the origin of the fundamental categories of human thought, or reason, not in individual perceptions, as Hume had argued, nor as a transcendent and innate aspect of the mind, as Kant had argued, but rather, in the shared emotional experience of those ritually produced moral forces created by the enactment of concrete practices in the midst of an assembled group.” Rawls, Anne W. Epistemology and Practice: Durkheim’s The Elementary Forms of Religious Life. 2004. Cambridge University Press. P. 10.


“Their ‘Major Transitions’ [Smith and Szathmary’s] identified uncontroversially important episodes in evolutionary history, but each of these episodes also changes some key evolutionary factor: the construction of new individuals; the increasing bandwidth and fidelity of inheritance; the establishment of new inheritance channels; the development of open-ended sources of variation.” Calcott, Brett & K. Sterelny, Eds. 2011. The Major Transitions In Evolution Revisited. MIT Press. P. 1. Reference is to Smith, Maynard & E. 1995. “The major evolutionary transitions.” Nature 374: 227-232. Also their book The Major Transitions in Evolution. 1995. Oxford University Press.


“Among the major transitions are episodes of the creation of new kinds of evolutionary agent: eukaryotic cells; multicelled animals; social insects. These episodes of the evolution of individuality show that selection acts on collectives of fitness-bearing agents, not just on those agents themselves, and that higher-level selection drives evolutionary trajectories.” Calcott, Brett & K. Sterelny, Eds. 2011. The Major Transitions In Evolution Revisited. MIT Press. Pp. 3-4.


“Instead of conceptualizing life as evolving through a fixed, though immense, space of organic design, and asking how that space is explored over time, Maynard Smith and Szathmary conceived of the space of biological possibility as itself evolving.” Calcott, Brett & K. Sterelny, Eds. 2011. The Major Transitions In Evolution Revisited. MIT Press. P. 4.


“Life in this universe has an importance far beyond our understanding, because it is life that created us from nothing. It is life that has given us the ability to survive. It is life that has given so much beauty to this earth. It is life through which God has given the ability to humans to be guided by his prophets through the books that he has given to them.

“Life is God’s natural gift to humanity. People owe their life to God. Each minute of life is being counted and is valued as much as gold. Life is a gift that nobody can take from another, not at any price. You should take care, treat life the way you would treat the most precious object, and be careful to use it the right way.” Zaeef, Abdul Salam. My Life with the Taliban. 2010. Columbia University Press. P. xlvi.


“The key to Gibson’s theory is that animals must actively explore and attend to their environments to pick up the available information...

“This active sampling allows animals to perceive not only the ‘invariant structure’ we described above, but also ‘perspective structure.’

“When an animal moves and transforms the optical array, this provides information about its own locomotion–this is perspective structure. A flowing perspective structure indicates movement, whereas an arrested perspective structure indicates that the organism is at rest. In Gibson’s theory, then, perception of the environment is always and simultaneously a form of self-perception (nicely embedding the animal in its environment in a mutualistic way). Barrett, Louise. Beyond the Brain: How Body and Environment Shape Animal and Human Minds. 2011. Princeton University Press. Pp. 106-7. Reference is to Gibson, J.J. The Ecological Approach to Visual Perception. 1979. Erlbaum.


“ ... behavior is not about producing the ‘right’ response given a particular stimulus, but often means producing the ‘response’ that subsequently leads to the ‘right’ stimulus.” Barrett, Louise. Beyond the Brain: How Body and Environment Shape Animal and Human Minds. 2011. Princeton University Press. P. 139.


“Andrew Pickering, a sociologist of science, who has written a wonderful book about the British ‘cyberneticians,’ including Grey Walter, suggests that we should refer to the brain and what it does as ‘performative’ rather than ‘representational ....’” Barrett, Louise. Beyond the Brain: How Body and Environment Shape Animal and Human Minds. 2011. Princeton University Press. P. 143. Reference is to Pickering, Andrew. The Cybernetic Brain: Sketches of Another Future. 2010. University of Chicago Press.


“Polanyi makes the point that these three factors of production [labor, land, and money] are not natural commodities because they are not produced for sale. He called them ‘fictitious commodities’ for this reason.” Jackson, Ross. Occupy World Street: A Global Roadmap for Radical Economic and Political Reform. 2012. Chelsea Green Publishing. P. 57. Reference is to Polanyi, Karl. The Great Transformation. 2001. Beacon Press.


“Polanyi argues that prior to the emergence of capitalism, the economy was embedded in society, i.e., subordinated to politics, religion, and social relationships, whereas a truly self-regulating market–the ideal of the merchant class–would essentially extricate the economy from society. Polanyi considered the very idea of an unregulated, self-adjusting market to be a utopia that could not exist for any time without destroying both man and his environment. It should be eminently clear that no market system can exist without government regulations, particularly regarding the ‘fictitious commodities’ of land, labor, and money, which do not behave as real commodities except in the abstract models of the economists. So in practice it is not a question of regulation or no regulation, but how much and what kind of regulation.

“Since the emergence of capitalism in the nineteenth century, the dynamic of what Polanyi called the ‘double movement’ has characterized the struggle between the merchant-class supporters of this unobtainable utopia on the one hand and needs of the citizens for a stable, secure, and satisfying social life, and supportive natural environment, on the other. The latter is, in its essence, a struggle for local democracy, which is the opposite pole of a self-regulating market society.” Jackson, Ross. Occupy World Street: A Global Roadmap for Radical Economic and Political Reform. 2012. Chelsea Green Publishing. P. 58. Reference is to Polanyi, Karl. The Great Transformation. 2001. Beacon Press.


“In other words Darwinian evolution necessarily involves continued diversification, but what if the outcomes are subject to repeated channeling? It may then transpire that the tree has a quite specific structure, and one that it is far from a random exploration of biological space.” Morris, Simon Conway. “The predictability of evolution: glimpses into a post-Darwinian world.” 2009. Naturwissenschaften. 96:1313-1337. P. 1317.


“I have outlined the concept of evolutionary inherency, that is, the notion that pre-existing configurations make subsequent evolutionary outcomes far more likely.” Morris, Simon Conway. “The predictability of evolution: glimpses into a post-Darwinian world.” 2009. Naturwissenschaften. 96:1313-1337. P. 1323.


“In a remarkable survey of the available mutational pathways that confer bacterial resistance to an antibiotic by the employment of B-lactamase, Weinreich et al. note that in their study that although more than a hundred pathways exist, in practice, nearly all of them are dead-ends. Thus, they conclude ‘that intramolecular interactions render many mutational pathways selectively inaccessible, which implies the protein tape of life ... might be surprisingly repetitive.’

“It seems inevitable that many deeper organizational principles remain to be discovered in biological systems.” Morris, Simon Conway. “The predictability of evolution: glimpses into a post-Darwinian world.” 2009. Naturwissenschaften. 96:1313-1337. P. 1326. Reference is to Weinreich, DM, Delaney NF, DePristo MA, Hartl, DL. 2006. “Darwinian evolution can follow only very few mutational pathways to fitter proteins.” Sciences. 312:111-114.


“... the reality in biology is not that very many things work ‘after a fashion,’ but to the contrary out of the unimaginably large possibilities of design hyperspace almost nothing works but when it does it usually works extremely well.” Morris, Simon Conway. “The predictability of evolution: glimpses into a post-Darwinian world.” 2009. Naturwissenschaften. 96:1313-1337. P. 1331.


“The same stone, for example, may function as shelter for the crab that hides beneath it, as an anvil for the thrush that uses it to break open snail shells, and as a missile for an angry human to hurl at an adversary. In Gibson’s terms, shelter, anvil and missile are all properties of the stone that are available to be taken up. For von Uexkuell, by contrast, they are qualities that are bestowed upon the stone by the need of the creature in question and in the very act of attending to it. The stone only becomes a shelter when the crab scuttles under it, an anvil when the thrush smashes the shell against it, and a missile when the man picks it up to throw. Outside of these activities, it was none of these things. Thus, far from fitting into a given corner of the world (a niche), it is the animal that fits the world to itself by ascribing functional qualities to the things it encounters and thereby integrating them into a coherent system of its own. To denote this system – the world as it is constituted within the animal’s circuit of perception and action – von Uexkuell used the term Umwelt. The life of every creature, von Uexkuell thought, was so wrapped up in its own Umwelt that no other worlds were accessible to it. It is as though each one were floating in its own particular ‘bubble’ of reality.” Ingold, Tim. “Point, Line and Counterpoint: From Environment to Fluid Space.” From: Berthoz, A. & Y. Christen (eds.). 2009. Neurobiology of “Umwelt”: How Living Beings Perceive the World. Springer. P. 146. References are to: Von Uexkuell, J. 1992. “A stroll through the worlds of animals and men: a picture book of invisible worlds.” Semiotica 89(4): 319-391 (originally published in 1934).


“The human practitioner is unique in inhabiting the world of the open. To explain what he meant, Heidegger asked his listeners to compare an inanimate object like a stone, an animal and a human being. How do they differ? His answer took the form of three theses: ‘The stone ... is worldless; the animal is poor in world; man is world-forming.” Ingold, Tim. “Point, Line and Counterpoint: From Environment to Fluid Space.” From: Berthoz, A. & Y. Christen (eds.). 2009. Neurobiology of “Umwelt”: How Living Beings Perceive the World. Springer. P. 147. Reference is to Heidegger, M. 1995. “The fundamental concepts of metaphysics: world, finitude, solitude. Translated by W. McNeil, N. Walker. Indiana University Press. [Based on a course presented in 1929-30, originally published in 1983.]


“... an environment is that which surrounds the organism, yet you cannot surround a bundle without wrapping it up, converting the very paths along which life is lived into boundaries within which it is contained. Instead, let us imagine ourselves, as did Charles Darwin in The Origin of Species, standing before ‘the plants and bushes clothing an entangled bank.’ Observe how the fibrous bundles comprising every plant and bush are entwined with one another so as to form a dense mat of vegetation. What we have been used to calling the environment reappears on the bank as an immense tangle of lines.” Ingold, Tim. “Point, Line and Counterpoint: From Environment to Fluid Space.” From: Berthoz, A. & Y. Christen (eds.). 2009. Neurobiology of “Umwelt”: How Living Beings Perceive the World. Springer. P. 150.


“The acteur reseau was intended by its originators (if not by those who have been beguiled by its translation as network) to be comprised of just such lines of becoming. Their inspiration came, in large measure, from the philosophy of Deleuze. As we have already seen, with acknowledgement to Deleuze, the line of the web does not link the spider to the fly, neither does the latter’s line of flight link it to the spider. Ensconced at the centre of its web, the spider knows that a fly has landed somewhere on the outer margins, as it sends vibrations down the threads that are picked up by the spider’s super-sensitive, spindly legs. And it can then run along the lines of the web to retrieve its prey. Thus the thread-lines of the web lay down the conditions of possibility for the spider to interact with the fly, but they are not themselves lines of interaction. If these lines are relations, then they are relations not between but along. Of course, as with the spider, the lives of organisms generally extend along not one but multiple lines, knotted together at the centre but trailing innumerable loose ends at the periphery. Thus each should be pictured, as Latour has latterly suggested, in the shape of a star ‘with a center surrounded by many radiating lines, with all sorts of tiny conduits leading to and fro.’ No longer a self-contained object like a ball that can propel itself from place to place, the organism now appears as an ever ramifying web of lines of growth. This is the Deleuzeian haecceity, famously compared to a rhizome. I personally prefer the image of the fungal mycelium. Indeed as the mycologist Alan Rayner has suggested, the whole of biology would be different had it taken the mycelium as the protoypical exemplar of the living organism. For it could not, then, have been built upon the presumption that life is contained within the absolute bounds of fixed forms. We would rather have a biology that starts from the fluid character of the life process, wherein boundaries are sustained only thanks to the continual flow of materials across them.” Ingold, Tim. “Point, Line and Counterpoint: From Environment to Fluid Space.” From: Berthoz, A. & Y. Christen (eds.). 2009. Neurobiology of “Umwelt”: How Living Beings Perceive the World. Springer. P. 152. References: Latour, Bruno. 2005. Reassembling the social: an introduction to actor-network theory. Oxford University Press. P. 177. Deleuze, G. & F.Guattari. 2004 A thousand plateaus: capitalism and schizophrenia. Translated by B. Massumi. Continuum. Originally published in 1980. P. 290. Rayner, Alan. 1997. Degrees of freedom: living in dynamic boundaries. Imperial College Press.


“Dividing an organism’s world into behavioral and biological factors has created counterproductive explanatory problems, often presented as a conflict between reductionism and explanation based on publicly accessible external variables. The main purpose of this paper is to suggest that an organism’s integrated repertoire of operant behavior has the status of a biological system, similar to other systems, like the nervous, cardiovascular, or immune systems.” Thompson, Travis. “Relations among functional systems in behavior analysis.” Journal of the Experimental Analysis of Behavior. 2007. 87, 423-440. P. 423.


“The integrated repertoire of behavioral units (operants) that have been acquired and maintained under the functional control of motivational or establishing operations, discriminative stimuli, mediating events conjoint with reinforced responses, and consequences, function as a biological system.” Thompson, Travis. “Relations among functional systems in behavior analysis.” Journal of the Experimental Analysis of Behavior. 2007. 87, 423-440. P. 423.


“Strictly speaking ‘Um-welt’ means the ‘world around’ in which animals and humans live. It can be translated in French by ‘Milieu.’ However, for von Uexkuell it includes the world of things in the environment, the perceived world, the signals emitted by both the subject and the things, and the actions that can be performed by each species. Above all, it includes the significance or meaning of things for each animal, in that they are potentially participating in the survival and social relations of the animal.” Berthoz, Alain. “The Human Brain ‘Projects’ upon the World, Simplifying Principles and Rules for Perception.” From: Berthoz, A. & Y. Christen (eds.). 2009. Neurobiology of “Umwelt”: How Living Beings Perceive the World. Springer. P. 18.


“Perceptual and effector worlds together form a closed unit, the Umwelt.” Von Uexkuell, Jakob. 1934. Streifzuege durch die Umwelten von Tieren und Menschen. Springer. English translation by C. Schiller. “A stroll through the worlds of animals and men. A picture book of invisible worlds.” in: Coll., Instinctive Behavior. 1957. P. 6. Quoted in Fagot-Largeault, Anne. “Anthropological Physiology: von Uexkuell, Portmann, Buytendijk.” From: Berthoz, A. & Y. Christen (eds.). 2009. Neurobiology of “Umwelt”: How Living Beings Perceive the World. Springer. P. 2.


“As the spider spins its threads, every subject spins his relations to certain characters of the things around him, and weaves them into a firm web which carries his existence.” Von Uexkuell, Jakob. 1934. Streifzuege durch die Umwelten von Tieren und Menschen. Springer. English translation by C. Schiller. “A stroll through the worlds of animals and men. A picture book of invisible worlds.” in: Coll., Instinctive Behavior. 1957. P. 14. Quoted in Fagot-Largeault, Anne. “Anthropological Physiology: von Uexkuell, Portmann, Buytendijk.” From: Berthoz, A. & Y. Christen (eds.). 2009. Neurobiology of “Umwelt”: How Living Beings Perceive the World. Springer. P. 2.


“Adolf Portmann (1897-1982) was a zoologist known for having developed the idea that human beings were born premature, and that the extra-uterine embryos we all were, found a second uterus in their social environment.” Fagot-Largeault, Anne. “Anthropological Physiology: von Uexkuell, Portmann, Buytendijk.” From: Berthoz, A. & Y. Christen (eds.). 2009. Neurobiology of “Umwelt”: How Living Beings Perceive the World. Springer. P. 3.


“Different sensory inputs may require the same motor output, and different sensory inputs that require the same motor output are said to form ‘categories’.” Mirolli, Marco & D. Parisi. “Language as a Cognitive Tool.” Minds & Machines. 2009. 19:517-528. P. 521.


“What are the consequences of this reciprocal functional linking of the sensory-motor network and the linguistic network, i.e., of possessing a language, for the organism’s categories? The answer is that categorization is enhanced by language. When the child hears and understands the language spoken by others, the child’s categories tend to become better categories, i.e., smaller and more distant clouds of points in the child’s neural network.” Mirolli, Marco & D. Parisi. “Language as a Cognitive Tool.” Minds & Machines. 2009. 19:517-528. Pp. 522-23.


“As Tomasello argues, the establishment of collaborative interaction, can only be achieved by animals mutually perceiving each other’s visible actions. It could not be achieved by way of vocalisations. A vocalisation can draw the attention of a recipient to its source, to the originator of the sound. But that sound cannot be used by itself to direct the attention of a recipient to something else that is to constitute a specific object for joint attention. One cannot point with a vocalisation. This can only be done through a visible action that serves to link, in someway, the actor to something in the environment in relation to which he is acting.” Kendon, Adam. “Language’s matrix.” 2009. Gesture. 9:3, 355-372. P. 359.


“A much better approach, it seems to me, and one that takes into consideration how utterances are actually produced in modern speakers, would be to start with the assumption that the transition into referential or language-like expressions involved hands and body, face and voice and mouth, all together, as an integrated ensemble. What so many writers on this topic – ‘gesture firsters’ and ‘speech firsters’ both – pay little attention to is the fact that modern humans, when they speak together in face-to-face situations, especially in the informal settings of everyday interactions, always mobilise face and hands and voice together in complex orchestrations.” Kendon, Adam. “Language’s matrix.” 2009. Gesture. 9:3, 355-372. P. 363.


“A more plausible approach would be to see that the diversification of languages comes about as a consequence of the way in which linguistic expressions serve to signify things in the world. They do this, not by signifying things directly but by signifying the concepts in terms of which the things in the world are construed. These concepts or conceptual categories are not dictated by anything in the world, they are, rather, the creations of communities of speakers....”

“There are no cognitive categories that are ‘given’ (except possibly at some very abstract level), so that the way one group may end up setting up linguistic categories can be rather different from the way another group may do this. The categorisations that language creates are the products of socially shared agreements, and these are free to vary within a very wide range....”

“Language differences can be (and are) exploited as sources of group pride and identity, and people may work to create and exaggerate such differences as part of the process of group differentiation, but the fundamental reason for language differentiation lies in the fact that languages are conceptual categorisation systems, freely created through local historical processes.” Kendon, Adam. “Language’s matrix.” 2009. Gesture. 9:3, 355-372. Pp. 368-69.


“Technique thus places the subject at the centre of activity, whereas technology affirms the independence of production from human subjectivity.” Ingold, Tim. The Perception of the Environment: Essays in livelihood, dwelling and skill. 2000. Routledge. P. 315.


“... technical evolution describes a process not of complexification but of objectification of the productive forces.” Ingold, Tim. The Perception of the Environment: Essays in livelihood, dwelling and skill. 2000. Routledge. P. 319.


“Thus in hunting, it is commonly supposed that the animal gives itself to be killed by the hunter who, as a recipient, occupies the subordinate position in the transaction. The spear, arrow or trap serves here as a vehicle for opening or consummating a relationship. If the arrow misses its mark, or if the trap remains empty, it is inferred that the animal does not as yet intend to enter into a relationship with the hunter by allowing itself to be taken. In that way, the instruments of hunting serve a similar purpose to the tools of divination, revealing the otherwise hidden intentions of non-human agents in a world saturated with personal powers of one kind and another. In short, whereas for farmers and herdsmen, the tool is an instrument of control, for hunters and gatherers it would better be regarded as an instrument of revelation.” Ingold, Tim. The Perception of the Environment: Essays in livelihood, dwelling and skill. 2000. Routledge. P. 320.


“Each of these sorts of phenomena–a function, reference, purpose, or value–is in some way incomplete. There is something not-there there. Without this ‘something’ missing, they would just be plain and simple physical objects or events, lacking these otherwise curious attributes. Longing, desire, passion, appetite, mourning, loss, aspiration–all are based on an analogous intrinsic incompleteness, an integral without-ness.

“As I reflect on this odd state of things, I am struck by the fact that there is no single term that seems to refer to this elusive character of such things. So, at the risk of initiating this discussion with a clumsy neologism, I will refer to this as an absential feature, to denote phenomena whose existence is determined with respect to an essential absence. This could be a state of things not yet realized, a specific separate object of a representation, a general type of property that may or may not exist, an abstract quality, an experience, and so forth–just not that which is actually present. This paradoxical intrinsic quality of existing with respect to something missing, separate, and possibly nonexistent is irrelevant when it comes to inanimate things, but it is a defining property of life and mind. A complete theory of the world that includes us and our experience of the world, must make sense of the way that we are shaped by and emerge from such specific absences. What is absent matters, and yet our current understanding of the physical universe suggests that is should not. A causal role for absence seems to be absent from the natural sciences.” Deacon, Terrence. Incomplete Nature: How Mind Emerged from Matter. 2012. W.W. Norton. Pp. 2-3.


“Dynamical systems theories are ultimately forced to explain away the end-directed and normative characteristics of organisms, because they implicitly assume that all causally relevant phenomena must be instantiated by some material substrate or energetic difference. Consequently, they are as limited in their power to deal with the representational and experiential features of mind as are simple mechanistic accounts.” Deacon, Terrence. Incomplete Nature: How Mind Emerged from Matter. 2012. W.W. Norton. P. 5.


“Teleology is like a mistress to a biologist: he cannot live without her but he’s unwilling to be seen with her in public.” Haldane, J.B.S. Quoted in: Deacon, Terrence. Incomplete Nature: How Mind Emerged from Matter. 2012. W.W. Norton. P. 107. Appears to be from: Bernal, J.D., (Ed). 1967. The Origin of Life. World Publishing Co.


“The concept of constraint is, in effect, a complementary concept to order, habit, and organization, because it determines a similarity class by exclusion.” Deacon, Terrence. Incomplete Nature: How Mind Emerged from Matter. 2012. W.W. Norton. Pp. 191-2.


“Constraints are what is not there but could have been, irrespective of whether this is registered by any act of observation.” Deacon, Terrence. Incomplete Nature: How Mind Emerged from Matter. 2012. W.W. Norton. P. 192.


“This way of characterizing disorder is exemplified by an information-theoretic means of measuring complexity termed Kolmogorov complexity, after the theoretician who first promoted its use, the Russian mathematician Andrey Nikolaevich Kolmogorov (1903-1987). It can most easily be understood in terms of a method for analyzing or generating a string of numbers. If the same string can be generated by an algorithm that is shorter than that string, it is said to be compressible to that extent. Such an algorithm effectively captures a form of redundancy that is not superficially exemplified in its product.” Deacon, Terrence. Incomplete Nature: How Mind Emerged from Matter. 2012. W.W. Norton. P. 196.


“So what may appear chaotic may be merely the result of a simple operation that tends to entwine with itself to the point that any regularity is obscured. Alternatively, being impossible to simplify means that there are only details to contend with, nothing simpler. Irrespective of whether all real phenomena are maximally algorithmically complex–as extreme nominalism would suggest–or are algorithmically compressible without residue–as extreme realism would suggest–a constraint view of orderliness still applies.” Deacon, Terrence. Incomplete Nature: How Mind Emerged from Matter. 2012. W.W. Norton. Pp. 196-7.


“Recasting the Realism/Nominalism debate in terms of dynamics and constraints eliminates the need to refer to both abstract generals, like organization, and simple particular objects or events lacking in organization. Both are simplifications due to our representation of things, not things in themselves. What exist are processes of change, constraints exhibited by those processes, and the statistical smoothing and the attractors that embody the options left by these constraints.” Deacon, Terrence. Incomplete Nature: How Mind Emerged from Matter. 2012. W.W. Norton. P. 197.


“For general purposes, then, it would be useful to distinguish between changes that must be forced to occur through extrinsic intervention and those that require intervention to prevent them from occurring....

“I will call changes in the state of a system that are consistent with the spontaneous, ‘natural’ tendency to change, irrespective of external interference, orthograde changes. The term literally refers to going with the grade or tilt or tendency of things, as in falling, or ‘going along with the flow.’ In contrast, I will call changes in the state of a system that must be extrinsically forced, because they run counter to orthograde tendencies, contragrade changes.” Deacon, Terrence. Incomplete Nature: How Mind Emerged from Matter. 2012. W.W. Norton. P. 223.


“Contragrade change is the natural consequence of one orthograde process influencing a different orthograde process...” Deacon, Terrence. Incomplete Nature: How Mind Emerged from Matter. 2012. W.W. Norton. P. 224.


“It is simply because the world is highly heterogeneous that there can be contragrade processes.” Deacon, Terrence. Incomplete Nature: How Mind Emerged from Matter. 2012. W.W. Norton. P. 224.


“Since orthograde processes ensue spontaneously, they are ubiquitously present, even during processes of contragrade (forced) changes. A contragrade change must therefore derive from two or more orthograde processes, each in some way undoing the other’s effects. To put this in the terms introduced in the previous chapter, each must constrain the other. The tendency of one orthograde process to realize the full range of its degrees of freedom (e.g., the diffusion into all potential locations) must diminish the tendency of another orthograde process to realize all its potential degrees of freedom.” Deacon, Terrence. Incomplete Nature: How Mind Emerged from Matter. 2012. W.W. Norton. P. 225.


“Rather than order or disorder, then, I suggest that we begin to think of entropy as a measure of constraint. An increase in entropy is a decrease in constraint, and vice versa.” Deacon, Terrence. Incomplete Nature: How Mind Emerged from Matter. 2012. W.W. Norton. P. 228.


“We can thus describe the increase in entropy as a decrease in constraints, and the second law can be restated as follows: In any given interaction, the global level of constraint can only decrease.” Deacon, Terrence. Incomplete Nature: How Mind Emerged from Matter. 2012. W.W. Norton. P. 229.


“Orthograde thermodynamic change occurs because it is an unperturbed reflection of the space of possible trajectories of change for that system. It is in this sense a consequence of the geometric properties of this probability space. An orthograde change just happens, irrespective of anything else, so long as there is any change occurring at all. I take this to be a reasonable way to reinterpret Aristotle’s notion of a formal cause in a modern scientific framework, because the source of the asymmetry is ultimately a formal or geometric principle.” Deacon, Terrence. Incomplete Nature: How Mind Emerged from Matter. 2012. W.W. Norton. Pp. 230-1.


“... Homeodynamics–coins a term that I think can more generally describe this most basic orthograde dynamic wherever we encounter it. It is a dynamic that spontaneously reduces constraints to their minimum and thus more evenly distributes whatever property is being changed from moment to moment and locus to locus.” Deacon, Terrence. Incomplete Nature: How Mind Emerged from Matter. 2012. W.W. Norton. Pp. 232-3.


“The second law of thermodynamics thus describes a tendency to spontaneously reduce constraint, while thermodynamic work involves the creation of constraint.” Deacon, Terrence. Incomplete Nature: How Mind Emerged from Matter. 2012. W.W. Norton. P. 247.


“What does this tell us in terms of morphodynamic processes in general? Using the Benard cell case as an exemplar, it demonstrates that if there are intrinsic interaction biases available (buoyancy differences, viscosity effects, and geometric distribution constraints in this case), the persistent imposition of constraint (constant heating) will tend to redistribute this additional constraint into these added dimensions of potential difference. Moreover, these additional dimensions are boundary conditions, to the extent that they are uniformly present across the system. This includes the geometric constraint, which is not derived from any material feature of the system or its components. Because these additional dimensions are systemwide and ubiquitous, they are also of a higher level of scale than the constraints of molecular interaction. So this transfer of constraints from molecular-level differences to global-level differences also involves the propagation of constraint from lower- to higher-order dynamics.

“The distinct higher-order orthograde tendency that characterizes the morphodynamics of Benard cell formation thus emerges from the lower-order orthograde tendency that characterizes fluid thermodynamics. This tendency to redistribute constraint to higher-order dimensions is an orthograde tendency of a different and independent kind than the spontaneous constraint dissipation that characterizes simpler thermodynamic systems.” Deacon, Terrence. Incomplete Nature: How Mind Emerged from Matter. 2012. W.W. Norton. Pp. 254-5.


“Life is characterized by the use of energy flowing in and out of an organism to generate the constraints that maintain its structural-functional integrity. Since organisms are subject to the incessant dissipative effects of the second law of thermodynamics, they additionally need to constantly impede certain forms of dissipation. Organisms take advantage of the flow of energy through them to do work to generate constraints that block some dissipative pathways as compared to others.” [An early description of teleodynamics] Deacon, Terrence. Incomplete Nature: How Mind Emerged from Matter. 2012. W.W. Norton. P. 263.


“... I will adopt the more descriptive term autogen for the whole class of related minimal teleodynamical systems. This term captures what is perhaps its most distinctive defining feature: being a self-generating system. In this respect, it is closely related to Maturana and Varela’s autopoiesis, though referring to a distinct dynamical unit process rather than a process more generally, for which I have reserved the more general term tel[e]odynamic. The term autogen is also easily modified to apply to a broader class of related forms by describing any form of self-encapsulating, self-repairing, self-replicating system that is constituted by reciprocal morphodynamic processes as autogenic, and describing the process, appropriately, as autogenesis.” Deacon, Terrence. Incomplete Nature: How Mind Emerged from Matter. 2012. W.W. Norton. P. 307.


“The term [autogenesis] is reserved for simple dynamical systems that accomplish self-generation by virtue of harnessing the co-dependent reciprocity of component morphodynamic processes.” Deacon, Terrence. Incomplete Nature: How Mind Emerged from Matter. 2012. W.W. Norton. Pp. 307-8.


“One might then describe an autogen as a hierarchic hypercyclic system, with each self-organizing component acting as supporting environment or context for the other.” Deacon, Terrence. Incomplete Nature: How Mind Emerged from Matter. 2012. W.W. Norton. Pp. 308-9.


“Autogenic organization only exists with respect to a relevant supportive environment. So autogenic individuation is also only defined with respect to a particular type of environment. Identity and environment are thus reciprocally defined and determined with respect to each other, because the same molecular configuration in a non-supportive environment lacks any of the defining properties of autogenesis. Indeed, the very possibility for autogen existence can be described as one of the possible micro configurations of a certain class of environments with the molecular constitution conducive to autogen formation.” Deacon, Terrence. Incomplete Nature: How Mind Emerged from Matter. 2012. W.W. Norton. P. 310.


“Morphodynamic processes are the only spontaneous processes that generate and propagate constraints, and autogens demonstrate that reciprocity between morphodynamic processes can preserve and replicate constraints.” Deacon, Terrence. Incomplete Nature: How Mind Emerged from Matter. 2012. W.W. Norton. P. 315.


“It should come as no surprise that an organism does not maximize the rate at which it generates entropy or the throughput of energy. Instead, an organism uses the flow of entropy to build constraints that ultimately divert and slow this process, increasing the amount of local work it can extract.” Deacon, Terrence. Incomplete Nature: How Mind Emerged from Matter. 2012. W.W. Norton. P. 318.


“So, whereas morphodynamic processes merely propagate and amplify constraints, teleodynamic processes additionally preserve them. This is the common theme of both life and evolution.” Deacon, Terrence. Incomplete Nature: How Mind Emerged from Matter. 2012. W.W. Norton. P. 318.


“Thus morphodynamic organization emerges due to the interaction of opposed thermodynamic processes (e.g., perturbation and equilibration), and it results in constraint amplification rather than constraint dissipation (i.e., increase in entropy). Analogously teleodynamic organization emerges due to reciprocally organized morphodynamic processes, and entropy ratcheting rather than entropy production. In this respect, autogen formation exemplifies the defining feature of an emergent phase transition–the appearance of a new form of orthograde organization.” Deacon, Terrence. Incomplete Nature: How Mind Emerged from Matter. 2012. W.W. Norton. P. 319.


“Emergence is, in effect, defined by a polarity reversal in orthograde dynamics with ascent in scale. Thus the orthograde signature of thermodynamic change is constraint dissipation, the orthograde signature of morphodynamic change is constraint amplification, and the orthograde signature of teleodynamic change is constraint preservation and correlation. The polarity reversal that defines the emergence of teleodynamics from morphodynamics is what characterizes life and evolution. A fit or interdependent correspondence between constraints in different domains is the essence of both biological adaptation and the relationship characterizing representational relationships.” Deacon, Terrence. Incomplete Nature: How Mind Emerged from Matter. 2012. W.W. Norton. P. 324.


“So long as contragrade change persists, work is involved ...” Deacon, Terrence. Incomplete Nature: How Mind Emerged from Matter. 2012. W.W. Norton. P. 327.


“Work is a spontaneous change inducing a non-spontaneous change to occur.” Deacon, Terrence. Incomplete Nature: How Mind Emerged from Matter. 2012. W.W. Norton. P. 335.


“Ultimately, the capacity of the perturbed system as a whole to be tapped to perform work at the level above that of molecular collision is a consequence of the distributional features of the incessant micro work, not the energy of the component collisions, which as a whole can increase, decrease, or remain unchanged. In other words, in thermodynamics the macro doesn’t simply reduce to the micro, even though it is dependent upon it. The macroscopic form of the distribution is the critical factor.” Deacon, Terrence. Incomplete Nature: How Mind Emerged from Matter. 2012. W.W. Norton. P. 336.


“This allows us to propose an even more general definition of work: it is simply the production of contragrade change.” Deacon, Terrence. Incomplete Nature: How Mind Emerged from Matter. 2012. W.W. Norton. P. 337.


“That is, we can begin to discern a basis for a form of causal openness in the universe. To frame these insights in somewhat more enigmatic and cosmic terms, we might speculate that whereas the conservation laws of science tell us that the universe is closed to the creation or destruction of the amount of possible ‘difference’ (the ultimate determinate of what constitutes mass-energy) available in the world, they do not restrict the distributional possibilities that these differences can assume, and it is distributional relationships which determine the forms that change can take.” Deacon, Terrence. Incomplete Nature: How Mind Emerged from Matter. 2012. W.W. Norton. P. 342.


“So to restate the closure or conservation laws a bit more carefully: the universe is closed to gain or loss of mass-energy and the most basic level of formal causality is unchanging, but it is open to organizational constraints on formal cause and the introduction of novel forms of efficient cause. Thus we have causal openness even in a universe that is the equivalent of a completely isolated system. New forms of work can and are constantly emerging.” Deacon, Terrence. Incomplete Nature: How Mind Emerged from Matter. 2012. W.W. Norton. P. 368.


“The vast power of evolvability thus is a consequence of the fact that natural selection is a process that regularly transforms incidental physical properties into functional attributes. An adaptation is the realization of a set of constraints on candidate mechanisms, and so long as those constraints are maintained, other features are arbitrary. But this means that with every adaptation, there are innumerable other arbitrary properties potentially brought into play.” Deacon, Terrence. Incomplete Nature: How Mind Emerged from Matter. 2012. W.W. Norton. Pp. 423-4.


“Evolution is not imposed design, but progressive constraint.” Deacon, Terrence. Incomplete Nature: How Mind Emerged from Matter. 2012. W.W. Norton. P. 426.


“... natural selection assumes the existence of processes of persistent non-equilibrium thermodynamics, self-maintenance, reproduction, and adaptation. It cannot therefore be the complete explanation for their origins, particularly for the origins of their teleodynamic character.” Deacon, Terrence. Incomplete Nature: How Mind Emerged from Matter. 2012. W.W. Norton. P. 429.


“I define symbionomics as the study of the emergence of complex systems through self-organization, self-selection, coevolution, and symbiosis.” De Rosnay, Joel. The Symbiotic Man: A New Understanding of the Organization of Life and a Vision of the Future. 2000. McGraw Hill. P. 31.


“An evolutionary convergence is occurring: technology is invading the biological world, and biology is invading the world of machines.” De Rosnay, Joel. The Symbiotic Man: A New Understanding of the Organization of Life and a Vision of the Future. 2000. McGraw Hill. P. 39.


“The coevolution of a society and its environment, with each determining the other, adds a new dimension in space and time.” De Rosnay, Joel. The Symbiotic Man: A New Understanding of the Organization of Life and a Vision of the Future. 2000. McGraw Hill. P. 39.


“A similar phenomenon exists in the birth, growth, and development of a city; the city is both a means of support and a consequence of the activity of the collective organism that lives in it, builds, it, and maintains its structure.” De Rosnay, Joel. The Symbiotic Man: A New Understanding of the Organization of Life and a Vision of the Future. 2000. McGraw Hill. P. 39.


“The digitization and circulation of information in networks is analogous to the introduction of currency into the networks of the economy. Before the introduction of currency, goods or services were bought and sold by barter, which made exchanges slow and limited them considerably. By creating additional space for expansion and by shrinking time and space, the introduction of currency led to explosive growth in the world economy.” De Rosnay, Joel. The Symbiotic Man: A New Understanding of the Organization of Life and a Vision of the Future. 2000. McGraw Hill. P. 51.


“The Internet is not a new technology; it is an integrated resource-sharing system, an informational ecosystem made up of numerous interdependent elements ...” De Rosnay, Joel. The Symbiotic Man: A New Understanding of the Organization of Life and a Vision of the Future. 2000. McGraw Hill. Pp. 54-5.


“From the point of view of macrobiology, the symbiosis between humans and cars is particularly illuminating. Humanity maintains a fleet of 500 million vehicles, extracts the energy that feeds them, and builds roads for their circulation, garages for their repair, and factories for their ‘reproduction.’ In return for the maintenance and reproduction of the automobile species, cars allow humans to travel at greater speeds, to act more effectively, to conquer distance, and they provide pleasure and social status. They are also, as we saw in the previous chapter, a source of disease for the social organism and of danger and pollution for the planetary organism. Like symbiotic partners that turn into parasites, they are endangering the future of the ecosphere.” De Rosnay, Joel. The Symbiotic Man: A New Understanding of the Organization of Life and a Vision of the Future. 2000. McGraw Hill. P. 76.


“... our environment is filled with biomechanical communications systems: door and drawer handles, keys, faucets; the steering wheel, clutch, and brake pedal of a car; the tiller of a boat; the control column and rudder of an airplane.” De Rosnay, Joel. The Symbiotic Man: A New Understanding of the Organization of Life and a Vision of the Future. 2000. McGraw Hill. Pp. 78-9.


“The marriage of virtual reality and biotics will lead to the ultimate interface between the human brain and that of the cybiont. Humans will then have access to a new inner universe. To the relationship between the real and the imaginary will be added the relationship between the real, the imaginary, and the virtual–a shared inner universe, the embryo of a planetary coconsciousness leading its own life, notwithstanding the limited existence of the symbiotic consciousnesses of which it is made up.” De Rosnay, Joel. The Symbiotic Man: A New Understanding of the Organization of Life and a Vision of the Future. 2000. McGraw Hill. P. 107.


“The cybiont is to the social macroorganism what Gaia is to the planetary ecosystem.” De Rosnay, Joel. The Symbiotic Man: A New Understanding of the Organization of Life and a Vision of the Future. 2000. McGraw Hill. P. 113.


“... at the present time it [the cybiont] has no need to move, since its life as a parasite of Gaia provides it with the energy needed for survival.” De Rosnay, Joel. The Symbiotic Man: A New Understanding of the Organization of Life and a Vision of the Future. 2000. McGraw Hill. P. 114.


“Like any living organism, the cybiont provides for its major basic functions: self-preservation, self-regulation, and self-repair. Using people and machines, it feeds itself, converts energy, digests, and eliminates its waste.” De Rosnay, Joel. The Symbiotic Man: A New Understanding of the Organization of Life and a Vision of the Future. 2000. McGraw Hill. P. 116.


“In an age of globalization, as the division of labor advances around the world, many problems are arising that Durkheim warned against. In particular the social function of religious practices is being confused with religious beliefs. If persons, in an attempt to overcome the increasing contingency and insecurity of modern life, turn to traditional religious communities that exclude nonbelievers, increased fragmentation will result. Practices, on the other hand, have the potential to be inclusive. It was Durkheim’s position that an international cult would have to be based on shared practices that do not discriminate between beliefs.” Rawls, Anne W. Epistemology and Practice: Durkheim’s The Elementary Forms of Religious Life. 2004. Cambridge University Press. P. 26.


“Durkheim also emphasizes the relationship between identical sounds and movements and the development of reason. His argument in this regard is essential to an understanding of his positions, because it places the emphasis, in explaining the origin of the categories, on the experience of enacting sounds and movements in common, not on learning words, or mastering systems of belief.” Rawls, Anne W. Epistemology and Practice: Durkheim’s The Elementary Forms of Religious Life. 2004. Cambridge University Press. P. 37.


“For Durkheim, the possibility of shared knowledge and mutual intelligibility depends entirely upon the collective enactment of those shared practices which produce moral force and through the experience of moral force the categories of the understanding. Without participation in ritual assemblies, and the performance of ritual practices, the categories would not be presented to experience, and all contact between minds would be lost.” Rawls, Anne W. Epistemology and Practice: Durkheim’s The Elementary Forms of Religious Life. 2004. Cambridge University Press. P. 39.


“Durkheim treats symbols as a surface phenomena beneath which lie concrete social relations. It is not a referential relationship, but a causal one. The concrete social relations, that is, the practices, cause the feelings that are ‘called up’ by the totemic symbol.” Rawls, Anne W. Epistemology and Practice: Durkheim’s The Elementary Forms of Religious Life. 2004. Cambridge University Press. P. 40.


“Rather, he [Durkheim] states the argument in a conditional form: Societies cannot exist where sameness of thought does not exist to a sufficient degree. Therefore, only groups that manage to develop religious rites that are able to cause the ideas essential to this sameness and unity of thought will become societies.” Rawls, Anne W. Epistemology and Practice: Durkheim’s The Elementary Forms of Religious Life. 2004. Cambridge University Press. P. 47.


“The internal coercion of the moral force of the categories is different from the experience of sense perception. In arguing that the categories have a social origin, Durkheim points out that they impose themselves on persons from the outside with an authority that sense perceptions do not have: ‘This is none other than the authority of society passing into certain ways of thinking that are the indispensable conditions of all common action.’ Moral force is what participants feel when the authority of the group is enacted by the practices and experienced directly. The point of the contrast between sense perception and moral force is that sensations do not impose themselves on us in this way. Sense perceptions can be doubted, moral forces cannot” Rawls, Anne W. Epistemology and Practice: Durkheim’s The Elementary Forms of Religious Life. 2004. Cambridge University Press. Pp. 64-5. Quote is from Durkheim, Emile. 1912. The Elementary Forms of the Religious Life. Translated by Karen Fields. The Free Press. P. 30.


“... Durkheim maintains that participation in the enactment of ritual social practices transforms the individual into a rational human being. However, the animal pre-rational nature of the individual remains intact. It is the tension between these two, the rational social being and the pre-rational individual, that constitutes dualism, according to Durkheim, not an inherent tension between the body and the mind, or between spiritual and material reality, as Kant and Descartes had argued.” Rawls, Anne W. Epistemology and Practice: Durkheim’s The Elementary Forms of Religious Life. 2004. Cambridge University Press. P. 74.


“Society is a reality sui generis.” Durkheim, Emile. 1912. The Elementary Forms of the Religious Life. Translated by Karen Fields. The Free Press. P. 29. Quoted in: Rawls, Anne W. Epistemology and Practice: Durkheim’s The Elementary Forms of Religious Life. 2004. Cambridge University Press. P. 79.


“The sacred Durkheim identifies with the group, the social, and with moral force. The profane he identifies with the individual (among other things). Because collective concepts are shared and transcend the individual, they are assigned by Durkheim to the realm of the sacred and not the profane.” Rawls, Anne W. Epistemology and Practice: Durkheim’s The Elementary Forms of Religious Life. 2004. Cambridge University Press. P. 100.


“Durkheim argues that ‘since the role of the social being in our single selves will grow ever more important as history moves ahead ... all evidence compels us to expect our effort in the struggle between the two beings within us to increase with the growth of civilization.’” Rawls, Anne W. Epistemology and Practice: Durkheim’s The Elementary Forms of Religious Life. 2004. Cambridge University Press. P. 101. Quote from: Durkheim, Emile. 1914 [1960] Montesquieu and Rousseau. University of Michigan Press. P. 339.


“Durkheim’s critique of religious anthropology parallels his critique of epistemology. The animists and naturists generally attempt to explain the sacred on the basis of sense perception and fail. They fall prey to Hume’s dilemma; that general ideas cannot be derived from sense perception. The Totemists, in an argument reminiscent of Kant, offer innate human tendencies as the origin of the sacred. In both cases, Durkheim argues, in a manner parallel to his criticisms of Kant and Hume, they have failed to explain the origin of the idea of sacredness. The animists, in particular Taylor, and the naturists, in particular Muller, must fail, Durkheim says, because sense perception cannot explain the origin of an idea, like the sacred, that has no counterpart in nature. Durkheim’s point here is similar to Hume’s argument that the idea of causality could not be empirically valid because no counterpart could be found for it in sense experience. Sacredness, not being a natural phenomena, cannot present itself to perception. The Totemists, and in this regard Durkheim, cite Frazier, because they are innatists, assume the existence of the phenomenon and therefore, like Kant, fail to provide any explanation at all for its origin.” Rawls, Anne W. Epistemology and Practice: Durkheim’s The Elementary Forms of Religious Life. 2004. Cambridge University Press. P. 110.


“Finally, in order to have an idea of a supernatural order of things, Durkheim argues that a society must first have an idea of a natural order of things. The idea of a supernatural order requires the explanation of a disjuncture between two orders of things....

“Consequently, he argues the origin of the belief in the supernatural cannot be reduced to being awestruck in the face of the unforeseen forces of nature, because events cannot be unexpected, unless there are background expectations against which they take place.” Rawls, Anne W. Epistemology and Practice: Durkheim’s The Elementary Forms of Religious Life. 2004. Cambridge University Press. P. 114.


“Durkheim then offers his final definition of religion: “A religion is a unified system of beliefs and practices relative to sacred things, that is to say, things set apart and forbidden-beliefs and practices which unite into one single moral community called a Church, all those who adhere to them.’ This means that religion is by definition collective. It also, by definition, relates to the sacred.” Rawls, Anne W. Epistemology and Practice: Durkheim’s The Elementary Forms of Religious Life. 2004. Cambridge University Press. P. 123.


“In other words, it is not the obligation that creates the collectivity, but the collectivity that creates the obligation.” Rawls, Anne W. Epistemology and Practice: Durkheim’s The Elementary Forms of Religious Life. 2004. Cambridge University Press. P. 123.


“Totemic symbols are not considered by Durkheim to be ideas. On the contrary, he treats them as physical objects, or marks. Their significance is not that they represent ideas either. What they signify are feelings that were once shared between members of a group, or more exactly, feelings that, once shared, made persons feel like members of a group. They call up collective moments. Such shared moments can be called up be a picture, things, or a word, and in so doing, the feelings that were once felt together are renewed.” Rawls, Anne W. Epistemology and Practice: Durkheim’s The Elementary Forms of Religious Life. 2004. Cambridge University Press. P. 149.


“He [Durkheim] argues that the sacred and profane occur in phases. Short periods that are considered sacred are followed by longer periods which are considered profane.” Rawls, Anne W. Epistemology and Practice: Durkheim’s The Elementary Forms of Religious Life. 2004. Cambridge University Press. P. 163.


“Viruses are by common definition neither organisms nor alive.” Brussow, Harald. “The not so universal tree of life or the place of viruses in the living world.” 2009. Philosophical Transactions of the Royal Society B. 364: 2263-2274. P. 2265.


“In the largest of the ocean studies, more than 91 per cent of the sequences from the viral DNA fraction did not have a significant hit in the sequence databases. From this observation, we have to conclude that the viral DNA sequence sphere is very large. Microbial ecologists working in the oceans provided data that independently support this conclusion. The first big surprise was the discovery of large numbers of viruses in coastal water. In eutrophic estuarine water, 107 viral particles were counted per millilitre of water. This is 10 times the amount of bacteria in this ecosystem. From the data of many ecological surveys, it was calculated that viruses are by far the most abundant ‘biological entities’ in the world’s oceans yielding a global level of more than 1030 viruses. Viruses are not only numerous, they are also a major cause of microbial mortality in the sea, rivaled only by grazing from protists.” Brussow, Harald. “The not so universal tree of life or the place of viruses in the living world.” 2009. Philosophical Transactions of the Royal Society B. 364: 2263-2274. P. 2269.


“Viruses play an important role in the ocean ecosystem by maintaining the genetic diversity of microbes according to the ‘killing the winning fraction’ concept. In addition, viruses power the microbial loop that maintains nutrients in the microbial world, preventing their flow into the marine food chain. Therefore, viruses play a major role in biogeochemistry.” Brussow, Harald. “The not so universal tree of life or the place of viruses in the living world.” 2009. Philosophical Transactions of the Royal Society B. 364: 2263-2274. P. 2269.


“If one combines the large number of ORFans in viral metagenome analyses and the sheer number of viruses in the biosphere, it is possible that the viral sequence space exceeds that of their prokaryotic hosts in size. These data are simply not compatible with the older concept that the viral genes escaped from cells.” Brussow, Harald. “The not so universal tree of life or the place of viruses in the living world.” 2009. Philosophical Transactions of the Royal Society B. 364: 2263-2274. P. 2270.


“Two central themes in Maynard Smith and Szathmary’s book develop this idea of change in the conditions that make evolutionary change possible. One concerns the expansion of mechanisms of hereditary–where richer and more accurate systems of the intergenerational flow of information evolve. The other focuses on the evolution of new levels of biological individuality; an evolutionary change after which previously independent entities now reproduce together, sharing their evolutionary fate. Both mark out core features of the Darwinian process. One is a radical change in the kind of individual from which evolving populations and lineages are built. The other is a change in the processes relating these individuals across generations. A third, less well-explored theme, concerns the generation of variation, which they touch on in their final chapter on language.... Thus, we see three core features of the Darwinian process of change–the subject of change, how change is passed on, and ways in which further change is generated–are all themselves subject to modification.” Calcott, Brett & K. Sterelny, Eds. 2011. The Major Transitions In Evolution Revisited. MIT Press. Pp. 4-5. Reference is to Smith, Maynard & E. 1995. “The major evolutionary transitions.” Nature 374: 227-232. Also their book The Major Transitions in Evolution. 1995. Oxford University Press.


“... David Queller has pointed out that there seem to be two very different transitions in individuality: ‘egalitarian’ and ‘fraternal’ transitions. Perhaps these should not be lumped together. Eukaryote evolution is the paradigm of an egalitarian transition, for the partnership that became the new Darwinian individual did not begin with an association between closely related individuals. In contrast, the evolution of multicelled organisms (and eusocial animals) is a fused alliance between close relatives. Explaining these two types of transition poses quite different challenges. In egalitarian transitions, differentiation between the partners, and hence the potential profits of specialization, come for free. But there is no automatic overlap of evolutionary interest, and no possibility of a division of reproductive labor. And so there are potentially unmanageable problems of conflict. In fraternal transitions, there is an overlap of evolutionary interest (in clones, identity), so the problem of conflict is less pressing. But the profit of cooperation is more elusive, as differentiation does not predate partnership.” Calcott, Brett & K. Sterelny, Eds. 2011. The Major Transitions In Evolution Revisited. MIT Press. P. 10. Reference is to Queller, David. 2000. “Relatedness and the fraternal major transitions.” Philosophical Transactions of the Royal Society B. 355: 1647-1656.


“Multicelled organisms have evolved many times, but only in a few cases have these lineages generated impressive disparity and diversity. The evolution of complex multicellularity requires the evolution of a higher-level unit with its own fitness values. But it requires more–the evolution of a developmental cycle–and that in turn requires a major advance in mechanisms of inheritance. Protist genes never have to contribute to building afresh the critical inner cellular structures of protists. The reproduction of these crucial intercellular structures can largely be reduced to growth and fission. In contrast, organs and tissues do not exist in miniature in fertilized ova. Complex multicelled organisms exist only because there are developmental cycles in which key structures of adult organisms are rebuilt from scratch in the new generation.” Calcott, Brett & K. Sterelny, Eds. 2011. The Major Transitions In Evolution Revisited. MIT Press. P. 11.


“A number of factors stabilize cooperation: relatedness, iterated interactions and reciprocity, mutualisms, and punishment or conflict mediation.” Calcott, Brett. “Alternative Patterns of Explanation for Major Transitions.” Pp. 35-51. From Calcott, Brett & K. Sterelny, Eds. 2011. The Major Transitions In Evolution Revisited. MIT Press. P. 38.


“Michod’s model explains the transition in V. carteri by showing that a split between germ and somatic line prevents the accumulation of defectors in the population. Without such a split, the defectors are more likely to build up and displace any cooperators.” Calcott, Brett. “Alternative Patterns of Explanation for Major Transitions.” Pp. 35-51. From Calcott, Brett & K. Sterelny, Eds. 2011. The Major Transitions In Evolution Revisited. MIT Press. P. 40.


“Most critically, though, in multicell systems, development routinely builds from scratch new structures in each generation. Tissues, organ systems, support structures, and circulatory systems all have to be built anew. That is not true when a prokaryote splits into two daughter cells. Its cell walls and many intercellular structures are continuously present and available through the process of gene replication and cell fission.” Sterelny, Kim. “Evolvability Reconsidered.” Pp. 83-100. From Calcott, Brett & K. Sterelny, Eds. 2011. The Major Transitions In Evolution Revisited. MIT Press. P. 91.


“Hence, the idea of a transition to a Darwinian world. Woese and his allies think such protocell evolution precedes a Darwinian transition, for the phenotype of a pretransition protocell depends more on its neighbors and those neighbors’ immediate ancestors than on the protocell’s own distant ancestors.” Sterelny, Kim. “Evolvability Reconsidered.” Pp. 83-100. From Calcott, Brett & K. Sterelny, Eds. 2011. The Major Transitions In Evolution Revisited. MIT Press. P. 93. Reference is to Woese, C. 2008. “The domains of life and their evolutionary implications.” From Dunn, M, L. Jorde, P. Little & S. Subramaniam (Eds.). Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. John Wiley & Sons.


“Explaining the evolution of evolvability turns into the project of explaining the origin and distribution of special developmental mechanisms, themselves novelties on which other novelties depend.” Sterelny, Kim. “Evolvability Reconsidered.” Pp. 83-100. From Calcott, Brett & K. Sterelny, Eds. 2011. The Major Transitions In Evolution Revisited. MIT Press. P. 95.


“The various hypotheses of the origin of life and the major transitions of evolution currently on offer, henceforward referred to as origins and transitions narratives–whether replicator-first, metabolism-first, RNA world, lipid world, peptide world, virus world, communal, gene-swapping progenotes, biological big bang, or panspermia–all share the assumption, usually tacit, that somehow selfishness entered the world. Put another way, they assume the emergence of the sort of self-preserving, self-organized complexity that provides a minimal basis for attributing selfishness to a system.” Lyon, Pamela. “To Be or Not To Be: Where is Self-Preservation in Evolutionary Theory?” Pp. 105-125. From Calcott, Brett & K. Sterelny, Eds. 2011. The Major Transitions In Evolution Revisited. MIT Press. P. 105.


“The evolution of traits adaptive at a given level of biological organization requires the existence–at that level–of the necessary prerequisites for Darwinian individuality. When the trait whose origin we wish to explain is reproduction, we face a dilemma: Appeals to natural selection would seem to presuppose the existence of collective reproduction–the very trait whose evolution requires explanation.” Rainey, Paul & BH. Kerr. “Conflicts among Levels of Selection as Fuel for the Evolution of Individuality.” Pp. 141-167. From Calcott, Brett & K. Sterelny, Eds. 2011. The Major Transitions In Evolution Revisited. MIT Press. P. 144.


“The absence of a means of collective reproduction does not mean that selection cannot act on collectives, but its capacity to do so is limited to selection at the level of collective viability.” Rainey, Paul & BH. Kerr. “Conflicts among Levels of Selection as Fuel for the Evolution of Individuality.” Pp. 141-167. From Calcott, Brett & K. Sterelny, Eds. 2011. The Major Transitions In Evolution Revisited. MIT Press. P. 145.


“Three phases can be identified in transitions in individuality. The aggregate phase is the least individuated, the group phase intermediately individuated, and the individual phase is the most. Each phase is characterized by a dominant fitness component. Differential expansion is the component associated with aggregates, differential persistence is associated with groups, and differential reproduction is characteristic of paradigm individuals. Evolutionary transitions to more individuated phases require the accumulation of additional fitness components, but new levels are attained once the expansive component of fitness is attained. This allows us to know that organisms in each of the three phases of individuality are at the same level if they share a common ancestor.” Simpson, Carl. “How Many Levels Are There?” Pp. 199-225. From Calcott, Brett & K. Sterelny, Eds. 2011. The Major Transitions In Evolution Revisited. MIT Press. Pp. 200-1.


“The obvious implication is that reduced material has been introduced to the three surface zones at a rate that is closely related to the oxygen and oxidised chemical increase in the environment.” Williams, R.J.P. & J.J.R. Frausto da Silva. The Chemistry of Evolution: The Development of our Ecosystem. 2006. Elsevier. P. 32.


“... we know today that about 2% of the retained energy on the Earth is used by life and it has increased continuously from the abiotic start, ...” Williams, R.J.P. & J.J.R. Frausto da Silva. The Chemistry of Evolution: The Development of our Ecosystem. 2006. Elsevier. P. 100.


“We must recognise, as stated above, that the only way we can account for evolution is if the chemicals produced became involved in a flow system that did not produce an all inclusive cycle, which is a terminal condition like that in the cyclic ozone layer.” Williams, R.J.P. & J.J.R. Frausto da Silva. The Chemistry of Evolution: The Development of our Ecosystem. 2006. Elsevier. P. 100.


“We wish to consider how the simple original resultant cell could lead, 3.5 billion years later, to an animal as complex as man. I shall explain why I do not consider it was due to pure chance alteration of a code. I shall claim that it is a direct consequence of a system of chemical reactions in coordinated flow and as such was inevitable as it was dependent on the inevitable original environment and its change, no matter how much the central line of progression of organisms is confused by the multitudes of varieties, so-called species, that arise at any one time. There is a main logical chemical progression of the whole of life.” Williams, R.J.P. 2011. “Chemical advances in evolution by and changes in use of space during time.” Journal of Theoretical Biology. 268: 146-159. P. 151.


“The evolutionary sequence was anaerobic, then aerobic prokaryotes, unicellular then multicellular eukaryotes, the last three dependent on a micro- then a macro-aerobic environment, with more and more compartments. This is the main line of change to 0.4 Ga independent of species. Moreover the last three coexist as the complex cells, alone, have not sufficient separate survival strength due to their complexity. In fact the majority of unicellular organisms supports the minority of multicelular organisms. This symbiosis is just an extra way of utilising space efficiently as in modern industrial practice where different locations provide different components.” Williams, R.J.P. 2011. “Chemical advances in evolution by and changes in use of space during time.” Journal of Theoretical Biology. 268: 146-159. P. 152.


“The Cambrian Explosion seen in fossils is due to the surge in oxidation to give cross-linked external matrices around 0.75-0.55 Ga, enabling the evolution of numerous shells and skeletons.” Williams, R.J.P. 2011. “Chemical advances in evolution by and changes in use of space during time.” Journal of Theoretical Biology. 268: 146-159. P. 153.


“At this point in the article I insert a general view of our holistic approach to chemical evolution which is based on observing the changes largely in the metal inorganic elements in the environment and those of organic chemicals based on them in cells. The reasons for using this approach are that the metal elements are common to both the environment and organisms in exactly the same form. Their concentrations in both can therefore be followed and compared, showing the mutual interaction and energisations of the different spaces, the environment and the cell compartments, including the cytoplasm.” Williams, R.J.P. 2011. “Chemical advances in evolution by and changes in use of space during time.” Journal of Theoretical Biology. 268: 146-159. P. 153.


“The remarkable fact appears to be that there is only one limiting set of free ion values in the cytoplasm, in all of the four classes of aerobic cells suggesting that this particular chemical condition is a unique solution to the problem of cell cytoplasmic activity.” Williams, R.J.P. 2011. “Chemical advances in evolution by and changes in use of space during time.” Journal of Theoretical Biology. 268: 146-159. Pp. 154-5.


“It is important to realise that the major changes of the chemistry of evolution were completed by 0.4 Ga. Thereafter evolution is largely diversity, not novelty, of chemistry.” Williams, R.J.P. 2011. “Chemical advances in evolution by and changes in use of space during time.” Journal of Theoretical Biology. 268: 146-159. P. 155.


“The increase in complexity of cells from prokaryotes to unicellular, then multicellular, organisms required more and more management. Staying with our wish to refer to metal ions, Fe2+ and Mg2+ remained as major controls of metabolic pathways in the cytoplasm in all cells, of both anaerobic and aerobic organisms. Control systems responsive to external changes became necessary for the vulnerable eukaryote cells. They evolved, using the available metal ion gradients, especially of calcium, and later of the pair of ions Na+/K+, for external/internal cell messages. The controls using all three ions arose from the need of the earliest prokaryotes for protection which created gradients of these ions with high concentration of Ca2+ and Na+ in the sea and later in extracellular fluids to low values in the cytoplasm. The flows of the two govern many cellular mechanical and chemical metabolic switches.” Williams, R.J.P. 2011. “Chemical advances in evolution by and changes in use of space during time.” Journal of Theoretical Biology. 268: 146-159. P. 155.


“Now complexity places great stress on the ability to organise. A remarkable feature of evolution in the broadest sense is not survival of the fittest, competition between individual organisms, but on survival of the whole, cooperative, symbiotic system. The development of unicellular eukaryotes is a major, little understood, symbiotic evolution. Utilising symbiosis is a new use of space. It was greatly increased in multicellular eukaryotes, plants and animals, as they come to rely on chemicals from lower organisms living independently, attached outside or even inside these eukaryotes. Plants depend on bacteria for nitrogen and on fungi for minerals. Plants and animals depend on vitamins, including the many essential coenzymes, and recent animals require additionally essential amino acids and sugars from many sources. They are obtained by feeding. The ensemble of organisms became a large cooperative network in an environment/organism system in which the definition of species becomes difficult. However, speciation is not important in main line chemical evolution. Man is an extreme example. We do not know how many organisms (species) man’s existence depends upon. The total complexity involves and is relieved by ever increasing use of biological plus environmental space.” Williams, R.J.P. 2011. “Chemical advances in evolution by and changes in use of space during time.” Journal of Theoretical Biology. 268: 146-159. P. 156.


“We have related symbiosis increases particularly to the difficulty of carrying increasing complexity in single cells whenever chemistry in the environment became more complicated and useful to cells but not directly related to the original maintained chemistry of the basic cell cytoplasm.” Williams, R.J.P. 2011. “Chemical advances in evolution by and changes in use of space during time.” Journal of Theoretical Biology. 268: 146-159. P. 156.


“Recall Hutchinson’s definition of the fundamental niche of a species: a hypervolume of environmental variables, ‘every point of which corresponds to a state of the environment which would permit the species to exist indefinitely.’ Most differences in niche concepts depend on the formulation and relative importance given to three interrelated points, considered in turn later: (1) the meaning of ‘exist indefinitely,’ (2) what kinds of variables constitute the hypervolume, and (3) the nature of feedback loops between a species and the variables composing the hypervolume.” Peterson, A. Townsend, J. Soberon, R. Pearson, R. Anderson, E. Martinez-Meyer, M. Nakamura & M. B. Araujo. Ecological Niches and Geographic Distributions. 2011. Princeton University Press. P. 9.


“Instead, we construct the multivariate environmental spaces for our definitions based on variables that are not dynamically affected by the species, like climate, topography, and perhaps some habitat features, in contrast to variables that are dynamically modified (linked), such as consumed resources or those that are subject to modification by niche construction. We use the term ‘dynamically linked’ in the sense of terms that appear as parameters in population equations versus appearing as dynamic state variables ... We call nonlinked variables ‘scenopoetic.’” Peterson, A. Townsend, J. Soberon, R. Pearson, R. Anderson, E. Martinez-Meyer, M. Nakamura & M. B. Araujo. Ecological Niches and Geographic Distributions. 2011. Princeton University Press. Pp. 11-2.


“The main meaning [of ‘niche’ underpinning this book] is explicitly geographic in nature, and is based on E-spaces composed of scenopoetic variables taken as conditions or requirements. These niches have been called ‘Grinnellian’ or ‘environmental.’” Peterson, A. Townsend, J. Soberon, R. Pearson, R. Anderson, E. Martinez-Meyer, M. Nakamura & M. B. Araujo. Ecological Niches and Geographic Distributions. 2011. Princeton University Press. P. 16.


“Of course, other extremes of niche meaning are possible and important; in particular, as we saw, niche concepts exist that are oriented toward community-ecology questions, defined at local scales, and including models of resource consumption and impacts. We will refer to this scale and meaning as ‘Eltonian niches.’” Peterson, A. Townsend, J. Soberon, R. Pearson, R. Anderson, E. Martinez-Meyer, M. Nakamura & M. B. Araujo. Ecological Niches and Geographic Distributions. 2011. Princeton University Press. P. 17.


“Grinnellian niches, defined as subsets of scenopoetic environmental spaces, are entirely different entities in this sense than Eltonian niches, defined in terms of zero-growth isoclines, impact vectors, and supply points.” Peterson, A. Townsend, J. Soberon, R. Pearson, R. Anderson, E. Martinez-Meyer, M. Nakamura & M. B. Araujo. Ecological Niches and Geographic Distributions. 2011. Princeton University Press. P. 17.


“In the classic niche literature, the only population interactions considered are competitive and predator-prey interactions. The inclusion of positive (mutualistic) interactors, however, represents an important gap in niche theory. Although we acknowledge this gap, we restrict our discussion to negative interactions, since available theory regarding Eltonian niches has disregarded mutualism almost entirely.” Peterson, A. Townsend, J. Soberon, R. Pearson, R. Anderson, E. Martinez-Meyer, M. Nakamura & M. B. Araujo. Ecological Niches and Geographic Distributions. 2011. Princeton University Press. P. 27.


“Water plays an indirect but crucial role in the story of life on earth through geophysical and astrophysical processes of which Henderson could have had not inkling. One of these is plate tectonics. Astrobiologists believe that a healthy planet must continually recycle material if equable conditions are to be maintained. For example, on earth, carbon becomes sequestered in carbonate rocks and is released again in the form of carbon dioxide when the rocks are subducted. Similarly, oxygen is prevented from building up to dangerous levels by tectonic activity, which continually exposes fresh material to be oxidized. Part of the reason Mars seems to be a dead planet is because its tectonic processes have ground to a halt. Water is a crucial ingredient in this story. If the earth’s crust were not hydrated, the basalt would be brittle. The water content gives the rock high plasticity that allows the plates to slide smoothly and material to flow steadily through the mantle.” Davies, Paul. “Fitness and the cosmic environment.” Pp. 97-113. From: Barrow, John, S.C. Morris, S. Freeland & C. Harper. (Eds.) Fitness of the Cosmos for Life: Biochemistry and Fine-Tuning. 2008. Cambridge University Press. P. 106.


“The central theme is the recognition of so-called ecomorphs. This term refers to unrelated species that evolve similar morphologies in response to equivalent functional demands within a given environment. As with other examples of convergence, the degrees of similarity are seldom precise, but can still be striking.” Morris, Simon C. “Tuning in the frequencies of life.” Pp. 197-224. From: Barrow, John, S.C. Morris, S. Freeland & C. Harper. (Eds.) Fitness of the Cosmos for Life: Biochemistry and Fine-Tuning. 2008. Cambridge University Press. P. 210.


“Let us consider the situation at two levels: the sequence level (which is the genotype because it is a direct translation from the evolving DNA molecules) and the structure level (which we can think of as the phenotype). As pointed out by Maynard Smith, as the sequence undergoes mutation, the mutated sequences must traverse a continuous network without passing through any intermediaries that are non-functioning. Thus, one seeks a connected network in sequence space for evolution by natural selection to occur. Considerable evidence accumulated since the pioneering suggestion of Kimura and King and Jukes shows that much of evolution is neutral. The experimental data strongly support the view that the ‘random fixation of selectively neutral or very slightly deleterious mutants occurs far more frequently in evolution than selective substitution of definitely advantageous mutants.’ Also ‘those mutant substitutions that disrupt less the existing structure and function of a molecule (conservative substitutions) occur more frequently in evolution than more disruptive ones.’ Thus, although one has a ‘random walk’ in sequence space that forms a connected network, there is no similar continuous variation in structure space.” Banavar, Jayanth & A. Maritan. “Life on earth: the role of proteins.” Pp. 225-255. From: Barrow, John, S.C. Morris, S. Freeland & C. Harper. (Eds.) Fitness of the Cosmos for Life: Biochemistry and Fine-Tuning. 2008. Cambridge University Press. P. 243. References: Maynard Smith, J. “Natural selection and concept of a protein space.” Nature. 225 (1970), 563; Kimura, M. “Evolutionary rate at the molecular level.” Nature. 217 (1968), 624; King, J. & T. Jukes. “Non-Darwinian evolution.” Science. 164 (1969), 788.


“There is increasing evidence that evolution along with natural selection allows nature to use variations on the same theme facilitated by the rich repertory of amino acids to create enzymes that are able to of catalyzing a remarkable array of diverse and complex tasks in the living cell. The key point, of course, is that a constant backdrop of folds not shaped by sequence but determined by physical law is necessary for molecular evolution to work in this manner. Were the folds not immutable and themselves subject to Darwinian evolution, the possibility of creating many subtle and wonderful variations on the same theme would not exist. The pre-sculpted landscape is the crucial feature that leads to a predetermined menu of immutable folds.” Banavar, Jayanth & A. Maritan. “Life on earth: the role of proteins.” Pp. 225-255. From: Barrow, John, S.C. Morris, S. Freeland & C. Harper. (Eds.) Fitness of the Cosmos for Life: Biochemistry and Fine-Tuning. 2008. Cambridge University Press. P. 244.


“Proteins, the workhorse molecules of life, are wonderful molecular machines that carry out a variety of functions and speed up chemical reactions by orders of magnitude. A single protein may have a variety of capabilities, but the work it does, although efficient, is monotonous. The situation changes dramatically when one has a collection of proteins organized in a network. These proteins interact with one another, catalyze chemical reactions, turn the gene on or off, and lead to the robust and coherent behavior that we associate with life.

The structure of the DNA molecule provides a beautiful explanation of how it is able to encode information and the mechanism underlying its replication. Proteins, on the other hand, are less well understood. One could ask what kind of a phase of matter one would choose to house protein structures in order to accommodate the important roles that these molecules of life play. Our work suggests that a very special, previously unstudied phase of matter is associated with the marginally compact phase of short tubes with a thickness specially tuned to be comparable to the range of attractive interactions promoting the compaction. This phase is a finite-size effect and exists only for relatively short tubes; it is poised near a phase transition of a new kind that lends itself to flexibility in the structure; the structures that one finds in the marginally compact phase are space-filling and modular in construction, being made up of two principal building blocks – helices and sheets; the total number of distinct folds is relatively small and only on the order of a few thousand or so, and proteins are able to fold rapidly and reproducibly into them. The price that nature pays for utilizing this novel phase of matter is the relative ease with which aggregation of multiple tubes can occur, leading to amyloid formation.

“In his insightful book, The Fitness of the Environment, Henderson extended the notion of Darwinian fitness to argue that ‘the fitness of [the] environment is quite as essential a component as the fitness which arises in the process of organic evolution.’ Strikingly, the chemistry of proteins ensures that they are self-tuned to occupy the marginally compact phase of short tubes. One cannot but marvel at how several factors – the steric interactions; hydrogen bonds, which provide the scaffolding for protein structures; the constraints placed by quantum chemistry on the relative lengths of the hydrogen and covalent bonds; the near planarity of the peptide bonds; and the key role played by water – all reinforce and conspire with one another to place proteins in this novel phase of matter.

“Proteins have proved to be difficult to understand because of (1) their inherent complexity with twenty types of amino acids and the role played by water; (2) their relatively short length compared with generic human-made polymers, which means they are therefore likely to be characterized by ‘non-universal’ behavior; and (3) the complexities associated with the random process of evolution. Nevertheless, our work suggests an underlying stunning simplicity. Although sequences and functionalities of proteins evolve, the folds that they adopted, which in turn determine function, seem to be determined by physical law and are not subject to Darwinian evolution.” Banavar, Jayanth & A. Maritan. “Life on earth: the role of proteins.” Pp. 225-255. From: Barrow, John, S.C. Morris, S. Freeland & C. Harper. (Eds.) Fitness of the Cosmos for Life: Biochemistry and Fine-Tuning. 2008. Cambridge University Press. Pp. 247-50. Reference is to: Henderson, L. 1913. The Fitness of the Environment: An Inquiry into the Biological Significance of the Properties of Matter. Macmillan.


“As well as being essentially invariant, it became apparent during the 1970s, as more structures were determined, that the structure of the folds is also basically hierarchical, consisting of secondary structural elements such as the α helix and β sheet combined into more complex motifs and that the same motifs (helix-turn-helix, β hairpin, etc.) recur in many different proteins. The hierarchic nature of fold structure and the recurrence of the same submotifs suggested that physical law is playing a major role in the ordering of global fold structure and further supported the notion that the folds might be a set of natural and lawful structures rather than contingent assemblages of matter.” Denton, Michael. “Protein-based life and protein folds.” Pp. 256-279. From: Barrow, John, S.C. Morris, S. Freeland & C. Harper. (Eds.) Fitness of the Cosmos for Life: Biochemistry and Fine-Tuning. 2008. Cambridge University Press. P. 263.


“A picture has emerged of a limited number of ahistorical forms that have been secondarily modified to perform a vast number of adaptive functions. A remarkable feature of these secondary adaptive substitutions is how few seem necessary to cause adaptive shifts in protein function.” Denton, Michael. “Protein-based life and protein folds.” Pp. 256-279. From: Barrow, John, S.C. Morris, S. Freeland & C. Harper. (Eds.) Fitness of the Cosmos for Life: Biochemistry and Fine-Tuning. 2008. Cambridge University Press. P. 264.


“The fact that the total number of theoretically possible protein structures that an individual amino acid chain of 150 residues might adopt – assuming that each peptide group has only three conformations – is 3150 or 1068 whereas the total number of permissible folds is of the order of 1000 graphically illustrates just how restrictive the laws of protein-fold form are. Whatever the actual figure, the total number of folds is bound to represent a tiny stable fraction of all possible polypeptide conformations, determined by the laws of physics. This further reinforces the notion that the folds, like atoms, represent a finite set of allowable physical structures that would recur throughout the cosmos wherever carbon-based life that utilizes the same twenty amino acids exists.” Denton, Michael. “Protein-based life and protein folds.” Pp. 256-279. From: Barrow, John, S.C. Morris, S. Freeland & C. Harper. (Eds.) Fitness of the Cosmos for Life: Biochemistry and Fine-Tuning. 2008. Cambridge University Press. Pp. 267-8.


“The discovery that the protein universe consists of a finite set of natural forms in a sense completes the molecular biological revolution, revealing finally – five decades after the nature and biological purpose of DNA and RNA were first elucidated – the essential nature of the second great class of biopolymers. It reveals that the purpose of the genetic system is to turn out endless adaptive variants of a set of invariant natural forms. The great complexity of the folds (among the most complex material structures known) indicates, perhaps more clearly than any other previous discovery in the biological sciences, that very great biological complexity may be lawful and need not necessarily be contingent.” Denton, Michael. “Protein-based life and protein folds.” Pp. 256-279. From: Barrow, John, S.C. Morris, S. Freeland & C. Harper. (Eds.) Fitness of the Cosmos for Life: Biochemistry and Fine-Tuning. 2008. Cambridge University Press. P. 269.


“Because each fold has been subjected to billions of years of selective fine-tuning for specific biochemical functions, efficient folding, and so forth, it is somewhat difficult to judge precisely which properties are universal, generic properties of the folds and which are secondarily evolved features. Nonetheless, as James and Tawfik point out, ‘An evolved function can only evolve if it is already present to some extent,’ and this presumably applies to all characteristics of the folds. Thus, four characteristics that contribute to their fitness are likely to be basic, intrinsic characteristics of the folds themselves: their architectural diversity, marginal stability, robustness, and possession of a hydrophobic core.

“The underlying molecular architectures of the folds are, as we have seen quite amazingly diverse. This architectural diversity is a major contributor to their biological fitness, providing the basis for the vast range of structural and functional molecular roles that they play within the cell.

“The folds exhibit a combination of robustness and marginal stability, both characteristics that confer important elements of fitness. In terms of marginal stability, the folds are nothing like the rigid conformations conveyed in textbook depictions. In fact, the energy difference between the native conformation of a fold and its denatured state is extraordinarily small – about 5-15 kcal/mol – not much more than the energy level of a single hydrogen bond, which is of the order of 2-5 kcal/mol. Studies by various groups, including those of Martin Karpus and Hans Frauenfelder indicate that a protein’s native structure consists of a large number of conformational substates. Instead of inhabiting a deep free-energy minimum, a ‘V-shaped’ bowl with steep sides ending in a unique deep pit, the folds inhabit a complex energy landscape that is more a ‘shallow U-shaped bowl’ with multiple small depressions on its base. These depressions are the substates, or alternative conformers, available to the fold, each of near-equivalent stability. Marginal stability is critical during folding, enabling the polypeptide chain to search conformational space for increasingly stable conformations. Marginal stability and the characteristic U-shaped energy landscape arise according to the ‘tube model’ of Banavar and Maritan from a ‘novel phase of matter in the vicinity of a phase transition’ in which the folds arise. The tube model also implies that few other polymers may exist that will exhibit discrete, stable, folded conformations associated with their characteristic marginal stability.

“It is this marginal stability and its consequences, the ability of folds to adopt many slightly different conformations, that have permitted the evolution of allosteric control mechanisms that link logical control circuits with catalysis in the same molecular fabric – a phenomenally sophisticated mechanism that Monod saw as the ‘second secret of life.’” Denton, Michael. “Protein-based life and protein folds.” Pp. 256-279. From: Barrow, John, S.C. Morris, S. Freeland & C. Harper. (Eds.) Fitness of the Cosmos for Life: Biochemistry and Fine-Tuning. 2008. Cambridge University Press. Pp. 270-1. References: James, L. & D. Tawfik. 2003. “Conformational diversity and protein evolution – a 60 year-old hypothesis revisited.” Trends in Biochemical Science. 28, 361-8; Karpus, M. & G. Petsko. 1990. “Molecular dynamics simulations in biology.” Nature. 347, 631-9; Frauenfelder, H., F. Parak & R. Young. 1988. “Conformational substates in proteins.” Annual Review of Biophysics and Biophysical Chemistry. 17, 451-79; Banavar, J. & A. Maritan. 2003. “Colloquium: geometrical approach to protein folding: a tube picture.” Reviews of Modern Physics. 75, 23-34; Banavar, J. & A. Maritan. 2003. “Comment on the protein folds as platonic forms.” Journal of Theoretical Biology. 223, 263-5.


“The rapid growth in understanding of biology, from structures to systems, seems likely to expose many more sensitivities of life to details of chemistry, physics, and history. The question has been posed as to whether these advance Henderson’s interpretation of fine-tuning of the environment or, more generally, what their anthropic significance is. In this chapter, we examine features of intermediary metabolism, whose universality and historical persistence suggest that they are not arbitrary products of chance.” Smith, Eric & H. Morowitz. “Framing the question of fine-tuning for intermediary metabolism.” Pp. 384-420. From: Barrow, John, S.C. Morris, S. Freeland & C. Harper. (Eds.) Fitness of the Cosmos for Life: Biochemistry and Fine-Tuning. 2008. Cambridge University Press. P. 384. Reference is to: Henderson, L. 1913. The Fitness of the Environment: An Inquiry into the Biological Significance of the Properties of Matter. Macmillan.


“We argue that much of biological order comes from arrangement and augmentation of near order in the underlying chemical world and that the uniqueness of life is often found in this augmenting relation, rather than in particular biological structures. What seems familiar and lawful to us about life is often the lawfulness of the underlying physical and chemical world, with which we have broad experience, as that order is expressed transparently through the living process. We are seeing the environment through life; the meaningful category distinctions are defined not by specific molecular structures, but by specific relations to the opportunities for structure formation in chemical and energetic relaxation.” Smith, Eric & H. Morowitz. “Framing the question of fine-tuning for intermediary metabolism.” Pp. 384-420. From: Barrow, John, S.C. Morris, S. Freeland & C. Harper. (Eds.) Fitness of the Cosmos for Life: Biochemistry and Fine-Tuning. 2008. Cambridge University Press. P. 385.


“Living systems combine a strictness of regularity with a profusion of innovation of structures, to a degree that seems unequaled in any other single class of phenomenon we recognize. They are uniform in many ways, but strikingly diverse in others. All organisms ever alive on earth, taken together, account for a tiny fraction of the conceivable physicochemical structures of comparable complexity, and their uniformity implies that, in a statistical sense, the realized instances are drawn over and over from that small subset of possibilities.” Smith, Eric & H. Morowitz. “Framing the question of fine-tuning for intermediary metabolism.” Pp. 384-420. From: Barrow, John, S.C. Morris, S. Freeland & C. Harper. (Eds.) Fitness of the Cosmos for Life: Biochemistry and Fine-Tuning. 2008. Cambridge University Press. P. 386.


“Adaptation produces sensitive dependence in living forms quite generally because it arises from growth with heritable variations. Differential growth rates (including survival and fecundity effects) appear exponentially with time in the population frequencies of inherited features, leading to sensitive dependence of population samples of phenotypes on small differences in their relations to environments. Under situations of resource constraint, this can result in competitive exclusion, through which not only the population mean, but all of its instances, may be strongly biased by small differences in viability. The relative growth rates themselves, which may not depend sensitively on environment by any natural measure, are termed ‘fitness’ in Darwinian population dynamics. Darwinian fitness is expressed through selection of individuals – each one a relatively complex package of adaptations – in response to the often complex characteristics of their environment. Therefore, it frequently leads to sensitive dependence of complex wholes on complex wholes.

“Henderson appears to have appealed to this latter aspect of fitness in characterizing the laws of chemistry and physics, as well as the earth’s environmental composition, as ‘fit for life.’ The observed physico-chemical environment is sensitive to his criterion that it be able to support life’s complexity and also its need for homeostasis, rather than being the result of any dynamic process that produces exponential dependence on initial conditions, and in that respect is unrelated to Darwinian fitness.

“Because of its variability, adaptability, and robustness, it seems likely that life will admit relatively few easy category distinctions, such as the carbaquist sensitivity to carbon abundance. Most of the ‘information’ in the structure of life, about either its necessary circumstances or its generating processes, will likely come from more specific structures, which typically emerge at higher levels of complexity. Thus, in addition to understanding the logic of anthropic argument and the flexibility in its use of empirical sensitivities, we must understand the different kinds of surprise carried by sensitivity in complex and simple systems.” Smith, Eric & H. Morowitz. “Framing the question of fine-tuning for intermediary metabolism.” Pp. 384-420. From: Barrow, John, S.C. Morris, S. Freeland & C. Harper. (Eds.) Fitness of the Cosmos for Life: Biochemistry and Fine-Tuning. 2008. Cambridge University Press. Pp. 387-8. Reference is to: Henderson, L. 1913. The Fitness of the Environment: An Inquiry into the Biological Significance of the Properties of Matter. Macmillan.


“Resilience and robustness can come from the same ability to track the environment that leads to convergence or from a quite different ability to absorb its variations, leading to a kind of antisensitivity. Such antisensitivity is not exclusive to life; the atmosphere generates many negative feedbacks that confer stability against geological and biogenic shocks. Indeed, the pH stability of blood arises from its positioning at a stable region of carbon dioxide solution chemistry in water. The fitness of the environment for life may depend on its richness in such stable regions, but not necessarily on the ability of natural selection to exploit those regions.” Smith, Eric & H. Morowitz. “Framing the question of fine-tuning for intermediary metabolism.” Pp. 384-420. From: Barrow, John, S.C. Morris, S. Freeland & C. Harper. (Eds.) Fitness of the Cosmos for Life: Biochemistry and Fine-Tuning. 2008. Cambridge University Press. P. 389.

“Heterotrophy is possible because all organisms are composed of roughly the same 300 small molecules (molecular mass < 500 Dal), into which all food is broken down before being used directly or being reassembled into several thousand kinds of polymer inside the organism. All major classes of these biomolecules are synthesized from the eleven carboxylic acids of the rTCA or TCA cycle, although sugars can also be photosynthesized from 3-phosphoglycerate by an alternate pathway.” Smith, Eric & H. Morowitz. “Framing the question of fine-tuning for intermediary metabolism.” Pp. 384-420. From: Barrow, John, S.C. Morris, S. Freeland & C. Harper. (Eds.) Fitness of the Cosmos for Life: Biochemistry and Fine-Tuning. 2008. Cambridge University Press. P. 390.


“We thus characterize life as a collection of physical and chemical processes of environmental constituents, augmented by biomolecules that are rare or absent in abiotic environments. Different levels of living structures, depending on their complexity, can behave more or less like the common reaction networks in the abiotic environment. In particular, those involving many reactions of small molecules that are strongly distinguished by free energies of formation or kinetics of functional groups may thoroughly and redundantly sample all allowed reactions with one another (a kinetic generalization of the notion of ergodic sampling in equilibrium statistical mechanics), selecting by familiar statistical means the favored species and pathways. More complex structures such as macromolecules – with a flatter energy landscape, more kinetically equivalent combinations, and lower turnover in reactions – are both more susceptible to accident and, as a result, more eligible to record information within the organism about the environment to which it must respond.

“Genes, compartments, and catalysts are regulatory structures that must be built from free energy and materials made available by metabolic reactions. The metabolites are smaller and simpler than the regulators, more of them are present in the ambient environment, and the possible reaction networks among them are more densely sampled than the possible networks producing complex structures. Thus, the reaction network of core metabolism is expected to be more nearly a bulk chemical process than the combinatorics of either nucleic acid or amino acid polymers.” Smith, Eric & H. Morowitz. “Framing the question of fine-tuning for intermediary metabolism.” Pp. 384-420. From: Barrow, John, S.C. Morris, S. Freeland & C. Harper. (Eds.) Fitness of the Cosmos for Life: Biochemistry and Fine-Tuning. 2008. Cambridge University Press. Pp. 394-5.


“Living processes contribute to thermochemical relaxation, but they are not the only ones to do so. Many processes in convective weather, chemistry, and engineered systems are examples of self-organized production of conduits for the transport of energy and transport or generation of entropy. Progression away from the unstable, unorganized state is frequently exponential, giving rise to a physical form of competitive exclusion similar to that seen in Darwinian population dynamics at a higher level of complexity. (Indeed, it is natural from a physical point of view to regard competition for bulk resources to build a metabolic energy-transducing channel as the origin of directional evolution in biology. Darwinian evolution is distinguished by the non-linearities it injects into this bulk process, making the genome the unit of inheritance and the individual the unit of selection.)

“As we expect many biological structures to achieve stability by exploiting statistical stability in the underlying chemical networks, so we expect biological organization to be most likely where it follows dynamically stable thermochemical relaxation pathways. Their stability can be driven by the free energy stress they relieve, by their use of near-equilibrium chemicals and reaction networks, or by the redundancy of random relaxation pathways leading to them. Thus, a continuation exists from physical self-organization to the energetically predictable biases to Darwinian fitness.” Smith, Eric & H. Morowitz. “Framing the question of fine-tuning for intermediary metabolism.” Pp. 384-420. From: Barrow, John, S.C. Morris, S. Freeland & C. Harper. (Eds.) Fitness of the Cosmos for Life: Biochemistry and Fine-Tuning. 2008. Cambridge University Press. P. 397.


“All of these observations combined lead us to believe that the development of modern life as a steady-state relaxation process in fact took place through the sequential emergence of two separate channels. The first in time, and the simple, was the emergence of reductive metabolism through autocatalytic networks either identical or similar to the rTCA [reductive tricarboxylic acid] cycle. All its reagents are small molecules that are selected by simple kinetic and physical properties from the complete set of CHO molecules of comparable size, and the reaction networks involving them are relatively densely sampled, either within the cycle or in the side-reactions that generate biomass from it.

“The reductive metabolic core reactions are close enough to bulk physical chemistry to be studied with the statistical mechanics of complete reaction networks of small molecules, yet produce the biomass necessary to support the full complement of compartments, catalysts, prosthetic groups, and genes. The scenario requiring minimal happy accidents is one in which most of the complexity of cellular life developed around this metabolism over the first 0.5-2 Gy.

“Reductive metabolism captures free energy ultimately produced by the fission of uranium, thorium, and potassium-40 in the earth’s mantle, but makes no use of the richer free energy stress from solar fusion reactions, other than exploiting liquid water as a solvent in the habitable zone. Photosynthesis captures this independent fusion energy source, but appears to have become accessible only with the molecular complexity of modern cells. It therefore evolved to be self-supporting by artificially generating reductant to synthesize critical components such as the porphyrins from molecules provided by the rTCA cycle.

“It is a remarkable example of life’s robustness that the compounds in the rTCA cycle survived the poisoning of the earth’s atmosphere by oxygenic photosynthesis to remain the core of biosynthesis. Photosynthesis of 3-phosphoglycerate as well as reductant enabled the direction of the cycle to be reversed, from self-generation to self-consumption, becoming the oxidative Krebs cycle.” Smith, Eric & H. Morowitz. “Framing the question of fine-tuning for intermediary metabolism.” Pp. 384-420. From: Barrow, John, S.C. Morris, S. Freeland & C. Harper. (Eds.) Fitness of the Cosmos for Life: Biochemistry and Fine-Tuning. 2008. Cambridge University Press. Pp. 402-3.


“We have argued that metabolic pathways are statistically favored relaxation channels in energetically stressed environments and that their universality and stability result at least partly from this function. Yet the only places we see these pathways capture a significant fraction of element abundances is within organisms. Once modern organisms exist, their greater efficiency than abiotic processes can scavenge useful reagents from the environment, lowering the residual energetic stress below the threshold to spontaneously induce life, so the dominance by organisms of these relaxation structures may not in itself be surprising. However, the essentially regulatory superstructure, which emerges with the complexity of cellular life to enhance efficiency, distinguishes living from all non-living relaxation phenomena that interact with the same reservoirs by means of the same active chemical bond types.” Smith, Eric & H. Morowitz. “Framing the question of fine-tuning for intermediary metabolism.” Pp. 384-420. From: Barrow, John, S.C. Morris, S. Freeland & C. Harper. (Eds.) Fitness of the Cosmos for Life: Biochemistry and Fine-Tuning. 2008. Cambridge University Press. P. 404.


“All the regulatory structures we have discussed have at least a qualitative category distinction from the reagents whose pathways we have argued are most like those of abiotic chemical networks. To function, all the regulators require polymerization of small molecules in the minimal set of 300. Although cell membranes form spontaneously by surface energy minimization, they are only stable with the addition of either amino-sugar or cellulose cell walls or with the addition of membrane-dissolved cholesterol and the cytoskeleton. Amino and nucleic acids are both generated along short pathways from the TCA [tricarboxylic acid cycle] core, but to be useful as catalysts and templates they must be polymerized with particular sequences.

“A qualitative difference arises between the somewhat sparse but orderly sampling of the reaction network among all small metabolites and the much sparser and more clearly contingent sampling of the space of synthesized polymers. The reactivity of biomass, a consequence of its reduction stoichiometry as shown in Figure 18.2, also induces small free energy differences among different sequences, making the energetic landscape of sequence space flat compared with that of the metabolites themselves.

“Polymer sequences are therefore much more likely to be governed by sampling bias in evolutionary history than are metabolites. One consequence of this degeneracy under permutations of sequence is that neutral models of population genetics can provide good first approximations for the evolution of traits that depend on complex syntheses, although this has also reduced most Darwinian arguments to rationalizations and led to the complaint that Darwinian evolution is not like other scientific theories. An important second point, however, is that only such neutral molecules are eligible, by possessing a degenerate configuration space with many states, to carry mutual information within the cell about those characteristics of the environment that it needs to anticipate. Although we have argued that it is an error to identify life with polymer chemistry and sparse sampling, we agree that a qualitative distinction of the informational and regulatory character of life emerges with this class.

“The regulatory structures have a universal relation to core metabolism that appears to be a distinguishing feature of life. First, they are of low metabolic load and can therefore exist in greater diversity than the metabolites they regulate. Thus, a typical cell contains as many as tens of thousands of kinds of polymers, most in small numbers, but only several dozen metabolic reagents, in amounts that scale with the mass of the organism, and perhaps 50 building blocks, cofactors, and prosthetic groups that are shared among the polymers.

“Second, whereas core metabolism generates net currents and an arrow of time from non-equilibrium thermal boundary conditions, regulatory structures inherit this arrow of time from metabolism, which generates their building blocks as raw materials for combinatorics. Thus, the plausible abstractions for metabolism are based on microscopically reversible thermodynamics and chemistry, with non-equilibrium boundary conditions. The more natural abstractions for regulatory structures are cellular automata or the growth-and-culling models of Darwinian population genetics. It is known that important prohibitions on the formation of order, such as the absence of phase transitions in one-dimensional systems, which apply to near-reversible processes, are not binding for cellular automata because of their time-reversal asymmetry and constructive dynamics. The opportunities for encoding stable information are naturally larger in these driven structures for dynamical, as well as sampling, reasons.

“Finally, because regulatory structures usually do not flow between the organism and its environment, and because they act catalytically within the organism, selection of these structures takes place only through their impacts on the rate of core metabolism and their ability to efficiently draw energy and material from it for self-reproduction. (It is implicit here that the fit participation of the organism in its living environment is almost always a leading factor impacting the net core metabolism of the ecology as a whole.) Those structures enabling greater bulk free energy transduction, more efficient synthesis, or reduced thresholds to autocatalysis either survive in expanded environments or exclude less efficient solutions in existing niches.

“We designate the reciprocal relation among components, having these three properties, as ‘feed-down’ of regulation onto core metabolism. This is a universal relational property of all living systems that provides an energetic foundation for Darwinian fitness and governs the emergence of complexity and innovation in evolution. Feed-down determines selection bias on catalytic schemata competing intraspecifically to be the surviving metabolic strategies of autotrophs and operates through material cycling, as well as energy capture, at the level of ecologies. To us, these three relational features of regulators to substrates – sparse sampling that leads to history dependence, but also to the ability to carry information about the environment; a limited gatekeeper role over the forms of organisms; and selection through feed-down reciprocity that operates both prior and subordinate to the gatekeeper role – are more fundamental to life than any single chemical class or physical structure.” Smith, Eric & H. Morowitz. “Framing the question of fine-tuning for intermediary metabolism.” Pp. 384-420. From: Barrow, John, S.C. Morris, S. Freeland & C. Harper. (Eds.) Fitness of the Cosmos for Life: Biochemistry and Fine-Tuning. 2008. Cambridge University Press. Pp. 406-8.


“... the really impressive aspect of an enzyme is not that it is a good catalyst for a given reaction but that it is an extremely bad catalyst–no catalyst at all, in fact–for virtually every other reaction... Specificity is what enzymes abundantly provide, and it is their specificity that ought to impress us, because it is specificity that allows all the reactions of life to proceed in an orderly fashion under the mild conditions that exist in a living cell.” Cornish-Bowden, Athel. The Pursuit of Perfection: Aspects of Biochemical Evolution. 2004. Oxford University Press. P. 4.


“Like any other catalyst, an enzyme does not determine the direction in which a reaction proceeds, nor even how far it will proceed given enough time. These are questions that are decided by energetic considerations that are independent of whether a catalyst is present or not; the catalyst only determines how fast the reaction proceeds toward equilibrium.” Cornish-Bowden, Athel. The Pursuit of Perfection: Aspects of Biochemical Evolution. 2004. Oxford University Press. P. 31.


“... most metabolic systems spend a large amount of their time in steady states, and we can go some way toward understanding how biochemical systems behave by restricting the discussion to steady states. In doing this, however, we should keep in mind that it is only a beginning, because many of the most interesting moments in the life of a cell involve transitions from one steady state to another.” Cornish-Bowden, Athel. The Pursuit of Perfection: Aspects of Biochemical Evolution. 2004. Oxford University Press. P. 87.


“... the appearance of metabolic steady states is a mathematical necessity that does not require natural selection or any other special mechanism to explain it ...” Cornish-Bowden, Athel. The Pursuit of Perfection: Aspects of Biochemical Evolution. 2004. Oxford University Press. P. 90.


“... negative feedback is very common in metabolism, positive feedback rare almost to the point of nonexistence.” Cornish-Bowden, Athel. The Pursuit of Perfection: Aspects of Biochemical Evolution. 2004. Oxford University Press. P. 131.


“Incidentally, in Rosen’s view evolution is secondary: one can imagine life forms that did not evolve (e.g., fabricated ones), but evolution without life is inconceivable.” Harold, Franklin. The Way of the Cell: Molecules, Organisms and the Order of Life. 2001. Oxford University Press. P. 223. Reference is to Rosen, R. Life Itself: A Comprehensive Inquiry into the Nature, Origin and Fabrication of Life. 1991. Columbia University Press.


“More generally speaking, the essence of life as such does not only concern the difference between a single living cell and its abiotic surroundings, but also the self-regulating system-wide properties spanning populations, ecosystems, or the entire biosphere. Thus, the emergence of pre-macromolecular collective systems with life-like properties steps in as the critical threshold for the origins of life.” Egel, Richard. “Integrative Perspectives: In Quest of a Coherent Framework for Origins of Life on Earth.” Pp. 289-360. From Egel, Richard, D. Lankenau & A. Mulkidjanian, Eds. Origins of Life: The Primal Self-Organization. 2011. Springer. P. 291.


“The semantics of life would be incomplete without mention of information, which is closely related to memory in any form. Evolutionary self-organization always depends on some kind of memory to evade stochastic equilibration in the flow of time. In modern life, the biochemical memory is primarily based on DNA ...” Egel, Richard. “Integrative Perspectives: In Quest of a Coherent Framework for Origins of Life on Earth.” Pp. 289-360. From Egel, Richard, D. Lankenau & A. Mulkidjanian, Eds. Origins of Life: The Primal Self-Organization. 2011. Springer. P. 294.


“Conceivably, self-organizing repositories of solely compositional and structural information have preceded the emergence of genetic memory.” Egel, Richard. “Integrative Perspectives: In Quest of a Coherent Framework for Origins of Life on Earth.” Pp. 289-360. From Egel, Richard, D. Lankenau & A. Mulkidjanian, Eds. Origins of Life: The Primal Self-Organization. 2011. Springer. P. 295.


“Comparing rather diverse kinetic phenomena has uncovered far-reaching similarities, as of tropical cyclonic depressions, orogenic island arcs, continental drainage patterns, or living organisms. All of these dynamic entities couple the dissipation of potential energy to collective flow and concerted redistribution of matter. As such, they are part of superior recycling systems at a global scale, which keep the entire Earth in a gradually evolving state of quasi-equilibrium. At different levels, the formation of stars and galaxies on the one hand, or socio-political interactions on the other, can likewise be ascribed to energy-dissipating aggregation.” Egel, Richard. “Integrative Perspectives: In Quest of a Coherent Framework for Origins of Life on Earth.” Pp. 289-360. From Egel, Richard, D. Lankenau & A. Mulkidjanian, Eds. Origins of Life: The Primal Self-Organization. 2011. Springer. P. 299.


“... it is worth noting that living organisms have exaggerated the roughness at the surface of the Earth enormously – starting at the molecular scale of catalytic sites at micelles or membranes, and culminating in the macroscopic appearance of forest communities or coral reefs.” Egel, Richard. “Integrative Perspectives: In Quest of a Coherent Framework for Origins of Life on Earth.” Pp. 289-360. From Egel, Richard, D. Lankenau & A. Mulkidjanian, Eds. Origins of Life: The Primal Self-Organization. 2011. Springer. P. 301.


“Certain macroscopic features of flow, energetics, and evolution in cascading pond and drainage systems formally resemble other processes, which at the molecular nanoscale have led to the organization of living matter. Repeated retardation of flow at intermediate energy potentials, as well as funneling of downward flow into conducting channels can be found again at the biochemical level in diverse reaction pathways. The retardation in reservoirs has an important buffer function, making energy and matter available more evenly than following environmental fluctuations directly.” Egel, Richard. “Integrative Perspectives: In Quest of a Coherent Framework for Origins of Life on Earth.” Pp. 289-360. From Egel, Richard, D. Lankenau & A. Mulkidjanian, Eds. Origins of Life: The Primal Self-Organization. 2011. Springer. P. 302.


“Inasmuch as the prebiotic evolution towards life on Earth has likely been governed by the structuring of catalytic surfaces in progressively greater detail, the assumption of some kind of primordial surface metabolism is quite valuable as a general evolutionary concept. Hence, this term as such should not be solely associated with the particular kind of pyrite-driven chemistry for which it was first proposed. In fact, the notion of catalytic surface interactions has earlier roots in clay-driven models of geochemical self-organization. Colloquially, the evolutionary potential of surface metabolism models has been referred to as ‘primordial pizza’ dynamics – in contrast with earlier notions of some ‘primordial soup’....” Egel, Richard. “Integrative Perspectives: In Quest of a Coherent Framework for Origins of Life on Earth.” Pp. 289-360. From Egel, Richard, D. Lankenau & A. Mulkidjanian, Eds. Origins of Life: The Primal Self-Organization. 2011. Springer. P. 302.


“In other words, the patchy environment where life can have started may best be conceived as biofilm-like molecular associations in some kind of geochemical reactor with many internal surfaces.” Egel, Richard. “Integrative Perspectives: In Quest of a Coherent Framework for Origins of Life on Earth.” Pp. 289-360. From Egel, Richard, D. Lankenau & A. Mulkidjanian, Eds. Origins of Life: The Primal Self-Organization. 2011. Springer. P. 303.


“The cash flow of energetic coupling in endergonic metabolic reactions is based on relatively few types of chemical bonds and compounds, as characterized by quantized energy release on the one hand and mechanical handles or anchor points on the other. The most readily convertable currency of metabolic energy coupling is represented by ATP and other pyrophosphate carriers. In the top-down ranking of universal metabolism, a close second is the prototype coenzyme, CoA, where thioester linkage activates carboxylic acid moieties for various transfer reactions.” Egel, Richard. “Integrative Perspectives: In Quest of a Coherent Framework for Origins of Life on Earth.” Pp. 289-360. From Egel, Richard, D. Lankenau & A. Mulkidjanian, Eds. Origins of Life: The Primal Self-Organization. 2011. Springer. P. 311.


“By and large, however, it is not unreasonable to assume a certain congruence between metabolic networks in modern life and a prebiotic protometabolism. In particular, the shell-like organization of metabolism can be rationalized in evolutionary terms, assuming that the inner shells assembled first in prebiotic, geochemical evolution.” Egel, Richard. “Integrative Perspectives: In Quest of a Coherent Framework for Origins of Life on Earth.” Pp. 289-360. From Egel, Richard, D. Lankenau & A. Mulkidjanian, Eds. Origins of Life: The Primal Self-Organization. 2011. Springer. P. 313.


“Although modern biocatalysts are wonderful in many ways, they cannot actually do miracles. Without proper substrates, all their marvelous capabilities would have no effect. What really matters is which potential substrates are present at a given moment in time, and which reactions can possibly lead to other compounds. Primordial catalysts can increase the rate of particular reactions over others and thereby influence the availability of substrates for other catalysts nearby. Inasmuch as entire ecosystems are capable of self-organization, it is the tenet of metabolism-first scenarios that self-organizing molecular ecosystems preceded the emergence and natural selection of cellular/genetic organisms.

“In terms of network analysis, emerging biocatalysts are both substrates and mediating agents. Acting collectively in a communicative system, this ultimately channelizes a flow of matter, as coupled to the conversion of environmental energy for metabolic work. The effective coupling of energy-rich compounds to endergonic reactions by emerging organic catalysts is arguably the most far-reaching accomplishment in prebiotic evolution ...” Egel, Richard. “Integrative Perspectives: In Quest of a Coherent Framework for Origins of Life on Earth.” Pp. 289-360. From Egel, Richard, D. Lankenau & A. Mulkidjanian, Eds. Origins of Life: The Primal Self-Organization. 2011. Springer. P. 314.


“Under general growth conditions, providing that the overall rate of covalent bond formation exceeds the rate of spontaneous degradation, the variety of different multimers is rising. Formally, this entails a random synthesizer function. Further feedback can then result from differential breakdown; if unstructured, flexible, idling multimers are purged before others that are tightly folded, substrate-bound, and stabilized. Complementary systems properties have been proposed by Dyson and Kauffman, assuming that, in a large set of different multimers, certain members will catalyse the formation of others. In a process of autocatalytic network closure, this provision will select for certain subsets where every member is catalysed in its formation by one or more members of the same set. Collectively, therefore, ‘selection at the chemical level can operate by the preferential survival of useful molecules.’” Egel, Richard. “Integrative Perspectives: In Quest of a Coherent Framework for Origins of Life on Earth.” Pp. 289-360. From Egel, Richard, D. Lankenau & A. Mulkidjanian, Eds. Origins of Life: The Primal Self-Organization. 2011. Springer. P. 316. References are: Dyson, F. 1985. Origins of Life. Cambridge University Press. Kauffman, S. 1993. The Origin of Order: Self-organization and selection in evolution. Oxford University Press. Subquote is from de Duve, C. 1987. “Selection by differential molecular survival: a possible mechanism of early chemical evolution.” Proc Natl Acad Sci USA. 84:8253-8256.


“As for activating free amino acids before their polymerization under early-earth conditions by other means, a conceivable mechanism is by reaction with isocyanic acid (HNCO), which supposedly entered the primordial atmosphere from volcanic sources. In a bold and ingenious revolving scheme, termed primary pump, this activation could have facilitated the stepwise elongation of prebiotic peptides, while cycling between tidal wetting at a flooded beach and intermittent desiccation.” Egel, Richard. “Integrative Perspectives: In Quest of a Coherent Framework for Origins of Life on Earth.” Pp. 289-360. From Egel, Richard, D. Lankenau & A. Mulkidjanian, Eds. Origins of Life: The Primal Self-Organization. 2011. Springer. P. 317.


“The thing primary pump and the SIPF [salt-induced peptide formation] reaction have in common is that they rely on local energizing in a generally anoxic atmosphere, as well as on the regular repetition of wet/drying cycles. Also, they probably would not have worked if they only had to rely on low average concentrations of amino acids in a primordial soup scenario, comprising the bulk of the entire ocean. Yet, in a patchy environment and in close association with a primordial geochemical reactor that already was generating a local stock pile of carboxylic and amino acids, the SIPF and/or primary pump reactions could have provided the critical link to kick-start the tentative biogenic reactor to proceed to the next level. Autonomous peptide formation should then take over, as energized by a system-internal means of amino acid activation and scaffold-guided polymerization of more and longer, yet still stochastic peptides.

“Neither the SIPF reaction nor the primary pump, however, have left directly traceable relics in modern metabolism. So their potential impact in kick-starting prebiotic peptide formation remains a matter of informed speculation.” Egel, Richard. “Integrative Perspectives: In Quest of a Coherent Framework for Origins of Life on Earth.” Pp. 289-360. From Egel, Richard, D. Lankenau & A. Mulkidjanian, Eds. Origins of Life: The Primal Self-Organization. 2011. Springer. P. 317.


“Metal chelation, such as phosphate binding in cups or nests can constrain relatively small peptides into rigid conformations, presenting quite specific binding epitopes for secondary interactions. In this pregenetic phase of uncoded peptide evolution, selective fitness had a quite literal dimension, dependent on physically fitting together complementary configurations and eliminating other peptides that did not fit in with any binding partner.

“Together with phosphorylated metabolites and cofactors, this colloidal community of peptides would further diversify by transpeptidation-like splicing reactions and various kinds of cross-linking, resulting in system-wide catalytic closure. To denote the relevance of this important evolutionary stage, the guiding concepts of a peptide world and a cofactor world can blend together in a tentative peptide-coenzyme world. At this dreamtime stage of prebiosis, regular RNA as a replicative macromolecule did not yet exist, and a prebiotic mode of ‘selection favored communities of molecules that collectively were best able to catalyze synthesis of their own constituents’. By this token, self-supportive – autotrophic – molecular ecosystems developed before any proto-cellular organisms, no matter whether the first of those would emerge as autotrophic or heterotrophic entities later on.” Egel, Richard. “Integrative Perspectives: In Quest of a Coherent Framework for Origins of Life on Earth.” Pp. 289-360. From Egel, Richard, D. Lankenau & A. Mulkidjanian, Eds. Origins of Life: The Primal Self-Organization. 2011. Springer. Pp. 318-9.


“Unlike most other catalysts, the ribosome itself is not directly involved in the chemical transpeptidation reaction as such; it does not form any reactive intermediate with the substrate. To the contrary, for most of its work cycle it actually forms a particularly unreactive intermediate, so as to protect the energy-rich peptide-bearing ester bond from accidental hydrolysis by ambient water molecules. Overall, the ribosome is essentially a reciprocating ratchet feeder for repetitive transpeptidation, from one ribonucleotide carrier to another. Assembled from many parts, it forms an exquisitely refined and complicated molecular machine. The processivity and quality controls that make it tick today must have gone through many evolutionary steps.” Egel, Richard. “Integrative Perspectives: In Quest of a Coherent Framework for Origins of Life on Earth.” Pp. 289-360. From Egel, Richard, D. Lankenau & A. Mulkidjanian, Eds. Origins of Life: The Primal Self-Organization. 2011. Springer. P. 320.


“Mineral surfaces appear suitable for the emergence of RNA polymerization, and tidal cycling may have assisted in the periodic separation of template and product in the primordial absence of efficient helicase activity. Up-concentration in the pore space of freezing sea-ice is likewise conducive of polymerization from activated monomers. With the emerging ability to replicate a given parental sequence and producing self-similar progeny molecules at higher frequencies than unrelated sequences, chemical evolution has passed a pivotal threshold, so as to enter competition between individual molecules for better reproducibility. Together with the emergent tendency for self-similar replication, the prolific exploration of sequence space to reach local or global optima should be greatly accelerated by means of molecular recombination quite early on.” Egel, Richard. “Integrative Perspectives: In Quest of a Coherent Framework for Origins of Life on Earth.” Pp. 289-360. From Egel, Richard, D. Lankenau & A. Mulkidjanian, Eds. Origins of Life: The Primal Self-Organization. 2011. Springer. Pp. 321-2.


“Except for the involvement of tRNAs and ribosomes in amino acid activation and trasnspeptidation reactions, all other natural ribozymes engage in splitting and joining of phosphodiester bonds during processing and maturation of RNA substrates. Among all the natural ribozymes, which generally are embedded in ribonucleo-protein (RNP) complexes, only RNase P and ribosomes facilitate more than a single reaction cycle, whereas others are used up in their first and only reaction. Besides, ribosomes act more as a mechanical shuttle and funneling aid than a genuine catalyst.” Egel, Richard. “Integrative Perspectives: In Quest of a Coherent Framework for Origins of Life on Earth.” Pp. 289-360. From Egel, Richard, D. Lankenau & A. Mulkidjanian, Eds. Origins of Life: The Primal Self-Organization. 2011. Springer. P. 326.


“The largest – and arguably most complicated – RNP machines are likewise engaged in the processing of RNA. These are the spliceosomes of eukaryotic cells, and there are two ancient kinds with only partly overlapping composition. Since the overwhelming majority of eukaryotic proteins are encoded by discontinuous bits and pieces in the genome, the corresponding transcripts need to be spliced into functional mRNAs, prior to meaningful translation by the ribosomes. It is the essential job of spliceosomes to remove all those intervening sequences (introns) – forming a branched byproduct (lariat) en route – and to join the adjacent coding parts (exons) together.

“There is a growing suspicion that spliceosomes indeed are ribozymes at heart. Yet, like ribosomes, they foremost are formidable RNP machines at large. In contrast with most other ribozymes, which esoterically engage in single-shot reactions, spliceosomes are rechargeable in an intricate cycle of dissociation and reassembly steps. Why this elaborate mechanism only prevails in eukaryotes, but is absent in bacteria and archaea, has intriguing implications for how to interpret the rooting of the universal Tree of Life. As tentative relics from an ancient RNA world are disproportionately more frequent in eukaryotic cells than in both bacteria and archaea, it is not entirely unreasonable to consider that the basic blueprint for eukaryotic cell organization, too, might be of more ancient vintage than commonly believed.” Egel, Richard. “Integrative Perspectives: In Quest of a Coherent Framework for Origins of Life on Earth.” Pp. 289-360. From Egel, Richard, D. Lankenau & A. Mulkidjanian, Eds. Origins of Life: The Primal Self-Organization. 2011. Springer. P. 327.


“The emergence of replicatable genes with particular metabolic functions is one thing: their integration into genomes is yet another. There are several modes of keeping functionally related genes together, all of which are biologically relevant to various extent. Most directly, the nucleic acid sequences of several genes can be connected into chromosomal entities. Also, groups of genes or their concatenates can be anchored at external scaffolds and/or be gathered in closed compartments. At the RNA world stage already – with or without the help of uncoded peptides – the RNA gene products had to be distinguished and separated from the generative templates (the genes themselves), which likewise consisted of RNA in the beginning. Furthermore, this principle had to cooperate with a growing tendency to gather functionally related genes on a common plasmid of chromosomal entity.” Egel, Richard. “Integrative Perspectives: In Quest of a Coherent Framework for Origins of Life on Earth.” Pp. 289-360. From Egel, Richard, D. Lankenau & A. Mulkidjanian, Eds. Origins of Life: The Primal Self-Organization. 2011. Springer. P. 328.


“The mutual entanglement of self-complication and self-simplification, which characterizes Darwinian evolution, likely goes back to precellular origins.” Egel, Richard. “Integrative Perspectives: In Quest of a Coherent Framework for Origins of Life on Earth.” Pp. 289-360. From Egel, Richard, D. Lankenau & A. Mulkidjanian, Eds. Origins of Life: The Primal Self-Organization. 2011. Springer. P. 332. Clarifying reference is: Conrad, M. 1990. “The geometry of evolution.” Biosystems 24:6181.


“As adaptive evolution gradually reduced the number of low-specificity components and, in turn, increased the length of sequences, expressing higher specificity and/or activity of system-supportive reactions, complementary tendencies for simplification and complication went hand in hand.” Egel, Richard. “Integrative Perspectives: In Quest of a Coherent Framework for Origins of Life on Earth.” Pp. 289-360. From Egel, Richard, D. Lankenau & A. Mulkidjanian, Eds. Origins of Life: The Primal Self-Organization. 2011. Springer. P. 333.


“As redundancy is required for many components at various levels, a simple genes-inside-vesicles model faces depletion by stochastic losses at each division and would hardly be viable early on. Instead, before long multi-genic plasmids and/or chromosomes had been established, together with effective proof reading, damage repair systems and segregation mechanisms, extensive masses of proto-cytoplasmic hydrogels had to remain connected in a state of confluence, spanning volumes much larger than presently seen in bacteria. Presumably, therefore, proto-cytoplasm and vesicular membranes coevolved for a long period, irrespective whether most of the membranes occurred inside or outside the proto-cytoplasm.” Egel, Richard. “Integrative Perspectives: In Quest of a Coherent Framework for Origins of Life on Earth.” Pp. 289-360. From Egel, Richard, D. Lankenau & A. Mulkidjanian, Eds. Origins of Life: The Primal Self-Organization. 2011. Springer. P. 333.


“... I am led by the notion that precellular systems were highly organized internally, before they could ever become miniaturized as genuine cells in the modern sense. In this scenario, precellular life is more concerned with sessile growth and spatial organization, than with periodic division at the earliest possible time. Such priorities are more related to the molecular ecology of biofilms, than to free-living, suspended individuals and populations.” Egel, Richard. “Integrative Perspectives: In Quest of a Coherent Framework for Origins of Life on Earth.” Pp. 289-360. From Egel, Richard, D. Lankenau & A. Mulkidjanian, Eds. Origins of Life: The Primal Self-Organization. 2011. Springer. P. 334.


“Seen from the vantage point of a coherent precellular molecular ecosystem, a direct path to eukaryotic cell organization poses no mystifying conundrum at any step.” Egel, Richard. “Integrative Perspectives: In Quest of a Coherent Framework for Origins of Life on Earth.” Pp. 289-360. From Egel, Richard, D. Lankenau & A. Mulkidjanian, Eds. Origins of Life: The Primal Self-Organization. 2011. Springer. P. 339.


“A particular trait of eukaryotic cells is no longer contested by any party – that mitochondria are of bacterial descent. In fact, modern eukaryotes have attained other endosymbionts repeatedly in various lineages, as commonly mediated by engulfment – phagocytosis without digestion.” Egel, Richard. “Integrative Perspectives: In Quest of a Coherent Framework for Origins of Life on Earth.” Pp. 289-360. From Egel, Richard, D. Lankenau & A. Mulkidjanian, Eds. Origins of Life: The Primal Self-Organization. 2011. Springer. P. 340.


“Presumably, the long transition from geochemical origins to organismal life has passed through several stages:

• Carboxylic acids, aldol phosphates, amino acids, heterocyclics, and other organic compounds accumulated in the multi-connected pore space of mineral-catalytic, and probably photon-activated, geochemical reactors.
• Self-stabilizing proto-metabolic networks coalesced as a mineral-cofactor world scenario.
• Peptide-like amino acid polymers added catalytic potential to water-hydrophobic interfaces, at proto-membranes of hydrogels in a peptide-cofactor world scenario.
• From a dual role of ribose phosphates, acting both in amino acid activation and in ribonucleotide polymerization, ribozymes and RNPd (RNA-peptide) complexes took over in a cofactor-assisted RNPd world scenario.
• By speeding up the generation of stochastic peptides, as followed by the adoption of sequence-specifying coding rules, the ever more sophisticated protoribosomes ushered in the currently prevailing regimen of RNA-encoded protein synthesis.
• The initially self-sufficient RNP (RNA-protein) world regimen was subsequently backed up by genomic DNA for higher genetic stability – the modern RNA- and protein-assisted DNA world.
• Presumably up to the RNP world level, a pervasive communal precellular system organized itself as a primarily photoautotrophic molecular ecosystem, mostly subject to K-selection.
• With the generation of autonomously viable and propagative cell-like systems (cellular escape), free-living populations of r-selected organisms could enrich the evolutionary scene, which quickly differentiated into multiple ecological niches, comprising both autotrophic producers and heterotrophic recyclers of various kinds.

“As for the sluggish, sessile, and communal precellular systems of the LUCAS era, we have no phylogenetic indication that any complex (non-bacterial) descendents survived on the bacterial side of the primal dichotomy. Only the planctobacterial superphylum may come closest to such an evolutionary relic. On the archaeal side, however, complex remnants were not necessarily wiped out altogether by the newly appearing r-selected prokaryotic cells. Instead, a mutual adjustment process let other precellular remnants specialize in recycling of particulate organic matter, including the engulfment of free-living cells. Eventually, some complex communal remnants organized themselves as more slowly evolving proto-eukaryotic macro-cells. The prokaryotic micro-cells, in turn, became smaller in size but more prolific and ubiquitous by sheer numbers. Mainly relying on phagocytosis of prokaryotic cells for a living, the complex macro-cells had no need to miniaturize. Instead, they could retain and perfect much higher degrees of cytoskeletal infrastructure and compartmentalization at subcellular levels. At least once in such engulfing cells, bacterial cells were retained as perpetuating proto-mitochondrial endosymbionts. These compound cells gave rise to all the eukaryotes of the modern era.” Egel, Richard. “Integrative Perspectives: In Quest of a Coherent Framework for Origins of Life on Earth.” Pp. 289-360. From Egel, Richard, D. Lankenau & A. Mulkidjanian, Eds. Origins of Life: The Primal Self-Organization. 2011. Springer. Pp. 342-4.


“One of the consequences of the sharpening differentiation among domains once suffused with the national, or the supranational, is that at the limit this can enable a proliferation of temporal and spatial framings and a proliferation of normative orders where once the dominant logic was toward producing unitary spatial, temporal, and normative framings. Even though this is a partial rather than all-encompassing development, its character is strategic.” Sassen, Saskia. Territory, Authority, Rights: From Medieval to Global Assemblages. 2006. Princeton University Press. P. 421.


“In earlier periods, including Bretton Woods, that [organizing] logic was geared toward building national states; in today’s phase, it is geared toward building global systems inside national states. One consequence of that difference in the economic arena, perhaps still the most legible domain, is the fact that in the earlier period the development of the world scale and the growth of international rivalry were directly related while today they are inversely related....

“The opposite dynamic was at work in the development of the earlier world scale. Where today’s global systems seek to over-ride interstate military conflict, those of the late 1800s and early 1900s fed such conflicts. Further, as they grow stronger, today’s global systems succeed more and more at diluting (or suppressing) rivalries among the major powers, while in the earlier period interstate rivalries became sharper as each of the major national powers grew stronger.” Sassen, Saskia. Territory, Authority, Rights: From Medieval to Global Assemblages. 2006. Princeton University Press. P. 16.


“In turn, as the formation of the national state and capitalism proceeded through the seventeenth century and onward through the twentieth century, the practices and projects that constituted the world scale evolved and reached considerable diversification of flows, institutionalization, and development of formidable administrative capacities. However, the organizing logics remained geared toward building national political economies.” Sassen, Saskia. Territory, Authority, Rights: From Medieval to Global Assemblages. 2006. Princeton University Press. Pp. 20-1.


“... globalization is not simply growing interdependence–its typical definition–but the actual production of spatial and temporal frames that simultaneously inhabit national structures and are distinct from national spatial and temporal frames as these have been historically constructed.” Sassen, Saskia. Territory, Authority, Rights: From Medieval to Global Assemblages. 2006. Princeton University Press. P. 23.


“The crux of the argument is that, in hominins, the act of opposing dominant individuals involves a form of cooperation. Thus, by tracking evidence in favor of enhanced cooperation, we can indirectly find evidence of hominins evolving the capacity to disrupt dominance hierarchies.” Dubreuil, Benoit. Human Evolution and The Origins of Hierarchies: The State of Nature. 2010. Cambridge University Press. P. 6.


“I argue that the most significant turning point between nonstate and state societies occurs when an individual is authorized to delegate to others the power to sanction normative transgressions. This is the beginning of political centralization and of the hierarchical integration that characterize many state institutions: the military, juridical, administrative, and (sometimes) religious systems.” Dubreuil, Benoit. Human Evolution and The Origins of Hierarchies: The State of Nature. 2010. Cambridge University Press. P. 8.


“Indeed, humans have the ability to share attention not only to physical objects but also to actions or events. Consequently, parents can draw the attention of children to stereotypical actions and attach a negative or positive sanction to them. This is basically what socialization is about: children learn through repetitive social sanctions that some actions are forbidden, permitted, or obligatory.” Dubreuil, Benoit. Human Evolution and The Origins of Hierarchies: The State of Nature. 2010. Cambridge University Press. P. 64.


“For instance, low-ranking male chimpanzees quickly learn that getting too close to a female in estrus can make high-ranking males quite angry. They quickly understand that it is advantageous to sneak into the bushes to avoid punishment. Non-human primates also have all kinds of ritual gestures to signal their good intentions. Many of these gestures are the outcome of social learning. Nonhuman primates develop expectations about social actions, and these expectations contribute to shaping their social preferences.

“There is no question that similar learning process shapes human expectations and social preferences. The difference, however, is that humans also develop a subset of expectations about actions that are sanctioned in the context of shared attention. This set of expectations can be qualified as ‘normative.’ In everyday life, normative expectations are frequently contrasted with other behavioral expectations. For instance, women often expect their employers to be upset if they find out that they are pregnant, but they generally do not expect to be blamed by their employers for being pregnant.” Dubreuil, Benoit. Human Evolution and The Origins of Hierarchies: The State of Nature. 2010. Cambridge University Press. P. 65.


“Philosopher John Searle has claimed that normative expectations in humans are distinctive in that they are ‘socially constructed.’ In the framework presented here, constructing normative expectations socially implies sharing attention to the action while attaching a positive or negative sanction to it. In the socialization process, basic norms take the form of stereotypical actions and scenes to which sanction will be attached overtly in the context of joint attention. In that sense, norms are similar to other conventional concepts on which natural language is based.” Dubreuil, Benoit. Human Evolution and The Origins of Hierarchies: The State of Nature. 2010. Cambridge University Press. Pp. 65-6.


“The mechanisms underlying normativity and sanction provide a solution to the collective problem of dominance. However, because they are general social mechanisms, they also secure cooperation in many other areas of social life.” Dubreuil, Benoit. Human Evolution and The Origins of Hierarchies: The State of Nature. 2010. Cambridge University Press. P. 67.


“What emerges from Table 2.1 is a punctuate evolution with two major behavioral transitions:

“1. Early Homo erectus sensu lato presents strong evidence of increased cooperation for two of the points that we examined: he was ecologically more flexible than his predecessors, probably because of his modern body, and he shifted to a higher quality diet.

“2. Homo heidelbergensis presents strong evidence of increased cooperation for all but one of the points discussed. There is no unambiguous evidence of long-term support for incapacitated individuals among these hominins, but this can easily be due to the scarcity of the fossil record. Even the much better known Neanderthal record has provided only a few indisputable specimens.”
[Four other points of evidence for cooperation: “Habitual use of fire, cooking, and reliance on large-game hunting; Prolonged infancy compared to apes; Secondary altriciality and modern birth mechanism; Reduced sexual dimorphism and restricted mating access”]
Dubreuil, Benoit. Human Evolution and The Origins of Hierarchies: The State of Nature. 2010. Cambridge University Press. Pp. 84-5.


“I have argued in this chapter that, with regard to cooperation and social norms, the archaeological record suggests that at least two major behavioral transitions occurred since our last common ancestor with chimpanzees. The first took place in early Homo erectus and can be related to a change in social motivations that made cooperative feeding more advantageous. It provoked a shift to a more versatile, higher quality diet, as well as the colonization of a new ecological niche. The second, which occurred in Homo heidelbergensis or slightly earlier, can be explained by enhanced cognitive control that facilitated investment in long-term public goods games such as cooperative breeding.

“If my argument is correct and these changes really occurred, they must have had a major impact on traditional dominance hierarchies. Had the early Homo erectus been interested in sharing attention with its conspecifics, it would have been more prone to engage in cooperative resistance against aggressive and violent individuals. A few hundred thousand years later, enhanced cognitive control could have given groups of Homo heidelbergensis the capacity to turn down the aspirations of their most aggressive members. We will never know exactly how our ancestors lived or the specific tactics they used to resist dominance. Nevertheless, the best guess as of now would be that a few hundred thousand years ago hominins were living in nearly egalitarian foraging bands, successfully resisting despotic individuals. Although dominance hierarchies were eradicated, modern status hierarchies had not yet been created. Homo erectus, Homo heidelbergensis, and Homo neanderthalensis had no more alpha males, but not yet a chief, a priest, or a president.” Dubreuil, Benoit. Human Evolution and The Origins of Hierarchies: The State of Nature. 2010. Cambridge University Press. P. 90.


“The African evidence suggests that, tens of thousands of years ago, populations of modern Homo sapiens began to formally organize their social life in building tribal networks in which local bands were embedded. In a species capable of building such institutions, hierarchies could reappear, given the right circumstances.” Dubreuil, Benoit. Human Evolution and The Origins of Hierarchies: The State of Nature. 2010. Cambridge University Press. P. 93.


“If the categorization of an individual as a ‘mother’ or as a ‘child’ can be based simply on behavioral cues, the successful construction of concepts such as ‘president,’ ‘chief,’ or ‘priest’ depends on our capacity to represent the point of view of other persons on the ascribed concept. It makes no sense to say that someone is a priest or a president if she has no idea what it means to be a priest or a president. At a minimum, I need to consider the status from my point of view and from the point of view of the other person. In sum, institution-making in humans builds on our capacity to consider and coordinate alternative perspectives on concepts. This capacity requires more than the faculty of language as it is ordinarily understood.

“1. It implies that we have the right affects and that we are interested in sharing attention with our conspecifics. I proposed in the previous chapter some reasons to believe that this ability was in place early in the human lineage.

“2. It implies executive functions such as inhibition and working memory, located in large part in the prefrontal cortex. Given the relative stasis of the frontal lobe during the last 500,000 years and the presence of long-term cooperative ventures in Homo heidelbergensis, these abilities were probably in place before the morphological and the behavioral modernization of Homo sapiens.

“3. Finally, it entails sufficient attentional flexibility to look simultaneously at a a person as a man or as a president, or at an object as a tool and as a ritual object. Such tasks rely heavily on the temporoparietal areas, and as these areas underwent significant reorganization in line with the globularization of the cranium, I propose that the cognitive modernization of Homo sapiens began there.”
Dubreuil, Benoit. Human Evolution and The Origins of Hierarchies: The State of Nature. 2010. Cambridge University Press. P. 136.


“Put briefly, my point is that the cognitive mechanisms underlying human behavioral modernization also stand behind the reappearance of hierarchies in our species. Hierarchies in modern humans are not of the same kind as those found in our closer relatives, but build on our ability for collective ascription of status. Humans can be bullies – there is no doubt about that – but leaders or rulers cannot be equated with alpha males. They can be violent and exploitative, but they do not need to be so.

“I think that evidence in favor of uniquely human social organization appears quite early in the archaeological record. As noted, the presence of raw materials from distant sources (>100 km) in MSA [Middle Stone Age] sites as old as 130,000 BP suggests that modern humans were already engaged in long-distance exchange networks at that time. Among modern foragers long-distance exchanges take place within tribal networks, in which corporate groups (clans, lineages, etc.) are institutionalized and are represented by specific individuals. It is tempting to see in Paleolithic personal ornaments instruments that were used to signal one’s place within such social systems.” Dubreuil, Benoit. Human Evolution and The Origins of Hierarchies: The State of Nature. 2010. Cambridge University Press. P. 137.


“When people struggle to monitor who is who, punishing defectors becomes more risky and less effective. People can thus go unpunished and break social norms with near impunity. The risk to the group of fission increases....”

“My contention is that local groups that grow beyond the level of a few dozen individuals have to find a cheaper strategy to monitor individual behavior. One way to do this is to focus monitoring on salient individuals and to take them as indicators of the trustworthiness of less salient ones. It is not surprising that most functions of headmen in egalitarian societies have to do with representing corporate groups (clans, lineages, tribes, and other sodalities).” Dubreuil, Benoit. Human Evolution and The Origins of Hierarchies: The State of Nature. 2010. Cambridge University Press. P. 164.


“Because normative violations have implications for collectives, certain members of a corporate group are often made implicitly or explicitly responsible for enforcing norms within the group. I term this second relational mechanism the ‘social division of sanction.’ By that, I mean that in such societies not everybody is equally responsible for sanctioning normative violations. Rather, normative expectations are created about who should sanction normative violations. In modern societies, for instance, there are explicit rules that specify that the right to sanction the burglar belongs to the judge and not to the victim.

“Philosopher of law Herbert L. Hart has aptly captured this point with his distinction between primary and secondary rules. To put it briefly, primary rules are rules of conduct. They prescribe how people should behave. In prelegal systems, their content is culturally defined by the disapprobation that attaches to specific actions. Rules of etiquette are probably the best examples of primary rules, but one can also think of rules prohibiting violence or prescribing help. In legal systems, primary rules can also be fixed by secondary rules; that is, rules that are defined with respect to other rules.” Dubreuil, Benoit. Human Evolution and The Origins of Hierarchies: The State of Nature. 2010. Cambridge University Press. Pp. 166-7. Reference is to Hart, Herbert. The Concept of Law. 1961. Clarendon Press.


“My contention is that, although the range of possible arrangements can vary indefinitely, growing group size depends on the ability to find institutions that relieve the burden on cognition by focusing social monitoring on a few salient individuals. If these individuals are turned into reliable indicators of the trustworthiness of larger groups, the costs of sanction may be prevented from rising.” Dubreuil, Benoit. Human Evolution and The Origins of Hierarchies: The State of Nature. 2010. Cambridge University Press. P. 169.


“... higher theory of mind and perspective taking are essential for creating both corporate groups and secondary rules. Consequently, only a species in which these abilities are well established would be able to generate the institutional arrangements that make it possible for human groups to grow beyond the size of the band. If higher theory of mind and perspective taking are unique to behaviorally modern humans, as I have argued, then archaic humans could not have created either local groups significantly larger than a few dozen individuals or tribal systems based on the aggregation of corporate groups.” Dubreuil, Benoit. Human Evolution and The Origins of Hierarchies: The State of Nature. 2010. Cambridge University Press. P. 170.


“The objective of this chapter was nevertheless to save one core assumption underlying neoevolutionary approaches. I am not referring to the idea of linearity or directionality of evolution, but to the assumption that there is some functional link between large societies and the emergence of hierarchies. I argued that this link can be explained by the cognitive and motivational mechanisms that make punishing strangers more expensive than punishing familiars. Growing group size thus depends on the existence of institutions that control the costs of sanction. These institutions can be corporate groups, indicating the trustworthiness of their members, or secondary rules, allowing for a social division of sanction.” Dubreuil, Benoit. Human Evolution and The Origins of Hierarchies: The State of Nature. 2010. Cambridge University Press. P. 186.


“In bacteriology, autotrophy has become determined by the growth of a pure culture in a strictly inorganic growth media, devoid of any organic compounds other than carbon dioxide (or carbonate) that serve as the sole source of carbon. Subsequent studies have uncovered other one carbon autotrophs that use carbon monoxide, carbon disulfide, methane and formic acid as the sole carbon source.” Srinivasan, V. & H. Morowitz. “What is an autotroph?” Arch Microbiology 2012 194:135-140. P. 135.


“As several autotrophs seem to lie near the root of the phylogenetic tree, the metabolist position suggests that the earliest organisms were chemoautotrophs. The core anabolism shows great similarity among chemoautotrophs indicating three possibilities: a single origin of metabolism, a best solution to anabolism, an only solution to anabolism.” Srinivasan, V. & H. Morowitz. “What is an autotroph?” Arch Microbiology 2012 194:135-140. P. 136.


“The last 60 years have witnessed chemists developing an understanding of organocatalysis and ligand field theory, both of which give demonstrable low-molecular-weight catalysts. We assume that transition-metal-ligand complexes are likely to have occurred in the deep ocean trenches by the combination of naturally occurring oceanic metals and ligands synthesized from the emergent CO2, H2, NH3, H2S, and H3PO4.” Morowitz, H., V. Srinivasan & E. Smith. “Ligand Field Theory and the Origin of Life as an Emergent Feature of the Periodic Table of Elements.” Biological Bulletin. 219:1-6. August 2010. P. 1.


“They [transition elements] are characterized as having atoms or ions with incomplete or complete shells of ‘d’ orbitals; the ones we are most interested in are groups 5 to 12 in the fourth period and molybdenum and tungsten in the next periods. They are part of a cluster of the periodic table called the ‘d’ block elements/chemicals. In present day biology they form a very small part of the mass of functioning cells, usually less than 1%, yet they play a central role as cofactors as well as essential components in perhaps half of all proteins. The best studied for their biological roles are vanadium, manganese, iron, cobalt, zinc, molybdenum, copper, and nickel.”

“As we noted, transition-metal complexes, or ‘d’ block complexes, consist of a central transition-metal atom or ion surrounded by molecules and ions, usually nonmetallic. When these surrounding structures are bonded or otherwise attached to the metal, they are called ligands. This is a restricted use of the word ligand used in ligand-field theory, which deals with molecular orbitals and bonding of the metals and ligands. Ligand in present-day biochemistry often refers to any molecular grouping that attaches to a protein.” Morowitz, H., V. Srinivasan & E. Smith. “Ligand Field Theory and the Origin of Life as an Emergent Feature of the Periodic Table of Elements.” Biological Bulletin. 219:1-6. August 2010. P. 2.


“In ligand field theory, orbitals are associated with the entire complex, thus allowing for more chemical subtlety. The orbitals are still weighted sums of atomic orbitals, but the s,p,d overlap renders the probability functions more global over the entire complex.” Morowitz, H., V. Srinivasan & E. Smith. “Ligand Field Theory and the Origin of Life as an Emergent Feature of the Periodic Table of Elements.” Biological Bulletin. 219:1-6. August 2010. P. 3.


“In a recent computational work, we sought to develop a broadly applicable set of algorithms to ask whether and under what environmental condition any two given species may be expected to display metabolic symbiosis.... Surprisingly, we found that for most organism pairs, it is possible to find a large number of putative environments that induce cross-feeding, i.e. that support growth of the joint model, but not of individual species. Hence, metabolism-based symbiotic interactions may be highly abundant in communities, and highly dependent on environmental composition and dynamics.” Klitgord, N. & D. Segre. “Ecosystems biology of microbial metabolism.” Current Opinion in Biotechnology. 2011. 22:541-546. P. 542.


“Genome-scale networks and algorithms are promising approaches toward studying small natural or engineered microbial ecosystems. An outstanding question is whether these approaches can be applied to the much larger number of interacting species present in most ecosystems, and whether large modular stoichiometric models are going to be useful and necessary. One potential answer to this question comes from metagenomic sequencing data, suggesting that while organism lineages fluctuate extensively through time and conditions, the functional (and more specifically metabolic) content of microbial communities displays dynamic stability and correlations with environmental parameters. On the one hand, it does not seem too surprising that the chemical make up of an environment (e.g. the available redox couples) should, at evolutionary time scales, determine what metabolic functions will be present in the microbial community. However, if this ‘metabolic determinism’ has truly been shaping the microbial world, this would have profound consequences on our understanding of life and its evolutionary history on our planet. Given this prospective of potential ecosystem-level principles of metabolic organization, it may be useful to explore stoichiometric models that consider a whole microbial community as a single ‘soup of enzymes’, disregarding the boundaries of individual species.” Klitgord, N. & D. Segre. “Ecosystems biology of microbial metabolism.” Current Opinion in Biotechnology. 2011. 22:541-546. P. 543.


“Indeed, in small-scale foraging social worlds, the cognitive problem of effective coordination is more demanding than that of detecting defection.” Sterelny, Kim. The Evolved Apprentice: How Evolution Made Humans Unique. 2012. Bradford Book, MIT Press. P. 10.


“Fruits are designed to be eaten. But plants do not welcome herbivore consumption of their storage organs, and hence they are protected both mechanically and chemically. It takes a well-informed mind to find these organs, extract them, and make them edible by soaking, cooking, and the like.” Sterelny, Kim. The Evolved Apprentice: How Evolution Made Humans Unique. 2012. Bradford Book, MIT Press. Pp. 13-4.


“The idea, then, is that positive feedback links social foraging and intergenerational social learning. Intergenerational learning provides much of the informational fuel that makes social foraging successful, and the rewards of social foraging support the life spans and expensive metabolisms that make extensive intergenerational learning possible.” Sterelny, Kim. The Evolved Apprentice: How Evolution Made Humans Unique. 2012. Bradford Book, MIT Press. P. 14.


“If specialists are more likely to successfully innovate in their field of specialization, as seems likely, positive connections will develop between elaborating social foraging, increased group size, and the rate of innovation.

“In sum, feedback loops form between individual cognitive capacity, social organization, and the pace of environmental change.” Sterelny, Kim. The Evolved Apprentice: How Evolution Made Humans Unique. 2012. Bradford Book, MIT Press. P. 18.


“The apprentice learning model has four important virtues. First, it identifies a form of learning that can be assembled incrementally. The reliable transmission of skill can begin as a side effect of adult activity, without adult teaching and without adaptations for social learning in the young. Once established, it then brings with it selection for cognitive and social changes that increase the reliability or reduce the cost of learning. Rudimentary but reliable skill transmission, however, does not presuppose the presence of such adaptations. Second, apprentice learning is known to support high-fidelity, high-bandwidth knowledge flow. Until recently, much technical competence in industrial society depended on apprentice learning. Virtually all technical competence in preindustrial societies depended on it. Third, the model fits ethnographic data quite well. Formal educational institutions and explicit teaching are not prominent parts of traditional society. But many forager societies organize and enhance children’s participation in economic activity, and this approach supports the transmission of traditional craft skills. Finally, the model can be shown to illuminate the archaeological record, ...” Sterelny, Kim. The Evolved Apprentice: How Evolution Made Humans Unique. 2012. Bradford Book, MIT Press. Pp. 35-6.


“For those who think of culture in this way, the emergence of decoration, public art, and ‘style’ is the archaeological signature of the transition from mere group membership to consciousness of membership. According to this view, the evolution of behavioral modernity is a cultural revolution, a transition from mere coexistence with others to identifying oneself with others. This transition is relatively recent; it took place (in this picture) somewhere between 120,000 and 50,000 years ago.” Sterelny, Kim. The Evolved Apprentice: How Evolution Made Humans Unique. 2012. Bradford Book, MIT Press. P. 49.


“However, symbols that serve as insignia of social place and identify are neither arbitrary nor displaced.” Sterelny, Kim. The Evolved Apprentice: How Evolution Made Humans Unique. 2012. Bradford Book, MIT Press. P. 51.


“In summary, then, the cultural learning characteristic of the Upper Paleolithic transition and later periods of human culture–social transmission with both a large bandwidth and sufficient accuracy for incremental improvement–requires individual cognitive adaptations for cultural learning, highly structured learning environments, and population structures that both buffer existing resources effectively and support enough specialization to generate a supply of innovation.” Sterelny, Kim. The Evolved Apprentice: How Evolution Made Humans Unique. 2012. Bradford Book, MIT Press. P. 61.


“Ecological cooperation selects for information sharing, and information sharing makes cooperative foraging more profitable and less risky. The critical premise of my argument was that cooperative foraging (of the hominin variety) depends on technology and expertise and hence selects for information sharing at and across generations.” Sterelny, Kim. The Evolved Apprentice: How Evolution Made Humans Unique. 2012. Bradford Book, MIT Press. P. 76.


“We are obligate, habitual, inveterate, and adapted social information pumps, sucking information and expertise from our social partners.” Sterelny, Kim. The Evolved Apprentice: How Evolution Made Humans Unique. 2012. Bradford Book, MIT Press. P. 76.


“But an alloparenting world selects for more than cuteness. It will select for (a) infant monitoring of mothers and others, (b) infant awareness of the differences among the others, and (c) infant awareness of others’ responses to its own action; awareness of joint attention and action. Once care is a negotiable quantity, babies are under selection for social skills, and that might help explain the recent results in developmental psychology suggesting that infants have a surprisingly rich theory of mind.” Sterelny, Kim. The Evolved Apprentice: How Evolution Made Humans Unique. 2012. Bradford Book, MIT Press. Pp. 87-8.


“But according to Marlowe, between perhaps 30,000 and 20,000 years ago, humans added spear throwers, the bow and arrow, and poison darts to their arsenal.

“All of this matters because the ability to kill at a distance changes the environment of cooperation. It became possible for individuals or small groups to kill large animals in relative safety. Large groups that hunt and kill together can share on the spot. The profit of joint activity is accrued together and in full view of all, so no informational problems arise in policing cooperation. Identifying and agreeing to a fair division of a joint resource is much less problematic if everyone is a roughly equal partner in a joint activity. Division becomes more problematic once individual success becomes highly variable (as individuals hunt alone or with favored partners), once the range of resources expands (making commensurability an issue), once role specialization becomes important, once reciprocation extends over time, and once individuals spend much of their time, and enjoy much of their success and failure, away from the eyes of the many. Cooperation is most stable in small, homogeneous groups.” Sterelny, Kim. The Evolved Apprentice: How Evolution Made Humans Unique. 2012. Bradford Book, MIT Press. P. 91. Reference is to Marlow, F.W. 2005. “Hunter-gatherers and human evolution.” Evolutionary Anthropology. 14:54-67.


“Kaplan, Hooper, and Gurven argue that egalitarian, cooperative social organization depends on four factors: (i) key resources cannot be monopolized by one or a few agents; (ii) all adult economic activity is highly skilled; (iii) female and male roles are complementary; and both are important; and (iv) communities are small, so that bottom-up mechanisms of norm enforcement, coordination, and decision work.” Sterelny, Kim. The Evolved Apprentice: How Evolution Made Humans Unique. 2012. Bradford Book, MIT Press. P. 92. Reference is to Kaplan, H., P. Hooper & M. Gurven. 2009. “The evolutionary and ecological roots of human social organization.” Philosophical Transactions of the Royal Society of London, Series B: Biological Sciences. 364:3289-3299.


“We are intelligent because cooperation is at once risky and too profitable to abandon.” Sterelny, Kim. The Evolved Apprentice: How Evolution Made Humans Unique. 2012. Bradford Book, MIT Press. P. 101.


“In short: if agents can commit–if commitment devices are available–agents can enhance fitness by constraining future choice. Constraining future choice enhances an agent’s capacity to deter. Credible threats secure resources that enhance fitness. Constraining future choice also enhances trustworthiness. Trustworthy agents can enter extended, profitable partnerships that cannot be stabilized by mutual surveillance.” Sterelny, Kim. The Evolved Apprentice: How Evolution Made Humans Unique. 2012. Bradford Book, MIT Press. P. 105.


“Internal mechanisms [those dependent on the “agent’s own psychology” and not on institutional support], in this view, were foundational to the solution of commitment dilemmas and hence to the evolution of human ultrasociality. In particular, Frank argues that our distinctive social and moral emotions are commitment devices....”

“As it happens, in hominin social worlds, the economic rewards of being trustworthy are important. Agents who care about keeping commitments tend to optimize their long-run economic welfare. As increasing resource take tends to increase fitness, there is selection for being trustworthy. Agents are trusted only if they can credibly commit; agents who can credibly commit gain an advantage thereby, and that explains the evolution of the commitment emotion complex. Commitment dilemmas were important to hominin social life. And so we evolved emotions that are motivationally powerful, emotions that are triggered by perceived violations of trust and fairness, emotions whose motivational saliences are relatively insensitive to utilitarian calculation, emotions whose occurrence are easily recognized and difficult to fake.” Sterelny, Kim. The Evolved Apprentice: How Evolution Made Humans Unique. 2012. Bradford Book, MIT Press. P. 107. Reference is to Frank, R. 1988. Pp. 57-77. “Cooperation through emotional commitment.” Evolution and the Capacity for Commitment. Editor, Nesse, R. Russell Sage Foundation.


“... commitment mechanisms do depend on costs, in three ways.”

“First, costs amplify effects of arousal. Some commitment signals are motivation bending rather than information carrying; they are Krebs-Dawkins signals. Their function is to change the motivational psychology of both sender and receiver rather than to reveal antecedently existing characteristics of the sender. Singing, for example, is a signal. But it has an affective impact on both sender and audience. Signal costs, I suggest, up-regulate the effects of such mood- and emotion-altering signals....

“By amplifying the salience of both reward and punishment, reinforcement is more effective in highly aroused situations. So joint action in emotionally amplified situations reinforces mutual bonds more powerfully than collective action in calmer emotional waters....

“Second costs are investments. We commit through niche alteration. But changing the world is not free.... Tattoos and facial scars are not (just) signals but interventions. They make cooperation within the group the right option in almost all circumstances, for the tattoos make shifting social networks much more difficult. In advertising your origins and affiliations, you inherit your allies’ enemies, whether or not you keep your allies’ support....

“Third, honesty has a by-product advantage. Honest signals can take advantage of by-products that increase their credibility for free. A dishonest signaler has to manufacture the evidence that makes a signal credible as well as produce the signal itself.” Sterelny, Kim. The Evolved Apprentice: How Evolution Made Humans Unique. 2012. Bradford Book, MIT Press. Pp. 110-1.


“Investment in building and maintaining relationships is a commitment device, because such relationships change the payoffs in triggering situations. If a triggering temptation arises, the costs of defection have been driven up. Defection will risk fracturing trust and hence forfeiting the profit from the investment necessary to build trust.” Sterelny, Kim. The Evolved Apprentice: How Evolution Made Humans Unique. 2012. Bradford Book, MIT Press. P. 117.


“But manipulation was a threat even in the small-scale, intimate social worlds of most human evolutionary history. But though real, this threat is not uniform. Other factors contribute to the robustness of honest signaling. The kind of information that flows, the nature of the channel, and the shape of the sender-receiver network are all relevant to honesty and deception. In sections 6.2 and 6.3, I argue that some forms of informational cooperation are much less prone to deceptive exploitation. In particular, I argue that the transmission of expertise is relatively immune to the problem of deception. That fact is important. It shows that some forms of informational cooperation can evolve and elaborate without requiring the prior or simultaneous evolution of complex cognitive tools.” Sterelny, Kim. The Evolved Apprentice: How Evolution Made Humans Unique. 2012. Bradford Book, MIT Press. Pp. 128-9.


“The Condorcet Jury Theorem makes the value of information-pooling in the face of uncertainty vivid. If each juror votes independently and has a better than 0.5 chance of being right, as the size of the jury goes up, the probability of a majority vote being right rises rapidly to near certainty. So agents gain access to reliable information about their environment if they have mutual knowledge of each agent’s assessment of noisy signals, together with trust in consensus. Imagine a foraging party trying to decide whether a swollen river is too dangerous to ford, which animal in a pack to target, how to interpret the ambiguous behavior of a neighboring group. There is no temptation to defect here. By voting honestly and accepting consensus, each agent trades an unreliable assessment of a relevant feature of the world for a much more reliable assessment. Information pooling protects not just against deception but against noise.” Sterelny, Kim. The Evolved Apprentice: How Evolution Made Humans Unique. 2012. Bradford Book, MIT Press. P. 137.


“This shows that in some respects, information sharing is less subject to defection problems than some forms of ecological and reproductive cooperation. When cooperation has a physical product, conflict and defection can arise over fair division of the product. A jointly produced informational product–for example, a more reliable assessment of the risks of a river crossing–is automatically available to all who have pooled their individual estimates. In this respect, it is more like successful collective defense than successful collective hunting.” Sterelny, Kim. The Evolved Apprentice: How Evolution Made Humans Unique. 2012. Bradford Book, MIT Press. P. 137.


“It follows that in a heterogeneous and changing environment, no one individual is personally exposed to all he or she needs to know about resources and dangers, threats and opportunities. Unless early hominins foraged together in a single convoy, differing individuals and teams experienced differing spatiotemporal patches of their home range. Together with a fission-fusion social organization, heterogeneity creates an informational gradient and thus a potentially advantageous division of epistemic labor.” Sterelny, Kim. The Evolved Apprentice: How Evolution Made Humans Unique. 2012. Bradford Book, MIT Press. P. 138.


“Many-to-many networks combined with sharing information in advance of action impose a veil of ignorance between a potentially Machiavellian agent and potential targets.... The upshot, then, is that in public signaling contexts, the chance that an attempted manipulation will be detected is quite high. Its rewards will rarely be both high and certain. Since the individual and collective benefits of local knowledge pooling are significant, we can expect a default for honest signaling.” Sterelny, Kim. The Evolved Apprentice: How Evolution Made Humans Unique. 2012. Bradford Book, MIT Press. P. 139.


“They [plausible candidate early evolving forms of information sharing] are low-risk forms of information sharing. Skill transmission, fast-fading ecological information, and long-shelf-life ecological information are all likely candidates for being early evolvers. The establishment of these early evolving forms of informational cooperation in hominin social worlds changed the nature of those social worlds, leading to selection for individual cognitive adaptations. Those extended the range of cultural learning, improved its fidelity and bandwidth, and managed the risks of deception. Moreover, the interaction of informational and ecological cooperation increased information gradients in hominin social groups and thus increased the potential profits of information sharing and communication. As forager skill levels increased, so did life expectancy, intensifying an intergenerational information gradient. Specialization and the division of labor likewise contribute to informational gradients, for specialization results in agents exploring different aspects and areas of their common range. These steeper gradients amplify the potential profits of communication, thus contributing to the positive feedback between cooperation, communication, and technical intelligence.” Sterelny, Kim. The Evolved Apprentice: How Evolution Made Humans Unique. 2012. Bradford Book, MIT Press. Pp. 148-9.


“One group can be fitter than another if it pumps more individual hominins into the next generation (multilevel selection 1). Or it can be fitter because it is more apt to produce descendant groups (multilevel selection 2). Sterelny, Kim. The Evolved Apprentice: How Evolution Made Humans Unique. 2012. Bradford Book, MIT Press. P. 178.


“Conventionally, Darwinian fitness is thing-based, measured in terms of replication of discrete things. In ‘traditional’ Darwinism, for example, the replicate is the offspring, while to a Neo-Darwinist, it is the atom of heredity, the gene. One can take a more physiological view of fitness as process, however, and here is where the future begins to creep back into our thinking about evolution. Processes have a dimension of timeliness that objects lack: they are properly quantified as rates. Processes are traditionally the purview of physiology, but they take on evolutionary import if they come to embody heritable memory. There is no real reason why they could not. Replicable genes qualify as heritable memory largely because they bias the future toward a particular state. The fitter gene is the one whose bias reaches further into the future. A physiological process can also bias the future, and by this criterion could also qualify as heritable memory. In this instance, the forward reach in time is embodied in persistence of the process: how likely it is that the orderly stream of matter and energy that embodies the process will persist in the face of whatever perturbations are thrown at it? A fit process is therefore a persistent process: if a particular catalytic milieu, or a particular embodied physiology, can more persistently commandeer a stream of energy and matter than can another, the more persistent stream will be the fitter. Homeostasis, therefore, is the rough physiological equivalent of genetic fitness: a more robust homeostasis will ensure a system’s persistence over a wider range of perturbations and further into the future than will a less robustly regulated system.

“A truly comprehensive theory of evolution, it seems, should be able to accommodate both thing-based and process-based fitness. One way to meld the two might be to define a new class of process-based heritable memory. Allow me to put forward a candidate: persistent environments created and managed by systems of Bernard machines. To differentiate these from thing-based replicators, I shall designate these persistent living environments as persistors. We place persistors and replicators at opposite ends of a spectrum of forms of heritable memory: object-oriented memory at one end and process oriented memory at the other.” Turner, J. Scott. The Tinkerer’s Accomplice: How Design Emerges from Life Itself. 2007. Harvard University Press. Pp. 218-9.


“Variation without persistence would mean that changes could not be maintained and built upon during evolution. And persistence without variation would bring evolution to a standstill.” Coen, Enrico. Cells to civilizations: The Principles of Change that Shape Life. 2012. Princeton University Press. P. 22.


“A vast range of arrangements can be produced simply by joining a few elements in different ways. I call this the principle of combinatorial richness.” Coen, Enrico. Cells to civilizations: The Principles of Change that Shape Life. 2012. Princeton University Press. P. 41.


“Our seven principles–population variation, persistence, reinforcement, competition, cooperation, combinatorial richness, and recurrence–and their interactions provide the driving force for these journeys, leading to the remarkable variety of organisms we see today. I have called this collection of seven principles and how they work together life’s creative recipe.” Coen, Enrico. Cells to civilizations: The Principles of Change that Shape Life. 2012. Princeton University Press. P. 60.


“Plant behavior is defined as the response to signals, and a plethora of external signals are sensed and acted upon by green plants. Resources (light, minerals, and water) figure strongly in a signals list that also includes numerous mecahanical influences such as wind, rain, and touch; gases such as ethylene and nitric oxide; soil compaction and particle structure; and numerous biotic features, such as identity of neighbors and disturbance, among many others.” Trewavas, Anthony. “Aspects of Plant Intelligence: Convergence and Evolution.” Pp. 68-110. From Morris, Simon C. The Deep Structure of Biology: Is Convergence Sufficiently Ubiquitous to Give a Directional Signal? 2008. Templeton Foundation Press. P. 69.


“Plants and animals differ fundamentally in the way they express behavior in response to signals. In plants, it is phenotypic plasticity; in animals, it is movement.” Trewavas, Anthony. “Aspects of Plant Intelligence: Convergence and Evolution.” Pp. 68-110. From Morris, Simon C. The Deep Structure of Biology: Is Convergence Sufficiently Ubiquitous to Give a Directional Signal? 2008. Templeton Foundation Press. P. 69.


“... unlike many animals, plants grow and develop throughout their life cycle. Embryogenesis continues throughout the life cycle, and the embryogenic meristems eventually form flowers. Environmental history can, thus, pass directly into reproduction. The Weismann proscription that the environment does not directly affect animal inheritance, because sexual cells are protected from environmental variation, is inapplicable to plants, strengthening the likelihood of neo-Lamarckian inheritance in plant evolution.” Trewavas, Anthony. “Aspects of Plant Intelligence: Convergence and Evolution.” Pp. 68-110. From Morris, Simon C. The Deep Structure of Biology: Is Convergence Sufficiently Ubiquitous to Give a Directional Signal? 2008. Templeton Foundation Press. Pp. 75-6.


“Light reflected from vegetation is richer in far-red wavelengths compared to red. Plants use that information along with its direction to predict not actual shade but to foresee the likelihood of shading at some stage in the future from a competitor. When a change in the balance of red to far-red radiation is perceived, an integrated adaptive response in phenotype structure results. New branches grow away from the putative competitor, stem growth is increased; the rate of branching diminishes, and such branches assume a more vertical direction; leaf area increases in anticipation of reduced incident flux; and the number of layers of leaf cells containing chlorophyll diminishes.” Trewavas, Anthony. “Aspects of Plant Intelligence: Convergence and Evolution.” Pp. 68-110. From Morris, Simon C. The Deep Structure of Biology: Is Convergence Sufficiently Ubiquitous to Give a Directional Signal? 2008. Templeton Foundation Press. P. 89.


“There are a number of organizational similarities between plants (trees, in particular) and social insect colonies.

• “Both trees and colonies contain large numbers of replaceable foragers: in the hive, for example, individual bees, in the tree leaf or branch root, meristems.
• “In both cases, reproductive and other functions are differentiated from the same uniform genetic line.
• “The hive colony is aggressive to invading outsiders, and entry points are guarded. Trees use allelopathy to damage local competitive species and possess induced defense reactions, such as natural pesticides, to kill herbivores or invading fungi. These defense reactions can be complex, involving chaotic pesticide production in different leaves so that the herbivore is uncertain whether the next leaf is edible or whether consumption kills.
• “A good source of food attracts more insect workers through positive feedback mechanisms and communication. Tree branches and leaves grow to exploit light patches, and roots proliferate in mineral-rich zones involving positive feedback mechanisms and communication.
• “Just as entry guards to hives and other foraging individuals in hives will altruistically sacrifice themselves to maintain the whole colony and, in particular, the queen, trees will altruistically abscise their foraging organs when parasitized by disease or damaged by herbivores. The abscission zone, a layer of a few cells at the base of the petiole and able to secrete cell wall weakening hydrolytic enzymes, will do so when signals are received from elsewhere in the plant and the leaf blade to commence abscission. The aim is maintenance of the whole individual for later reproduction. Again, leaves and roots can altruistically abscise if resources of minerals and water are short to ensure the future integrity of the individual plant.
• “Hive and tree behaviors are dependent on complex communication, assessment of external status, and behavioral (plasticity) change. If one is regarded as intelligent, so must the other.”
Trewavas, Anthony. “Aspects of Plant Intelligence: Convergence and Evolution.” Pp. 68-110. From Morris, Simon C. The Deep Structure of Biology: Is Convergence Sufficiently Ubiquitous to Give a Directional Signal? 2008. Templeton Foundation Press. P. 92.


“However, other organisms have developed intelligence in a very different way from animals. Here, intelligence does not localize in a defined place like a brain but is a property of the whole system. Animals learn by exchanging dendritic connections between different cells, constructing new neural pathways and changing information flow. Analogously, bacteria learn by exchanging genes from other bacteria, altering information flow. Cells learn by changing directions of information flow through signal transduction pathways. Plants learn by changing information flow via chemical communication much as social insects do.” Trewavas, Anthony. “Aspects of Plant Intelligence: Convergence and Evolution.” Pp. 68-110. From Morris, Simon C. The Deep Structure of Biology: Is Convergence Sufficiently Ubiquitous to Give a Directional Signal? 2008. Templeton Foundation Press. P. 94.


“I argue that we do better to conceptualize functions as effects of systemic components that contribute to more-general capacities of the larger system. Emphasis falls upon the structure and organization of natural systems and the work accomplished by components of such systems. The function of the mammalian heart is to pump blood because pumping contributes in significant ways to certain capacities of the circulatory system. Functions are essentially systemic; history is not essential. Functions typically have a history, to be sure, including a selective history, but pumping would have been the function of the heart even if some other device had beaten it out early in the evolution of mammals. Functions are contributions to systemic capacities and, while selection can preserve or eliminate those functions, selection is not their source.” Davies, Paul Sheldon. Norms of Nature: Naturalism and the Nature of Functions. 2003. MIT Press. P. xiii.


“Thus, although systemic functions are not defined by reference to historical success, they are defined in terms of capacities to contribute to the exercise of some higher-level capacity. They are defined in terms of the capacity for systemic success. Thus, when the capacity to contribute is absent, so too is the systemic function.” Davies, Paul Sheldon. Norms of Nature: Naturalism and the Nature of Functions. 2003. MIT Press. P. 212.


“For a finite-size flow system to persist in time (to live), its configuration must evolve in such a way that provides easier access to the currents that flow through it.” Bejan, Adrian & J.P. Zane. Design in Nature: How the Constructal Law Governs Evolution in Biology, Physics, Technology, and Social Organization. 2012. Doubleday. P. 3.


“Flow systems have two basic features (properties). There is the current that is flowing (for example, fluid, heat, mass, or information) and the design through which it flows.” Bejan, Adrian & J.P. Zane. Design in Nature: How the Constructal Law Governs Evolution in Biology, Physics, Technology, and Social Organization. 2012. Doubleday. P. 3.


“Where the second law commands that things should flow from high to low, the constructal law commands that they should flow in configurations that flow more and more easily over time.” Bejan, Adrian & J.P. Zane. Design in Nature: How the Constructal Law Governs Evolution in Biology, Physics, Technology, and Social Organization. 2012. Doubleday. P. 19.


“Determinacy is a condition common to many (but not all) animals, in which the body boundaries of ‘individuals’ are localized: these individuals cannot be in two or more places at once and they inevitably die within a fairly fixed span of time. Such individuals may be free to move about, but they have little freedom to remodel their own body boundaries other than by moulting or adding on extra segments as they get older. Although animals which accomplish the latter, e.g. snakes and worms, are sometimes described as indeterminate, they generally repeat rather than remodel their previous boundary and so are better thought of as ‘modular.’

“Since determinate individuals have a more or less fixed life span, they have to reproduce if their genes are to survive. This situation may, fundamentally, be related to the abilities of animals to ingest food and to locate further supplies using various means of locomotion. It contrasts with the indeterminacy of many plants, fungi, actinomycetes and colonial animals such as hydroids, which are not fully motile and which receive and/or absorb energy sources. These indeterminate organisms have at least the potential to grow indefinitely, until or unless they encounter some external limit to their expansion. Reproduction therefore provides them with the scope to disperse and reassort their genetic information in the long term, rather than being an absolute necessity for individual furtherance in the short term.” Rayner, Alan. Degrees of Freedom: Living in Dynamic Boundaries. 1997. Imperial College Press. P. 69.


“A general property of relatively indeterminate systems is that they branch, having first become ‘polarized’ by producing an elongating structure that typically extends at its tips....”

“These important processes in indeterminate development, namely polarization, branching, integration and degeneration correspond with patterns that are common to all kinds of fluid-dynamical systems.” Rayner, Alan. Degrees of Freedom: Living in Dynamic Boundaries. 1997. Imperial College Press. Pp. 78-9.


“The intuitive appeal of the idea that at least some human thought processes are indeterminate is evident in such widely used phrases as ‘streams of consciousness’ and ‘lateral thinking.’ Most people, when asked how it feels to think about a complex, unfamiliar problem might well describe something akin to a foraging fungal mycelium. Thoughts radiate out from some inner space, as though searching out easier passages and circumventing obstacles, eventually cross-connecting with one another and becoming focused along particular channels. This kind of thinking has sometimes been described as ‘water logic,’ and often yields varied solutions that depend sensitively on circumstances....

“There therefore seem to be two contrasting kinds [of] problem solving–the one prescriptive and precise but inflexible, the other innovative and versatile but prone to wander.” Rayner, Alan. Degrees of Freedom: Living in Dynamic Boundaries. 1997. Imperial College Press. Pp. 89-90.


“At the outset, I want to recall that there are two basic kinds of approaches to explaining the existence of biological phenomena–adaptational and organizational.” Rayner, Alan. Degrees of Freedom: Living in Dynamic Boundaries. 1997. Imperial College Press. P. 94.


“One way of proliferating involves expanding in all directions (isotropic expansion). Any system which continues to expand in this way retains its original shape and symmetry; i.e, it just gets larger. However, the surface area of its boundary relative to its volume is inevitably reduced as the distance between the boundary and the core of the system increases. This makes it harder and harder to keep the interior adequately supplied with resources brought in from outside.

“These limitations on isotropic expansion are the compelling reasons usually given for why living systems in general and cells in particular cannot just get larger, and therefore have to divide. Further reasons lie in the fact that without division it is impossible to produce specialized components or to disperse to new locations.

“Where the products of division do not dissociate, prospects open up for them to follow distinctive developmental paths–to differentiate–whilst still being able to be interconnected and so divide labour efficiently.” Rayner, Alan. Degrees of Freedom: Living in Dynamic Boundaries. 1997. Imperial College Press. P. 97.


“Depending on the degree of freedom of genetic transfer, the ultimate consequence of gene flow may be envisaged to be either the formation of gene pools or the formation of genetic networks. The concept of a gene pool basically assumes that genes have complete freedom to move around within a population boundary, so that their distribution amongst individuals is random....”

“In genetic networks, genes are distributed locally amongst interbreeding individuals. No individual is capable of containing all the genetic information available in the population as a whole, and so each individual can be regarded as a differentiated component of the system, capable of occupying a distinctive niche.” Rayner, Alan. Degrees of Freedom: Living in Dynamic Boundaries. 1997. Imperial College Press. P. 117.


“The three known mechanisms of genetic transfer between bacteria are conjugation, transduction and transformation. Conjugation involves a sex-like process in which one cell, often described as ‘male’ acts as a donor, attaching by means of ‘sex pili’ to a ‘female’, recipient cell.

“Tranduction involves the intervention of a third party, a virus or ‘bacteriophage’, as the agent of transfer....”

“Transformation involves the uptake of ‘foreign’ DNA by a bacterial cell from its immediate environment rather than directly from another cell or virus particle.” Rayner, Alan. Degrees of Freedom: Living in Dynamic Boundaries. 1997. Imperial College Press. Pp. 118-9.


“... it is debatable whether fungal mycelia should be regarded as multicellular because although they can be compartmented by septa, the latter allow considerable protoplasmic communication. In some sense, therefore, mycelia represent the most extreme result of the diversification and integration of a single cell,...” Rayner, Alan. Degrees of Freedom: Living in Dynamic Boundaries. 1997. Imperial College Press. P. 131.


“The way that this re-organisation [in developing embryos] occurs contrasts markedly between most higher plants and animals, presumably reflecting the relative indeterminacy and determinacy of these organisms.

“Basically, in higher plants, the embryo becomes polarized and new cells are added at the apices of the resultant elongated structure either by proliferation of a single apical cell, or of sets of dividing cells known as ‘meristems’. The apical meristems occur at the tips of shoots and roots and are responsible for the production of cells which give rise to all the tissues of what is known as the ‘primary plant body’. In woody plants, secondary lateral meristems known as ‘cambria’ then give rise to the conductive tissues within bark (‘phloem’) and wood (‘xylem’), thickening the roots and stems in the process. The localization of cell division within apical meristems also occurs in colonial Cnidaria and Bryozoa and is a basic feature of indeterminate multicellular structures, analogous to the extending tips of hyphae and other cellular filaments.

“By contrast, in the majority of animal embryos the production of new cells for the body as a whole occurs within all the developing organs and tissues and so is not localized.” Rayner, Alan. Degrees of Freedom: Living in Dynamic Boundaries. 1997. Imperial College Press. P. 133.


“For this programme [the “precise sequence” of development of an animal embryo] to operate successfully, it is important for the developing embryo to be buffered, as far as is possible, from the effects of a variable external environment. With some important exceptions, and in marked contrast to indeterminate forms, the programme is therefore followed without reference to external conditions.” Rayner, Alan. Degrees of Freedom: Living in Dynamic Boundaries. 1997. Imperial College Press. P. 135.


“Higher plants typically consist of two complementary, potentially competitive, but ultimately interconnected and interdependent systems–roots and shoots. Root systems consist both of highly branched, short-lived, absorptive components (‘short roots’) and indefinitely extending, explorative and conductive components (‘long roots’). The absorptive roots gather and the conductive roots distribute soil solution. Shoot systems likewise consist both of indefinitely extending axes which explore the aerial environment and assimilative offshoots (typically, leaves) which harvest sunlight by means of photosynthesis.” Rayner, Alan. Degrees of Freedom: Living in Dynamic Boundaries. 1997. Imperial College Press. P. 146.


“For there can be no doubt about it; drawing on the energy assimilated by individual human beings, our infrastructures are evolving in the characteristic patterns of indeterminate systems.” Rayner, Alan. Degrees of Freedom: Living in Dynamic Boundaries. 1997. Imperial College Press. P. 152.


“In versatile systems, degeneracy provides means for recycling and renewal rather than demise. Death, the abandonment of old contextual boundaries, becomes a way of life.” Rayner, Alan. Degrees of Freedom: Living in Dynamic Boundaries. 1997. Imperial College Press. P. 156.


“Determinate systems diversify from outside-in, i.e differentiation occurs within an external boundary that ceases to expand with the passage of time. Indeterminate systems diversify from inside-out, with the external boundary continuing to expand and change its form.” Rayner, Alan. Degrees of Freedom: Living in Dynamic Boundaries. 1997. Imperial College Press. Pp. 159-60.


“Indeterminate organisms are versatile both in the variety of functionally distinctive offshoots–leaves, flowers, polyps, fungal fruit bodies etc–that they can produce, and in the form of the interconnections between these offshoots.

“The offshoots are commonly composed of tissues, and are often referred to as ‘organs’ equivalent to those of determinate organisms. However, they are generally produced externally and at varied places and/or times–not internally and once-and-for-all. They therefore correspond more with alternative phenotypes than with organs, although the fact that they remain interconnected makes it easy to view them as components of the same system.” Rayner, Alan. Degrees of Freedom: Living in Dynamic Boundaries. 1997. Imperial College Press. P. 168.


“... through the interplay of differentiation, integration and degeneracy, all living systems undergo cyclic patterns of change. These patterns are brought about by four fundamental processes that vary the flow of energy within and across contextual boundaries in different but complementary ways: conversion, regeneration, distribution and recycling.

“Conversion processes characteristically follow a phase during which energy has been gathered in (‘assimilated’) from the external environment. They both immobilize and seal the boundary of a system, or segment of a system, so conserving energy and producing ‘dormant’ survival capsules. Seeds, spores, cysts and storage organs of various kinds all result from conversion processes....

“Distribution involves the sealing but not the immobilization of parts of the boundary of a system which are connected, directly or indirectly, to assimilative regions. Resources taken in through the assimilative regions can then drive expansion of the sealed components which are thereby able to negotiate restrictive environments that would not otherwise sustain growth. Explorative structures of all kinds are driven in this way....

“Regeneration allows the resumption of energy-gathering processes, through the production of open, mobile boundaries, when supplies of available resources are either renewed outside a survival structure or encountered by an explorative or dispersal structure....

“Recycling occurs when internal partitioning allows resources to be redistributed from locations that no longer participate in energy-gathering or exploration to sites where these processes are being sustained. It is therefore associated with the degeneration of former boundaries, such as occurs during metamorphosis, fairy ring-formation and amnesia.” Rayner, Alan. Degrees of Freedom: Living in Dynamic Boundaries. 1997. Imperial College Press. Pp. 181-2.


“They [“‘self-organization’ and ‘complexity’ theories”] do not recognize the role played by dynamic boundaries both in the emergence and the sustainment of ordered structures. Indeed, they imply that, due to dissipation, life cannot persist for any length of time in resource-restricted environments.

“However, processes of boundary-fusion, boundary-sealing and boundary-redistribution all provide means for reducing dissipation, allowing energy to be maintained within the system rather than lost to the outside. Since they lead to more coherent, more persistent organizations in which the discreteness of individual units is blurred, these processes may be referred to as ‘self-integrational’.” Rayner, Alan. Degrees of Freedom: Living in Dynamic Boundaries. 1997. Imperial College Press. P. 184.


“The thesis I will start off with is that a fallacy is a form of reasoning that for some applications is bad and for others is good; roughly speaking, it is bad for logic but, for instance, good for surviving.” Bardone, Emanuele. Seeking Chances: From Biased Rationality to Distributed Cognition. 2011. Springer. P. 1.


“From the perspective of classical logic, a fallacy is a pattern of poor reasoning which appears to be a pattern of good reasoning.” Bardone, Emanuele. Seeking Chances: From Biased Rationality to Distributed Cognition. 2011. Springer. P. 2.


“... practical agents operate in cognitive economies, where the agent access to cognitive resources encounters limitations such as:
• bounded information
• lack of time
• limited computational capacity.”
Bardone, Emanuele. Seeking Chances: From Biased Rationality to Distributed Cognition. 2011. Springer. Pp. 4-5.


“Abduction is defined by Magnani as the process in which a hypothesis is created/selected and then evaluated.” Bardone, Emanuele. Seeking Chances: From Biased Rationality to Distributed Cognition. 2011. Springer. P. 12. Reference is to Magnani, L. Abduction, Reqason, and Science. Processes of Discovery and Explanation. 2001. Kluwer Academic/Plenum Publishers.


“Abduction – considered as the process of hypothesis generation and evaluation – plays an important role in the evaluation of arguments (whether a real shift has occurred or not): insofar as an alleged ignoratio elenchi is evaluated and then accepted by the audience – in a dialectical and rhetorical context – it becomes a good argument.

“In the three cases of ignoratio elenchi illustrated above, the abductive skills involved concern the ability of turning information about people, and the social characters they represent, into relevant knowledge supporting one view rather than another. In the argumentum ad hominem this ability is related to the formulation of those abductive inferences, which successfully employ and evaluate the information discrediting your opponent. In the argumentum ad verecundiam the abductive process involved is connected to the selection of experts and authorities who may be recognized as such by a certain audience. Finally, the case of the argumentum ad populum involves the selection of the majority to be heeded, taking its composition into account.” Bardone, Emanuele. Seeking Chances: From Biased Rationality to Distributed Cognition. 2011. Springer. P. 13.


“The three fallacies can be easily considered in the light of group-serving behaviors as well. For instance, discrediting your opponent – the argumentum ad hominem – can be considered as a means of controlling ideas and behaviors, which do not fit within the group.” Bardone, Emanuele. Seeking Chances: From Biased Rationality to Distributed Cognition. 2011. Springer. P. 16.


“Fallacies are part of a kind of rationality that in the following I will call biased rationality.” Bardone, Emanuele. Seeking Chances: From Biased Rationality to Distributed Cognition. 2011. Springer. P. 21.


“In other terms, to use Simon’s own definition, ‘rationality is bounded when it falls short of omniscience’.” Bardone, Emanuele. Seeking Chances: From Biased Rationality to Distributed Cognition. 2011. Springer. P. 23. Reference is to Simon, H.A. 1979. “Rational decision making in business organizations.” American Economic Review. 69, 493-513.


“The idea of homo heuristicus stems from the rejection of two main assumptions about accuracy and effort. The first is that a heuristic always involves a trade-off to be reached between accuracy and effort, as they are basically conflicting concepts....

“The second assumption can be called the ‘principle of total evidence’. The principle of total evidence – introduced by Carnap and explicitly mentioned by Gigerenzer and colleagues – states that it is always better to take into account the total evidence available in order to determine whether or not a certain hypothesis or course of action is justified or rational: that is, having more information is always better than having less information. Or, to put it simply, more is always more, and less is always less.

“Contrary to these two beliefs, Gigerenzer and colleagues argued, and managed to provide empirical evidence to support the idea, that heuristics are not always accuracy-effort trade-offs. On certain occasions, one can attain higher accuracy with less effort.” Bardone, Emanuele. Seeking Chances: From Biased Rationality to Distributed Cognition. 2011. Springer. P. 31. Reference is to, among others: Gigerenzer, G. 2000. Adaptive thinking: Rationality in the Real World. Oxford University Press.


“The availability bias means seizing the first impression one comes up with about a person, an object or a situation....”

“The primacy bias consists in interpreting certain clues in light of those presented earlier....”

“The halo effect is further specification of the availability bias and the primacy bias. Basically, it occurs when a person judges a situation, an object or another person relying only one good trait. An example is a script presented in good handwriting.” Bardone, Emanuele. Seeking Chances: From Biased Rationality to Distributed Cognition. 2011. Springer. Pp. 32-3.


“Ecological validity is the term introduced by Brunswik to refer to the situation in which a given proximal stimulus acts as a valuable indicator of a certain distal state or event; ecological validity is a normative measure about how diagnostic certain proximal stimuli are with respect to a given distal event.” Bardone, Emanuele. Seeking Chances: From Biased Rationality to Distributed Cognition. 2011. Springer. P. 40. Reference is to Brunswik, Egon. 1952. The Conceptual Framework of Psychology. University of Chicago Press.


“As people follow the so-called ‘wisdom of the crowd’, the bandwagon has the cognitive effect of diminishing the total level of information available to the group. If at an individual level conformity allows people to make a decision when lacking competence and knowledge, at a group level this could be catastrophic especially when facing change and/or difficulties.” Bardone, Emanuele. Seeking Chances: From Biased Rationality to Distributed Cognition. 2011. Springer. P. 44.


“Conformity enhances the probability that a given behavior or trait will become common in a group or population. In doing so, it reduces eco-cognitive variation within a group and consequently makes learning by imitation less profitable. In fact, as reported by Castro et al. imitators ‘do poorly when they are common and individual learners are rare’.” Bardone, Emanuele. Seeking Chances: From Biased Rationality to Distributed Cognition. 2011. Springer. P. 44. Reference is to Castro, L., M. Toro & F. Ayala. 2004. “The evolution of culture: from primate social learning to human culture.” Proceedings of the National Academy of Sciences of the United States of America. 101(27), 10235-10240.


“... humans like other creatures do not simply live their environment, but they actively shape and change it looking for suitable chances. In doing so, they construct cognitive niches through which the offerings provided by the environment in terms of cognitive possibilities are appropriately selected and/or manufactured to enhance their fitness as chance seekers.” Bardone, Emanuele. Seeking Chances: From Biased Rationality to Distributed Cognition. 2011. Springer. P. 49.


“I call the entire cycle the ‘externalization process,’ and it can be summarized as follows: human beings overcome their internal limitations by (1) externalizing and disembodying thoughts, ideas, solutions, and then (2) re-projecting internally that occurring outside in the external invented structure to find new ways of thinking.” Bardone, Emanuele. Seeking Chances: From Biased Rationality to Distributed Cognition. 2011. Springer. P. 50.


“Basically, composite intentionality refers to situations in which the intentionality resulting from an action we take is made up of our own in coordination with that emerging from the interaction with an artefact. The intentionality resulting from interaction in smart environments is indeed highly composite,...” Bardone, Emanuele. Seeking Chances: From Biased Rationality to Distributed Cognition. 2011. Springer. P. 65.


“... I define behaviors such as altruism as group-projecting behaviors, meaning that groups are projections of an higher unit of evolution. That is, every time an individual behaves altruistically it acts as if the group actually exists....”

“The relevance of group-projecting behavior introduces quite a speculative issue, that is however useful in order to better understand the allegedly evolutionary meaning of groups. According to Stearns we are ‘stalled part way through a major evolutionary transition from individual to groups’.” Bardone, Emanuele. Seeking Chances: From Biased Rationality to Distributed Cognition. 2011. Springer. P. 72. Reference is to Stearns, S. 2007. “Are we stalled part way through a major evolutionary transition from individual to group?” Evolution 61(10), 2275-2280.


“... I may claim that affordances are chances that are ecologically rooted. They are ecological[ly] rooted because they rely on the mutuality between an agent (or a perceiver) and the environment.” Bardone, Emanuele. Seeking Chances: From Biased Rationality to Distributed Cognition. 2011. Springer. P. 79.


“They [Zhang and Patel] maintain that affordances can be also related to the role of distributed representations extended across the environment and the organism. These kinds of representation come about as the result of a blending process between two different domains: on one hand the internal representation space, that is the physical structure of an organism (biological, perceptual, and cognitive faculties); on the other the external representation of space, namely, the structure of the environment and the information it provides. Both these two domains are described by constraints so that the blend consists of the allowable actions.” Bardone, Emanuele. Seeking Chances: From Biased Rationality to Distributed Cognition. 2011. Springer. Pp. 79-80. Reference is to Zhang, J & V. Patel. 2006. “Distributed cognition, representation, and affordance.” Cognition & Pragmatics. 14(2), 333-341.


“Patel and Zhang’s idea tries to clarify that affordances result from a hybridizing process in which the environmental features and the agent’s ones in terms of constraints are blended into a new domain which they call affordance space. Taking a step further, Patel and Zhang define affordances as allowable actions.” Bardone, Emanuele. Seeking Chances: From Biased Rationality to Distributed Cognition. 2011. Springer. P. 80. Reference is to Zhang, J & V. Patel. 2006. “Distributed cognition, representation, and affordance.” Cognition & Pragmatics. 14(2), 333-341.


“As argued by these authors, hidden affordances are those affordances specified by the information not available at the time of the interaction, but drawn from past experiences. The same event or place can have different affordances to different organisms but also multiple affordances to the same organism. Following D. Normal’s perspective, affordances suggest a range of chances: ...” Bardone, Emanuele. Seeking Chances: From Biased Rationality to Distributed Cognition. 2011. Springer. P. 80. References are: Rader, N. & L. Vaughn. 2000. “Infant reaching to a hidden affordance: evidence for intentionality.” Infant Behavior and Development. 23, 531-541. Norman, Donald. 1988. The Design of Everyday Things. Addison Wesley.


“Indeed, we may be afforded by the environment, if we can detect those signs and cues from which we may abduce the presence of a given affordance. [relating to semiotics]” Bardone, Emanuele. Seeking Chances: From Biased Rationality to Distributed Cognition. 2011. Springer. P. 89.


“My idea is that the human agent abductively regulates his relationship with the environment. That is, the human agent is constantly engaged in controlling his own behavior through continuous manipulative activity. Such manipulative activity (which is eco-cognitive one) hangs on to abductive anchors, namely, affordances that permit the human agent to take some part of the environment as local representatives of some other. So, the human agent operates in the presence of abductive anchors, namely, affordances, that stabilize environmental uncertainties by directly signaling some pre-associations between the human agent and the environment (or part of it).” Bardone, Emanuele. Seeking Chances: From Biased Rationality to Distributed Cognition. 2011. Springer. P. 89.


“The idea that an affordance is not a resource but rather, something that offers information about one, allows it to be seen as anything involving some eco-cognitive dimension.” Bardone, Emanuele. Seeking Chances: From Biased Rationality to Distributed Cognition. 2011. Springer. P. 89.


“From a theoretical perspective we may argue that human beings function as a kind of adapting task-transforming representation. The term ‘task-transforming representation’ was introduced by Hutchins to refer to the fact that external artifacts shape the structure of a task – its representation – helping people solve the problem they are facing. A tool may transform the structure of a task:

1. Redistributing the cognitive load;
2. Rearranging constraints and action possibilities;
3. Unearthing additional computational abilities;
4. Increasing the number of operations while reducing mental costs.

“In the case of adapting affordances the cognitive load is reduced by means of a transformation, which adapts the structure/representation of the task to allow a person to detect latent environmental chances. Caregivers and the intentional gaze are fair examples, as they show how people adaptively manipulate the representations their fellows have of the environment to favor or facilitate the exploitation of latent affordances.” Bardone, Emanuele. Seeking Chances: From Biased Rationality to Distributed Cognition. 2011. Springer. Pp. 92-3. Reference is to Hutchins, E. 1995. Cognition in the Wild. MIT Press.


“Adapting affordances are those affordances that help the agent exploit latent environmental possibilities providing additional clues.” Bardone, Emanuele. Seeking Chances: From Biased Rationality to Distributed Cognition. 2011. Springer. P. 93.


“... docility is thought to be the concept able to connect a pro-social attitude like altruism to human cognition. Docility will be described as the attitude or tendency underlying those learning processes, which involve various forms of reliance on social channels.” Bardone, Emanuele. Seeking Chances: From Biased Rationality to Distributed Cognition. 2011. Springer. P. 101.


“Going beyond Simon, docility can be considered as a kind of adaptation that facilitates the process of distributing cognitive functions to the environment, and makes that a major basis for decision making. From our birth we operate this kind of delegation, first to our parents, and then to other people. After that we begin to select and distinguish between people from whom to learn something important or insignificant,...” Bardone, Emanuele. Seeking Chances: From Biased Rationality to Distributed Cognition. 2011. Springer. P. 106. Reference is to Simon, H. 1993. “Altruism and economics.” The American Economic Review. 83(2), 156-161.


“As I put it, docility has both an active and passive side. Developing this line of thought, the active side can be further articulated into three main elements; thus, docility can be viewed also as the tendency

1. To share one’s own information;
2. To give a public and social dimension to one’s thought/work;
3. To render communication easier by creating, maintaining, and developing standards, or standard-fidelity.” Bardone, Emanuele. Seeking Chances: From Biased Rationality to Distributed Cognition. 2011. Springer. Pp. 107-8.


“We would like to emphasize that formation and maintaining of increasingly complex biopolymers could proceed only if supported by a constant flow of utilizable energy. This consideration severely constrains otherwise plausible hypotheses of origin of life under impact bombardment that tend to treat emergence of life as a one-time event.” Mulkidjanian, Armen & Michael Galperin. 2007. “Physico-Chemical and Evolutionary Constraints for the Formation and Selection of First Biopolymers: Towards the Consensus Paradigm of the Abiogenic Origin of Life.” Chemistry & Biodiversity. Vol. 4. Pp. 2003-2015. P. 2005.


“An important chemical constraint, which often remains unrecognized, is the reversibility of most (bio)chemical reactions. Therefore, any scheme that explains biopolymer formation under certain environmental conditions should also be able to explain why the synthesis of the given biopolymers would not be followed by their immediate hydrolysis. One cannot help noting that, in virtually all papers describing origin of life, the corresponding schemes contain unidirectional arrows, instead of bidirectional ones. However, the mechanisms that underlie that unidirectionality are almost never described.” Mulkidjanian, Armen & Michael Galperin. 2007. “Physico-Chemical and Evolutionary Constraints for the Formation and Selection of First Biopolymers: Towards the Consensus Paradigm of the Abiogenic Origin of Life.” Chemistry & Biodiversity. Vol. 4. Pp. 2003-2015. P. 2005.


“The rule of chemical conservation implies that the chemical composition of living beings is more conservative than the chemical composition of their environment. Therefore, the conserved organismal chemistry can retain information about the ancient environmental conditions. The most popular manifestation of this principle is the similarity between the chemical composition of sea water and the internal liquids of multicellular animals. The latter are characterized by high sodium content even if organisms live in fresh water or on the land. In this case, high sodium content appears to reflect the emergence of the first multicellular organisms in the sea waters. Less broadly acknowledged example of chemical conservation is the highly reduced state of the cell interior even in those organisms that inhabit oxygenated environments.” Mulkidjanian, Armen & Michael Galperin. 2007. “Physico-Chemical and Evolutionary Constraints for the Formation and Selection of First Biopolymers: Towards the Consensus Paradigm of the Abiogenic Origin of Life.” Chemistry & Biodiversity. Vol. 4. Pp. 2003-2015. P. 2006.


“Alternatively, we have argued that the UV irradiation might play a positive role upon the very origin of life by serving both as energy source and a principal selective factor in the formation of pre-biological structures. Indeed, the above noted extremely efficient deactivation of the UV quanta by nitrogenous bases allows them to protect the compounds to which they are attached from the UV-induced breakage. In particular, the UV-damage to the sugar-phosphate bond was shown to decrease in the presence of adenine entity; due to this phenomenon, the backbone breaks in RNA and DNA seem to happen 103 – 104 times less frequent than the UV-damage to the nitrogen bases proper....

“It seems quite unlikely that the extremely effective UV-quenching by all five major nucleobases is just incidental. Therefore, we suggested that the nucleobases were initially recruited as UV protectors.” Mulkidjanian, Armen & Michael Galperin. 2007. “Physico-Chemical and Evolutionary Constraints for the Formation and Selection of First Biopolymers: Towards the Consensus Paradigm of the Abiogenic Origin of Life.” Chemistry & Biodiversity. Vol. 4. Pp. 2003-2015. P. 2008.


“In the UV-illuminated primordial world the probability of a UV-breakage was more than real for any compound. Correspondingly, those that succeeded to bind (trap) a UV-quencher got a selective advantage. Hence, the primordial polymerization could be driven by a mechanism that resembled natural selection with the most UV-resistant polymers living longer.” Mulkidjanian, Armen & Michael Galperin. 2007. “Physico-Chemical and Evolutionary Constraints for the Formation and Selection of First Biopolymers: Towards the Consensus Paradigm of the Abiogenic Origin of Life.” Chemistry & Biodiversity. Vol. 4. Pp. 2003-2015. P. 2012.


“In sum, only at continental geothermal springs, the formation of organic nitrogen-, phosphor-, and sulfur-containing compounds could be supported by two different fluxes of reducing equivalents resulting from the abiotic photosynthesis and the hydrothermal alteration of the iron-containing rocks. In addition, only continental environments could be characterized by wet-dry cycles, favorable for condensation reactions.” Mulkidjanian, Armen. “Energetics of the First Life.” Pp. 3-27. From Egel, Richard, D. Lankenau & A. Mulkidjanian, Eds. Origins of Life: The Primal Self-Organization. 2011. Springer. P. 11.


“In a previous work four rules of metabolic evolution were stated as follows:...

“1. Any enzymatic reaction is also chemically possible without the enzyme, although in that case it would occur much more slowly and without a well-defined specificity.

“2. All the intermediates of a chain of reactions to be used ultimately in a metabolic sequence must resist rapid decomposition. The strongest reason for this assumption is evolutionary; at the beginning of the pathway design every rudimentary enzymatic reaction occurred very slowly, so unstable intermediates could not have been used.”

“3. Material availability (Opportunism): Any material to be used by the new pathway must exist in another metabolic process which was originally developed for a different purpose. Design of this new pathway must preserve the function of the previous one whose material has been used. An inverse chronological application of this rule would eventually lead to the origin of metabolism; on the primordial Earth the first available compounds had to have been made through spontaneous chemical processes.

“4. Kinetic and thermodynamic compatibility: The new pathway cannot have a reaction involving any thermodynamic or kinetic incompatibility with a previous one that is operating simultaneously in the same space.”
Melendez-Hevia, Enrique, N. Montero-Gomez & F. Montero. “From prebiotic chemistry to cellular metabolism–The chemical evolution of metabolism before Darwinian natural selection.” 2008. Journal of Theoretical Biology. 252(2008) 505-519. P. 506.


“Life evolved through Darwinian natural selection, and its earliest form appeared when natural selection became possible. Thus, the appearance of the minimal material necessary for natural selection to work could not be produced by natural selection itself, but by a previous selection that we shall call ‘chemical selection’. This consists of an increase and enlargement of certain specific chemical processes based on specific kinetic and thermodynamic features that can increase the reaction rate. Yet without considering the existence of enzymes as catalysts specific for particular reactions, there are a number of different mechanisms that can enhance the reaction rates based only on the stoichiometry of the pathways, i.e., without ‘external’ catalysts: (a) stoichiometric catalysis, which occurs in all metabolic cycles, as the feeder (or starter) does as a catalyst itself; (b) stoichiometric autocatalysis, which occurs in some cycles when the global reaction yields more amount of the feeder than its entrance, so promoting the enlargement of the reaction; (c) thermodynamic cooperativity, which is a property of a process in which physical or chemical positive interactions among the end products enhance the stability of the final structure promoting their production. This effect is typical in the construction of polymers, as these processes imply an initiation step, which is usually difficult, as it is delayed by a positive energy change, followed by another of elongation that is much easier; and (d) thermodynamic push of certain specific processes by products originated in others; e.g., ATP production will promote biosynthetic reactions, and NADPH production will promote reductive processes.” Melendez-Hevia, Enrique, N. Montero-Gomez & F. Montero. “From prebiotic chemistry to cellular metabolism–The chemical evolution of metabolism before Darwinian natural selection.” 2008. Journal of Theoretical Biology. 252(2008) 505-519. Pp. 508-9.


“The formose reaction and the structure of the metabolic map can explain that metabolism could start from glucose, but it was obviously necessary to develop a pathway capable of producing it from mineral material (CO2 and H2O), as a necessary step to divorcing metabolism from prebiotic chemistry.” Melendez-Hevia, Enrique, N. Montero-Gomez & F. Montero. “From prebiotic chemistry to cellular metabolism–The chemical evolution of metabolism before Darwinian natural selection.” 2008. Journal of Theoretical Biology. 252(2008) 505-519. P. 514.


“The materials necessary for natural selection had to be achieved beforehand, by ‘chemical selection’. As this process operates through selecting the reagents and reactions independent of their Darwinian selective value, it can only be driven by increasing the rate of the reactions as a consequence of their own chemical features. Thus, in this process, catalytic, autocatalytic and cooperative effects, as well as thermodynamic driving by available substrates or forces, such as energy currency and reductive power that can favour certain reactions, could have played a critical role, enhancing their probability.” Melendez-Hevia, Enrique, N. Montero-Gomez & F. Montero. “From prebiotic chemistry to cellular metabolism–The chemical evolution of metabolism before Darwinian natural selection.” 2008. Journal of Theoretical Biology. 252(2008) 505-519. P. 516.


“Chemolithotrophic microbes are faced with the problem of extracting energy from narrow redox zones in marine environments. The free-living species typically occur in biofilms on sulfidic rocks or in filamentous mats like Beggiatoa spp., absorbing reduced gases from the substrate below and oxygen from the ambient water above. Symbiotic microbes, however, can span broader oxic-anoxic boundaries by exploiting the behavior, physiology and morphology of their animal hosts....

“The sessile vestimentiferan tubeworm, Riftia pachyptila, grows up to 1.5 m in length. It absorbs dissolved sulfide and oxygen from the ambient bottom water with a feathery plume (the obturaculum) and delivers the gases through its circulatory system to the trophosome, a specialized organ housing thiotrophic endosymbionts. Riftia has a leathery tube that allows it to flex and relocate its plume among water masses that are variably sulfidic or oxygenated. Other species have rigid tubes that penetrate deeply into anoxic sediments, allowing absorption of sulfides through the worm’s posterior end.” Vrijenhoek, Robert. “Genetics and Evolution of Deep-Sea Chemosynthetic Bacteria and Their Invertebrate Hosts.” Pp. 15-49. From The Vent and Seep Biota: Aspects from Microbes to Ecosystems. 2010. Edited by Kiel, Steffen. Springer Verlag. P. 16.


“The global average of human density for ice-free land is not a very meaningful measure. Cultivated area is the proper denominator: it now supplies about 85% of all food, and the global anthropomass now amounts to almost 200 kg/ha of arable land and permanent plantations; China’s mean is almost 500 kg/ha, and the country’s most intensively cultivated provinces support 600-700 kg of humanity per hectare of arable land. This means that in densely populated regions, human biomass is now more abundant than that of all soil invertebrates. In contrast, the average densities of the two large African primates, chimpanzees and gorillas, are mostly less than 1 kg/ha of their now so limited habitats.” Smil, Vaclav. The Earth’s Biosphere: Evolution, Dynamics, and Change. 2002. MIT Press. Pp. 186-7.


“Completely transformed surfaces include all arable land and areas under permanent crops, whose total the Food and Agriculture Organization puts at 15 million km2, and the surface claimed by settlements, industries, transportation links, and water reservoirs. Urbanized areas, so vividly outlined by nighttime satellite sensing of lights, now amount to about 5 million km2, and water reservoirs cover about 500,000 km2. Human activities have thus entirely refashioned at least 20 million km2, or 15% of all ice-free land surface....

“Permanent pastures, totaling about 34 million km2, are thus the largest area that has been modified to different degrees by human actions. Tree plantations and forests actively managed for goods and services total about 6.5 million km2. Road building, logging, and fires have degraded large areas of remaining forests....

“Adding up these impacts reveals that the total area strongly or partially imprinted by human activities is about 70 million km2, or no less than 55% of all nonglaciated land.” Smil, Vaclav. The Earth’s Biosphere: Evolution, Dynamics, and Change. 2002. MIT Press. Pp. 239-40.


“Yet another way to look at the extent and the intensity of the recent transformation of the biosphere is to estimate the share of GPP consumed or otherwise processed, managed, or destroyed by human actions. Vitousek et al. put this ‘appropriation’ of the global terrestrial NPP at as much as 40%, but even their lower-bound estimate of about 25% illustrates the intensity of the biosphere’s transformation.” Smil, Vaclav. The Earth’s Biosphere: Evolution, Dynamics, and Change. 2002. MIT Press. P. 240.


“The aggregate mass of machines already greatly exceeds that of humans. The dry-matter anthropomass is about 100 Mt, whereas the mass of motor vehicles (cars, buses, and trucks) alone is now an order of magnitude larger, in excess of 1Gt. And machines now need more carbon every year than humans do. The global food harvest now amounts to about 1.3 Gt C per year, whereas almost 1 Gt of fossil carbon (mostly metallurgical coke and hydrocarbon feedstocks) is used annually to produce metals and plastics from which machines are assembled, and about 4 Gt C are used each year to power them, either directly with coal, oil, and natural gas, or indirectly with electricity generated in thermal stations.” Smil, Vaclav. The Earth’s Biosphere: Evolution, Dynamics, and Change. 2002. MIT Press. P. 269.


“Isenhower and colleagues demonstrated that individuals are able to distinguish the boundaries between an affordance for oneself and an affordance for a dyad, ie the point at which an individual action must become a joint action in order to accomplish the goal.” Davis, Tehran, M. Riley, K. Shockley & S. Cummins-Sebree. 2010. “Perceiving affordances for joint actions.” Perception. Vol. 39, Pp. 1624-44. P. 1625. Reference is Isenhower, R.W., M. Richardson, C. Carello, R. Baron & K. Marsh. 2010. “Affording cooperation: Embodied constraints, dynamics, and action-scaled invariance in joint lifting.” Psychonomic Bulletin & Review. 17: 342-347.


“While being able to perceive what actions another person is capable of performing may be useful when predicting what the other person is about to do, perceiving affordances for another may also provide information relative to the constraints on possible interactions and joint action. A major issue when considering joint action is how the action planning of two distinct individuals becomes integrated to guide shared behavior. One possible explanation is that individuals’ perception of a shared affordance may facilitate the ‘embodying’ of other agents. That is, perception of the shared affordance acts as a medium through which individuals gain information relative to social perception – action processes involved in a joint action.” Davis, Tehran, M. Riley, K. Shockley & S. Cummins-Sebree. 2010. “Perceiving affordances for joint actions.” Perception. Vol. 39, Pp. 1624-44. P. 1642.


“From a computational viewpoint, shared representations help solving interaction problems in that they afford an interactive strategy for coordination that makes action selection and understanding easier.” Pezzulo, G. & H. Dindo. 2011. “What should I do next? Using shared representations to solve interaction problems.” Exp Brain Res. 211: 613-630. P. 616.


“Our analysis suggests that agents engaged in joint actions do not solve their problems individually, but ‘distribute’ some of them externally; in this sense, the agent-environment dynamics and the agent-agent dynamics are part of the problem-solving strategy. Indeed, our graphical model formulation emphasized that the two agents are coupled at the level of cognitive variables as well as at the physical level of interaction.” Pezzulo, G. & H. Dindo. 2011. “What should I do next? Using shared representations to solve interaction problems.” Exp Brain Res. 211: 613-630. P. 626.


“Theories of common ground formation propose similar arguments as those that we made regarding shared representations, in that common ground is a facilitator of interactions. However, these theories typically assume that both agents know what is shared, which is not essential in our model. Despite so, theories of common ground can be considered as complementary to our proposal, as they emphasize interactive dynamics and the coordination of co-actors at the level of cognitive processing, not only of overt behavior. Furthermore, these theories have provided illuminating analyses of important elements for coordination that should be incorporated in any model that aims to scale up to the complexity of human interactions.” Pezzulo, G. & H. Dindo. 2011. “What should I do next? Using shared representations to solve interaction problems.” Exp Brain Res. 211: 613-630. P. 626.


“It is noteworthy, however, that there has been little study of the interaction between the chemistry of life and cognitive or adaptive behavior. In general, models that focus on the self-organization of chemical systems work with a set of fixed boundary conditions, making adaptive behavior unnecessary for system survival. And conversely, models that study behavior tend to abstract away everything except the sensory, control, and motor mechanisms.

“This is, perhaps, starting to change. There has been a series of recent models that explore the interaction between processes that determine how a system is constituted (metabolism) and mechanisms through which the system influences its interaction with its environment (behavior). These models include computer simulations as well as real chemical systems, and they have led to some interesting reconceptualizations: Metabolic processes can be thought of as robust or even adaptive, able to intelligently modulate behavioral strategies; remarkably simple chemical reactions can perform chemotaxis; and in a range of bacteria, metabolism-based behavior appears to be more common than previously thought.” Egbert, Matthew, X. Barandiaran & E. Di Paolo. 2012. “Behavioral Metabolution: The Adaptive and Evolutionary Potential of Metabolism-Based Chemotaxis.” Artificial Life. 18: 1-25. P. 2.


“In parallel with the omission of behavior in the study of the origin of life, studies of minimal adaptive behavior have almost completely ignored the role of metabolism as sustaining or modulating behavioral patterns. Adaptive behavior is generally understood and modeled as optimizing some value function or as maintaining essential variables under viability constraints. However, there is generally no reference to the dynamics of the biological organization (e.g., metabolism) that serves as the basis of these viability constraints ....” Egbert, Matthew, X. Barandiaran & E. Di Paolo. 2012. “Behavioral Metabolution: The Adaptive and Evolutionary Potential of Metabolism-Based Chemotaxis.” Artificial Life. 18: 1-25. P. 3.


“However, recent experimental data provides counterevidence for the metabolism-independence assumption. Many bacteria display clear cases of what is called metabolism-dependent chemotaxis, including E. coli, Azospirillum brasilense, Rhodobacter sphaeroides, and Pseudomonas putida. Such cases have attracted renewed attention to the interplay between metabolism and behavior. Experiments have shown that nonmetabolizable structural analogues of metabolizable attractants (i.e., molecules that bind to chemoattractant receptors but are not metabolizable) do not produce a positive behavioral response in bacteria. It has also been shown that inhibition of the metabolism of a chemical attractant completely abolishes chemotaxis to and only to this attractant. And, in a slightly more complex scenario, when a sufficient quantity of a metabolizable compound is present in the environment, bacteria cease to be attracted to other attractants. The most-studied cases of metabolism-dependent chemotaxis are those concerning energy-taxis, which involve the modulation of behavior in a manner that is sensitive to the energetic needs of the bacteria.” Egbert, Matthew, X. Barandiaran & E. Di Paolo. 2012. “Behavioral Metabolution: The Adaptive and Evolutionary Potential of Metabolism-Based Chemotaxis.” Artificial Life. 18: 1-25. P. 3.


“Figure 1 illustrates the three different types of relationship between metabolism and chemotaxis that we have mentioned: metabolism-independent chemotaxis (long thought to be the default case); metabolism-dependent chemotaxis, where different aspects of metabolic dynamics (e.g., in the electron transport system) modulate existing sensorimotor pathways; and metabolism-based chemotaxis, where metabolites directly modulate motor activity.” Egbert, Matthew, X. Barandiaran & E. Di Paolo. 2012. “Behavioral Metabolution: The Adaptive and Evolutionary Potential of Metabolism-Based Chemotaxis.” Artificial Life. 18: 1-25. P. 4.


“The type of interactions shown in the experiments above, between behavior, metabolism, and evolution, we have termed behavioral metabolution, which we define as the evolution of behavior and metabolism in such a way that: (a) behavior drives the evolution of metabolism (by exploring, selecting, and/or climbing chemical environments that are beneficial to metabolism), and (b) changes in metabolism affect behavior and the evolution of behavioral patterns (e.g., changes in metabolism could lead to the improvement and fixation of the adaptive response).” Egbert, Matthew, X. Barandiaran & E. Di Paolo. 2012. “Behavioral Metabolution: The Adaptive and Evolutionary Potential of Metabolism-Based Chemotaxis.” Artificial Life. 18: 1-25. P. 16.


“In the standard approach, variation is internal and selection is considered as an environmental feature, but in behavioral metabolution it is the environment that provides a variety of chemicals to be selected by the behaving protocell and retained by its metabolism and/or recurrent chemotactic patterns. If the environment is sufficiently stable in its provision of a specific chemical species, the retention of a reactant beneficial to the protocells’ metabolism can be inherited through continued interaction with that environment. Metabolism-based chemotactic protocells can therefore be considered to instantiate the evolutionary principles in this nontraditional way: Variation can be both internal (the result of behavioral encounters / collisions giving rise to new molecular species) and external (the result of behavioral encounters in a rich environment), and selective retention can also be internal (by contribution to autocatalysis) or external (by repetitive gradient climbing or behavioral selection of an environmental compound).” Egbert, Matthew, X. Barandiaran & E. Di Paolo. 2012. “Behavioral Metabolution: The Adaptive and Evolutionary Potential of Metabolism-Based Chemotaxis.” Artificial Life. 18: 1-25. P. 19.


“The process of evolution has generated an enormous diversity of behavioral and physiological interactions, far surpassing the diversity of interactions possible in chemical and physical systems.” Camazine, S., J-L. Deneubourg, N. Franks, J. Sneyd, G. Theraulaz & E. Bonabeau. Self-Organization in Biological Systems. 2001. Princeton University Press. P. 3.


“Most self-organizing systems use positive feedback. This may be surprising since most biologists probably are more familiar with negative feedback, a mechanism commonly used to stabilize physiological processes (homeostasis) and avoid undesirable fluctuations.” Camazine, S., J-L. Deneubourg, N. Franks, J. Sneyd, G. Theraulaz & E. Bonabeau. Self-Organization in Biological Systems. 2001. Princeton University Press. P. 15.


“In other words, information from the local environment and work-in-progress can guide further activity. As a structure such as a termite mound develops, the state of the building process continually provide new information for the builders.

“In the study of social insects, the term stigmergy has been used to describe such recursive building activity. ‘In stigmergic labor it is the product of work previously accomplished, rather than direct communication among nestmates, that induces the insects to perform additional labor.’” Camazine, S., J-L. Deneubourg, N. Franks, J. Sneyd, G. Theraulaz & E. Bonabeau. Self-Organization in Biological Systems. 2001. Princeton University Press. P. 23. Subquote is from Wilson, E. O. 1971. The Insect Societies. Harvard University Press. P. 229.


“... self-organized pattern-formation relies on positive feedback, negative feedback, and a dynamic system involving large numbers of actions and interactions.

“With such self-organization, environmental randomness can act as the ‘imagination of the system,’ the raw material from which structures arise. Fluctuations can act as seeds from which patterns and structures are nucleated and grow.” Camazine, S., J-L. Deneubourg, N. Franks, J. Sneyd, G. Theraulaz & E. Bonabeau. Self-Organization in Biological Systems. 2001. Princeton University Press. P. 26.


“The one characteristic that rodents and other mammals do not share with primates is heavy reliance on vision. The expansion and specialization of this sense has resulted in the other changes that immediately identify animals as primates, even for novices in natural history. A mammal is readily recognizable as a primate if it has a relatively small snout, eyes that face forward, and a fairly large head that encloses a fairly large brain. The primate brain has become larger in part to accommodate the expansion of the visual system, even to the extent of influencing parts of the cerebral cortex that are not the main visual areas in the brain.” Isbell, Lynne. 2009. The Fruit, the Tree, and the Serpent: Why We See So Well. Harvard University Press. P. 10.


“Many hypotheses for the origin of primates have been proposed over the years. Most have focused on reconstructing a lifestyle that included a unique diet or a unique way that proto-primates moved about in their environment. These include the Arboreal theory, the (Nocturnal) Visual Predation hypothesis, the Angiosperm/Omnivore hypothesis, and the Camouflage-Breaking hypothesis.” Isbell, Lynne. 2009. The Fruit, the Tree, and the Serpent: Why We See So Well. Harvard University Press. P. 36.


“According the the Arboreal theory, the sense of smell is not particularly useful in the trees and so primates lost much of their olfactory ability. It was replaced by expansion of the visual system, which, in the three-dimension, complex environment of tropical forests, also required coordination of hands with eyes to maneuver along the branches.” Isbell, Lynne. 2009. The Fruit, the Tree, and the Serpent: Why We See So Well. Harvard University Press. P. 37.


“He pointed out that there are many arboreal mammals that survive and reproduce quite well without grasping hands, nails, orbital convergence, and forward-facing eyes. Tree squirrels are one familiar example. Cartmill also pointed out that many arboreal mammals still retain excellent olfactory capability, and so life in the trees cannot alone explain primates’ weakened olfactory sense. Again using a comparative approach, Cartmill proposed an alternative model he originally called the Visual Predation hypothesis. Cartmill proposed that stalking and grabbing insects at close range while on small-diameter branches at lower levels of tropical forests favored the entire suite of primate characteristics.” Isbell, Lynne. 2009. The Fruit, the Tree, and the Serpent: Why We See So Well. Harvard University Press. P. 38. Reference is to Cartmill, M. 1974. “Rethinking primate origins.” Science 184: 436-443.


“... Sussman suggested that the first primates were not committed insectivores but were omnivores, primarily eating fruits and other plant foods while taking insects more opportunistically. Sussman hypothesized that the first primates were able to take advantage of the appearance of angiosperms (flowering plants), which had begun to spread throughout the world. Angiosperms today include grasses, herbs, small shrubs, and enormous tropical trees, but he suggested that the first primates lived and ate among early angiosperms, which were small shrubs with small-diameter branches. The new foods offered by angiosperms included fruits and flowers, many of which were small and located in the dim light of forest understories.” Isbell, Lynne. 2009. The Fruit, the Tree, and the Serpent: Why We See So Well. Harvard University Press. Pp. 39-40. Reference is to Sussman, R. 1991. “Primate origins and the evolution of angiosperms. American Journal Primatology. 23:209-223.


“Crompton argued that orbital convergence would be useful for discriminating between any number of small targets. For arboreal animals, such targets would also include branches used during locomotion. He thus offered what I call here the Camouflage-Breaking hypothesis. He argued that orbital convergence and grasping hands would have been useful not only for capturing insects and finding and eating small fruits but also for aiming for and leaping to small branches in the complex three-dimensional environments that are typical of tropical forests.” Isbell, Lynne. 2009. The Fruit, the Tree, and the Serpent: Why We See So Well. Harvard University Press. P. 41. Reference is to Crompton, R. 1995. “‘Visual predation,’ habitat structure, and the ancestral primate niche.” Pp. 11-30. In Alterman, L., G. Doyle, & M. Izard. Eds. Creatures of the Dark: The Nocturnal Prosimians.” Plenum Press.


“I use visual system to refer to all the parts of the brain that give us the ability to see. It is the broadest term of all, but it can be separated into the lateral geniculate nucleus (LGN) visual system and the superior colliculus-pulvinar (SC-pulvinar) visual system. I use pathway to describe a distinct set of neural connections going from the eye to various other parts of the brain. There are three of them: the magnocellular (M) pathway, the parvocellular (P) pathway, and the koniocellular (K) pathway. Finally, I use stream to describe the conceptual idea that several functions related to vision in the primate brain, e.g., object recognition/assessment and spatial localization/self-movement, can be separated to some degree.” Isbell, Lynne. 2009. The Fruit, the Tree, and the Serpent: Why We See So Well. Harvard University Press. P. 46.


“Although all mammals have a retina in each eye, the primate retina is a bit different. Only primates (but not all prosimians) have a retinal fovea. This is a pit, or depression, in the retina that allows clear central vision for distinguishing between exceedingly small objects,...” Isbell, Lynne. 2009. The Fruit, the Tree, and the Serpent: Why We See So Well. Harvard University Press. P. 47.


“Visual processing streams appear to be unique to primates because of the great increase in number of areas in the primate brain that are involved in vision.” Isbell, Lynne. 2009. The Fruit, the Tree, and the Serpent: Why We See So Well. Harvard University Press. P. 49.


“These differences in the complexity of the LGN reveal that the P pathway has not only expanded more in primates than in other mammals but also has expanded more in anthropoid primates than in prosimians, and more in catarrhines than platyrrhines [New World primates]. The P pathway is largely responsible for our own excellent central vision, fine visual acuity, and our ability to see rich color, all of which help us to perceive objects in our environment.” Isbell, Lynne. 2009. The Fruit, the Tree, and the Serpent: Why We See So Well. Harvard University Press. P. 50.


“Compared with prosimians, the anthropoid LGN visual system is even more expansive and orbital convergence is even closer. We know this because the number of P layers varies within primates, and as Barton showed, the degree of orbital convergence is positively correlated with the number of neurons in the P layers in primates. This suggests that there was some greater selective pressure on anthropoids that favored even more acute vision for identifying objects and even better stereopsis for distinguishing between relative depths of objects also in the lower visual field and for cutting through camouflage of objects in the lower visual field. The presence of a fovea in anthropoids but not in all prosimians is also consistent with the idea that anthropoids uniquely benefited from clearly seeing and identifying objects that were close by and in front of them.” Isbell, Lynne. 2009. The Fruit, the Tree, and the Serpent: Why We See So Well. Harvard University Press. P. 64.


“Visual systems simply cannot expand much in mammals that cannot afford to weaken their reliance on olfaction (or echolocation).” Isbell, Lynne. 2009. The Fruit, the Tree, and the Serpent: Why We See So Well. Harvard University Press. P. 112.


“When angiosperms evolved they did something that was different from the gymnosperms. Instead of using abiotic forces such as fire, water, or the wind to help them reproduce, they began to use animals. These angiosperms evolved flowers, nectar, and fleshy fruits enclosing still-protected seeds to entice some animals to pollinate other flowers and to disperse their seeds. The plants gained because animals are more accurate and efficient than abiotic forces such as wind in placing pollen among flowers, and more predictable than abiotic forces such as fire in casting seeds away from the parent tree.” Isbell, Lynne. 2009. The Fruit, the Tree, and the Serpent: Why We See So Well. Harvard University Press. P. 115.


“Visual expansion became possible with both the evolution of pleasantly scented, tasty fruits and flowers and the exploitation of these foods by some vertebrates, including birds and mammals. Unlike animal and plant predators, however, those non-flying mammals that took advantage of this new food source could afford a weaker olfactory system without jeopardizing their ability to find food. Since there was no foraging cost associated with olfactory reduction, their visual systems were no longer constrained. Today, the mammals with the best vision tend to be those with diets heavily weighted toward fruits. These include primates, the most frugivorous order of mammals in existence today, and bats, coming in at a distant second.” Isbell, Lynne. 2009. The Fruit, the Tree, and the Serpent: Why We See So Well. Harvard University Press. Pp. 115-6.


“The neuroprotectant property of glucose might help explain the permissive influence of frugivory on visual and brain expansion. The hypothesis is that as females began to eat fruits, and plants began to make fruits more attractive, a diet richer in glucose could have initiated a positive feedback loop in which greater consumption and more rapid metabolism of sugars by mothers both allowed greater CO activity to occur during development of fetal visual systems and other parts of the brain because more glucose provides more energy, making it possible for metabolic and glutamatergic activity to increase, and was required because glucose is a neuroprotectant against increased glutamate exposure. Over evolutionary time, this could have resulted in greater neural growth, resulting in more complex visual systems and larger brains.” Isbell, Lynne. 2009. The Fruit, the Tree, and the Serpent: Why We See So Well. Harvard University Press. P. 119.


“To summarize, I am suggesting that frugivory made it possible for visual systems (and brains) to expand in primates because the glucose in fruits protected the K and P pathways from glutamate excitotoxicity as the pathways expanded. The K pathway expanded under selection to better detect snakes preconsciously while the P pathway expanded in concert, to evaluate the K pathway’s initial response, to help fuel visual expansion, and to protect it during expansion. The addition of trichromatic color vision to the P pathway was a later contribution that enabled frugivorous primates to find the more glucose-rich foods more efficiently.” Isbell, Lynne. 2009. The Fruit, the Tree, and the Serpent: Why We See So Well. Harvard University Press. P. 121.


“‘it may well be necessary, as Professor Gregory has recommended, to discontinue the use of the word symbiosis, substituting for it the more appropriate term ‘functional field.’ ... If this were done, questions could profitably be raised regarding the degree of integration of symbiotic associations considered as a function of the intensity of the field established and of the internal and external resistances surmounted in its establishment.’” Sapp, Jan. 2010. “On the Origin of Symbiosis.” Pp. 5-18. From Seckbach, Joseph & M. Grube, Eds. Symbioses and Stress: Joint Ventures in Biology. Springer Verlag. P. 16. Reference is to Gregory, F., F. Baker, P. Fildes, A. Felix, G. Bond, R. Synge & S. Elsden. 1952. “A discusion on symbiosis involving micro-organisms, general discussion.” Proc. Royal Society London B. 139: 202-207.


“While neo-Darwinian evolutionists continue to trivialize significance of symbiosis as a mode of evolutionary innovation, others argue that the concept of the organism needs to be enlarged to embrace the symbiotic complex, or ‘symbiome.’” Sapp, Jan. 2010. “On the Origin of Symbiosis.” Pp. 5-18. From Seckbach, Joseph & M. Grube, Eds. Symbioses and Stress: Joint Ventures in Biology. Springer Verlag. P. 16.


“The concepts of function and semiosis are intertwined. Both are teleological concepts in the sense of being determined with respect to an end (or other than itself)–a specifically correlated absent content. Although it is unclear whether these two properties of living processes are exactly co-extensive, it is clear that although time-asymmetrical, irreversible physical processes are found in the prebiotic physical-chemical world, teleological processes that are specially organized with respect to specific ends or referents are unique to living processes.

“If we conceive of a function as a process organized around an implicitly represented end, then these two classes of phenomena must be considered entirely co-extensive.” Kull, Kalevi, T. Deacon, C. Emmeche, J. Hoffmeyer & F. Stjernfelt. “Theses on Biosemiotics: Prolegomena to a Theoretical Biology.” Pp. 25-41. Emmeche, Claus & K. Kull, Eds. 2011. Towards a Semiotic Biology: Life is the Action of Signs. Imperial College Press. P. 27.


“Another way to put this is to say that hemoglobin function is not intrinsic to its molecular structure. Rather it is relational – hemoglobin may be seen as a carrier of contstitutive absence, in the sense that the molecule’s properties are constituted not only by intrinsic features, but by extrinsic features of its historical and physical functional contexts. In effect, the missing oxygen with respect to which hemoglobin structure has evolved has become its defining characteristic. In this respect, one can understand the structure of hemoglobin as a ‘representation’ of both oxygen and its role in the cellular molecular processes of metabolism. The function of hemoglobin is in this way also what affords the possibility of it having representational character. This function relates to the ‘needs’ or self-maintenance conditions of some agent.” Kull, Kalevi, T. Deacon, C. Emmeche, J. Hoffmeyer & F. Stjernfelt. “Theses on Biosemiotics: Prolegomena to a Theoretical Biology.” Pp. 25-41. Emmeche, Claus & K. Kull, Eds. 2011. Towards a Semiotic Biology: Life is the Action of Signs. Imperial College Press. Pp. 29-30.


“The difficulty of making predictions about biological phenomena is that the functions are plurally realizable and thus subject to considerable variation. As a result, the physical-chemical details necessarily provide an incomplete account. Functional requirements do, however, constrain the physical-chemical substrates that can be recruited.” Kull, Kalevi, T. Deacon, C. Emmeche, J. Hoffmeyer & F. Stjernfelt. “Theses on Biosemiotics: Prolegomena to a Theoretical Biology.” Pp. 25-41. Emmeche, Claus & K. Kull, Eds. 2011. Towards a Semiotic Biology: Life is the Action of Signs. Imperial College Press. P. 31.


“A semiotic niche is defined as the totality of signs or cues in the surroundings of an organism–signs that it must be able to meaningfully interpret to ensure its balance and welfare. The semiotic niche includes the traditional ecological niche factors, but now the semiotic dimension of these factors is also emphasized.” Kull, Kalevi, T. Deacon, C. Emmeche, J. Hoffmeyer & F. Stjernfelt. “Theses on Biosemiotics: Prolegomena to a Theoretical Biology.” Pp. 25-41. Emmeche, Claus & K. Kull, Eds. 2011. Towards a Semiotic Biology: Life is the Action of Signs. Imperial College Press. P. 38.


“Volumes have been produced to solve the problem of how to justify the concept of function inside a non-teleological frame of understanding. And this is where natural selection comes in, for natural selection will tend to optimize the capacity of species to meet the functional challenges of their ecological niche conditions. Functionality is exactly what natural selection is supposed to produce.

“The term ‘function’ in biology is understood as the answer to a question about why some object or process has evolved in a system. In other words, what is it good for? A function thus refers forward in time from the object or process, along some chain of causation to the goal or success. This inversed arrow of time (future directedness) immediately sets functions apart from other kinds of mechanisms that always refer backward along some chain of causation explaining how the feature occurred. Darwinists, however, are not worried about the teleological character of functions because they believe that natural selection will ultimately account for them through ordinary mechanistic causation. Thus, as often noted by Darwinists, adaptive traits are not explained by the consequences the will or can have but by the consequences they already have had in ancestor populations. The consequences in other words precede the effect they explain, and selection does not therefore challenge the mechanistic paradigm of traditional biology. So, as the explanation goes, the teleology implied by the concept of function is only an ‘as if’ teleology, i.e., a teleonomy.” Hoffmeyer, Jesper. “Biology is Immature Biosemiotics.” Pp. 43-65. Emmeche, Claus & K. Kull, Eds. 2011. Towards a Semiotic Biology: Life is the Action of Signs. Imperial College Press. P. 44.


“... contrary to physically based interactions, semiotic interactions do not depend on any direct causal connection between the sign vehicle and the effect. Instead the two events are connected through the intervention of an interpretative response. The point is that in semiotic interactions the causal machinery of the receptive system is itself in charge of producing the behavior, and it thus only needs to acquire a sensitivity towards the sign as an inducing factor. The biochemical machinery underlying the response is not, therefore, restricted by any bonds deriving from the chemistry of the releasing sign.” Hoffmeyer, Jesper. “Biology is Immature Biosemiotics.” Pp. 43-65. Emmeche, Claus & K. Kull, Eds. 2011. Towards a Semiotic Biology: Life is the Action of Signs. Imperial College Press. Pp. 60-1.


“... open-ended evolution includes then two distinct properties. (1) An immense number of potential forms, and (2) a basic unpredictability of the paths evolution will take.” Pattee, Howard & K. Kull. “Between Physics and Semiotics.” Pp. 213-233. Emmeche, Claus & K. Kull, Eds. 2011. Towards a Semiotic Biology: Life is the Action of Signs. Imperial College Press. P. 214. Kull speaking.


“The physical basis of the immense number of forms is a consequence of the immense number of linear sequences of material units that laws cannot distinguish because of their similar energy or similar stability. This is the genetic memory. Only some forms of ‘frozen accident’ or higher level selection process affects which memory sequences survive over time. Not only are the initial sequences unpredictable, but their physical structure appears to be largely arbitrary. Natural selection is also unpredictable because of its complexity and the indefinite time period over which selection continues to work.” Pattee, Howard & K. Kull. “Between Physics and Semiotics.” Pp. 213-233. Emmeche, Claus & K. Kull, Eds. 2011. Towards a Semiotic Biology: Life is the Action of Signs. Imperial College Press. P. 214. Pattee speaking.


“The inexorable character of physical law is often misunderstood to imply determinism. This is not the case. There are innumerable structures in the universe that physical laws do not determine. It is also important to understand why lawfully indeterminate does not mean physically indistinguishable.

“Since all the basic laws of physics are expressed in terms of energy, systems with two or more states with the same energy are lawfully indeterminate. However, in many cases we can distinguish these states by measurements of their initial conditions. These law-equivalent states are often called degeneracies or symmetries.

“A common example is chirality, or left and right handedness. Chemically, amino acids and proteins can be left or right handed, and they cannot be distinguished by the laws that they both obey.” Pattee, Howard & K. Kull. “Between Physics and Semiotics.” Pp. 213-233. Emmeche, Claus & K. Kull, Eds. 2011. Towards a Semiotic Biology: Life is the Action of Signs. Imperial College Press. P. 215. Pattee speaking.


“The concept of absolute determinism as envisioned by Laplace and philosophers like Dennett, has turned out in physics to be an unsupportable and unproductive way of thinking. Determinism is an untestable metaphysical concept. First of all, measurement processes are irreversible and therefore dissipative and subject to error, so determinism is not empirically verifiable. All the fundamental laws are consistent only with a probabilistic universe. We have enough ‘freedom’ just because of the undeterminable or equivalent probabilities of many structures, like polymer sequences.” Pattee, Howard & K. Kull. “Between Physics and Semiotics.” Pp. 213-233. Emmeche, Claus & K. Kull, Eds. 2011. Towards a Semiotic Biology: Life is the Action of Signs. Imperial College Press. P. 217. Pattee speaking.


“In physics a constraint is a local structure that limits the motions of otherwise ‘free’ particles that are governed only by the laws of motion. However, the concept of constraint is also used to describe levels of hierarchical organizations. Generally speaking, each higher level requires a constraint that is described by fewer observables than the lower level description. More precisely, a constraint is an alternative simplified description of structures that are not usefully described by the behavior at a more detailed lower level.

A simple example is a closed box that limits the detailed motions of the gas molecules inside. The box itself is also made of molecules, but they are constrained by chemical bonds to form a solid structure. So we simplify the description of the box by describing only its geometric boundaries, and we ignore the detailed molecular structure of the box itself. Such constraints are also called ‘boundary conditions.’” Pattee, Howard & K. Kull. “Between Physics and Semiotics.” Pp. 213-233. Emmeche, Claus & K. Kull, Eds. 2011. Towards a Semiotic Biology: Life is the Action of Signs. Imperial College Press. Pp. 217-8. Pattee speaking.


“To be more precise, you never have ‘freedom from laws’ but only freedom from initial or boundary conditions. You have to make a clear distinction between laws and constraints. Laws are universal and inexorable. Nothing is free of laws. Constraints are local structures that obey laws but are not determined or predictable by laws. Memory is a special type of constraint that can alter or control the lawful course of local events. Polanyi’s phrase ‘harnessing the laws’ is apt.” Pattee, Howard & K. Kull. “Between Physics and Semiotics.” Pp. 213-233. Emmeche, Claus & K. Kull, Eds. 2011. Towards a Semiotic Biology: Life is the Action of Signs. Imperial College Press. P. 220. Pattee speaking. Reference is to Polanyi, Michael. 1968. “Life’s irreducible structure.” Science 160:1308-1312.


“A thing in the physical world is just one, whereas in the semiotic world it is always many, it just cannot be one until it has a meaning. Semiosis makes the world plural. Like, for instance, a painting – physically, it is a concrete pattern of pigments, but semiotically it is many things that can be recognized (or to what it refers).” Pattee, Howard & K. Kull. “Between Physics and Semiotics.” Pp. 213-233. Emmeche, Claus & K. Kull, Eds. 2011. Towards a Semiotic Biology: Life is the Action of Signs. Imperial College Press. P. 226. Kull speaking.


“Physics and semiotics have two very different cultures, and biochemistry is a third culture. The problem is even worse because all these areas have subcultures with their special foci and terminologies.

“I’m sure you are aware of this culture problem. The two of us are both motivated to try to resolve our different language problem by discussions like this one. Unfortunately this is not the common motivation of most biochemists. When they are confronted with the biosemiotics perspective, they often resist semiotic expression of the problems of life as nothing but restatements of what they describe in their well-developed material language, which they regard as a more scientific description of life.

“It is not clear to me what biosemiotics wants to be. All I can suggest is that if its practitioners want it to be accepted as science rather than as philosophy, they must focus more on empirically decidable models, rather than emphasizing its linguistic and philosophical foundations. In other words, if biosemiotics claims that symbolic control is the distinguishing characteristic of life, and if it also claims to be a science, then it must clearly define symbols and codes in empirical scientific terms that are more familiar to physicists and molecular biologists.” Pattee, Howard & K. Kull. “Between Physics and Semiotics.” Pp. 213-233. Emmeche, Claus & K. Kull, Eds. 2011. Towards a Semiotic Biology: Life is the Action of Signs. Imperial College Press. P. 230. Pattee speaking.


“... in Costa Rica, the tropical biologist and conservationist Dan Janzen had argued that the biggest fruits, those that now sit unmoved beneath their shady mothers, evolved to be dispersed by the now-extinct megafauna, species that disappeared along with the pronghorn’s predators. Janzen’s idea arose from his observations in 1979 of the three-foot-long pods of the Cassia grandis tree. Thirty years later, Janzen seems just as right and those fruits remain just as unmoved. To paraphrase the paleontologist Paul S. Martin, we live in a time of ghosts, their prehistoric presence hinted at by the largest sweet-tasting fruits. Many of the fruits that humans have come to favor seem to have evolved to be carried from one place to another in the temporary vehicle of a giant mammal’s guts–papayas make the list, as do avocados, guava, cherimoya, osage oranges, and the foul-smelling but delicious durian.” Dunn, Rob. 2011. The Wild Life of Our Bodies: Predators, Parasites, and Partners that Shape who we are Today. Harper Collins. P. 29.


“Let’s call it the pronghorn principle. The pronghorn principle has two elements: First, all species have physical characteristics and genes that relate to the ways in which they interact with other species. Second, when those other species are removed, such features become anachronistic or worse....

“Pick any organism on Earth and as much of its biology is defined by how it interacts with other species as is influenced by the basics of living, eating, breathing, and mating. Interactions among species are part of the tangled bank to which Darwin referred. What the Byerses newly understood in the context of the pronghorn was the consequences of removing the species our bodies evolved to interact with, be they predators (as in the case of the cheetah), mutualists like the animals that once dispersed the giant American fruits, or even parasites and disease.” Dunn, Rob. 2011. The Wild Life of Our Bodies: Predators, Parasites, and Partners that Shape who we are Today. Harper Collins. P. 30. Reference is to Byers, John. Built for Speed, A Year in the Life of Pronghorn. 2003. Harvard University Press.


“They [microbes in our guts especially for early humans] provided vitamin K where it was once scarce, but just as importantly, they allowed us to extract extra calories from our food, up to 30 percent extra.” Dunn, Rob. 2011. The Wild Life of Our Bodies: Predators, Parasites, and Partners that Shape who we are Today. Harper Collins. P. 81.


“For much of our primate history, we spent hours a week picking and savoring wild fruits. The fruits benefited us. We also benefited their seeds by ‘depositing them’ wherever we relieved ourselves. Some plant species spread around the world in this way, using latrines as stepping-stones. In this regard our ancestors were like toucans, emus, monkeys, and the many other species that serve plants as seed dispersers. We ate other things, of course. We searched out some insects–the queens of ants, for example, or the grubs of large beetles–but, for most of our story, the plants were the mainstay of our vessel. Today when we look out at our evolutionary partners, the ones not in our bodies, we see a very different scene. No less than half of all wild forests and grasslands have been replaced by agricultural and other intensively managed land uses. On these managed lands, we nurture a tiny minority of Earth’s species, our domesticates, whether corn, rice, wheat, or more rarely, something else. These species are still our mutualists, but in a very different way from the papaya tree growing like a phoenix out of the outhouse. In making the transition from gathering thousands of species to farming far fewer, we caused both our favored species and our disfavored species to evolve, but they were not the only ones. We evolved too.” Dunn, Rob. 2011. The Wild Life of Our Bodies: Predators, Parasites, and Partners that Shape who we are Today. Harper Collins. Pp. 111-2.


“The answer Tishkoff found in East Africa was that the ability of human adults to digest lactase evolved more than once. It evolved once in Europeans, around 9,000 to 10,000 years ago, at about the time that archaeological evidence and cow genes point to the domestication of cows in Europe. It then evolved again, at least three times, in Africa, beginning around 7,000 years ago, again just about when evidence suggests cows were domesticated for the second time. At least twice (and probably more like four times) upon a time, aurochsen were domesticated.” Dunn, Rob. 2011. The Wild Life of Our Bodies: Predators, Parasites, and Partners that Shape who we are Today. Harper Collins. Pp. 126-7. Reference is to Scheinfeldt, L., S. Soi & S. Tishkoff. 2010. “Working Toward a Synthesis of Archaeological, Linguistic, and Genetic Data for Inferring African Population History.” Proceedings of the National Academy of Sciences. 107: 8931-8938.


“In fact, it seems possible that in each place that agriculture arose, our bodies changed, independently and differently. Our great human variety reflects, in no small part, the great variety of ways in which we came to depend on individual species, a new less diverse set of species, to make it through the toughest years.

“In the villages of our descent, we turned to these new species and latched on, the way a baby first latches on to its mother. We had been brave and independent, but in those moments, we gave in. We would live, for each day after, where and how those species needed us to live in order to benefit from what they offered. We made an evolutionary contract from which we have never since been separated. It is far easier to divorce your spouse than to divorce agriculture.” Dunn, Rob. 2011. The Wild Life of Our Bodies: Predators, Parasites, and Partners that Shape who we are Today. Harper Collins. Pp. 127-8.


“Imagine a crab that proceeds through four acts in its performance–finding a mollusk, picking it up, breaking in, and then actually killing and eating it. At some tasks, it rarely fails. It finds prey without trouble. It kills with deadly certainty once it has broken through the shell. What it most often fails to do is to get through the shell. Breaking in is hard to do, and so what mollusks have done over time is to change most in those features that prevent the crabs from breaking in. This was Vermeij’s law: prey respond to predators’ weaknesses, the ways they fail rather than the ways they succeed. The main caveat is that the prey must vary genetically in traits related to the predators’ weakness, but in most cases they do. Now that crabs are everywhere, almost all shells in the ocean are thick and hard ....” Dunn, Rob. 2011. The Wild Life of Our Bodies: Predators, Parasites, and Partners that Shape who we are Today. Harper Collins. Pp. 172-3.


“Each year we have farmed more sugarcane and sugar beets. Now they are joined by corn farms. On such farms, a useful food is farmed to produce nutritionally useless sweet high-fructose corn syrup. In 2010, more than 400,000 square kilometers of Earth were dedicated to the farming of sugar beets and sugar-cane, an area the size of California. A similar quantity of land is dedicated to the corn used to produce corn syrup.

“When millions of humans continue to starve each year, the fact that we have allotted an area this large to a substance for which none of us has any real need is a sign of just how beholden we are to our taste buds....

“Back in East Africa, no one follows the honeyguide anymore. It has stopped coming to villages. The children who once chased it pursue lollypops instead.” Dunn, Rob. 2011. The Wild Life of Our Bodies: Predators, Parasites, and Partners that Shape who we are Today. Harper Collins. Pp. 187-8.


“Our senses, coupled with our power, changed the world so quickly and universally that it is easy to forget what the world used to be like. Today, roughly 60 percent of the earth’s surface is managed by humans for production, and most of that land is devoted to one or another kind of grass. Nearly all humans on Earth live by water. Many of us tend to live by water because we need it, but also because we tend to prefer it. It pulls at us like gravity and makes us feel good. Once upon a time, though, before modern humans, there were more forests and larger animals. Rats were rare, as were mice and roaches. Even grasslands were not nearly so common, and the flowering plants that have arisen around us had not yet called to our senses. In many places, the coastlines along which we now so easily walk were hidden beyond dunes tens of feet high, dunes that while useful to us in protecting our shores, obscured our views. The views won, and so in general the dunes are gone, reduced to a minor row of hills that does little ....” Dunn, Rob. 2011. The Wild Life of Our Bodies: Predators, Parasites, and Partners that Shape who we are Today. Harper Collins. Pp. 197-8.


“Preutz and Bertolani reported the first habitual use of tools by chimpanzees to secure vertebrate prey. The apes of Fongoli, Senegal, used sharpened sticks as skewers to hunt lesser bushbabies from their nests in tree cavities. Making these instruments involved a hierarchically organized sequence of up to five steps, flexible enough to allow some steps to be omitted and others repeated. Some of the observed episodes involved more than one tool being used to probe a single cavity.” Wynn, Thomas, R. Adriana Hernandez-Aguilar, L. Marchant & W. McGrew. 2011. “‘An Ape’s View of the Oldowan’ Revisited.” Evolutionary Anthropology. 20:181-197. P. 182. Reference is to Preutz J. & P. Bertolani. 2007. “Savanna chimpanzees, Pan troglodytes verus, hunt with tools.” Current Biology 17:412-417.


“Hernandez-Aguilar, Moore, and Pickering reported for the first time that chimpanzees use tools to excavate the underground storage organs (USOs) of plants.” Wynn, Thomas, R. Adriana Hernandez-Aguilar, L. Marchant & W. McGrew. 2011. “‘An Ape’s View of the Oldowan’ Revisited.” Evolutionary Anthropology. 20:181-197. P. 183. Reference is to Hernandez-Aguilar, RA, J. Moore & TR Pickering. 2007. “Savanna chimpanzees use tools to harvest the underground storage organs of plants. Proc Natl Acad Sci USA. 104:19210-19213.


“A tool set is ‘two or more tools [used] in an obligate sequence to achieve a single goal. Brewer and McGrew first described a tool set. In that case, a female chimpanzee used four types of tools in series to extract honey. Since then, tool sets have been seen in wild communities for obtaining honey, sap, and social insects. The largest known tool set comprises five tools used to get honey. A specific order in the use of each tool of the set is needed to reach the goal.” Wynn, Thomas, R. Adriana Hernandez-Aguilar, L. Marchant & W. McGrew. 2011. “‘An Ape’s View of the Oldowan’ Revisited.” Evolutionary Anthropology. 20:181-197. P. 183. Reference is to Brewer, S. & W. McGrew. 1990. “Chimpanzees use of a tool-set to get honey.” Folia Primatology. 54:100-104.


“Based on long-term studies, these white-faced capuchins show notable parallels with chimpanzees, such as social hunting, meat-sharing, and interpopulational behavioral variation. However, in the last 10 years, it is C. libidinosus (bearded capuchin) that has leapt to prominence...

“Overall, the tool kits of capuchin monkeys rival or even exceed those of chimpanzee populations in scope and complexity, if not yet in size.” Wynn, Thomas, R. Adriana Hernandez-Aguilar, L. Marchant & W. McGrew. 2011. “‘An Ape’s View of the Oldowan’ Revisited.” Evolutionary Anthropology. 20:181-197. P. 187.


“Since 1989, the picture of non-human primate technology-based adaptations has broadened dramatically. From termite fishing at Gombe and nut cracking at Tai, which formed the core of the 1989 analysis, the known tool-based activities of chimpanzees have expanded to encompass a much greater variety of tools, including tool sets, composite tools, and compound tools, and a greater variety of foods accessed and processed. Moreover, it is clear that much of this activity depends on sequentially and hierarchically organized actions that allow flexibility in task completion. Chimpanzees represent the high end of a range of reliance on tool-assisted activities now documented for other apes, and also monkeys.” Wynn, Thomas, R. Adriana Hernandez-Aguilar, L. Marchant & W. McGrew. 2011. “‘An Ape’s View of the Oldowan’ Revisited.” Evolutionary Anthropology. 20:181-197. P. 187.


“In nut cracking, Carvalho and colleagues reported that a large flake detached from an anvil was then reused as a hammer. They stressed that although such fracturing may have been accidental, the result was a tool produced by another tool. Unintentional products of chimpanzee percussion activities were also identified in the excavated archeological assemblages at Tai. Although accidental stone tool-making by apes is not the same as intentional knapping of stones by hominins, it is an important occurrence and allows for the hypothesis that the unintentional fracture of anvil margins was the first step in the evolution of stone knapping.” Wynn, Thomas, R. Adriana Hernandez-Aguilar, L. Marchant & W. McGrew. 2011. “‘An Ape’s View of the Oldowan’ Revisited.” Evolutionary Anthropology. 20:181-197. P. 192. Reference is to Carvalho, S, E. Cunha, C. Sousa & T. Matsuzawa. 2008. “Chaines operatoires and resource exploitation strategies in chimpanzee nut-cracking (Pan troglodytes).” Journal of Human Evolution. 55:148-163.


“These authors found that normal participants were better able to report a target when it was presented in interaction with a partner object but only under conditions in which the stimuli could be perceptually integrated (e.g., with a short interval between the objects). Green and Hummel proposed that objects placed in co-locations for action could be grouped together and attended as a single ‘unit.’” Yoon, EY, G. Humphreys & MJ Riddoch. “The Paired-Object Affordance Effect.” 2010. Journal of Experimental Psychology: Human Perception and Performance. 36, 4:812-824. P. 813. Reference is to Green, C., & J. Hummel. 2006. “Familiar interacting objects are perceptually grouped.” Journal of Experimental Psychology: Human Perception and Performance. 32, 1107-1119.


“In order for a structure to evolve there must be a reasonable probability that genetic variation carries it from one adaptive peak to another; at the same time the structure should not be overly unstable to phenotypic perturbations, as this is incompatible with occupying a peak. Organizations that are complex in terms of numbers of components and interactions are more likely to meet the peak-climbing condition, but less likely to meet the stability condition. Biological structures that are characterized by a high degree of component redundancy and multiple weak interactions satisfy these conflicting pressures.” Conrad, Michael. “The geometry of evolution.” 1990. BioSystems, 24:61-81. P. 61.


“The picture is that a very special class of structures is particularly amenable to evolution, and that these are themselves selected through the Darwinian mechanism of variation and selection. The chief characteristic of this special class of structures is that it must satisfy at one and the same time two conflicting conditions. The first is that the organism be stable, that it sit in a developmental basin of attraction. This is more likely as the number of components in the organism and the number of interactions among them decreases, on the simple grounds that the chance of a valley occurring in the phase space of a system decreases with its dimensionality. The second condition is that the adaptive peaks corresponding to these basins of attraction should be close enough together to be connected by single genetic changes. But this is more likely as the number of components and interactions increases, since pathways between peaks in the adaptive peak space correspond to pathways between valleys in the basin space. The only way for a system to satisfy both conditions is to have many redundant components with multiple weak interactions. In this case the developmental system can have many genetically related homomorphic images. The extra components and weak interactions that allow for this special situation are costs to the individual organism; the structure that is more amenable to evolution will be functionally less effective from the thermodynamic point of view. Nevertheless the amenability-increasing structural features inevitably hitchhike along with the advantageous traits whose evolution they facilitate.” Conrad, Michael. “The geometry of evolution.” 1990. BioSystems, 24:61-81. P. 62.


“Clearly we have arrived at a contradiction. A genetic-developmental organization must be slightly unstable to allow for evolution, but this is incompatible with the stability required for fitness. The resolution is not too difficult. It is only necessary to organize the phenotypic dynamics to be unstable to mutation and other genetic perturbation, but stable to the physiological class of perturbations.” Conrad, Michael. “The geometry of evolution.” 1990. BioSystems, 24:61-81. P. 69.


“At the level of the gene and organism the principle [of self-complication] may be stated thus: the complexity of biological organization increases because (buffered) dynamic instability in response to genetic variations is advantageous to evolutionary self-organization....

“The principle of self-complication contrasts with what has been termed the principle of self-simplification. Some authors have argued that complex systems, because they are unstable, will self-simplify. This is a reasonable assumption, except for those special cases in which the structure of complexity confers extra stability. Our analysis suggests that complication in terms of redundant components and weak interactions will in general facilitate the achievement of stability and that biological organization is a consequence of self-complicating as well as self-simplifying processes.” Conrad, Michael. “The geometry of evolution.” 1990. BioSystems, 24:61-81. Pp. 78-9.


“Actually our whole discussion has used a rather naive definition of complexity Many other definitions exist. According to the algorithmic definition of Chaiten and Kolmogoroff, the complexity of a pattern can be represented by the length of the shortest computer program that can generate the pattern. A truly random (not pseudorandom) pattern is thus the most complex. Redundancy means that some of the features of the pattern are related to each other by a rule. Thus our principle of self-complication has a self-simplifying aspect when looked at from the point of view of the Chaiten-Kolmogoroff definition. The Chaiten-Kolmogoroff complexity of an evolutionary system would increase less in the course of evolution than would the complexity as measured by the number of components and interactions. Evolutionary systems would move toward some situation intermediate between order and randomness. From the point of view of constructing scientific theories this is of course the most complex (difficult) region. Pure randomness, no matter how complex from the standpoint of Chaiten-Kolmogoroff, lends itself to probabilistic models; while highly ordered situations lend themselves to group theory. The organizations that are best suited to evolution are precisely those that are most ill suited to the classical standards of scientific description.” Conrad, Michael. “The geometry of evolution.” 1990. BioSystems, 24:61-81. P. 79.


“... a different and completely valid scenario is that the entities that gave rise to the lineages of the three different domains of life were actually the result of independent cellularisation events in an evolving population of precells. However, the concept of a distinct LUCA becomes ambiguous in this case, and as a consequence it is more appropriate to speak of the Last Universal Common Ancestral State (LUCAS).” Guzman, Marcelo. “Abiotic Photosynthesis: From Prebiotic Chemistry to Metabolism.” Pp. 85-105. From Egel, Richard, D. Lankenau & A. Mulkidjanian, Eds. Origins of Life: The Primal Self-Organization. 2011. Springer. P. 86.


“While metabolism supplies the monomers from which the replicators (i.e., genes) are made, replicators alter the kinds of chemical reactions occurring in metabolism. Only then can natural selection, acting on replicators, power the evolution of metabolism.” Guzman, Marcelo. “Abiotic Photosynthesis: From Prebiotic Chemistry to Metabolism.” Pp. 85-105. From Egel, Richard, D. Lankenau & A. Mulkidjanian, Eds. Origins of Life: The Primal Self-Organization. 2011. Springer. P. 87.


“Here are only three such models [to explain the origin of life]: (1) the RNA-first world, (2) the compartmentalistic approach, and (3) the proposal of nonenzymatic metabolism.... Among the many other models to explain the origin of life is the thioester world and the glyoxylate scenario.” Guzman, Marcelo. “Abiotic Photosynthesis: From Prebiotic Chemistry to Metabolism.” Pp. 85-105. From Egel, Richard, D. Lankenau & A. Mulkidjanian, Eds. Origins of Life: The Primal Self-Organization. 2011. Springer. P. 90.


“Universal metabolism rationalizes that all the possible metabolic cycles are partially common and converge in the r-TCA cycle through at least one of the intermediates. In consequence, this cycle is proposed to be fundamental to the origin of life. Enzymes, specialized proteins able to catalyze all these metabolic reactions, appeared later in metabolism, speeding up the reactions, and eventually took over the complete control of these networks. The deep consequence is that metabolic networks arose before the origin of macromolecules with highly specialized catalytic properties or enzymes.

“The model is not absolutely accepted, least so by supporters of the RNA-first world scenario, whose main concern relates to the catalytic properties of the minerals involved in the organization of the chemical system.” Guzman, Marcelo. “Abiotic Photosynthesis: From Prebiotic Chemistry to Metabolism.” Pp. 85-105. From Egel, Richard, D. Lankenau & A. Mulkidjanian, Eds. Origins of Life: The Primal Self-Organization. 2011. Springer. P. 92.


“Nonenzymatic metabolism requires overcoming the high activation energies (Ea) for the chemical reactions involved. Enzymes have the ability of catalyzing those reactions by decreasing Ea and making possible many energetically unfavorable reactions. In addition, the active sites where the reactions take place in enzymes have a tridimensional geometry of high order where the actual concentration of reactants is considerably larger than in the surroundings. Cairns-Smith explored an idea first suggested by Bernal. Cairns-Smith showed that clay mineral surfaces, in an aqueous environment, can adsorb organic molecules, enhancing their concentration. Clay surfaces also behave as a mold for polymerization reactions to take place.” Guzman, Marcelo. “Abiotic Photosynthesis: From Prebiotic Chemistry to Metabolism.” Pp. 85-105. From Egel, Richard, D. Lankenau & A. Mulkidjanian, Eds. Origins of Life: The Primal Self-Organization. 2011. Springer. P. 93.


“To date, there are six known carbon fixation pathways used by living organisms. One of them, the r-TCA cycle is often proposed as the leading candidate to be the first carbon fixation mechanism because it operates in ancient green sulfur bacteria. Additionally, all six mechanisms share at least a common intermediate ....” Guzman, Marcelo. “Abiotic Photosynthesis: From Prebiotic Chemistry to Metabolism.” Pp. 85-105. From Egel, Richard, D. Lankenau & A. Mulkidjanian, Eds. Origins of Life: The Primal Self-Organization. 2011. Springer. P. 96.


“The photocatalytic principle consists in the absorption of a photon in the wave-length band of absorption of the mineral. The most extensively studied mineral for this application is sphalerite, the cubic form of zinc sulfide.... The novelty of this mechanism is to provide complementary oxidation and reduction reactions that occur at the same time in the tiny nano- to micro-meter diameter scale colloidal particles.” Guzman, Marcelo. “Abiotic Photosynthesis: From Prebiotic Chemistry to Metabolism.” Pp. 85-105. From Egel, Richard, D. Lankenau & A. Mulkidjanian, Eds. Origins of Life: The Primal Self-Organization. 2011. Springer. Pp. 98-9.


“In the early terrestrial environment, the genetic information that was embedded in the RNA sequences could lead to self replication and to phenotypes with catalytic properties. In the case of the proto-ribosome, it is likely that the more efficient and more stable RNA dimers that functioned as proto-ribosomes by positioning the substrates in a spatial arrangement similar to the modern one, could have autoreplicated. Thus, the surviving ancient pockets became the templates for the ancient ribosomes. In a later stage these molecular entities underwent optimization from non-genetic peptide bond formation towards performing genetically driven translation.” Davidovich, Chen, M. Belousoff, A. Bashan & A. Yonath. “The evolving ribosome: from non-coded peptide bond formation to sophisticated translation machinery.” Resarch in Microbiology. 2009. 160: 487-492. P. 489.


“The emergence of Life required an apparatus for synthesizing polypeptides capable of performing catalytic or other life supporting tasks, i.e. the ribosome. The proto-ribosome, which served as the precursor for the modern translation machinery by its capacity to autonomously catalyze peptide bonds forming non-coded amino acid oligo- or polymers, is suggested to have appeared by spontaneous dimeric assembly of two self-folding RNA chains. These pocket-like dimers offered a catalytic site for favorable positioning of the substrates involved in peptide bond formation and simple elongation. Our studies show that it is likely that the proto-ribosome is still embedded in the core of the modern ribosome, and that the tendency for dimerization of the proto-ribosome, a prerequisite for obtaining the catalytic center, is intrinsically linked to the sequences and the folds of its two components, thus indicating functional selection at the molecular level in the prebiotic era.” Davidovich, Chen, M. Belousoff, A. Bashan & A. Yonath. “The evolving ribosome: from non-coded peptide bond formation to sophisticated translation machinery.” Resarch in Microbiology. 2009. 160: 487-492. P. 491.


“An important consequence of this view is that the agent and the environment constitute a single system, i.e. the two aspects are so intimately connected that a description of each of them in isolation does not make much sense.” Nolfi, Stefano. “Behaviour as a Complex Adaptive System: On the Role of Self-Organization in the Development of Individual and Collective Behaviour.” ComPlexUs. 2005. 2:195-203. P. 196.


“The various forms of learning have traditionally been treated as separate creations, much as species were treated by pre-Darwinian biologists. This long-standing position is indefensible, however. Just as systematists, comparative zoologists, biochemists, and ethologists have reconstructed evolutionary hierarchies showing the origins of species, structures, proteins, and instincts, so also comparative psychologists (or others) should in principle be able to find hierarchical relationships linking most or all known forms of learning. The present work addresses this question, and offers a cladogram linking ninety-seven processes.” Moore, Bruce. “The evolution of learning.” 2004. Biological Reviews. 79:301-335. P. 302.


“Habituation has been defined as a response decrement ‘occurring as the result of repeated [or prolonged] stimulation,’ and not attributable to fatigue or sensory adaptation.” Moore, Bruce. “The evolution of learning.” 2004. Biological Reviews. 79:301-335. P. 303. Quote is from Harris, J. 1943. “Habituatory response decrement in the intact organism.” Psychological Bulletin. 40:385-422.


“Dishabituation, in which abrupt stimuli reduce habituation, is rather like sensitization. But it brings habituated reactions back to normal, or near-normal, whereas sensitization enhances normal reflexes.” Moore, Bruce. “The evolution of learning.” 2004. Biological Reviews. 79:301-335. P. 305. Quote is from Harris, J. 1943. “Habituatory response decrement in the intact organism.” Psychological Bulletin. 40:385-422.


“Sensitization is ordinarily an after-effect of negative reinforcement. It occurs when mere presentation of a reinforcing stimulus, typically an aversive one, potentiates reactions from the species-typical repertoire.” Moore, Bruce. “The evolution of learning.” 2004. Biological Reviews. 79:301-335. P. 305. Quote is from Harris, J. 1943. “Habituatory response decrement in the intact organism.” Psychological Bulletin. 40:385-422.


“While conditioning and sensitization are similar, they differ in at least two ways. Conditioning is associative, while sensitization is not, and it is a long-term (semi-permanent) effect, unlike simple sensitization.” Moore, Bruce. “The evolution of learning.” 2004. Biological Reviews. 79:301-335. P. 305. Quote is from Harris, J. 1943. “Habituatory response decrement in the intact organism.” Psychological Bulletin. 40:385-422.


“Here we present evidence from a diversity of sources supporting the hypothesis that a fuller answer [to how hominin evolution could compete with a guild of specialist carnivores] lies in the evolution of a new socio-cognitive niche, the principal components of which include forms of cooperation, egalitarianism, mindreading (also known as ‘theory of mind’), language and cultural transmission, that go far beyond the most comparable phenomena in other primates.” Whiten, Andrew & D. Erdal. “The human socio-cognitive niche and its evolutionary origins.” 2012. Philosophical Transactions of the Royal Society: B. 367: 2119-2129. P. 2119.


“Under thermodynamic criteria, any biological system is no more ordered than a piece of rock of equivalent weight. The difference between them is in the kinetics and ability to remember favorable structurization scenarios.” Ivanitskii, G.R. “21st century: what is life from the perspective of physics?” 2010. Uspekhi Fizicheskikh Nauk. 180 (4) 337-369. P. 334.


“In other words, biological evolution proceeds in two distinct modes: as the existence of short-living organisms, and via mutations in the long-lived genetic code.” Ivanitskii, G.R. “21st century: what is life from the perspective of physics?” 2010. Uspekhi Fizicheskikh Nauk. 180 (4) 337-369. P. 342.


“It can be concluded that the greatest event in the course of natural evolution was the appearance of primitive memory for at least one cycle of environmental changes.” Ivanitskii, G.R. “21st century: what is life from the perspective of physics?” 2010. Uspekhi Fizicheskikh Nauk. 180 (4) 337-369. P. 344.


“The main point is that variations in the random process of environmental changes enabled living organisms to develop a memory strategy for the selection of advantageous mutations and modifications at different hierarchical levels from macromolecules to the biospshere as a whole; simultaneously, they learned how to survive in the course of evolution. In other words, the mechanism of selection consists in a gradual alteration of living matter responsiveness in time and space using memory of preceding results. This mechanism was realized in different modes at different stages of evolution by changing the pitch and the length of the genetic code, a set of biochemical reactions, inner links, exchange operation of learning for reproduction rate, etc. Selection gave advantages to the best forms of living matter and enabled them to build up new hierarchical levels of regulation by combining simultaneously arising elements, which promoted the transformation of both chaotic and deterministic environmental processes into the symbiotic deterministic-chaotic process inside the living organism.” Ivanitskii, G.R. “21st century: what is life from the perspective of physics?” 2010. Uspekhi Fizicheskikh Nauk. 180 (4) 337-369. P. 352.


“It is worth noting that the mass of living matter on our planet is still rather small (2.4 - 3.6 x 1012 metric tons, dry weight), or less than 10-6 of Earth’s mass. But the load it exerts on the planet is determined by kinetics, not mass, of living matter, i.e., by the energy being exhausted as it is consumed. According to different but close estimates, a few billion species have disappeared from Earth during the 4.5 billion years of organic evolution. All these organisms had to let the entire matter contained in the envelope of Earth (the atmosphere, hydrosphere, lithosphere) pass many times through their organs, tissues, and cells. Thereby, they not only reproduced themselves, but also transformed atmospheric air, oceanic waters, and a huge mass of mineral substance into the products of their vital functions.” Ivanitskii, G.R. “21st century: what is life from the perspective of physics?” 2010. Uspekhi Fizicheskikh Nauk. 180 (4) 337-369. P. 353


“Much of evolution is coevolution—the process of reciprocal evolutionary change between interacting species driven by natural selection. Most species survive and reproduce only by using a combination of their own genome and that of at least one other species either directly or indirectly. Species evolve to a large degree by co-opting and manipulating other free-living species or by acquiring the entire genomes of other species through parasitic or mutualistic symbiotic relationships. The evolution of biodiversity is therefore largely about the evolution of interaction diversity.” Thompson, John. The Geographic Mosaic of Coevolution. 2005. University of Chicago Press. Pp. 3-4.


“We are also beginning to understand better the profound effects of coevolution on human societies. Human history is partly a history of coevolution with the parasites and pathogens that have shaped the spread of our species and our cultures worldwide. The story of human agriculture is to a great degree the story of human-induced coevolution between crop plants and rapidly evolving parasites and pathogens.” Thompson, John. The Geographic Mosaic of Coevolution. 2005. University of Chicago Press. Pp. 4-5.


“In the past, discussions of the relevance of science for the interpretation of reality, including human existence, were based on the simplifications of physics. However, the close relationship of alternative interpretations of living matter (in terms of either simplifying generality or complex specificity and its extensive network of conceptual continuity) suggests that the understanding of living, rather than inanimate systems, would be of greater use in reconciling the simplifying and complex qualities of reality. With its emphasis on specificity, biology becomes a focal point in the discussion of the simple/complex relationship, a pivotal area in bridging the gap between the abstract realities of mechanistic physics and the concrete realities of human society. It legitimizes biological systems as models for establishing conceptual continuity as a way of understanding complexity.” Hermann, Heinz. From Biology to Sociopolitics: Conceptual Continuity in Complex Systems. 1998. Yale University Press. Pp. 7-8.


“Inherent in the scientific thought of past centuries has been the resolve to create a representation of reality that is free of complexity. Examination and discussion of complexity as a noteworthy concept in its own right was to be avoided. Phenomena that could not be reduced to the simplicity of ideal systems were to be disregarded. Ignoring complexity seemed quite plausible, as long as some mathematical formalization could be regarded as the only necessary and sufficient requirement for understanding of nonideal systems. This tendency became particularly frequent in dealing with biological systems. Physiology texts published at the turn of the century could boast that their mathematical correlations of physiological parameters gave physiology a status comparable to that of physics.” Hermann, Heinz. From Biology to Sociopolitics: Conceptual Continuity in Complex Systems. 1998. Yale University Press. Pp. 125-6.


“This hope for relieving the burdensome and frustrating complexity of human existence through a simplified representation of reality, to be able to make complexity tolerable by subsuming it under a unifying system of thought, has been a pervasive goal of Western culture since the days of ancient Greece to the present....

“These developments [demonstrations of necessary complexity in “nonideal systems of physics, biology, or sociopolitics”] suggest that humanity may have to abandon its dreams of simple realities and at last come to terms with the overriding complexity of both individual and social existence. The response to this change, the way we perceive reality, will very likely become an initial determining condition and characteristic of our future.

“Three types of responses to complexity can be distinguished: resignation; escape of denial; acceptance and attempted mastery.” Hermann, Heinz. From Biology to Sociopolitics: Conceptual Continuity in Complex Systems. 1998. Yale University Press. Pp. 204-6.


“I shall try to show that our major trouble, and the reason why it is taking the Kuhnian revolution so long to complete itself, is that we have no theory of the cell or organism that explains how either of these [the environment or genes] manages to constrain or collapse an enormously complex realm of possibility to a given adaptive reality. Until we do, if Kuhn was right, we will have to go on repairing a defective genetic paradigm that looks for answers in simplistic genetic programs of one sort or another.” Strohman, Richard. “Epigenesis and Complexity: The coming Kuhnian revolution in biology.” 1997. Nature Biotechnology. Volume 15: 194-200. Pp. 194-5.


“Normal science is an approach that reveals genetic maps related to biological function, but the directions for reading the maps are not included in the package. And the real secrets of life are obviously in those missing directions–in the rules and constraints that organize genetic agents into functional arrays. These rules and constraints are more than likely embedded in the organization of life rather than in the catalogue of the organization’s agents, and we have mistaken the former for the latter.” Strohman, Richard. “Epigenesis and Complexity: The coming Kuhnian revolution in biology.” 1997. Nature Biotechnology. Volume 15: 194-200. P. 197.


“The Kuhnian revolution in which we are now embedded is all about the special qualities of living matter and of discoveries, now underway, and still to come, of the very special boundary conditions that harness the material forces to the purposeful pursuits of organisms. The evidence that these boundary conditions must be present is everywhere. Their absence from our current theories of life is at the root of confusion coming from genetic determinism.” Strohman, Richard. “Epigenesis and Complexity: The coming Kuhnian revolution in biology.” 1997. Nature Biotechnology. Volume 15: 194-200. P. 197.


“The entire landscape of theory in biology is changing before us. We are trying to fit dynamic nonlinear change into a linear theory of the gene, and it will not fit there. And this lack of fit has also been forecast for years by organismal biologists and by population geneticists like Richard Lewontin.” Strohman, Richard. “Epigenesis and Complexity: The coming Kuhnian revolution in biology.” 1997. Nature Biotechnology. Volume 15: 194-200. P. 199.


“The biosphere is dominated, in terms of both physical abundance and genetic diversity, by primitive life forms, prokaryotes and viruses. These ubiquitous organisms evolve in ways unimaginable and unforeseen in classical evolutionary biology.” Koonin, Eugene. 2009. “The Origin at 150: is a new evolutionary synthesis in sight?” Trends in Genetics. V. 25. No. 11. Pp. 473-5. P. 473.


“We now think of the entire world of prokaryotes as a single, huge network of interconnected gene pools, and the notion of the prokaryotic pangenome is definitely here to stay.” Koonin, Eugene. 2009. “The Origin at 150: is a new evolutionary synthesis in sight?” Trends in Genetics. V. 25. No. 11. Pp. 473-5. P. 473.


“In general, the species concept does not apply to prokaryotes and is of dubious validity for unicellular eukaryotes as well.” Koonin, Eugene. 2009. “The Origin at 150: is a new evolutionary synthesis in sight?” Trends in Genetics. V. 25. No. 11. Pp. 473-5. P. 474.


“Equally outdated is the (neo-) Darwinian notion of the adaptive nature of evolution; clearly, genomes show very little if any signs of optimal design, and random drift constrained by purifying in all likelihood contributes (much) more to genome evolution than Darwinian selection.” Koonin, Eugene. 2009. “The Origin at 150: is a new evolutionary synthesis in sight?” Trends in Genetics. V. 25. No. 11. Pp. 473-5. P. 474.


“Whereas emergence seems to be required to explain numerous biological phenomena, fundamentalist reductionism flatly denies its existence: in all cases the whole is no more than the sum of its parts. Thus, biology of the 20th century was in the strange position of having to contort itself to conform to a world view (fundamentalist reductionism) that 20th century physics was simultaneously in the process of rejecting.” Woese, Carl. 2004. “A New Biology for a New Century.” Microbiology and Molecular Biology Reviews. 68(2):173-186. P. 174.


“Our task now is to resynthesize biology; put the organism back into its environment; connect it again to its evolutionary past; and let us feel that complex flow that is organism, evolution, and environment united. The time has come for biology to enter the nonlinear world.” Woese, Carl. 2004. “A New Biology for a New Century.” Microbiology and Molecular Biology Reviews. 68(2):173-186. Pp. 179-80.


“The genes in a genome thus fall into fairly discrete categories depending upon these HGT [prevalence of horizontal gene transfer] characteristics. One category could be called ‘cosmopolitan genes.’ These would be specialty genes, genes that come and go as environmental circumstances change. Cosmopolitan genes are special life style genes; they allow adaptation to unusual environments....

“Then there are the genes whose functions are central to general cellular metabolism and so are crucial for the cell’s existence under any (natural) condition. For the majority of the main metabolic pathways, alternatives appear to exist, i.e., different enzymes catalyzing the same reaction, different pathways from one compound to another, etc....

“Finally there are the genes that define the organizational fabric of the cell, those that give the cell its basic character. By and large genes of this type are highly and idiosyncratically woven into the cellular fabric.” Woese, Carl. 2004. “A New Biology for a New Century.” Microbiology and Molecular Biology Reviews. 68(2):173-186. P. 181.


“In all likelihood primitive cells were loosely connected conglomerates, in which the connections among the parts were relatively few in number and imprecise in specification, and primitive cellular organization was likely minimal and largely horizontal in nature.” Woese, Carl. 2004. “A New Biology for a New Century.” Microbiology and Molecular Biology Reviews. 68(2):173-186. P. 181.


“The aboriginal processes of DNA replication and transcription could not be as complex and, so, as precise as are their modern equivalents because both of these mechanisms today are dependent upon large proteins. Imprecise primitive genome replication implies that primitive genomes could comprise relatively few (unique) genes. This in turn argues for simplicity of primitive cell designs and a general looseness and imprecision in those designs.” Woese, Carl. 2004. “A New Biology for a New Century.” Microbiology and Molecular Biology Reviews. 68(2):173-186. P. 182.


“The world of primitive cells feels like a vast sea, or field, of cosmopolitan genes flowing into and out of the evolving cellular (and other) entities. Because of the high levels of HGT [horizontal gene transfer], evolution at this stage would in essence be communal, not individual.” Woese, Carl. 2004. “A New Biology for a New Century.” Microbiology and Molecular Biology Reviews. 68(2):173-186. P. 182.


“... I assert that it was one such transition that took the cell out of its initial primitive state in which HGT dominated the evolutionary dynamic (and evolving cells had no stable genealogical records and evolution was communal) to a more advanced (modern) form (where vertical inheritance came to dominate and stable organismal lineages could exist). The obvious choice of a name for this particular evolutionary juncture would be Darwinian threshold or Darwinian transition, for it would be only after such a saltation had occurred that we could meaningfully speak of species and of lineages as we know them.” Woese, Carl. 2004. “A New Biology for a New Century.” Microbiology and Molecular Biology Reviews. 68(2):173-186. P. 182.


“The order in which the three cell designs crossed their respective Darwinian thresholds is, then, the bacterial first, the archaeal second, and finally the eucaryotic.” Woese, Carl. 2004. “A New Biology for a New Century.” Microbiology and Molecular Biology Reviews. 68(2):173-186. P. 184.


“[In the 19th and 20th centuries] Physics provided the ultimate explanations. Biology, as no more than complicated chemistry, was at the end of the line, merely providing baroque ornamentation on the great edifice of understanding that was physics–the hierarchy physics–>chemistry–>biology is burned into the thinking of all scientists, a pecking order that has done much to foster in society the (mistaken) notion that biology is only an applied science.” Woese, Carl. 2004. “A New Biology for a New Century.” Microbiology and Molecular Biology Reviews. 68(2):173-186. P. 185.


“This article has touched on only some of the conflicts between the Luhmannian and emergentist traditions. But these divisions are so fundamental that we are justified in seeing these two systems of thought as competing paradigms of social systems theory. First, they have radically different understandings of the core concept of system; for Luhmann, the fundamental units of social systems are communicative events, whereas for emergentists, systems are entities and are composed of entities, and events are produced by their causal interaction. Second, while contemporary emergentism sees higher level properties as products of mechanisms that depend on the properties of lower level parts and the relations between them, a central element of Luhmann’s theory is autopoiesis–a model of systems that denies the influence of lower level properties on the behavior of the higher level system. Third, the two traditions are primarily concerned with quite different core problems that imply very different styles of theory: for emergentists, the resolution of the core problem of reductionism provides resources for developing causal theory, whereas for Luhmann, the resolution of the core problem of self-reference entails the analysis of the meaning of communications.” Elder-Vass, Dave. “Luhmann and Emergentism: Competing Paradigms for Social Systems Theory.” 2007. Philosophy of the Social Sciences. 37:408-432. Pp. 428-9.


“At the most basic level, the parameters describing human society are the same as those for any other vertebrate group. The most obvious of these is the tendency to be social itself, namely to live in groups made up of known individuals. Other basic parameters that appear to be common across humans and non-humans are more prolonged parental relationships, which might be either sex or both, kin-based relationships among resident adults, sex-based patterns of dispersal, more or less prolonged relationships between adult males and females, with one or more partners, some degree of tolerance of the presence of other members of the ‘society’, a lack of presence of equivalent tolerance for members of another group (or at least a different pattern of behaviour) and some degree of structured or repeated style of relationship between individuals (e.g., dominance, submission, friendliness, aggression, etc.).” Foley, Robert & C. Gamble. “The ecology of social transitions in human evolution.” 2009. Philosophical Transactions of the Royal Society: B. Pp. 3267-79. Pp. 3267-8.


“The ability to focus attention so single-mindedly on the making of an object, and its constant repetition across three continents and many millennia, is testament to a high level of attention in practical operations....

“But this Acheulean gaze was not the only derived human trait that appeared at this time [from 2 to 1 Mya]. Using the correlation between brain and community size, Dunbar has proposed that hominins in this period possessed a theory of mind and accompanying orders of intentionality. Gamble has argued for the importance of behaviours that amplified the strength and persistence of social bonds in such an advanced hominin cognition. These would include social laughter and crying as well as other mood enhancers such as collective dance and music.” Foley, Robert & C. Gamble. “The ecology of social transitions in human evolution.” 2009. Philosophical Transactions of the Royal Society: B. Pp. 3267-79. P. 3274.


“It is generally accepted that fission-fusion is an important element of chimpanzee social organization and that it may have been enhanced among the earlier hominins. However, among modern humans, fission-fusion occurs at a different order of magnitude. Individuals, families, bands, etc. can split up for very long periods of time, and disperse over large distances, while still maintaining a common social network....

“A further indication of a significant change in ranging patterns comes from the evidence that lithic raw materials were extracted and transported over greater distances than before. [speaking of the time between 300ka and 200ka ago]” Foley, Robert & C. Gamble. “The ecology of social transitions in human evolution.” 2009. Philosophical Transactions of the Royal Society: B. Pp. 3267-79. P. 3275.


“At this point [200 to 10ka ago], a fundamental shift that goes beyond the normal range of the socioecological model occurred. Technological dependence, spatially restricted and controlled staples such as domesticates, defended flocks, fields, and stores, opened the possibility for greater male control over access to resources at local, regional and inter-regional scales. If we take it as axiomatic to the model that female reproduction is dependent upon access to resources, and males by access to females, then the open-ended model becomes closed when males themselves control the resources. Complex social structures that interweave marriage patterns and resources, which characterize all human societies, represent an entirely novel socioecology that is uniquely human.” Foley, Robert & C. Gamble. “The ecology of social transitions in human evolution.” 2009. Philosophical Transactions of the Royal Society: B. Pp. 3267-79. Pp. 3275-6.


“One such point is that if the ‘community’, in the sense used to describe both chimpanzee groups and human social units, was present from the last common ancestor to the emergence of modern humans, the key development is the addition of social structures both below–families and descent groups–and above–shared political systems, segmentary lineage systems and trade networks. The community, however, remains the core and the basis for elaboration....”

“Human society is essentially a chimpanzee community with exploded fission-fusion; a society that has achieved release from the constraints of proximity that dominate the negotiation and often daily affirmation of social bonds and hierarchies among primates.” Foley, Robert & C. Gamble. “The ecology of social transitions in human evolution.” 2009. Philosophical Transactions of the Royal Society: B. Pp. 3267-79. Pp. 3276-7.


“Nevertheless, tradition, even post-Darwinian tradition, excludes our doings from natural history. It may acknowledge our effects on the natural world–at times (though less often in recent times) even celebrate them–but these effects are treated as impingements, and never incorporated into our conception of self-organization. Yet to put this exclusion so baldly is to make its absurdity self-evident, and to invite us to challenge the entire tradition on which it rests.” Fox Keller, Evelyn. 2005. “Ecosystems, Organisms, and Machines.” BioScience. 55(12):1069-1074. P. 1073.


“Indeed, Gergely & Csibra have recently elaborated an account explaining why the existence of relatively ‘opaque’ cultural conventions (there is no causal structure or else it is difficult to see this structure) requires both that human adults be specifically adapted for pedagogy toward children and that human children be specifically adapted for recognizing when adults are being pedagogical–which is typically indicated by the same behavioural signs as cooperative communication in general, such things as eye contact, special tones of voice and so forth (and indeed teaching may be seen as one manifestation of human cooperative communication in general). Gergely and Csibra emphasize that when children detect pedagogy, they assume that they are supposed to be learning something otherwise opaque to them that applies to the world in a general way.” Tennie, Claudio, J. Call & M. Tomasello. 2009. “Ratcheting up the ratchet: on the evolution of cumulative culture.” Philosophical Transactions of the Royal Society: B. 364, 2405-2415. P. 2411. Reference is to Gergely, G. & G. Csibra. “Sylvia’s recipe: the role of imitation and pedagogy in the transmission of cultural knowledge.” From Roots of human sociality: culture, cognition, and human interaction. 2006. Enfield, N. & S. Levenson, Eds. Pp. 229-255. Berg Publishers.


“These three additional processes–teaching, social imitation and normativity–represent the contribution of humans’ special forms of cooperation to the process of cultural transmission across generations.” Tennie, Claudio, J. Call & M. Tomasello. 2009. “Ratcheting up the ratchet: on the evolution of cumulative culture.” Philosophical Transactions of the Royal Society: B. 364, 2405-2415. P. 2412.


“When distributing two parts of a task between two actors, we found that each actor represented not only his or her own part of the task but also the other’s part of the task. Compared with performing the same part of the task alone, acting together led to increased demands on executive control, as actors needed to decide whether it was their turn or the other’s turn to act. Finally, using fMRI, we found evidence that acting together led to increased brain activity in areas involved in self-other distinction. Thus, these findings suggest that humans have a strong tendency to take others’ tasks (and the related intentions) into account, while at the same time possessing mechanisms to keep them apart.” Knoblich, Guenther & N. Sebanz. 2008. “Evolving intentions for social interaction: from entrainment to joint action.” Philosophical Transactions of the Royal Society: B. 363, 2021-31. P. 2025.


“Combining simultaneous affordance with joint intentionality allows one to address the issue of how different actors perform non-identical actions upon the same object to achieve a joint goal. For example, the way people lift a two-handled basket depends on whether they lift it alone or together. When alone, a person would normally grasp each handle with one hand. When together, one person would normally grasp the left handle with his/her right hand and the other person would grasp the right handle with his/her left hand. Thus, embedded in joint intentionality, simultaneous affordance changes into a joint affordance, inviting two different actions from two co-actors.” Knoblich, Guenther & N. Sebanz. 2008. “Evolving intentions for social interaction: from entrainment to joint action.” Philosophical Transactions of the Royal Society: B. 363, 2021-31. P. 2026.


“The creation of enduring artefacts opened up a whole new world of affordances and ways of interacting with the world in a direct manner. The resulting fact that artefacts embody socially transmitted knowledge about ways of interacting with objects is hardly ever acknowledged in the research on object perception.” Knoblich, Guenther & N. Sebanz. 2008. “Evolving intentions for social interaction: from entrainment to joint action.” Philosophical Transactions of the Royal Society: B. 363, 2021-31. P. 2027.


“We hypothesize that this new social world, created by rapid cultural adaptation, led to the genetic evolution of new, derived social instincts. Cultural evolution created cooperative groups. Such environments favoured the evolution of a suite of new social instincts suited to life in such groups including a psychology which ‘expects’ life to be structured by moral norms, and that is designed to learn and internalize such norms. New emotions evolved, like shame and guilt, which increase the chance the norms are followed. Individuals lacking the new social instincts more often violated prevailing norms and experienced adverse selection. They might have suffered ostracism, been denied the benefits of public goods, or lost points in the mating game. Cooperation and group identification in inter-group conflict set up an arms race that drove social evolution to ever-greater extremes of in-group cooperation. Eventually, human populations came to resemble the hunter-gathering societies of the ethnographic record.” Boyd, Robert & P. Richerson. 2009. “Culture and the evolution of human cooperation.” Philosophical Transactions of the Royal Society: B. 364, 3281-3288. P. 3286.


“Universal symbiogenesis is the process whereby new entities are introduced because of the interactions between (different) previously independently existing entities. These interactions encompass horizontal mergings and the new entities that emerge because of this are called symbionts. The process is irreversible and discontinuous.” Gontier, Nathalie. 2007. “Universal symbiogenesis: An alternative to universal selectionist accounts of evolution.” Symbiosis. 44, 167-81. Pp. 174-5.


“Green showed that complex systems are isomorphic to networks (nodes linked to edges).” Paperin, Greg, D. Green & S. Sadedin. 2011. “Dual-phase evolution in complex adaptive systems.” Journal of the Royal Society: Interface. 8, 609-629. P. 610. Reference is to Green, David. 1993. Emergent behavioiur in biological systems.” From Complex systems: from biology to computation. Green, David & T. Bossomaier, Eds. IOS Press. Pp. 24-33.


“State spaces of dynamic systems form directed networks in which the states are nodes and the transitions define edges. Thus, system dynamics can be modelled in terms of state-transition networks, allowing the application of graph-theoretical analysis techniques. Sparse connectivity of state-transition networks often implies simple behaviour, while richly connected state-transition networks are associated with chaotic behaviour.” Paperin, Greg, D. Green & S. Sadedin. 2011. “Dual-phase evolution in complex adaptive systems.” Journal of the Royal Society: Interface. 8, 609-629. P. 610.


“But it is perhaps owing to the work of Gould and Lewontin as well as Goodwin that many contemporary biologists are now aware of the fallacy of pure ‘selectionism’, according to which natural selection is the sole, almighty sculptor of all phenotypic traits. Natural constraints in organismal design, emanating from the inescapable laws of chemistry, physics and even mathematics, as well as from history, present prefabricated modules of high complexity for natural selection to choose from. But the complexity itself is not the work of natural selection.” Huang, Sui. 2011. “The molecular and mathematical basis of Waddington’s epigenetic landscape: A framework for post-Darwinian biology?” Bioessays 34: 149-157. P. 150.


“Network dynamics is, then, the coordinated change of the expression levels, x1(t), x2(t), x3(t)..., of all the genes in a GRN [gene regulatory network] as a consequence of the entirety of the regulatory interactions displayed as connections (wiring) in the fixed ‘wiring diagram’. In other words: strictly speaking, when talking about GRNs, there are no ‘dynamic networks’. Instead, ‘network dynamics’ is a legitimate term indicating the characteristic dynamic behaviour exhibited by a given network.

“Thus, it is crucial to distinguish between two separate timescales: network dynamics (the coordinated change of the expression levels xi(t) of the genes of a given network) takes place within one organisms’ lifetime, during which the wiring diagram of that network does not change. By contrast, a change of the structure, or ‘rewiring’ of the network, is the result of a genomic mutation (which may, for instance, affect how a regulatory gene controls its target gene) and occurs at the evolutionary time scale.” Huang, Sui. 2011. “The molecular and mathematical basis of Waddington’s epigenetic landscape: A framework for post-Darwinian biology?” Bioessays 34: 149-157. P. 153.


“Gene network dynamics readily accounts for Waddington’s genetic assimilation, the related Baldwin effect, Neo-Lamarckism and other epigenetic phenomena presented by critics of Neo-Darwinism.” Huang, Sui. 2011. “The molecular and mathematical basis of Waddington’s epigenetic landscape: A framework for post-Darwinian biology?” Bioessays 34: 149-157. P. 156.


“The heterogeneous field of systems biology can be described as the study of the ‘dynamic interactions between components of a living system, between living systems and their interaction with the environment.’” Drack, Manfred & O. Wolkenhauer. 2011. “System approaches of Weiss and Bertalanffy and their relevance for systems biology today.” Seminars in cancer Biology. 21: 150-155. P. 153. Subquote is from Pastori, G., V. Simons & M. Bogaert. 2008. “Systems biology in the European research area.” ERASysBio Partners.


“Systems biology has its roots in new experimental and measurement methods, and aims for a dynamic understanding of the behaviour of mostly small systems. Broadly speaking Weiss and Bertalanffy started from the whole and saw it as a system, while systems biology started from the parts and works on ever more inclusive systems.

“O’Malley and Dupre distinguish two types of approaches. The first one is referred to as ‘systems-theoretic biology,’ which strives for laws or fundamental principles. The second is termed ‘pragmatic systems biology’ of the post-genomic era, where high-tech tools and sophisticated computational models are utilised to study the interplay between the parts (mostly molecules) of a living system.” Drack, Manfred & O. Wolkenhauer. 2011. “System approaches of Weiss and Bertalanffy and their relevance for systems biology today.” Seminars in cancer Biology. 21: 150-155. P. 154.


“The system approach of Weiss and Bertalanffy must be reconciled with approaches in systems biology: the former start with the whole, the latter with the dynamically interacting parts.” Drack, Manfred & O. Wolkenhauer. 2011. “System approaches of Weiss and Bertalanffy and their relevance for systems biology today.” Seminars in cancer Biology. 21: 150-155. P. 154.


“From this discussion, tentative agreement among many geographers seemed to have emerged, at least temporarily, regarding several interrelated ideas about the ontological nature of scale:

“1. Scales (at least those most obviously relevant to social theorists) are socially produced and contested.
“2. Consequently, scales are not known a priori, but must instead be understood according to the processes producing them.
“3. Because many causal processes operate across multiple scales, comprehending most social phenomena will demand a poly-scalar approach.”
Chapura, Mitch. 2009. “Scale, causality, complexity and emergence: rethinking scale’s ontological significance.” Transactions of the Institute of British Geographers. 34: 462-474. P. 463.


“If causality can operate across multiple scales, agency can as well. As with causality, we should expect our perception of agency to be inextricably tied to the resolution at which we observe a panarchic system.

“The immune system illustrates this point well. A variety of specialised cells exist to find and destroy or neutralise pathogens that have entered the body. Observed at the cellular scale, the behaviour of macrophages, neutrophils, and eosinophils etc. appears quite purposeful. They ‘discriminate’ between different pathogens and ‘seek out’ those which they may ‘attack’ and will even alter their ‘attack strategy’ so as to most effectively neutralise the pathogen....

“Without the proper functioning of my immune system I could not exist. Yet I am not consciously aware of its actions, nor do I control the billions of cells constantly at work....

“Of course ‘I’ can influence my immune system, for better or for worse, by eating a healthy diet, taking medications etc. Still, my ability to causally influence my immune system, i.e. my agency, remains incomplete and indirect. Acting to influence my immune system as a whole is not equivalent to directing the complex operations of its components’ seemingly purposeful behaviours. Moreover, my actions cannot be understood in isolation from my semiotic and material milieux. Let us imagine, for example, that, experiencing symptons of illness, I consume an antibiotic. The very possibility of this action results from my participation in socio-material systems larger than ‘me’. Perhaps most saliently, without the narratives, practices and technologies of contemporary biomedicine, including the ‘germ theory of illness’ and the consequent creation of ingestible antibacterial substances, the dissemination of knowledge through medical educational institutions, and the production and sale of my specific antibiotic by a pharmaceutical corporation, my actions would be both unintelligible and impossible....

“Insofar as my immune system is both composite and component, the agency in question is itself a poly-scalar phenomenon.” Chapura, Mitch. 2009. “Scale, causality, complexity and emergence: rethinking scale’s ontological significance.” Transactions of the Institute of British Geographers. 34: 462-474. Pp. 467-8.


“Based on Hutchinson’s general concept, the niche describes the set of abiotic and biotic conditions where a species can persist. Many ecologists favour a concept of the niche based on resources and species interactions at the local scale (i.e. an Eltonian niche concept). On the other hand, more biogeographically oriented ecologists often prefer a concept focusing on the environmental conditions determining the large-scale distribution of species (i.e. a Grinnellian niche concept). I consider these to represent equally valid conceptualizations of different aspects of the general Hutchinsonian niche concept....” Wiens, John. 2011. “The niche, biogeography and species interactions.” Philosophical Transactions of the Royal Society: B. 366: 2336-2350. P. 2336.


“Species range limits are not simply set by unsuitable abiotic and biotic conditions at their range margins, but also by the failure of individuals to adapt to those unsuitable conditions....

“Therefore, to explain large-scale biogeographic patterns, we also need to explain why species do not simply adapt to the ecological conditions at the margins of their geographic ranges and continue expanding their ranges. Without such limits, every species could be everywhere, and again there would be few non-random biogeographic patterns. Niche conservatism is simply the idea that species will retain similar ecological traits over time.” Wiens, John. 2011. “The niche, biogeography and species interactions.” Philosophical Transactions of the Royal Society: B. 366: 2336-2350. P. 2338.


“By contrast, there have been five origins of the long-tailed ecomorph [of snakelike lizards], giving a somewhat clearer picture for this morph. These origins exhibit a biogeographic pattern that is largely consistent with the idea that the origin of one morph in a region restricts subsequent origins of that same ecomorph in the same region....

“Thus, even if competition may constrain the same ecomorph from evolving multiple times in the same region in most regions around the world, competion does not prevent the build-up of many species of the same ecomorph in sympatry within a region (at least at the broad scale)....

“Thus, species interactions seem to limit the rate of body-size evolution, but they do not prevent co-occurrence of species with similar size.” Wiens, John. 2011. “The niche, biogeography and species interactions.” Philosophical Transactions of the Royal Society: B. 366: 2336-2350. P. 2344.


“Space and time are not static containers for material objects. They are ‘dynamic process manifolds’ that incorporate the interaction of determinism and contingency. Scales and scaling are generated by the behavior of the phenomena.” Stallins, J. Anthony. 2012. “Scale, causality, and the new organism-environment interaction.” Geoforum. 3: 427-441. P. 430. Subquote is from Rhoads, B. 2006. “The dynamic basis of geomorphology reenvisioned.” Annals of the Association of American Geographers. 96 (1): 1323-1340.


“In other words, epistemology and ontology recursively influence one another. How the world is verified and observed – whether through the senses or indirectly through technology – contributes to the ontologies that become evident in it.” Stallins, J. Anthony. 2012. “Scale, causality, and the new organism-environment interaction.” Geoforum. 3: 427-441. P. 431.


“Organisms may carry and even reinforce a particular set of omic influences around with them. These dynamics exemplify how the causality of molecular biology has aligned with geography. The landscapes of the cell have a contingent, generative potential.” Stallins, J. Anthony. 2012. “Scale, causality, and the new organism-environment interaction.” Geoforum. 3: 427-441. P. 432.


“Health scholars now speak of the ‘diseaseome’, the interacting networks of genetic, cellular, and social interactions implicated in disease.” Stallins, J. Anthony. 2012. “Scale, causality, and the new organism-environment interaction.” Geoforum. 3: 427-441. P. 437.


“Scale, boundaries, and their ongoing negotiation could be considered a defining feature of life. Organisms remake boundaries to promote and inherit their own version of stability and predictability.” Stallins, J. Anthony. 2012. “Scale, causality, and the new organism-environment interaction.” Geoforum. 3: 427-441. P. 438.


“In this article, we argue that the considerable social differences that exist among different cultures affect not only their beliefs about specific aspects of the world but also (a) their naive metaphysical systems at a deep level, (b) their tacit epistemologies, and (c) even the nature of their cognitive processes–the ways by which they know the world. More specifically, we put forward the following propositions, which we develop in more detail later.

“1. Social organization directs attention to some aspects of the field at the expense of others.
“2. What is attended to influences metaphysics, that is, beliefs about the nature of the world and about causality.
“3. Metaphysics guides tacit epistemology, that is, beliefs about what it is important to know and how knowledge can be obtained.
“4. Epistemology dictates the development and application of some cognitive processes at the expense of others.
“5. Social organization and social practices can directly affect the plausibility of metaphysical assumptions, such as whether causality should be regarded as residing in the field versus the object.
“6. Social organization and social practices can influence directly the development and use of cognitive processes such as dialectical versus logical ones.”
Nisbett, Richard, K. Peng, I. Choi & A. Norenzayan. 2001. “Culture and Systems of Thought: Holistic Versus Analytic Cognition.” Psychological Review. 108 (2): 291-310. Pp. 291-2.


“One of the most remarkable characteristics of the ancient Greeks was the location of power in the individual. Ordinary people developed a sense of personal agency that had no counterpart among the other ancient civilizations....”

“The ancient Chinese provide a particularly valuable contrast to the Greeks. The Chinese counterpart to the Greek sense of personal agency was a sense of reciprocal social obligation or collective agency.” Nisbett, Richard, K. Peng, I. Choi & A. Norenzayan. 2001. “Culture and Systems of Thought: Holistic Versus Analytic Cognition.” Psychological Review. 108 (2): 291-310. P. 292.


“In Confucianism there was no thought of knowing that did not entail some consequence for action.” Munro, D. 1969. The Concept of Man in Early China. Stanford University Press. P. 55. Quoted in Nisbett, Richard, K. Peng, I. Choi & A. Norenzayan. 2001. “Culture and Systems of Thought: Holistic Versus Analytic Cognition.” Psychological Review. 108 (2): 291-310. P. 293.


“The cognitive differences between ancient Chinese and Greeks can be loosely grouped under the heading of holistic versus analytic thought. We define holistic thought as involving an orientation to the context or field as a whole, including attention to relationships between a focal object and the field, and a preference for explaining and predicting events on the basis of such relationships. Holistic approaches rely on experience-based knowledge rather than on abstract logic and are dialectical, meaning that there is an emphasis on change, a recognition of contradiction and of the need for multiple perspectives, and a search for the ‘Middle Way’ between opposing propositions. We define analytic thought as involving detachment of the object from its context, a tendency to focus on attributes of the object to assign it to categories, and a preference for using rules about the categories to explain and predict the object’s behavior. Inferences rest in part on the practice of decontextualizing structure from content, the use of formal logic, and avoidance of contradiction.” Nisbett, Richard, K. Peng, I. Choi & A. Norenzayan. 2001. “Culture and Systems of Thought: Holistic Versus Analytic Cognition.” Psychological Review. 108 (2): 291-310. P. 293.


“A fundamental intellectual difference between the Chinese and the Greeks was that the Chinese held the ‘view that the world is a collection of overlapping and interpenetrating stuffs or substances... [This contrasts] with the traditional Platonic philosophical picture of objects which are understood as individuals or particulars which instantiate or ‘have’ properties’ that are themselves universals.” Nisbett, Richard, K. Peng, I. Choi & A. Norenzayan. 2001. “Culture and Systems of Thought: Holistic Versus Analytic Cognition.” Psychological Review. 108 (2): 291-310. P. 293. Subquote is from Hansen, C. 1983. Language and Logic in Ancient China. University of Michigan Press. P. 30.


“The relationship view versus the rule stance is well illustrated by the difference between the holistic approach to medicine characteristic of the Chinese and the effort to find effective rules and treatment principles in the West. Surgery was common in the West from a very early period because the idea that some part of the body could be malfunctioning was a natural one to the analytic mind. But the idea of surgery was ‘heretical to ancient Chinese medical tradition, which taught that good health depended on the balance and flow of natural forces throughout the body.’” Nisbett, Richard, K. Peng, I. Choi & A. Norenzayan. 2001. “Culture and Systems of Thought: Holistic Versus Analytic Cognition.” Psychological Review. 108 (2): 291-310. P. 294. Subquote is from Hadingham, E. 1994. “The mummies of Xinjiang.” Discover. 15(4): 68-77. P. 77.


“In the Chinese intellectual tradition, there is no necessary incompatibility between the belief that A and not A both have merit. Indeed, in the spirit of the Tao or yin-yang principle, A can actually imply that not A is also the case–the opposite of a state of affairs can exist simultaneously with the state of affairs itself.” Nisbett, Richard, K. Peng, I. Choi & A. Norenzayan. 2001. “Culture and Systems of Thought: Holistic Versus Analytic Cognition.” Psychological Review. 108 (2): 291-310. P. 294.


“We believe that social organization affects cognitive processes in two basic ways: indirectly by focusing attention on different parts of the environment and directly by making some kinds of social communication patterns more acceptable than others.” Nisbett, Richard, K. Peng, I. Choi & A. Norenzayan. 2001. “Culture and Systems of Thought: Holistic Versus Analytic Cognition.” Psychological Review. 108 (2): 291-310. P. 294.


“Thus the results of several studies indicate that East Asians rely less on rules and categories and more on relationships and similarities in organizing their worlds than do Americans. East Asians preferred to group objects on the basis of relationships and similarity, whereas Americans were more likely to group objects on the basis of categories and rules.” Nisbett, Richard, K. Peng, I. Choi & A. Norenzayan. 2001. “Culture and Systems of Thought: Holistic Versus Analytic Cognition.” Psychological Review. 108 (2): 291-310. P. 301.


“Examples of rules about contradiction that have played a central role in the Western intellectual tradition include the following:

“1. The law of identity: A = A. A thing is identical to itself.

“2. The law of noncontradiction: A =/ [not equal] not-A. No statement can be both true and false.

“3. The law of the excluded middle: Any statement is either true of false....

“Peng and Nisbet characterized dialecticism in terms of three principles.

“1. The principle of change: Reality is a process that is not static but rather is dynamic and changeable. A thing need not be identical to itself at all because of the fluid nature of reality.

“2. The principle of contradiction: Partly because change is constant, contradiction is constant. Thus old and new, good and bad, exist in the same object or event and indeed depend on one another for their existence.

“3. The principle of relationship or holism: Because of constant change and contradiction, nothing either in human life or in nature is isolated and independent, but instead everything is related. It follows that attempting to isolate elements of some larger whole can only be misleading.”
Nisbett, Richard, K. Peng, I. Choi & A. Norenzayan. 2001. “Culture and Systems of Thought: Holistic Versus Analytic Cognition.” Psychological Review. 108 (2): 291-310. P. 301. Reference is to Peng, K. & R. Nisbett. 1999. “Culture, dialectics, and reasoning about contradiction.” American Psychologist. 54: 741-54.


“Chinese civilization was based on agriculture, which entailed that substantial cooperation with neighbors was necessary to carry out economic activities in an effective way.... Social scientists since Marx have observed that economic and social arrangements such as these are generally associated with ‘collectivist’ or ‘interdependent’ social orientations as distinguished from ‘individualistic’ or ‘independent’ social orientations that are characteristic of societies with economies based on hunting, fishing, trading, or the modern market economy....

“The Greek ecology conspired against an agrarian base, consisting as it does mostly of mountains descending to the sea. This sort of ecology was more suited to herding and fishing than to large scale agriculture. The sense of personal agency that characterized the Greeks could have been the natural response to the genuine freedom that they experienced in their less socially complex society.” Nisbett, Richard, K. Peng, I. Choi & A. Norenzayan. 2001. “Culture and Systems of Thought: Holistic Versus Analytic Cognition.” Psychological Review. 108 (2): 291-310. P. 303.


“Mere inertia would not result in contemporary differences in the way people think. We propose that systems of thought exist in homeostasis with the social practices that surround them.” Nisbett, Richard, K. Peng, I. Choi & A. Norenzayan. 2001. “Culture and Systems of Thought: Holistic Versus Analytic Cognition.” Psychological Review. 108 (2): 291-310. P. 304.


“Perhaps the most pervasive and important of all practices that operate to sustain the cognitive differences are those having to do with language and writing....”

“1. The basic writing system of Chinese and other East Asian languages has been essentially pictographic. It can be maintained that the Western alphabet is more atomistic and analytic by nature and ‘is a natural tool for classifying and served as a paradigm for codified law, scientific classification, and standardized weights and measures.’

“2. The actual grammar of Indo-European languages encourages thinking of the world as being composed of atomistic building blocks, whereas East Asian languages encourage thinking of the world as continuous and interpenetrating. ‘[R]ather than one-many, the Chinese language motivates a part-whole dichotomy.’

“3. East Asian languages are highly contextual in every sense. Because of their multiple meanings, words must be understood in the context of sentences. Because of the minimal nature of syntax in Sinitic languages, context is important to understanding sentences. In contrast, Heath has shown that language socialization for middle-class American children quite deliberately decontextualizes language. Parents try to make words understandable independent of verbal context and utterances understandable independent of situational context.

“4. Although Western toddlers learn nouns at a much more rapid rate than they learn verbs, the reverse appears to be true for Chinese. Moreover, Western toddlers hear more noun phrases from their mothers, whereas East Asian children hear more verbs.

“5. ‘Generic’ noun phrases–that is, those referring to categories and kinds (e.g., ‘birds,’ ‘tools,’ as opposed to exemplars such as ‘sparrow,’ ‘hammer’)–are more common for English speakers than for Chinese speakers, perhaps because Western languages mark in a more explicit way whether a generic interpretation of an utterance is the correct one.

“6. Consistent with the above findings about category usage, Ji and Nisbett found that English-speaking Chinese used relationships more and categories less when they grouped words in Chinese than when they did so in English.

“Thus there are some good reasons to believe that social practices and cognitive ones maintain each other in a state of equilibrium. Cognitive practices may be highly stable because of their embeddedness in larger systems of beliefs and social practices.” Nisbett, Richard, K. Peng, I. Choi & A. Norenzayan. 2001. “Culture and Systems of Thought: Holistic Versus Analytic Cognition.” Psychological Review. 108 (2): 291-310. Pp. 304-5. First subquote is from Logan, R. 1986. The Alphabet Effect. Morrow. P. 55. Second subquote is from Hansen, C. 1983. Language and Logic in Ancient China. University of Michigan Press. P. vii. Reference on point 3 is to Heath, S. 1982. “What no bedtime story means: Narrative skills at home and school. Language in Society. 11: 49-79. Reference on point 6 is to Ji, L. & R. Nisbett. 2001. Culture, language and Categories. University of Michigan unpublished manuscript.


“The assumption of universality of cognitive processes lies deep in the psychological tradition. We believe that the results discussed here force consideration of the possibility that an indefinitely large number of presumably ‘basic’ cognitive processes may be highly malleable.” Nisbett, Richard, K. Peng, I. Choi & A. Norenzayan. 2001. “Culture and Systems of Thought: Holistic Versus Analytic Cognition.” Psychological Review. 108 (2): 291-310. P. 305.


“It is ironic that, just as our evidence indicates that some cognitive processes are highly susceptible to cultural influence, other investigators are providing evidence that some cognitive content may not be very susceptible to cultural influence. Naive theories of mechanics and physics, naive theories of biology and naive theory of mind appear so early and are apparently so widespread that it seems quite likely that at least some aspects of them are largely innate and resistant to social modification.” Nisbett, Richard, K. Peng, I. Choi & A. Norenzayan. 2001. “Culture and Systems of Thought: Holistic Versus Analytic Cognition.” Psychological Review. 108 (2): 291-310. P. 305.


“Thus, it appears that the assumption that cognitive content is learned and indefinitely malleable and the assumption that cognitive processes are universally the same and biologically fixed may both be quite wrong.” Nisbett, Richard, K. Peng, I. Choi & A. Norenzayan. 2001. “Culture and Systems of Thought: Holistic Versus Analytic Cognition.” Psychological Review. 108 (2): 291-310. P. 306.


“We are urging the view that metaphysics, epistemology, and cognitive processes exist in mutually dependent and reinforcing systems of thought, such that a given stimulus situation often triggers quite different processes in one culture than in another.” Nisbett, Richard, K. Peng, I. Choi & A. Norenzayan. 2001. “Culture and Systems of Thought: Holistic Versus Analytic Cognition.” Psychological Review. 108 (2): 291-310. P. 306.


“The basic premise of world-systems analysis is that historical social systems have lives.” Lee, Richard. 2011. “The Modern World-System: Its Structures, Its Geoculture, Its Crisis and Transformations.” Pp. 27-40. Palumbo-Liu, David, B. Robbins & N. Tanoukhi, Eds. Immanuel Wallerstein and the Problem of the World. Duke University Press. P. 27.


“There was a third set of structures that were just as constitutive of the modern world-system as those in the arenas of production and distribution (the economic), and coercion and decision-making (the political).... The third arena has come to be conceptualized as that of cognition and intentionality, the structures of knowledge.” Lee, Richard. 2011. “The Modern World-System: Its Structures, Its Geoculture, Its Crisis and Transformations.” Pp. 27-40. Palumbo-Liu, David, B. Robbins & N. Tanoukhi, Eds. Immanuel Wallerstein and the Problem of the World. Duke University Press. P. 29.


“From the beginning of the long sixteenth century, the practices of knowledge production took the form of a complex of processes that produced over time an intellectual and institutional hierarchy, a set of structures, within which legitimate knowledge was progressively defined as the ‘other’ of societal and moral values. Values, the foundations on which the humanities have been built, could be based on ‘authorities,’ but in the end were open and contestable, and thus relative, whereas the universal truths produced by what eventually became the sciences were presented as singular and not open to interpretation.” Lee, Richard. 2011. “The Modern World-System: Its Structures, Its Geoculture, Its Crisis and Transformations.” Pp. 27-40. Palumbo-Liu, David, B. Robbins & N. Tanoukhi, Eds. Immanuel Wallerstein and the Problem of the World. Duke University Press. Pp. 29-30.


“The pursuit of objectivity, that is, the view from nowhere that canceled agency and history, that in fact negated subjectivity however conceived, took the form of the progressive privileging of formal rationality. This formal rationality moved disinterested calculation to the fore as a generalized means of instrumental action, to the detriment of substantive rationality, the normative pursuit of specifically situated ends.” Lee, Richard. 2011. “The Modern World-System: Its Structures, Its Geoculture, Its Crisis and Transformations.” Pp. 27-40. Palumbo-Liu, David, B. Robbins & N. Tanoukhi, Eds. Immanuel Wallerstein and the Problem of the World. Duke University Press. P. 30.


“These then are the three analytically distinct but functionally, and existentially, inseparable structural arenas of the modern world-system: the axial division of labor, the interstate system, and the structures of knowledge. They define a singular ‘world.’ And that world is unique in human history in that from the time of its emergence it has expanded to incorporate the entire globe. It is this world, then, that constitutes the unit of analysis of the world-systems perspective.” Lee, Richard. 2011. “The Modern World-System: Its Structures, Its Geoculture, Its Crisis and Transformations.” Pp. 27-40. Palumbo-Liu, David, B. Robbins & N. Tanoukhi, Eds. Immanuel Wallerstein and the Problem of the World. Duke University Press. P. 32.


“‘Utopistics’ is the name Wallerstein gives to the mode of social analysis appropriate for these times; it is a mode of analysis that privileges the differentiation of possible from impossible alternatives for the future. World-systems analysis, as Wallerstein himself has constantly and consistently maintained, has always been an interpretative approach or perspective, always taking into consideration of course that it is the modern world-system that is the unit with which the analyst is concerned, rather than a ‘theory’ to be proven or an explanatory or causal framework grounding prediction.” Lee, Richard. 2011. “The Modern World-System: Its Structures, Its Geoculture, Its Crisis and Transformations.” Pp. 27-40. Palumbo-Liu, David, B. Robbins & N. Tanoukhi, Eds. Immanuel Wallerstein and the Problem of the World. Duke University Press. Pp. 38-9.


“To what extent is evolution ruled by the chance of contingency, versus the necessity of convergence? For Gould all is contingent; for Conway Morris, the question is, would an intelligent biped still have four fingers and a thumb?” Lane, Nick. 2005. Power, Sex, Suicide: Mitochondria and the Meaning of Life. Oxford University Press. P. 23.


“Dolphins and bats developed sonar navigation systems independently, and we invented our own sonar system before we knew that dolphins and bats took soundings in this way. All these systems are exquisitely complex and beautifully adapted to needs, but the fact that each has evolved independently on several occasions implies that the odds against their evolution were not so very great.

“If so, then convergence outweighs contingency, or necessity overcomes chance. As Richard Dawkins concluded, in The Ancestors Tale: ‘I am tempted by Conway Morris’s belief that we should stop thinking of convergent evolution as a coulourful rarity to be remarked and marvelled at when we find it. Perhaps we should come to see it as the norm, exceptions to which are occasions for surprise.’” Lane, Nick. 2005. Power, Sex, Suicide: Mitochondria and the Meaning of Life. Oxford University Press. P. 24. Subquote is from Dawkins, Richard. 2004. The Ancestor’s Tale: A Pilgrimage to the Dawn of Life. Weidenfeld & Nicolson.


“If you divide the luminosity of the sun by its mass, each gram of solar mass yields about 0.0002 milliwatts of energy, which is 0.0000002 joules of energy per gram per second. Now let’s assume that you weigh 70 kg, and if you are anything like me you will eat about 12600 kilojoules (about 3000 calories) per day. Converting this amount of energy averages 2 millijoules per gram per second or about 2 milliwatts per gram–a factor of 10000 greater than the sun. Some energetic bacteria, such as Azotobacter, generate as much as 10 joules per gram per second, outperforming the sun by a factor of 50 million.” Lane, Nick. 2005. Power, Sex, Suicide: Mitochondria and the Meaning of Life. Oxford University Press. P. 67.


“In an average person, ATP is produced at a rate of 9 X 1020 molecules per second, which equates to a turnover rate (the rate at which it is produced and consumed) of about 65 kg every day.” Lane, Nick. 2005. Power, Sex, Suicide: Mitochondria and the Meaning of Life. Oxford University Press. P. 80.


“So the three great energy highways of life, respiration, fermentation, and photosynthesis, all generate ATP, another profound example of the fundamental unity of life.” Lane, Nick. 2005. Power, Sex, Suicide: Mitochondria and the Meaning of Life. Oxford University Press. P. 80.


“In a broad sense, respiration generates energy using proton pumps. The energy released by redox reactions is used to pump protons across a membrane. The proton difference across the membrane corresponds to an electric charge of about 150 mV. This is the proton-motive force, which drives the ATPase motor to generate ATP, the universal energy currency of life.

“Something very similar happens in photosynthesis. In this case, the sun’s energy is used to pump protons across the chloroplast membrane in an analogous fashion to respiration. Bacteria, too, function in the same way as mitochondria, by generating a proton-motive force across their outer cell membrane. For anyone who is not a microbiologist, there is no field of biology more confusing than the astonishing versatility with which bacteria generate energy. They seem to be able to glean energy from virtually anything, from methane, to sulphur, to concrete. This extraordinary diversity is related at a deeper level. In each case, the principle is exactly the same: the electrons pass down a redox chain to a terminal electron acceptor. In each case the energy derived from the redox reactions is used to pump protons across a membrane.

“Such a deep unity is noteworthy not just for its universality, but perhaps even more because it is such a peculiar and roundabout way of generating energy....

“It seems that pumping protons across a membrane is as much a signature of life on earth as DNA. It is fundamental.” Lane, Nick. 2005. Power, Sex, Suicide: Mitochondria and the Meaning of Life. Oxford University Press. P. 91.


“Bacteria have dozens of membrane transporters, many of which use the proton-motive force to pump nutrients into the cell, or waste products out. Instead of using ATP to power active transport, bacteria use protons: they hive off a little energy from the proton gradient to power active transport....

“In short, bacteria are basically proton-powered. Even though the ATP is said to be the universal energy currency, it isn’t used for all aspects of the cell. Both bacterial homeostasis (the active transport of molecules in and out of the cell) and locomotion (flagellar propulsion) depend on proton power rather than ATP.” Lane, Nick. 2005. Power, Sex, Suicide: Mitochondria and the Meaning of Life. Oxford University Press. Pp. 92-3.


“To me, all this [the universality of harnessing proton gradients] hints at the deep antiquity of proton pumping. It is the first and foremost need of the bacterial cell, its life-support machine. It is a deeply unifying mechanism, common to all three domains of life, and central to all forms of respiration, to photosynthesis, and to other aspects of bacterial life, including homeostasis and locomotion. It is in short a fundamental property of life. And in line with this idea, there are good reasons to think that the origin of life itself was tied to the natural energy of proton gradients.” Lane, Nick. 2005. Power, Sex, Suicide: Mitochondria and the Meaning of Life. Oxford University Press. P. 93.


“A single E. coli bacterium weighs about a trillionth of a gram. Seventy-two cell divisions in a day corresponds to an amplification of 272, which is an increase in weight from 10-12 grams to 4000 metric tons. In two days, the mass of exponentially doubling E. coli would be 2664 times larger than the mass of the Earth!

“Luckily this does not happen, and the reason is that bacteria are normally half starved.” Lane, Nick. 2005. Power, Sex, Suicide: Mitochondria and the Meaning of Life. Oxford University Press. P. 114.


“In other words, to thrive, bacteria must replicate their genome faster than the competition, and to do so requires either a smaller genome or more effective energy production.” Lane, Nick. 2005. Power, Sex, Suicide: Mitochondria and the Meaning of Life. Oxford University Press. P. 115.


“Konstantinos Konstantinidis and James Tiedje, at Michigan State University, examined all 115 fully sequenced bacterial genomes. They found that the bacteria with the largest genomes (about 9 or 10 million letters, encoding 9000 genes) dominate in environments where resources are scarce but diverse, and where there is little penalty for slow growth, in particular the soil.” Lane, Nick. 2005. Power, Sex, Suicide: Mitochondria and the Meaning of Life. Oxford University Press. P. 115. Reference is to Konstandinidis, K. & J. Tiedje. “Trends between gene content and genome size in prokaryotic species with larger genomes.” 2004. Proceedings of the National Academy of Sciences USA. 101: 3160-3165.


“Overall, then we see the dynamic balance of two different trends in bacteria–the tendency to gene loss, which reduces the bacterial genome to the smallest possible size in the prevailing conditions, and the accumulation of new genes by means of lateral gene transfer, according to need.” Lane, Nick. 2005. Power, Sex, Suicide: Mitochondria and the Meaning of Life. Oxford University Press. P. 120.


“The more we learn about bacteria, the harder it becomes to make valid generalizations about them. In recent years, we have discovered bacteria with straight chromosomes, with nuclei, cytoskeletons, and internal membranes, all traits once considered to be unique prerogatives of the eukaryotes. One of the few definitive differences that hasn’t evaporated on closer inspection is gene number. Why is it that there are no bacteria with more than 10 million DNA letters, when, as we noted in Chapter 1, the single-celled eukaryote Amoeba dubia has managed to accumulate 670 billion letters–67000 times more letters than the largest bacteria, and for that matter 200 times more than humans? How did the eukaryotes manage to evade the reproductive constraints imposed on bacteria? The answer that I think gets to the heart of the matter was put forward by Tibor Vellai and Gabor Vida in 1999, and is disarmingly simple. Bacteria are limited in their physical size, genome content, and complexity, they say, because they are forced to respire across their external cell membrane.” Lane, Nick. 2005. Power, Sex, Suicide: Mitochondria and the Meaning of Life. Oxford University Press. P. 121. Reference is to Vellai, T. & G. Vida. 1999. “The origin of eukaryotes: The difference between prokaryotic and eukaryotic cells.” Proceedings of the Royal Society of London B: Biological Sciences. 266: 1571-1577.


“So bacteria are under a strong selection pressure for small size whereas eukaryotes are not.... Whereas large size is penalized in bacteria, it actually pays dividends in eukaryotes. For example, large size enables a change in behaviour or lifestyle. A large energetic cell does not have to spend all its time replicating its DNA, but can instead spend time and energy developing an arsenal of protein weapons. It can behave like a fungal cell, and squirt lethal enzymes onto neighbouring cells to digest them before absorbing their juices. Or it can turn predator and live by engulfing smaller cells whole, digesting them inside itself. Either way, it doesn’t need to replicate quickly to stay ahead of the competition–it can simply eat the competition.... A parallel with human society is the larger communities made possible by farming: with more manpower, it was possible to satisfy food production and still have enough people left over to form an army, or invent lethal new weapons. The hunter-gathers [sic] couldn’t sustain such a high population and were bound to lose out to the numerous and specialized competition.” Lane, Nick. 2005. Power, Sex, Suicide: Mitochondria and the Meaning of Life. Oxford University Press. P. 126.


“Among cells, it is interesting that predation and parasitism tend to pull in opposite directions. As a rule of thumb, parasites are regressive in character, and in this regard the eukaryotic parasites are no exception.” Lane, Nick. 2005. Power, Sex, Suicide: Mitochondria and the Meaning of Life. Oxford University Press. P. 126.


“So phagocytosis is made possible by three factors: the ability to change shape (which requires losing the cell wall, then developing a far more dynamic cytoskeleton); sufficiently large size to physically engulf prey; and a plentiful supply of energy.” Lane, Nick. 2005. Power, Sex, Suicide: Mitochondria and the Meaning of Life. Oxford University Press. P. 127.


“In the world of replicating systems, however, a system is stable (in the sense of being persistent and maintaining a presence) if it does react–to make more of itself, and those replicating entities that are more reactive, in that they are better at making more of themselves, are more stable (in the sense of being persistent) than those that aren’t. This is almost a paradox–greater stability is associated with greater reactivity. We therefore call the kind of stability associated with replicating systems a dynamic kinetic stability.” Pross, Addy. 2012. What is Life? How Chemistry Becomes Biology. Oxford University Press. P. 73.


“In 1989, Richard Dawkins alluded to a fundamental law of nature which applies to both the biological as well as the broader physicochemical world: the survival of the most stable.... Once it is evident that matter is not immutable, that it is susceptible to chemical change, then it necessarily follows that matter will tend to be transformed from less persistent to more persistent forms, in other words, from less stable to more stable.” Pross, Addy. 2012. What is Life? How Chemistry Becomes Biology. Oxford University Press. P. 76. Reference is to Dawkins, Richard. 1989. The Selfish Gene. Oxford University Press.


“... Darwinism did bring about a sense of unity within biology, but the troubling consequence of that unification, of enormous value in itself, has been a growing isolation of the subject from the physical sciences to which it must necessarily connect.” Pross, Addy. 2012. What is Life? How Chemistry Becomes Biology. Oxford University Press. P. 117.


“But the chemistry-biology nexus runs much deeper. Ecology is an established branch of biology and would seem to be quite unrelated to chemistry. However, as Gerald Joyce, the remarkable Scripps biochemist, reported in 2009, there is an intimate connection between the two. A key ecological principle, termed the competitive exclusion principle, states: ‘Complete competitors cannot exist’ or, expressed in its positive form: ‘Ecological differentiation is the necessary condition for coexistence.’” Pross, Addy. 2012. What is Life? How Chemistry Becomes Biology. Oxford University Press. P. 128. Reference is to Joyce, Gerald & S. Voytek. 2009. “Niche partitioning in the coevolution of two distinct RNA.” PNAS. 106: 7780-5.


“But here’s the important point. Manfred Eigen and Peter Schuster discovered that the population of replicating RNAs that is generated by this exploration of the fitness landscape does not consist of one single sequence, but rather a population of RNAs of differing sequences, centred around the most successful sequence (termed the wild type) within that population. This population of varied sequences was termed a quasispecies....” Pross, Addy. 2012. What is Life? How Chemistry Becomes Biology. Oxford University Press. P. 143. Reference is to Eigen, M. & P. Schuster. 1979. The Hypercycle: A Principle of Natural Self-Organization. Springer-Verlag.


“Thermodynamic stability is an intrinsic property of any system and is measured in closed systems, in which energy and resources are continually supplied. That makes comparisons of DKS [dynamic kinetic stability] highly problematic....

“Despite the difficulties we’ve discussed in our ability to formally quantify DKS, two crude measures of DKS are actually available. These are the steady-state population number for a given replicating entity and the length of time that the replicating population has managed to maintain itself.” Pross, Addy. 2012. What is Life? How Chemistry Becomes Biology. Oxford University Press. Pp. 145-7.


“In the case of replicating systems and their clear tendency to become transformed into more effective replicating systems, the driving force can now be identified as the drive toward greater DKS. In other words, the biological term ‘maximizing fitness’ is just the biological expression of the more fundamental and more ‘physical concept–maximizing DKS.” Pross, Addy. 2012. What is Life? How Chemistry Becomes Biology. Oxford University Press. P. 148.


“... DNA does not just catalyse its own formation. Through the processes of transcription into messenger RNA and the subsequent translation of the messenger RNA sequence into an amino acid sequence (proteins), it also acts as a catalyst, a catalyst for the synthesis of other materials.... Change the DNA sequence and you end up with a different protein structure. What that means therefore is that DNA is not just an autocatalyst, but also a highly specific catalyst.... A moment’s thought suggests therefore that the term ‘information in its biological context is just ‘specific catalysis’ when considered in a chemical context.” Pross, Addy. 2012. What is Life? How Chemistry Becomes Biology. Oxford University Press. Pp. 151-2.


“We see then that the material world can in some sense be subdivided into two parallel worlds–the ‘regular’ chemical world and the replicative world.” Pross, Addy. 2012. What is Life? How Chemistry Becomes Biology. Oxford University Press. P. 155.


“In fact, the moment some non-metabolic (downhill) [he equates metabolic here with energy-gathering] replicator acquired an energy-gathering capability, could be thought of as the moment that life began. At that moment the replicating system would be free to pursue its replicating ‘agenda’ despite associated energy costs, and significantly, through the incorporation of that energy-gathering system the conflicting requirements of DKS and the Second Law would be accommodated.” Pross, Addy. 2012. What is Life? How Chemistry Becomes Biology. Oxford University Press. P. 158.


“... in regular chemistry matter is stable if it doesn’t react. But in the world of replicating systems, matter is stable (in the sense of being persistent) if it does react, to make more of itself.” Pross, Addy. 2012. What is Life? How Chemistry Becomes Biology. Oxford University Press. P. 163.


“Biology then is just a particularly complex kind of replicative chemistry and the living state can be thought of as a new state of matter, the replicative state of matter, whose properties derive from the special kind of stability that characterizes replicating entities–DKS. That leads to the following working definition of life: a self-sustaining kinetically stable dynamic reaction network derived from the replication reaction.” Pross, Addy. 2012. What is Life? How Chemistry Becomes Biology. Oxford University Press. Pp. 163-4.


“As already stated, in the world of replicators the stability that matters is DKS and not thermodynamic stability. And why is it that those entities that are stable in a DKS sense are invariably unstable in a thermodynamic sense? Simply, because DKS depends on the system continually reacting in order to replicate, to make more of itself, and that actually requires the system to be reactive, to be unstable.” Pross, Addy. 2012. What is Life? How Chemistry Becomes Biology. Oxford University Press. P. 168.


“The topology of the world of replicating systems is inherently divergent.” Pross, Addy. 2012. What is Life? How Chemistry Becomes Biology. Oxford University Press. P. 173.


“What we classify as individual living entities may themselves be thought of as components of a network–the ever-expanding life network.” Pross, Addy. 2012. What is Life? How Chemistry Becomes Biology. Oxford University Press. P. 186.


“So a biosphere that has overwhelmed our planet should not be interpreted in terms of an invasion by billions of individual life forms, but by an ever-expanding living network.” Pross, Addy. 2012. What is Life? How Chemistry Becomes Biology. Oxford University Press. P. 189.


“The many definitions [of “political ecology”] together suggest that political ecology represents an explicit alternative to ‘apolitical’ ecology, that it works from a common set of assumptions, and that it employs a reasonably consistent mode of explanation.” Robbins, Paul. 2004. “Political Ecology: A Critical Introduction. Blackwell Publishing. P. 5.


“The first lesson to draw is that the dominant contemporary accounts of environmental crisis and ecological change (ecoscarcity and modernization) tend to ignore the significant influence of political economic forces. As we shall see, this is to ignore the most fundamental problems in contemporary ecology. The other lesson is that apolitical ecologies, regardless of claims to even-handed objectivity, are implicitly political. It is not so much that political ecology is ‘more political’ than these other approaches to the environment. Rather it is simply more explicit in its normative goals and more outspoken about the assumptions from which its research is conducted.” Robbins, Paul. 2004. “Political Ecology: A Critical Introduction. Blackwell Publishing. P. 11.


“Indeed, as political ecologists continually emphasize, the environment is not a malleable thing outside of human beings, or a tablet on which to write history, but instead a produced set of relationships that include people, who, more radically, are themselves produced.” Robbins, Paul. 2004. “Political Ecology: A Critical Introduction. Blackwell Publishing. P. 209.


“For geographers, this process of categorization (binary or otherwise) is of particular interest because basic themes within our particular subject matter – environment, space and place – are frequently used in creating collective and personal identities. Many of us identify with places, at a variety of scales – from our home, through our street and neighbourhood, town and region, up to a nation-state. In part, we are who we are because of what places we choose to associate with.” Cloke, Paul & R. Johnston. “Deconstructing Human Geography’s Binaries.” From Cloke, Paul & R. Johnston, Eds. 2005. Spaces of Geographical Thought. SAGE Publications. Pp. 1-20. P. 2.


“The aim of this book is to argue that the mind-body problem is not just a local problem, having to do with the relation between mind, brain, and behavior in living animal organisms, but that it invades our understanding of the entire cosmos and its history.” Nagel, Thomas. 2012. Mind and Cosmos: Why the Materialist Neo-Darwinian Conception of Nature is Almost Certainly False. Oxford University Press. P. 3.


“As the plank-moving studies illustrate, affordances are different for every kind of perception-action system, whether that is a system of an individual completing a task with only their body, or an individual completing a task with tools, or pairs of individuals completing a task. Research on tool use in solo action offers an important demonstration of the consequences of embedding for the individual. When we take up a tool, for instance, it becomes a part of our perception-action system, extending our body’s boundaries and allowing us to capitalize on other affordances of our environment.” Marsh, Kerry, L. Johnston, M. Richardson & R. Schmidt. 2009. “Toward a radically embodied, embedded social psychology.” European Journal of Social Psychology. 39: 1217-1225. Pp.. 1218-9.


“We hypothesize that becoming a temporary unit of social action with another person also involves creation of a new perception-action system with new capabilities. The individual becomes embedded in a social unit, with a reality of its own. By engaging in joint perception or joint action with another, our actions serve to impact and define the social unit of which we are a part, and in turn our actions are constrained and channeled by participation in this relationship or group.” Marsh, Kerry, L. Johnston, M. Richardson & R. Schmidt. 2009. “Toward a radically embodied, embedded social psychology.” European Journal of Social Psychology. 39: 1217-1225. P. 1219.


“Importantly, the patterns of behavior that occur between two individuals, rocking independently in separate chairs–with no mechanical linkages, only informational links–obey the same universal dynamics as coupled components (arms) within a single body.” Marsh, Kerry, L. Johnston, M. Richardson & R. Schmidt. 2009. “Toward a radically embodied, embedded social psychology.” European Journal of Social Psychology. 39: 1217-1225. P. 1219.


“The challenge to the normal way of thinking is to take rather seriously that causality resides at the level of the interaction, rather than in our head.” Marsh, Kerry, L. Johnston, M. Richardson & R. Schmidt. 2009. “Toward a radically embodied, embedded social psychology.” European Journal of Social Psychology. 39: 1217-1225. P. 1220.


“Someone touches us on the shoulder, calls our name, or a passing stranger glances at us, and this is a catalyst, a rapid switching mechanism for switching from an autonomous individual mode of action to being pulled temporarily into a ‘social eddy’ with another, a dynamic patterning, a dance that includes rich nonverbal (and perhaps verbal) behavior, responsivity, mutuality, and coordination of behavior.” Marsh, Kerry, L. Johnston, M. Richardson & R. Schmidt. 2009. “Toward a radically embodied, embedded social psychology.” European Journal of Social Psychology. 39: 1217-1225. P. 1222.


“Converging evidence from neurophysiology, neuropsychology and experimental psychology suggests that there are multiple representations of space, each with its own properties, but in a simplified manner, we can distinguish between three spatial representations originating from the body: the space covering the surface of our body (personal space), the space immediately surrounding our body (peripersonal space) and the space that falls far away from our body and it is unreachable by a simple arm movement (extrapersonal space).” Costantini, Marcello, E. Ambrosini, G. Tieri, C. Sinigaglia & G. Committeri. 2010. “Where does an object trigger an action? An investigation about affordances in space.” Exp Brain Research. 207:95-103. P. 96.


“Another feature is equally important: systems are not inherently closed. They have a relative stability and thus an organizational closure, but at the same time they are open for influences from their surroundings.” Rosslenbroich, Bernd. 2011. “Outline of a concept for organismic systems biology.” Seminars in Cancer Biology. 21: 156-164. P. 158.


“... a system is relatively closed as well as relatively open at the same time. Coincidences of this type, where two opposing principles are present simultaneously, are a typical feature of organic life and can be found in many other examples as well.” Rosslenbroich, Bernd. 2011. “Outline of a concept for organismic systems biology.” Seminars in Cancer Biology. 21: 156-164. P. 158.


“Similarly, we now understand that in terms of both numbers and genetic diversity, the microbial world not only dominates the biosphere but is almost impossible to sample properly. This point is, of course, even more emphatically made if one includes in this calculation the virosphere, which we regard as an intrinsic aspect of the microbial world, not to be separated from it.” Woese, Carl & N. Goldenfeld. 2009. “How the Microbial World Saved Evolution from the Scylla of Molecular Biology and the Charybdis of the Modern Synthesis.” Microbiology and Molecular Biology Reviews. 73(1):14-21. P. 16.


“Biology is a study, not in being, but in becoming.... A discipline whose perspective is that of classical 19th century physics is inherently incapable of dealings with the problems of a nonlinear world, which is nonreductionist, non-deterministic (acausal), and works in terms of fields and emergent properties, not a static world of particles with linear relationships among them....

“Thus, in the early decades of the 20th century, molecular biology’s fundamental reductionist perspective was innocuous–especially when there were many problems that could benefit from a (simple) reductionist approach. It was another thing altogether when molecular biology began reconceptualizing biology in an exclusively reductionist fashion.” Woese, Carl & N. Goldenfeld. 2009. “How the Microbial World Saved Evolution from the Scylla of Molecular Biology and the Charybdis of the Modern Synthesis.” Microbiology and Molecular Biology Reviews. 73(1):14-21. P. 17.


“We have seen that molecular biology, the dominant biological discipline of the time, did not even recognize the evolutionary process as a scientific problem. Given its overview, molecular biology took evolution simply as biological epiphenomenology, ‘historical accident’–which means that evolutionary considerations have no bearing whatsoever on any fundamental understanding of living systems.” Woese, Carl & N. Goldenfeld. 2009. “How the Microbial World Saved Evolution from the Scylla of Molecular Biology and the Charybdis of the Modern Synthesis.” Microbiology and Molecular Biology Reviews. 73(1):14-21. P. 18.


“What makes the treatment of evolution by biologists of the last century insufferable scientifically is not the modern synthesis per se. Rather, it is the fact that molecular biology accepted the synthesis as a complete theory unquestioningly–thereby giving the impression that evolution was essentially a solved scientific problem with its roots lying only within the molecular paradigm.” Woese, Carl & N. Goldenfeld. 2009. “How the Microbial World Saved Evolution from the Scylla of Molecular Biology and the Charybdis of the Modern Synthesis.” Microbiology and Molecular Biology Reviews. 73(1):14-21. P. 18.


“Despite the growing consensus in many disciplines about the important role that the material world plays in the structuring of human cognitive operations the precise question of the causal efficacy of things in the human cognitive system, has, surprisingly, evoked limited collaboration between archaeology, anthropology and neuroscience. This attitude of what we may call ‘epistemic neglect of the object’, is symptomatic of a more general tendency in the mainstream cognitive sciences to leave material culture outside the cognitive equation proper. Even embodied and situated perspectives in cognitive science, which explicitly recognize the intrinsic relationship between brain/body and environment, often seem oblivious to the actual material medium that envelops and shapes our lives.” Malafouris, Lambros. 2010. “The brain-artefact interface (BAI): a challenge for archaeology and cultural neuroscience.” SCAN. 5, 264-273. P. 265.


“Lastly, new imaging data show that neural circuits supporting stone toolmaking partially overlap with language circuits, which suggests that these behaviors share a foundation in more general human capacities for complex, goal-directed action and are likely to have evolved in a mutually reinforcing way.” Malafouris, Lambros. 2010. “The brain-artefact interface (BAI): a challenge for archaeology and cultural neuroscience.” SCAN. 5, 264-273. P. 267.


“However, as Ludwik Fleck observed in 1935, ‘every new finding raises at least one new problem: namely an investigation of what has just been found’. New knowledge, in turn, allows for new options without delivering secure criteria for how these new options need to be handled.

“The contemporary explosion of knowledge or the observation that our current age is the beginning of a knowledge society thus has a little remarked on corollary: new knowledge also means more ignorance. Thus, surprising events will occur more frequently and become more and more likely. If this is the case, handling ignorance and surprise becomes one of the distinctive features of decision making in contemporary society.” Gross, Matthias. 2010. Ignorance and Surprise: Science, Society, and Ecological Design. MIT Press. P. 1. Reference is to Fleck, Ludwick. 1935 (1979). Genesis and Development of a Scientific Fact. University of Chicago Press. P. 51.


“I believe that both interpretations–the one that claims that precaution means paralysis and the one that says that precaution must be a key feature in regulatory politics–have not dealt seriously with the importance of ignorance and surprise. The critics ascribe a ‘better safe than sorry’ attitude to the precautionary principle and recommend turning back to cost-and-benefit analyses and risk assessments based on known facts, thus ignoring the inevitability of uncertainty and ignorance. Proponents of the precautionary principle have not yet delivered any effective strategies for determining what exactly is to be done when decisions have to be made promptly and risk assessments or computer models cannot help in any meaningful way.” Gross, Matthias. 2010. Ignorance and Surprise: Science, Society, and Ecological Design. MIT Press. P. 4.


“Hans-Jorg Rheinberger has argued that what makes the physical, technical, and procedural basis for an experiment work is that it is deliberately arranged to generate surprises.” Gross, Matthias. 2010. Ignorance and Surprise: Science, Society, and Ecological Design. MIT Press. P. 5.


“In the following, a surprising event is understood as an occurrence that triggers awareness of one’s own ignorance.” Gross, Matthias. 2010. Ignorance and Surprise: Science, Society, and Ecological Design. MIT Press. P. 5.


“Although there has been no consensus on a full definition for the word ‘niche’, a general description of the concept illustrates the key underlying idea: a niche is a (hyper-) volume in a set of dimensions which expresses the capability of a species to exploit resources.” Wennekes, Paul, J. Rosindell & R. Etienne. 2012. “The Neutral–Niche Debate: A Philosophical Perspective.” Acta Biotheor. 60:257-271. P. 261.


“Each species has a fundamental niche, which is the n-dimensional space in which they can theoretically survive. However, most species will have competitors whose niches may partially or wholly overlap their own. The species that is more efficient in the overlapping part of their fundamental niches will, in a process which is known as niche partitioning or competitive exclusion, attempt to exclude the other species by outcompeting them. This can lead to two scenarios; either one species will win and the other will go extinct, or, in a reaction to the evolutionary pressure, one or both species may undergo a change in specialization away from the contested part (character displacement), effectively reducing the niche-overlap between the two species, thus avoiding extinction. The realized niche of a species is the part of their fundamental niche that they actually occupy.” Wennekes, Paul, J. Rosindell & R. Etienne. 2012. “The Neutral–Niche Debate: A Philosophical Perspective.” Acta Biotheor. 60:257-271. Pp. 261-2.


“The biosphere is dominated, in terms of both physical abundance and genetic diversity, by primitive life forms, prokaryotes and viruses. These ubiquitous organisms evolve in ways unimaginable and unforeseen in classical evolutionary biology.... We now think of the entire world of prokaryotes as a single, huge network of interconnected gene pools, and the notion of the prokaryotic pangenome is definitely here to stay.” Koonin, Eugene. 2009. “The Origin at 150: is a new evolutionary synthesis in sight?” Trends in Genetics. Vol 25 (11) 473-5. P. 473.


“In general, the species concept does not apply to prokaryotes and is of dubious validity for unicellular eukaryotes as well.” Koonin, Eugene. 2009. “The Origin at 150: is a new evolutionary synthesis in sight?” Trends in Genetics. Vol 25 (11) 473-5. P. 474.


“Like the universal genetic code, the Krebs cycle and the ATP, chemiosmosis is universal to all life, and appears to have been a property of the last universal common ancestor, LUCA.” Lane, Nick. 2009. Life Ascending: The Ten Great Inventions of Evolution. W.W. Norton & Co. P. 31.


“And the great advantage of a gradient is that a single reaction can be repeated again and again just to generate one single ATP molecule. If one particular reaction releases a hundredth of the energy needed to generate one ATP, the reaction is simply repeated a hundred times, building up the gradient step by step until the proton reservoir is big enough to generate a single ATP. Suddenly the cell can save up; it has a pocket full of small change.” Lane, Nick. 2009. Life Ascending: The Ten Great Inventions of Evolution. W.W. Norton & Co. P. 32.


“Acids are defined in terms of protons: an acid is rich in protons, an alkali poor. So bubbling alkaline fluids into acidic oceans produces a natural proton gradient. In other words the mineral cells in Russell’s alkaline vents are naturally chemiosmotic.” Lane, Nick. 2009. Life Ascending: The Ten Great Inventions of Evolution. W.W. Norton & Co. P. 32.


“This paints an extraordinary portrait of the last common ancestor of all life on earth. If Martin and Russell are right–and I think they are–she was not a free-living cell but a rocky labyrinth of mineral cells, lined with catalytic walls composed of iron, sulphur and nickel, and energised by natural proton gradients. The first life was porous rock that generated complex molecules and energy, right up to the formation of proteins and DNA itself.” Lane, Nick. 2009. Life Ascending: The Ten Great Inventions of Evolution. W.W. Norton & Co. P. 33. Reference is to Russell, M.J., & W. Martin. 2004. “The rocky roots of the acetyl CoA pathway.” Trends in Biochemical Sciences. 29:358-63.


“Predation escalates size, of course, driving arms races between predator and prey.... With oxygen, then, predation pays; and with predators size pays. So oxygen makes large organisms not just feasible but also probable.”

“It also helps build them. The protein that gives animals their tensile strength is collagen. This is the main protein of all connective tissues, whether calcified in bones, teeth and shells, or ‘naked’ in ligaments, tendons, cartilage and skin. Collagen is by far the most abundant protein in mammals, making up a remarkable 25 per cent of total body protein.... Collagen is composed of some unusual building blocks, which require free oxygen to form cross-links between adjacent protein fibres, giving the overall structure a high tensile strength. The requirement for free oxygen means that large animals, protected with shells or strong skeletons, could only evolve when atmospheric oxygen levels were high enough to support collagen production ...

“Is oxygen necessary to give strength or just a random ingredient that happened to be incorporated and then forever remained part of the recipe? We don’t really know, but it’s striking that higher plants, too, need free oxygen to form their structural support, in the shape of the immensely strong polymer lignin, which gives wood its flexible strength. Lignin is formed in a chemically haphazard way, using free oxygen to form strong cross-links between chains.” Lane, Nick. 2009. Life Ascending: The Ten Great Inventions of Evolution. W.W. Norton & Co. Pp. 62-3.


“... there is around 26,000 times more ‘dead’ organic carbon trapped in the earth’s crust than in the entire living biosphere. Each atom of carbon is the antithesis of a molecule of oxygen in the air.... So far, despite our vainglorious efforts to burn all the known reserves of fossil fuels, we have lowered the oxygen content of the air by a mere two or three parts per million, or about 0.001 per cent.” Lane, Nick. 2009. Life Ascending: The Ten Great Inventions of Evolution. W.W. Norton & Co. P. 64.


“Once they had adopted the phagocytic way of life, eukaryotes were no longer bound by the endless drudgery of bacterial life, and specifically the need to streamline themselves for fast replication. Eukaryotes didn’t have to compete with bacteria; they could just eat them and digest them within, at their leisure. Freed from the need for speed, those first eukaryotes could accumulate DNA and genes, giving them scope for enormously greater complexity. Jumping genes helped swell eukaryotic genomes up to thousands of times the normal bacterial size.” Lane, Nick. 2009. Life Ascending: The Ten Great Inventions of Evolution. W.W. Norton & Co. P. 116.


“What is startling is that meiosis begins by duplicating all the chromosomes, to give four sets per cell. These are then mixed and matched–the technical term is ‘recombined’–to generate four entirely new chromosomes, each one taking a bit from here and a bit from there. Recombination is the real heart of sex.” Lane, Nick. 2009. Life Ascending: The Ten Great Inventions of Evolution. W.W. Norton & Co. P. 126.


“The great advantage of sex is that it allows good genes to recombine away from the junk residing in their genetic backgrounds, while at once preserving a great deal of the hidden genetic variability in populations.” Lane, Nick. 2009. Life Ascending: The Ten Great Inventions of Evolution. W.W. Norton & Co. P. 139.


“Intriguingly, the fossil record points to a rather abrupt change in complexity following the greatest mass extinction in the history of our planet, that at the end of the Permian period, 250 million years ago, when 95 per cent of all species are thought to have vanished. After this great extinction wiped the slate clean, nothing was ever the same again.

“The world was complex enough before the Permian, of course. On land there were giant trees, ferns, scorpions, dragonflies, amphibians, reptiles. The seas were full of trilobites, fish, sharks, ammonites, lampshells, sea lilies and corals. A cursory inspection might suggest that some of these ‘types’ have changed, but that the ecosystems were not so very different; yet a detailed inventory says otherwise.

“The complexity of an ecosystem can be estimated by the relative number of species: if a handful of species dominate, and the rest carve out a marginal existence, then the ecosystem is said to be simple. But if large numbers of species coexist together in similar numbers, then the ecosystem is far more complex, with a much wider web of interactions between species. By totting up the number of species living together at any one time in the fossil record, it’s possible to come up with an ‘index’ of complexity, and the results are somewhat surprising. Rather than a gradual accrual of complexity over time, it seems there was a sudden gearshift after the great Permian extinction. Before the extinction, for some 300 million years, marine ecosystems had been split roughly fifty-fifty between the simple and complex; afterwards, complex systems outweighed simple ones by three to one, a stable and persistent change that has lasted another 250 million years to this day. So rather than gradual change there was a sudden switch. Why?

“According to palaeontologist Peter Wagner, at the Field Museum of Natural History in Chicago, the answer is the spread of motile organisms. The shift took the oceans from a world that was largely anchored to the spot–lampshells, sea lilies, and so on, filtering food for a meagre low-energy living–to a new, more active world, dominated by animals that move around, even if as inchingly as snails, urchins and crabs. Plenty of animals moved around before the extinction, of course, but only afterwards did they become dominant. Why this gearshift took place after the Permian mass extinction is unknown, but might perhaps relate to the greater ‘buffering’ against the world that comes with a motile lifestyle. If you move around, you often encounter rapidly changing environments, and so you need greater physical resilience. So it could be that the more motile animals had an edge in surviving the drastic environmental changes that accompanied the apocalypse. The doomed filter feeders had nothing to cushion them against the blow.” Lane, Nick. 2009. Life Ascending: The Ten Great Inventions of Evolution. W.W. Norton & Co. Pp. 145-6.


“So motility brings with it a need to deal with rapidly changing environments, more interactions between plants and other animals, new lifestyles like predation, and more complex ecosystems. All these factors encouraged the development of better senses and a faster pace of evolution, simply to keep up, not just among animals, but among many plants too.” Lane, Nick. 2009. Life Ascending: The Ten Great Inventions of Evolution. W.W. Norton & Co. P. 147.


“Sight is quite a rarity. Eyes are absent, at least in a conventional sense, from the plant kingdom, as well as from the fungi, algae and bacteria. Even in the animal kingdom eyes are not at all common property. There are said to be thirty-eight fundamentally different models of body plan – phyla – in the animal kingdom, yet only six of them ever invented true eyes....

“If we add them all up, we find that 95 per cent of all animal species have eyes: the handful of phyla that did invent eyes utterly dominates animal life today.” Lane, Nick. 2009. Life Ascending: The Ten Great Inventions of Evolution. W.W. Norton & Co. P. 172.


“For now let’s just note that sight gives far more information about the world than smell, hearing, or touch possibly can, for the earth is drenched in light, and we can hardly avoid being seen. Many of the most marvellous adaptations of life are a response to being seen, whether strutting for sex in the case of a peacock or a flower, parading the great armoured plates of a stegosaurus, or careful concealment in the world of a stick insect.” Lane, Nick. 2009. Life Ascending: The Ten Great Inventions of Evolution. W.W. Norton & Co. P. 173.


“The human retina consumes even more oxygen than the brain, per gram, making it the most energetic organ in the body,...” Lane, Nick. 2009. Life Ascending: The Ten Great Inventions of Evolution. W.W. Norton & Co. P. 175.


“The cost of living for a mammal in the cold is a hundred times that of a lizard. Even in temperate conditions, say around 20° C, a pleasant spring day in much of Europe, the gap is huge, around thirtyfold. To support such a prodigious metabolic rate, the mammal must burn up thirty times more food than a reptile. It must eat as much in a single day, every single day, as a lizard eats in a whole month. Given that there’s no such thing as a free lunch, that’s a pretty serious cost.

“So there it is: the cost of being a mammal or a bird starts at around ten times the cost of being a lizard and is often far higher. What do we get for our expensive lifestyle? The obvious answer is niche expansion. While hot blood may not pay in the desert, it enables nocturnal foraging, or an active existence over winter in temperate climates, both of which are denied to lizards.” Lane, Nick. 2009. Life Ascending: The Ten Great Inventions of Evolution. W.W. Norton & Co. P. 209.


“The onset of hot-bloodedness in the development of animals today lends support to the idea that hot blood is more about turbocharging visceral organs than heat production.” Lane, Nick. 2009. Life Ascending: The Ten Great Inventions of Evolution. W.W. Norton & Co. P. 214.


“It is then most significant that one of the things that the cosmologies of Plato and Newton have in common is that they lack the notion of evolution, in either the biological or the astronomical sense. Stuck with a universe in which past and future cannot fundamentally differ from each other, we see how those things that we now understand as born and bound in time are instead set as timeless oppositions. Thus, both Plato’s myth [The Statesman, pilot of the universe with hand on the rudder] and Newton’s universe are framed in terms of a duality in which the intelligence of a god who exists outside the universe is forever opposed to the imagined tendency of material things to disintegrate to chaos.” Smolin, Lee. 1997. The Life of the Cosmos. Oxford University Press. P. 143.


“In biology textbooks one reads that a living thing is something that shares the characteristics of metabolism, reproduction, and growth. There are, however, two problems with such a definition. The first is that it is not very insightful; it tells us nothing, for example, about why those characteristics are often found together, or about why things with these characteristics exist in the universe. The second problem is that any definition of life that may be applied to a single organism gives the false impression that a solitary living thing could exist in our universe.”

“In the first chapter, we examined the image of the warm, living Earth in the midst of a cold and dead cosmos, and we have since seen the extent to which this is an absurd idea. The same problems hold, even more strongly and clearly for the notion of a living thing in isolation. Certainly on Earth we never find a tree or an animal living alone on an otherwise dead island. Instead, we know of no place on or even near the surface of the Earth that does not contain life of some kind. Thus, the one planet we know which is not dead is not just a rock decorated with life in a few corners. It is a planet teeming with life.

“Of course, we don’t have access to any other life except on our own planet. But it is impossible that a single individual of any of the species with which we are familiar could live alone on any planet. It is almost equally difficult to imagine a planet populated by only one species. The reason is that each species plays a role in the great cycles that circulate material around the biosphere. We breath in oxygen and exhale carbon monoxide. Plants do the opposite, freeing the oxygen in carbon dioxide for our later use. We could not survive very long without plants for the elementary reason that all of the free oxygen now in the biosphere was rather recently produced by them.

“This holds, not only for the oxygen we breath, but for the nutrients we eat, and for the other gases in the atmosphere: the nitrogen, carbon, and so forth. The life of any plant or animal cannot then be usefully conceived, except as embedded in the great system of the biosphere. This is particularly true if what we are interested in is a conception of life that could be useful for our project of understanding why life exists from the framework of physics and cosmology.” Smolin, Lee. 1997. The Life of the Cosmos. Oxford University Press. Pp. 145-6.


“For example, when a species becomes extinct, those that eat it are in big trouble, as are those that live in it, while those it eats are suddenly in a different situation. In many cases, this is all; only a few other species are affected by the extinction. But in some cases many species will be affected, for example, if that species produced a waste product, like oxygen, that is necessary for the life of many other species.

“By modeling the effects of mutations and extinctions in such a complex network of relationships, Bak, Kauffman, and others have found that collective effects dominate the patterns of extinction and successful mutations, so that the evolution of the biosphere can only be understood as a single, coupled system.” Smolin, Lee. 1997. The Life of the Cosmos. Oxford University Press. P. 150.


“We may then turn to the first part of the definition [of life: “A living system is a self-organized non-equilibrium system ...”] and ask what conditions are necessary for the universe to contain self-organized, non-equilibrium systems. The answer is that either their existence is transitory, so that sooner or later the whole universe will come to equilibrium, or the universe as a whole must itself be a self-organized, non-equilibrium system. The reason for this is that it is impossible to have a self-organized, non-equilibrium system which exists permanently inside of a larger system which is itself in thermal equilibrium. It is not hard to see why. Part of the definition of a self-organized, non-equilibrium system is that it has a flow of energy through it. The energy enters the system at one point from the outside, which we may call the source, and leaves at another, which we may call the sink. Now, it follows from elementary ideas about heat that the source and the sink must be at different temperatures; in particular the source must be hotter than the sink. This is because of the simple fact that heat flows from hot regions to cold regions.

“This means that the source and the sink cannot themselves be parts of a single system in thermal equilibrium because, if they were, they would be at the same temperature and no heat would flow. As the source and the sink are parts of the environment surrounding our self-organized, non-equilibrium system, this means that the environment cannot itself be in equilibrium.”

“This is the case with every living organism on Earth. We live because we can take in energy that is at a higher temperature than the heat that we relinquish to our environments.” Smolin, Lee. 1997. The Life of the Cosmos. Oxford University Press. P. 158.


“We look around and see that our universe is beautiful and that, with its enormous variety of phenomena spread out over every scale from the nuclear to the cosmological, it resembles more the ancient city than the modern shopping center. Could this beautiful universe be the result of the construction of a single planner? Certainly, it is difficult to imagine any human planner choosing the laws of nature carefully enough to result in a universe with such a variety of phenomena. Indeed, as we saw in earlier chapters, to choose the laws of physics so that such a variety of phenomena results, let alone so that the universe is not simply a gas in equilibrium, requires that many parameters be finely tuned, some to as many as sixty decimal places. Of course, God is imagined to have infinite power, and we cannot limit what might be possible for him. But exactly for this reason, if we believe in the picture of a universe made by the providential choice of an eternal and fundamental theory, must we not also believe in God?

“On the other hand, perhaps for the first time in human history, we know enough to imagine how a universe like ours might have come to be without the infinite intelligence and foresight of a god. For is it not conceivable that the universe is as we find it to be because it made itself; because the order, structure and beauty we see reflected at every scale are the manifestations of a continual process of self-organization, of self-tuning, that has acted over very long periods of time? If such a picture can be constructed, it may be possible to understand the fact that the universe has structure and phenomena at every scale, not as some enormous accident or coincidence requiring the fundamental theory to be so finely tuned, but merely as evidence that the maker of the universe is nothing more or less than the random and statistical process of its own self-organization.” Smolin, Lee. 1997. The Life of the Cosmos. Oxford University Press. P. 176.


“How is it possible for us to discover any truth that is true always? The only reasonable answer to this question, which really just emphasizes Kant’s point in a different way, is that mathematical and logical truths may be true for all time because they are not really about anything that exists. They are only about possible relations. Thus, it is a mistake–a kind of category error–to imagine that the theorems of mathematics are about some ‘other’ or ‘Platonic’ realm that exists outside of time. The theorems of mathematics are outside of time because they are not about the real. On the contrary, anything that exists must exist inside of time.

“If we insist that existence means existence bounded by time, we can reverse the trap that the old metaphysics imposed on us, in which all that really exists–the true Being–exists only eternally, while those things that exist in time are only appearances, only faint reflections of what is really real. If existence requires time, then there is no need and no place for Being, for the absolute and transcendent Platonic world. That which exists is what we find in the world. And that which exists is bound by time, because to exist something must be created by processes that act in time to create the novel out of what existed before.” Smolin, Lee. 1997. The Life of the Cosmos. Oxford University Press. P. 188.


“To be bothered by this [liar’s paradox, Goedel’s theorem], we must think of mathematics as some timeless reality, such that anything that is true about it is true forever. If we stick to the view that logic and mathematics are about nothing, and that all that exists is bound in time, then these difficulties may be seen in a different light. If we construct a real system, say a computer or a living thing, that is capable of self-reference, then what we have done is to construct a feedback loop. Self-reference in a real entity must exactly be the possibility that its state at the next moment is a function of its state now. In a real system, which can have only one state at a time, self-reference must be understood as something that happens in time.

“As we saw in the last few chapters, feedback is an essential element of any process of self-organization. And processes of self-organization are what gives our world structure. Thus, self-reference, which leads to paradox when we try to envision knowledge as timeless, leads instead to structure and organization when it is realized as a real process that acts over time in the real world.” Smolin, Lee. 1997. The Life of the Cosmos. Oxford University Press. P. 189.


“Thus, belief in a final theory shares with a belief in a god the idea that the ultimate cause of things in this world is something that does not live in the world but has an existence that, somehow, transcends it. This is why the belief in god and belief in the existence in a final theory are both related to the metaphysical idea that what is really true about the world is true about a timeless transcendent realm and not about the world of the things we see around us.

“There is still another issue that arises if we aim to give up on the idea that the goal of physics is the discovery of a final theory, in which the properties of the elementary particles are fixed by first principles, independent of the history of the universe. For it might seem that if we give up on the idea that there is a single final theory, we may also be giving up on the possibility of gaining a complete and objective description of the world. Is it possible then to have objective knowledge, if that knowledge does not tell us how the world of appearances is constructed out of what ultimately exists?

“I would like to argue that the answer to this question is, in fact, yes. It is, to begin with, not really the case that the aspiration to discover the final theory, or apprehend the true Being, has really helped the project of gaining objective knowledge. It is true that it is often presumed that objective knowledge, to the extent that it is possible, is knowledge of some absolute reality that lies beyond the subjective appearances. But it seems to me that to equate the world of appearances with the subjective is to make a kind of category error. What we have given to us, from which we will deduce all possible knowledge, is nothing other than the appearances of the world. If objective knowledge exists at all, must it not be knowledge about the world of appearances? Must it not then be possible to construct or deduce any real knowledge from the appearances alone? Do we, as observers who live in the world, have any other choice?

“The idea that objective knowledge must be about something other than the appearances carries with it a presumption that it is possible to imagine a view or a picture of the world that is somehow more true than the views of human observers. Such a view would not be limited to the incomplete and incompletely reliable views of observers present in the world. It might be a view of the world in its entirety, as it is.

“But such a view cannot be the view of any real observer living in the world. It could only be the view of some imagined being who is outside the world. In this way the idea that there is a world behind the appearances, an absolute Being, a world as it is, carries with it, in every context in which it appears, the dream that there is a view of the world from outside of it. And if one subscribes to this dream, then it is clear that the ultimate justification for objective knowledge must lie not in any incomplete view from inside the world, but in this all encompassing view from the outside. Thus, if one believes in the possibility of this view from outside the world, one is led to identify objective knowledge with knowledge of the absolute world behind the appearances. All other knowledge is at best incomplete and tainted by subjectivity.

“If such a view were possible, then we would certainly like to aspire to it, for we would all like to have a kind of knowledge which is liberated from our situation, just as, indeed, we would all like not to die. The questions is then, is such a view possible? Or, at least, is it conceivable?

“I do not think that such a view can be achieved; we can learn this from both relativity theory and quantum theory.” Smolin, Lee. 1997. The Life of the Cosmos. Oxford University Press. Pp. 199-200.


“Thus the metaphor of the universe we are trying now to imagine, which I would like to set against the picture of the universe as a clock, is an image of the universe as a city, as an endless negotiation, an endless construction of the new out of the old. No one made the city, there is no city-maker, as there is a clock-maker. If a city can make itself, without a maker, why can the same not be true of the universe?” Smolin, Lee. 1997. The Life of the Cosmos. Oxford University Press. P. 299.


“Given a network of catalyzed chemical reactions, a (sub)set R of such reactions is called:

“1. Reflexively autocatalytic (RA) if every reaction in R is catalyzed by at least one molecule involved in any of the reactions in R;

“2. F-generated (F) if every reactant in R can be constructed from a small ‘food set’ F by successive application of reactions from R;

“3. Reflexively autocatalytic and F-generated (RAF) if it is both RA and F.”
Hordijk, Wim, J. Hein & M. Steel. 2010. “Autocatalytic Sets and the Origin of Life.” Entropy. 12, 1733-1742. P. 1735.


“Thus, autocatalytic cycles, hypercycles, and collectively autocatalytic sets can all be seen as particular instances of RAF sets.” Hordijk, Wim, J. Hein & M. Steel. 2010. “Autocatalytic Sets and the Origin of Life.” Entropy. 12, 1733-1742. P. 1736.


“Finally, and perhaps most importantly, the RAF framework has provided strong support for the claim that autocatalytic sets indeed have a high probability of occurrence, even with very moderate levels of catalysis. Our computational results in [previous journal article] indicate that only a linear growth in catalytic activity (with system size) is necessary for RAF sets to appear with high likelihood in Kauffman’s binary polymer model. This was subsequently verified analytically. The level of catalysis necessary for RAF sets to occur in our simulations is between 1 and 2 reactions per molecule, a number which is (bio)chemically quite realistic, especially for proteins. This is in stark contrast to the exponential growth required in Kauffman’s original argument, and therefore re-instates his claim that in ‘sufficiently complex chemical reaction systems’ autocatalytic sets will arise almost inevitably. Moreover, we have provided a formal way of quantifying ‘sufficiently complex’, in terms of the level of catalysis required. These results, combined with existing experimental evidence, make autocatalytic sets a serious and plausible candidate for consideration in origin of life scenarios.” Hordijk, Wim, J. Hein & M. Steel. 2010. “Autocatalytic Sets and the Origin of Life.” Entropy. 12, 1733-1742. P. 1738. Reference is to Hordijk, W. & M. Steel. “Detecting autocatalytic, self-sustaining sets in chemical reaction systems.” J. Theor. Biol. 2004, 227, 451-461.


“Mimicry is a form of convergent evolution in which one species independently evolves a morphology very similar to that of another species simply in order to fool a third species.” McGhee, George. 2011. Convergent Evolution: Limited Forms Most Beautiful. MIT Press. P. 8.


“Mimicry is similar to camouflage, where species evolve morphologies that converge on the form of either a living or a nonliving model in order to blend into the surroundings so that the camouflaged species cannot be seen.” McGhee, George. 2011. Convergent Evolution: Limited Forms Most Beautiful. MIT Press. P. 8.


“Hansell identifies five architectural behaviors found in nest-building birds, listed here in terms of increasing behavioral complexity: stacking, entangling, Velcro-fastening, stitching, and weaving.” McGhee, George. 2011. Convergent Evolution: Limited Forms Most Beautiful. MIT Press. P. 213. Reference is to Hansell, M. 2005. Animal Architecture. Oxford University Press.


“We can easily visualize a universe in which every species is morphologically different from every other species, and in which each species has its own unique ecological role, or niche, in nature. That universe does not exist. Instead, we live in a universe where convergence in evolution is rampant at every level, from the external forms of living organisms down to the very molecules from which they are constructed, from their ecological roles in nature to the way in which their minds function.” McGhee, George. 2011. Convergent Evolution: Limited Forms Most Beautiful. MIT Press. Pp. 245-6.


“The hypothetical universe in which every species has its own unique functional morphology, is morphologically different from every other species, does not exist.” McGhee, George. 2011. Convergent Evolution: Limited Forms Most Beautiful. MIT Press. Pp. 250-1.


“In modeling the evolution of the development of multicellular organisms, Newman et al. start with four different kinds of physical and chemical patterning mechanisms: diffusion gradients, sedimentation gradients, reaction-diffusion mechanisms, and chemical oscillation mechanisms. Most importantly, these four patterning mechanisms are found in nonliving as well as living chemical systems. Then Newman et al. add two basic cell properties: differential adhesion and cell ppolarity.” McGhee, George. 2011. Convergent Evolution: Limited Forms Most Beautiful. MIT Press. P. 258. Reference is to Newman, S., G. Forgacs & G. Mueller. 2006. “Before programs: The physical origination of multicellular forms.” International Journal of Developmental Biology. 50:289-299.


“In an extended study, Newman argues that nine ‘dynamical patterning modules’ (or DPMs) in particular exist within the spectrum of hypothetical developmental forms, and that ‘the DPMs, in conjunction with cell-type-defining and switching networks, transformed simple, spherical topologically solid cell clusters into hollow, multilayered, elongated, segmented, folded, and appendage-bearing structures. They thus founded the pathways that evolved into the developmental programs of modern animals.’

“In conclusion, Newman et al. and Newman suggest that the evolution of development on Earth may have been a two-stage process: metazoans originated from multicellular forms and structures first assembled by predominantly physical mechanisms, and then subsequently evolved genetic mechanisms to perpetuate the functionally successful morphologies formed in the first stage.” McGhee, George. 2011. Convergent Evolution: Limited Forms Most Beautiful. MIT Press. P. 259. References are: Newman, S., G. Forgacs & G. Mueller. 2006. “Before programs: The physical origination of multicellular forms.” International Journal of Developmental Biology. 50:289-299; Newman, S. 2010. “Dynamical patterning modules.” From Evolution: The Extended Synthesis. Edited by M. Pigliucci & G. Mueller. Pp. 281-306. MIT Press.


“Bodies can ‘express ecology’ by being sufficiently plastic, by taking on different structure, form or composition in different environments. Part of the phenotypic variation between organisms, especially differences between isolated populations and unrelated individuals, may be fixed and reflect differences in genetic make-up. Some of the variation develops in interaction with the particularities of the environment in which an organism finds itself. This part, indicated by the term phenotypic plasticity, can be further subcategorized on the basis of whether phenotypic changes are reversible and occur within a single individual, and whether the changes occur, or do not occur, in seasonally predictable, cyclical ways. The non-reversible phenotypic variation between genetically similar organisms that originates during development, developmental plasticity, has attracted much empirical and theoretical attention, including the publication of several monographs. In contrast, the subcategory of phenotypic plasticity that is expressed by single reproductively mature organisms throughout their life, phenotypic flexibility–reversible within-individual variation–has remained little explored and exploited in biology. This is surprising, because, as we shall discover, intra-individual variation most readily provides insights into the links between phenotypic design, ecological demand functions (performance) and fitness.” Piersma, Theunis, & J. van Gils. 2011. The Flexible Phenotype: A Body-Centred Integration of Ecology, Physiology, and Behaviour. Oxford University Press. P. 3.


“The field that studies the balance between the elemental make-up of animals and their food is called ‘ecological stoichiometry’, an area of research that has flourished over the last decade. One of the best-known applications of stoichiometric principles to ecology is the Redfield ratio, named after Alfred C. Redfield, an oceanographer from Harvard and the Woods Hole Oceanographic Institute. He discovered a remarkably constant ratio between carbon (C), nitrogen (N), and phosphorus (P), both in the world’s oceans and in the phytoplankton living in them, and which he explained by the continuous degradation of phytoplankton keeping this ratio in the water column constant. In more recent times, larger datasets and more precise measurements have yielded some small modifications here and there, but overall they still support the generality of the magic ratio 106:16:1 in the offshore ocean.” Piersma, Theunis, & J. van Gils. 2011. The Flexible Phenotype: A Body-Centred Integration of Ecology, Physiology, and Behaviour. Oxford University Press. P. 26.


“The term symmorphosis comes from Greek, as technical biological terms tend to, with ‘morphosis’ meaning ‘formation’ and ‘symmorphosis’ literallly meaning ‘balanced formation’ (think of symmetry). In 1981, Taylor and Weibel provided the following definition: ‘state of structural design commensurate to functional needs resulting from regulated morphogenesis, whereby the formation of structural elements is regulated to satisfy but not exceed the requirements of the functional system’. Symmorphosis thus predicts that all structural elements of a body, or at the least its subsystems, are fine-tuned to each other and to overall functional demand. Because a serial system is as strong as the weakest link, any element in the chain that would be stronger than the weakest would be wasteful.” Piersma, Theunis, & J. van Gils. 2011. The Flexible Phenotype: A Body-Centred Integration of Ecology, Physiology, and Behaviour. Oxford University Press. P. 36. Reference is to Taylor, C. & E. Weibel. 1981. “Design of the mammalian respiratory system. I. Problem and strategy.” Respiratory Physiology. 44:1-10.


“Symmorphosis, the principle that evolved body designs avoid excess capacity, e.g. in cascades of serial physiological processes, such as the respiratory chain, is now widely accepted as a useful, heuristic design principle. As we will see later in the book, like other criteria used in optimality-driven evaluations of organismal performance, symmorphosis is better seen as a useful null hypothesis, than as a hypothesis with very precise and rigid criteria for rejection. The discussion of safety factors has demonstrated how an evaluation of cases where simple, economy-based expectations are not upheld, develops our biological insight.” Piersma, Theunis, & J. van Gils. 2011. The Flexible Phenotype: A Body-Centred Integration of Ecology, Physiology, and Behaviour. Oxford University Press. P. 49.


“So, if animals are pushed very hard, under some conditions, they can raise the ceiling from working at 5 times BMR [basal metabolic rate] to working at 7 times BMR. As we have seen, endurance athletes in energy balance can push their performance levels to 5 times BMR, but not further. We have also seen that free-living birds, except in the case of marathon migrants, generally do not work harder than 4 times BMR. The considerable gap between the maximum sustained working level of 4 times BMR that hard-working parent birds are prepared to give, and the physiological maxima of 5-7 times BMR that can be achieved under exceptional conditions, makes evolutionary sense if working hard comes at a survival cost. If very hard work precipitously increases the likelihood of death (e.g. because of free-radical derived oxidative DNA and tissue damage), without leading to compensatory increases in reproductive output, evolutionary trade-offs would select for animals that are not prepared to work harder than what we can call the ‘optimal working capacity’.” Piersma, Theunis, & J. van Gils. 2011. The Flexible Phenotype: A Body-Centred Integration of Ecology, Physiology, and Behaviour. Oxford University Press. P. 67.


“Highly predictable changing environments would select for polyphenism in short-lived organisms and life-cycle staging in long-lived organisms. The lower the predictability of environmental variation, the better it is for organisms to respond opportunistically, rather than seasonally scheduled. Developmental plasticity would then describe the kind of variable responses: organisms encountering unpredictably variable environments in the course of their life would benefit from plasticity being reversible, i.e. showing phenotypic flexibility. If environmental variation cannot be predicted, organisms might go into bet hedging (generating differently adaptive phenotypes at random) in shorter-lived organisms. In theory at least, especially longer-lived animals could also cope with extravagant changeability of the environment by not adjusting the phenotype at all, i.e. show robustness.” Piersma, Theunis, & J. van Gils. 2011. The Flexible Phenotype: A Body-Centred Integration of Ecology, Physiology, and Behaviour. Oxford University Press. P. 94.


“If animals can combine prior information about the environment with new information about a current option (be it a patch, a prey, a mate, or whatever), they can markedly improve their assessment of the value of the current option, and thus improve fitness. This is the essence of ‘Bayesian’ updating, named after Thomas Bayes (1702-61), an Anglican priest interested in probability theory. Just to give you a simple example of Bayesian updating in practice: imagine a patch in which a forager has found two prey items during the first minute of search. Should it continue searching or should it leave this patch? If the environment is structured such that a patch can only contain two prey items at most, then the forager should definitely move on. By contrast, if patches can contain many more than just two items, then the forager should stay, especially if it took little time to find these two items. Thus, knowing your environment (in a statistical, probabilistic sense) greatly improves your assessment abilities; without knowledge about your environment, it is much harder to make the right choices. A popular example of Bayesian updating in humans is the so-called ‘Monty Hall problem’, named after an American quizzmaster. Imagine you are participating in a TV game in which you have to select one out of three closed doors. Behind one of these doors stands a car, behind each of the other two doors stands a goat. You will take home either a car or a goat, depending on which door you choose. Once you have selected your door, the friendly quizmaster, who knows what stands behind each door, helps you by opening one of the other two doors for you, with a goat behind it. Knowing this, or, in Bayesian terms, updating your prior expectation with new sampling information, should you switch to the other closed door? The answer is yes; by switching, your chance of winning the car increases from 1 in 3 to 2 in 3. The intuitive, but incorrect, answer is that there is no need to switch doors, since your chances would only increase from 1 in 3 to 1 in 2, irrespective of whether you switch or not!” Piersma, Theunis, & J. van Gils. 2011. The Flexible Phenotype: A Body-Centred Integration of Ecology, Physiology, and Behaviour. Oxford University Press. Pp. 122-3.


“In this book we have offered a progression of ideas that support the view that, although bodies and environments are recognizable entities, they really are inseparable. In this final chapter we extend this view to evolution–the inheritance of, and selection for, randomly variable phenotypic traits across generations. What we find is that evolutionary change needs systems of inheritance, but we also find that the genetic system that we all work with is just one of five such possible inheritance systems. Since organisms not only provide the beginnings and nurture of their offspring, but also build the environments in which they and their offspring live, there are very tight feedbacks of reciprocal causation, both in the development of organisms and in the relationships between the developing organism and their environments. Bodies are earth, and we would do well to acknowledge that in the ways that we study them.” Piersma, Theunis, & J. van Gils. 2011. The Flexible Phenotype: A Body-Centred Integration of Ecology, Physiology, and Behaviour. Oxford University Press. P. 184.


“It turns out there is something very special about the nanoscale when it comes to converting different forms of energy into each other. Intriguingly, only at the nanoscale are many types of energy, from elastic to mechanical to electrostatic to chemical to thermal, roughly of the same magnitude. This creates the exciting possibility that the molecules in our bodies can spontaneously convert different types of energy into one another. Molecules and small, nanoscale particles can have substantial fluctuations in energy as they take energy from the molecular storm (thermal energy), use it to convert, for example, chemical energy to electrical energy, and then release the energy again into the surrounding chaos. By contrast, smaller structures, such as atoms or nuclei, have binding energies that are too large to allow thermal energy fluctuations, unless the temperature (along with thermal energy) is extremely high (thousands or millions of degrees). At such high temperatures, molecules are unstable and the formation of complex structures needed for life is impossible. On the other hand, at scales much larger than a nanometer, mechanical and electrical energies are too high to be subject to thermal fluctuations. At this scale, everything becomes deterministic, and objects do not spontaneously change shape or assemble themselves–which are attributes needed for life.

“Thus, the nanoscale is truly special. Only at the nanoscale is the thermal energy of the right magnitude to allow the formation of complex molecular structures and assist the spontaneous transformation of different energy forms (mechanical, electrical, chemical) into one another.” Hoffmann, Peter. 2012. Life’s Ratchet: How Molecular Machines Extract Order from Chaos. Basic Books. Pp. 122-4.


“The hallmark of a tightly coupled molecular motor is that it goes through well-defined cycles, using up a fixed number of ATP molecules during each step. Nevertheless, random motion is the drive behind the motor’s locomotion, as it ultimately moves the legs of the motor forward–of course, rectified by the allosteric interaction of the motor’s legs with ATP.

“Loosely coupled motors, by contrast, rely more heavily on random motion and have no fixed step cycle.” Hoffmann, Peter. 2012. Life’s Ratchet: How Molecular Machines Extract Order from Chaos. Basic Books. P. 162.


“As demonstrated, kinesin, a tightly coupled motor, uses the molecular storm to push its feet forward. The allosteric tilting of the molecule helps bias the movement in the forward direction, but where does the tilt come from? Any change in shape of a molecule is ultimately the result of the molecular storm’s pushing the molecule in the direction of reduced energy, that is, into a valley of its energy landscape. A molecular motor will simply not work if the temperature is too low to provide sufficient random thermal motion. Even the most tightly controlled motor needs the chaos of the thermal dance to traverse transition states and find its way on an every-changing energy landscape.” Hoffmann, Peter. 2012. Life’s Ratchet: How Molecular Machines Extract Order from Chaos. Basic Books. Pp. 167-8.


“In our cells, directed motion, ‘purposeful’ activity, is created by the action of molecular ratchets–molecular machines, enzymes, and motors, which by degrading free energy and due to their asymmetric structures, can rectify the random motions of the molecular storm to create order.” Hoffmann, Peter. 2012. Life’s Ratchet: How Molecular Machines Extract Order from Chaos. Basic Books. P. 225.


“For our purposes, a shared lexicon is a consensus on a set of distinctions.” Hutchins, Edwin & B. Hazlehurst. “How to invent a shared lexicon: the emergence of shared form-meaning mappings in interaction.” From Goody, Esther (Ed.) 1995. Social Intelligence and Interaction: Expressions and Implications of the Social Bias in Human Intelligence. Cambridge University Press. P. 55.


“Virtually all work in connectionist modelling today models aspects of the cognition of individuals. Our theoretical stance suggests that it might be useful to consider the properties of communities of networks. Of particular interest here is the fact that in traditional connectionist modelling, the programmer constructs the world of experience from which the networks learn. In a community of networks the behaviour of other networks might also be an important source of structure from which each network could learn. Connectionist programmers refer to the output patterns to be learned as the ‘teachers’ for their networks. With a community of networks, we can let an important part of the teaching be embodied in the behaviour of other networks. Thus, where traditional network modelling is concerned only with the relation of structure in the environment to internal structure, a model of interactions in a community of networks adds the universe of communicational artifacts to the picture.”

“It is easy to show that consensus among two networks can be achieved by taking the output of each as the teacher for the other.” Hutchins, Edwin & B. Hazlehurst. “How to invent a shared lexicon: the emergence of shared form-meaning mappings in interaction.” From Goody, Esther (Ed.) 1995. Social Intelligence and Interaction: Expressions and Implications of the Social Bias in Human Intelligence. Cambridge University Press. P. 59.


“The hand and mouth are the two most complex and flexible effectors of the human body and are regulated by neighbouring or even partialy overlapping neural circuits.” Stout, Dietrich & T. Chaminade. 2009. “Making Tools and Making Sense: Complex, Intentional Behaviour in Human Evolution.” Cambridge Archaeological Journal. 19(1): 85-96. P. 86.


“Functional brain imaging results suggest that meaningful correspondences do exist between language and ESA (early stone age) tool-making, and furthermore that that [sic] these correspondences are to be found at increasingly higher levels of organization in more sophisticated stone technologies.” Stout, Dietrich & T. Chaminade. 2009. “Making Tools and Making Sense: Complex, Intentional Behaviour in Human Evolution.” Cambridge Archaeological Journal. 19(1): 85-96. P. 86.


“Kinematic studies reveal that grasping movements with the hand affect concurrent movements of the mouth, with larger manual target objects being associated with wider, faster opening of the mouth and with increased power of the voice spectrum during syllable pronunciation. PMv [frontal lobe ventral premotor cortex] has thus been characterized as producing an ‘action vocabulary’ across a wide array of different behaviours, reflecting a more general role in processing sequentially structured events.” Stout, Dietrich & T. Chaminade. 2009. “Making Tools and Making Sense: Complex, Intentional Behaviour in Human Evolution.” Cambridge Archaeological Journal. 19(1): 85-96. P. 87.


“Overlapping PMv [frontal lobe ventral premotor cortex] contributions to phonological processing and object manipulation provide evidence of a specific neurobehavioural correspondence between language and manual action involving this region. In particular, this correspondence is found at the level where discrete articulatory and prehensile elements are assembled into short goal directed action units, such as grasping an object or pronouncing an intonational phrase.” Stout, Dietrich & T. Chaminade. 2009. “Making Tools and Making Sense: Complex, Intentional Behaviour in Human Evolution.” Cambridge Archaeological Journal. 19(1): 85-96. P. 88.


“It is nothing new to propose an evolutionary link between language and tool-making. In 1871, Darwin himself argued that ‘To chip a flint into the rudest tool... demands the use of a perfect hand... the structure of the hand in this respect may be compared with that of the vocal organs’. In more recent years, however, many archaeologists have instead stressed the dissimilarities between language and stone tool-making. Brain-imaging studies of ESA [early stone age] tool-making provide important new empirical support for the early intuitions of Darwin, as well as for more recent proposals regarding the co-evolution of language and technology.” Stout, Dietrich & T. Chaminade. 2009. “Making Tools and Making Sense: Complex, Intentional Behaviour in Human Evolution.” Cambridge Archaeological Journal. 19(1): 85-96. Pp. 91-2. Reference is to Darwin, Charles. 2004 (1871). Descent of Man, and Selection in Relation to Sex. Penguin Books. P. 69.


“The conclusions we may draw from these observations are that humans are generally oblivious to rates and proportions (which are transitory) and that they constantly search for causal relations (which are invariant).” Pearl, Judea. Causality: Models, Reasoning, and Inference. 2000. Cambridge University Press. P. 182.


“The word ‘counterfactual’ is a misnomer, since it connotes a statement that stands contrary to facts or, at the very least, a statement that escapes empirical verification. Counterfactuals are in neither category; they are fundamental to scientific thought and carry as clear an empirical message as any scientific law.” Pearl, Judea. Causality: Models, Reasoning, and Inference. 2000. Cambridge University Press. P. 217.


“These possibilities trigger an important basic question: “is ‘explanation’ a concept based on general causes (e.g., ‘Drinking hemlock causes death’) or singular causes (e.g., ‘Socrates’ drinking hemlock caused his death’)? Causal effect expressions P(y |do(x)) belong to the first category whereas counterfactual expressions P(Yx’ = y’ | x,y) belong to the second, since conditioning on x and y narrows down world scenarios to those compatible with the most specific information at hand: X = x and Y = y.” Pearl, Judea. Causality: Models, Reasoning, and Inference. 2000. Cambridge University Press. P. 222.


“If, on the other hand, we base explanations solely on singular-event considerations (i.e., necessary causation), then various background factors that are normally present in the world would awkwardly qualify as explanations. For example, the presence of oxygen in the room would qualify as an explanation for the fire that broke out, simply because the fire would not have occurred were it not for the oxygen. That we judge the match struck, not the oxygen, to be the actual cause of the fire indicates that we go beyond the singular event at hand (where each factor alone is both necessary and sufficient) and consider situations of the same general type–where oxygen alone is obviously insufficient to start a fire. Clearly, some balance must be struck between the necessary and the sufficient components of causal explanation, and the present chapter illuminates this balance by formally explicating the basic relationships between these two components.” Pearl, Judea. Causality: Models, Reasoning, and Inference. 2000. Cambridge University Press. P. 285.


“Yet despite its ubiquity in natural thoughts, actual causation is not an easy concept to formulate. A typical example considers two fires advancing toward a house. If fire A burned the house before fire B, we (and many juries nationwide) would surely consider fire A ‘the actual cause’ for the damage, though either fire alone is sufficient (and neither one was necessary) for burning the house. Clearly, actual causation requires information beyond that of necessity and sufficiency; the actual process mediating between the cause and the effect must enter into consideration.” Pearl, Judea. Causality: Models, Reasoning, and Inference. 2000. Cambridge University Press. P. 309.


“Thus, the distinction between type and token claims is a matter of degree in the structural account. The more episode-specific evidence we gather, the closer we come to the ideals of token claims and actual causes.” Pearl, Judea. Causality: Models, Reasoning, and Inference. 2000. Cambridge University Press. P. 311.


“The overriding ideas in this solution [to the second riddle of causation – figuring out what difference it makes to know that something is causal] are:

“First – treating causation as a summary of behavior under interventions; and

“Second – using equations and graphs as a mathematical language within which causal thoughts can be represented and manipulated.

“And to put the two together, we need a third concept: Treating interventions as a surgery over equations.” Pearl, Judea. Causality: Models, Reasoning, and Inference. 2000. Cambridge University Press. P. 344.


“In summary, intervention amounts to a surgery on equations (guided by a diagram) and causation means predicting the consequences of such a surgery.” Pearl, Judea. Causality: Models, Reasoning, and Inference. 2000. Cambridge University Press. P. 347.


“Changes in size are not a consequence of changes in shape, but the reverse: changes in size often require changes in shape. To put it another way, size is a supreme regulator of all matters biological. No living entity can evolve or develop without taking size into consideration. Much more than that, size is a prime mover in evolution. There is abundant evidence for the natural selection of size, for both increases and decreases. Those size changes have the remarkable effect that they guide and encourage novelties in the structure of all organisms. Size is not just a by-product of evolution, but a major player.” Bonner, John Tyler. 2006. Why Size Matters: From Bacteria to Blue Whales. Princeton University Press. P. 2.


“The rules [“correlations in which various properties of organisms vary with size”] are as follows:

“RULE 1 Strength varies with size.

“RULE 2 Surfaces that permit diffusion of oxygen, of food, and of heat in and out of the body, vary with size.

“RULE 3 The division of labor (complexity) varies with size.

“RULE 4 The rate of various living processes varies with size, such as metabolism, generation time, longevity, and the speed of locomotion.

“RULE 5 The abundance of organisms in nature varies with their size.”
Bonner, John Tyler. 2006. Why Size Matters: From Bacteria to Blue Whales. Princeton University Press. P. 5.


“... a larger animal could not even exist unless its cells had a reduced rate of metabolism. It would either starve or burst into flames, or both.” Bonner, John Tyler. 2006. Why Size Matters: From Bacteria to Blue Whales. Princeton University Press. P. 124.


“There is good evidence that a tree starts declining in its growth when it becomes so tall that the water and nutrients can no longer effectively reach the growing tips of the outer stems.” Bonner, John Tyler. 2006. Why Size Matters: From Bacteria to Blue Whales. Princeton University Press. P. 133.


“The present research examined a dynamic way in which cognition may be shaped and maintained by culture and found evidence that culturally specific patterns of attention may be at least partially afforded by the perceptual environment.” Miyamoto, Yuri, R. Nisbett & T. Masuda. 2006. “Culture and the Physical Environment.” Psychological Science. Vol. 17, No. 2, Pp. 113-9. P. 118.


“The present research suggests a dynamic process through which attention can be shaped and sustained by the perceptual environment. Given the fact that such perceptual environments have been historically constructed and maintained by people repeatedly exposed to a culturally specific perceptual environment, we believe that the current exploration sheds light on possible processes of mutual constitution of cognitive processes and sociocultural environment.” Miyamoto, Yuri, R. Nisbett & T. Masuda. 2006. “Culture and the Physical Environment.” Psychological Science. Vol. 17, No. 2, Pp. 113-9. P. 118.


“Cells are characterized by the presence of genetic information, of a metabolism and of compartments; there has been an ongoing debate on the features that came first. This debate has also been complicated by an excessive simplification of positions. But the simultaneous requirement of two or all of the sub-systems can be considered a likely possibility as well. Independent of that choice, a metabolic contribution cannot be precluded as the presence of genetic material or that of membrane components requires synthetic pathways supporting, for example, a preparatory metabolism variant of the genetic polymer first option. Therefore, the chemical free energy released or used in these pathways represents an essential component in the majority of the hypotheses on the origin of life.” Pascal, Robert & L. Boiteau. 2011. “Energy flows, metabolism and translation.” Philosophical Transactions of the Royal Society: B. 366, 2949-2958. P. 2949.


“A trait has high ‘broad sense’ heritability in a population to the extent that the existing variation for that trait in the population is due to genetic variation. If variance in a trait is entirely due to genetic variance, broad sense heritability is 1.0; if it is entirely due to variance in non-genetic factors, broad sense heritability is 0.0.” Bateson, Patrick & P. Gluckman. 2011. Plasticity, Robustness, Development and Evolution. Cambridge University Press. P. 13.


“The developmental biologist Frederik Nijhout has proposed a formal approach to robustness in which he suggests that the developing organism is robust if it is unable to detect changes in the environment or is resistant to them.” Bateson, Patrick & P. Gluckman. 2011. Plasticity, Robustness, Development and Evolution. Cambridge University Press. P. 21. Reference is to Nijhout, H.F. 2002. “The nature of robustness in development.” Bioessays. 24, 553-563.


“William Homan Thorpe brought together the insights of European ethology and holistic psychology with the vast corpus of work on the various mechanisms of learning from American and Russian laboratories, as well as those from psychology departments worldwide. Thorpe classified learning into five categories: habituation, classical conditioning, instrumental conditioning, latent learning and insight learning. Some forms of learning such as behavioural imprinting, which Thorpe discussed in his chapter on insight learning, and the acquisition of song in birds may be restricted to early development, but most can take place throughout life.

“One of the most primitive changes in behaviour in response to experience is non-specific. Sensitisation usually results from exposure to an alarming stimulus (such as a blow-up toy snake suddenly becoming inflated), which elicits a variety of defensive or aversive reactions from the animal. Subsequently, many other potentially aversive stimuli (such as loud sounds) will have the same effect even though this would not have been the case had the animal not been previously sensitised.” Bateson, Patrick & P. Gluckman. 2011. Plasticity, Robustness, Development and Evolution. Cambridge University Press. Pp. 39-40. Reference is to Thorpe, W. H. 1956. Learning and Instinct in Animals. Methuen.


“DNA sequences that do not code for proteins were previously called ‘junk DNA’ and comprise the bulk of the mammalian genome. However, much of this codes for RNAs that are not translated into proteins. The recognition of the critical biological significance of these sequences has been one of the major discoveries of recent years. Many non-coding RNA molecules act as regulatory factors either by association with intra-nuclear proteins or by binding to the DNA. They are likely to play a major role in conferring specificity to these epigenetic processes.” Bateson, Patrick & P. Gluckman. 2011. Plasticity, Robustness, Development and Evolution. Cambridge University Press. Pp. 57-8.


“Unlike the forms of plasticity that occur early in development, much of the capacity to learn can occur throughout life.” Bateson, Patrick & P. Gluckman. 2011. Plasticity, Robustness, Development and Evolution. Cambridge University Press. P. 76.


“Various mechanisms that generate robustness and are involved in plasticity coexist to allow the development of an integrated phenotype or a variety of alternative phenotypes. Successful lineages of sexually reproducing organisms require compatibility between the genomic architecture and the phenotypes at a number of levels. This requires a level of robustness in development. But organisms living within variable environments also require plasticity to cope with environmental change. To ensure their utility, these mechanisms must be integrated with those that maintain the species’ characteristics.” Bateson, Patrick & P. Gluckman. 2011. Plasticity, Robustness, Development and Evolution. Cambridge University Press. P. 79.


“Two fundamental issues have remained in bridging the gap between the neo-Darwinist camp and those who seek to emphasise the importance of development in evolution. The first has been the need to provide molecular mechanisms that would explain the role of development in evolutionary processes. The second has been the need to demonstrate the generality of developmental processes impacting on evolution.” Bateson, Patrick & P. Gluckman. 2011. Plasticity, Robustness, Development and Evolution. Cambridge University Press. P. 82.


“For example, robustness due to insensitivity to the environment might simply reflect a species having been stable in an unchanging ecological niche over evolutionary time; plasticity would have had relatively little utility. Alternatively, where sensitivity to environmental cues might induce harm, mechanisms to render the developing organism insensitive to the environment may be under active Darwinian selection. Viviparity in some reptiles and fish, the firm eggshell of birds, and the placental barrier of mammals all represent evolved systems to create environmental insensitivity.” Bateson, Patrick & P. Gluckman. 2011. Plasticity, Robustness, Development and Evolution. Cambridge University Press. P. 85.


“These terms [“nature and nurture”] refer to different domains and should not be contrasted directly; one is a state and the other a process. Nature, we argued, should refer to the fully developed characteristics of an organism, and nurture to the ways in which those characteristics were derived.” Bateson, Patrick & P. Gluckman. 2011. Plasticity, Robustness, Development and Evolution. Cambridge University Press. P. 124.


“A robust phenotype is often supposed to be one produced by processes that are difficult to disrupt (developmental non-malleability), and one that is difficult to modify once it has developed (post-developmental non-malleability). However, as we have seen in Chapter 3, developmental and post-developmental robustness do not necessarily go together and are not based on unitary processes. A trait that is robust with respect to its development may not also be robust with respect to its continuance, and vice versa. As noted in Chapter 3, developmental malleability may be followed by non-malleability, as in many examples of alternative phenotypes found throughout the animal kingdom. The same is true for humans, as in the case of sexual differentiation or differentiation of the visual pathway. Conversely developmental non-malleability may be followed by considerable malleability, as in the case of the human smile, which reliably appears in infants during the fifth or sixth week after birth and is successively greatly modified by social interactions and cultural influences.” Bateson, Patrick & P. Gluckman. 2011. Plasticity, Robustness, Development and Evolution. Cambridge University Press. Pp. 125-6.


“The realisation that the many processes of development interact and are intertwined is crucial in order to make progress in biology and cognitive science.” Bateson, Patrick & P. Gluckman. 2011. Plasticity, Robustness, Development and Evolution. Cambridge University Press. P. 129.


“Robustness and plasticity are complementary and intertwined and must be considered together.” Bateson, Patrick & P. Gluckman. 2011. Plasticity, Robustness, Development and Evolution. Cambridge University Press. P. 130.


“Disturbance can be thought of as any more or less sudden environmental circumstance which makes resources newly available for exploitation. It is often caused by human beings. Fire, toxic pollutants, extreme weather conditions, wave action and ploughing all provide examples of ‘destructive disturbance’ which eliminate established biological communities or parts of communities. By contrast, taking the lid off a pot of jam, pruning a tree, and burying animal or plant remains in soil are examples of ‘enrichment disturbance’ which adds or exposes resources to living systems.

“Disturbance therefore results in temporary plenty. In so doing it causes what is known as ‘R’- or ‘r’-selection. This kind of selection favours open-bounded entities that are quick to arrive on the scene, exploit the most readily assimilable resources and then reproduce as supplies become restricted. Such entities are competitive with respect to arrival and exploitation, i.e. in terms of ‘primary resource capture’. They also have relatively unspecialized requirements for resources and little need to adjust to heterogeneous conditions other than by reproducing. Regenerative processes are therefore emphasized, allowing very rapid rates of proliferation and dissemination of reproductive units through space and time. Variation produced by recombinatorial, developmental or behavioural mechanisms tends to be minimized.” Rayner, Alan. Degrees of Freedom: Living in Dynamic Boundaries. 1997. Imperial College Press. Pp. 187-8.


“After the goldrush [a disturbance], increased access to resources by any one entity or group can only be achieved by means of trade or takeover. The ability of each entity to retain or gain resources now depends on mechanisms affecting the self-integration and degeneration of contextual boundaries.... For the moment, their [mechanisms] main significance lies in the fact that they result in the ‘combative’ and ‘collaborative’ ecological strategies of entities that develop in circumstances where there is a potentially high incidence of competitors. Such circumstances cause ‘C’-selection.

“Since C-selected entities inhabit heterogeneous environments over relatively long time intervals, during which they may have a wide variety of close encounters with others, they tend to possess a high degree of versatility. This versatility is associated with an emphasis on conversional processes–which permit retention of resources, and distributive processes–which enable invasion of hostile territory. Recycling processes that enable redistribution to defensive or invasive ‘battlefronts’ are often also important. The formation of co-operative networks and partnerships allows new capabilities that can also enhance combative prowess. C-selected entities can be expected to be genetically variable at the population level of organization and developmentally or behaviourally variable at the individual level.” Rayner, Alan. Degrees of Freedom: Living in Dynamic Boundaries. 1997. Imperial College Press. Pp. 188-9.


“Stress or adversity can be thought of as any more or less continuously imposed kind of environmental extreme, other than a high incidence of competitors, which inhibits the proliferation of the majority of entities under consideration. Particularly in terrestrial environments, many stress factors may ultimately operate by compromising the mechanisms that circumvent or protect from oxygen toxicity.

“Those relatively few ‘S’- or ‘A’-selected entities which can tolerate, or indeed develop best in the relative absence of competitors under stressed conditions, do so because they have specialized attributes. For example, organisms inhabiting deserts have attributes which protect them from desiccation and extremes of temperature.

“S-selection, like C-selection, is a feature of relatively stable environments (hence both C- and S-selection represent different aspects of K-selection) and especially favours attributes associated with protective, conversional processes. Co-operative interactions and distributive processes that allow emigration can also be an asset. Purely S-selected entities, in being highly specialized, tend to lack versatility. However, S-selection is often associated with individual life cycle stages or alternative phenotypes of versatile organisms.” Rayner, Alan. Degrees of Freedom: Living in Dynamic Boundaries. 1997. Imperial College Press. P. 189

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