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“There are many circumstances under which novelties emerge, and I allocate them to arenas of evolutionary causation that include association (symbiotic, cellular, sexual, and social), functional biology (physiology and behavior), and development and epigenetics. Think of them as three linked circus rings of evolutionary performance, under the ‘big top’ of the environment. Natural selection is the conservative ringmaster who ensures that tried-and-true traditional acts come on time and again.” Reid, Robert. Biological Emergences: Evolution by Natural Experiment. 2007. MIT Press. P. 5.
 

“... in general, organic compounds are molecular and do not form continuously bonded lattices in contrast with a large number of such inorganic compounds....

“They readily form long-chain, electrical insulating, polymers, sometimes cross-linked, of very high molecular weight.  Hence they were very difficult to characterise at first and very little was really known about them until after 1850 AD, while inorganic compounds had already been studied, albeit often in a rough and ready way, for more than 3000 years.”  Williams, R.J.P. & J.J.R. Frausto da Silva.  The Chemistry of Evolution: The Development of our Ecosystem.  2006.  Elsevier.  P. 57.
 

“Any principle proper to ecology will remain valid over only a finite domain of space and time. For ecologists, the universe is packed with ‘bubbles,’ each of which delimits the principles and processes endemic to that domain: that is, the universe is ‘granular’ in nature.” Ulanowicz, Robert. A Third Window: Natural Life beyond Newton and Darwin. 2009. Templeton Foundation Press. P. 124.


“Contrast two evolutionarily distant relatives: the intestinal bacterium Escherichia coli and its host, ourselves. We span the spectrum of complexity in living organisms. The bacterium has minimal capability for perceiving and reacting to short-term changes in its environment, whereas the major portion of our body is devoted to these tasks.

“Escherichia coli cells commit less than 5% of their molecular machinery to motion and perception, allowing only the simplest of responses....”

“Our bodies, in contrast, are built for specific, directed motion under the control of detailed perception. The bulk of our body weight is dedicated to sense, reaction, and motion.” Goodsell, David S. The Machinery of Life. Springer Verlag. 1998. p. 50.


“Although we have written of the origin of the eukaryotes as one of the ‘major transitions,’ it was in fact a series of events: the loss of the rigid cell wall, and the acquisition of a new way of feeding on solid particles; the origin of an internal cytoskeleton, and of new methods of cell locomotion; the appearance of a new system of internal cell membranes, including the nuclear membrane; the spatial separation of transcription and translation; the evolution of rod-shaped chromosomes with multiple origins of replication, removing the limitation on genome size; and , finally, the origin of cell organelles, in particular the mitochondrion and, in algae and plants, the plastid. Of these events, at least the last two qualify as major transitions in the sense of being major changes in the way genetic information is stored and transmitted.” Smith, John Maynard, and Eörs Szathmary. The Origins of Life. Oxford University Press. 1999. Quoted Morowitz, Harold. The Emergence of Everything. Oxford University Press. 2002. Pps. 91-2.


“When interacting with the world, organisms must protect and isolate themselves, but at the same time, they must sense and respond to changing conditions. To perform these opposing functions, modern organisms have developed a bewildering variety of different molecular machines. The molecular machines of synthesis and energy production, discussed above, are nearly identical in all living organisms; the differences between organisms appear mainly in this third class of function.” Goodsell, David S. The Machinery of Life. Springer Verlag. 1998. p. 49.


“An autonomous agent must be an autocatalytic system able to reproduce and able to perform one or more thermodynamic work cycles.” Kauffman, Stuart. Investigations. Oxford University Press. 2000. p. 49.


“At first glance, scepticism about a principled internal/external boundary looks absurd. Organisms are enclosed by physical structures. These barriers are essential for the metabolic integrity of the organism. From the point of view of physiology, the organism/environment distinction is both sharp and important. It does not follow that the boundary is principled when we consider development and evolution. Oyama is sceptical about the importance of the organism/environment interface in developmental biology because she does not think development is driven by discrete chunks of information, some of it internal and guiding the development of genetic traits, and some of it external, guiding an organism’s learning. In her view, the information needed in the development of every trait is constructed from both internal and external sources. Oyama might be wrong, but she cannot be refuted by appeal to the boundary’s importance for metabolic integrity.

“If the existence of a principled boundary is an open question in developmental biology, it is even more open in evolutionary biology. The metabolic argument for the boundary has even less grip. For the ‘organic systems’ in question do not have skins. For when Godfrey-Smith talks of organisms, he has in mind not single organisms but organism lineages. For example:

“‘... the organic system in question does play a role in determining whether... a given environmental pattern is relevant to it or not.... But the properties of the organic system that make the environmental pattern relevant need not be the same properties that the environmental pattern can help to explain.... The organism, by virtue of one set of organic properties, makes it the case that a given environmental pattern is relevant.’

“Lineages do not have skins. They have no metabolic integrity to preserve. It is not at all obvious that there is a principled demarcation in the causal history of an evolving lineage into external and internal factors. For example, Godfrey-Smith counts game theoretic and other frequency dependent effects in evolution as external factors. But these equally well can be thought of as internal to the lineage; they are after all features of the evolving population. So the set of evolutionary causes may not divide in any clean way into internal and external factors.” Sterelny, Kim. The Evolution of Agency and Other Essays. Cambridge University Press. 2001. p. 187. Subquote is from Godfrey-Smith, Peter. Complexity and the Function of Mind in Nature. Cambridge University Press. 1996. p. 155.


“Case 1: Two communities live along the northwest Pacifc coast of North America. One subsists largely on marine mammals, such as seals and sea lions; the members hunt in small, silent parties, roving widely. The other community focuses on fish, especially schools of salmon; its members hunt in big noisy groups and stay close to home. Both societies speak the same language, but with distinct dialects that differ even from clan to clan.

“Case 2: Two populations live 250 kilometers apart, separated by high mountains. One group erects towers of glued sticks on a painted black mossy base, decorated in stereotyped style with black, brown, and gray snail shells, acorns, sticks, stones, and leaves. The other population erects woven-stick huts on an unpainted green mossy base, decorated with much individual variation, using fruits, flowers, fungus, and butterfly wings, of every color imaginable except a few shades of brown, gray, and white.

Case 3: Different groups colonized different types of forest, where they found little competition. The empty niches allowed remarkable innovation: these are the only societies known to build arboreal residence. Each group invented a range of efficient techniques to harvest staple foods, focused on the seeds of conifers. The processing techniques require social transmission from one generation to the next; youngsters deprived of such tradition would starve.

None of these case studies is of humans. The first is not a society of sea-going canoe-hunters of marine vertebrates, such as the Kwakiutl, but are orcas, or killer whales. The second is not a highland New Guinean horticultural society such as the Eipo, but a population of bowerbirds. The third is not a seafaring, exploratory colonizer of uninhabited islands, such as the ancestral Polynesians, but black rats.” de Waal, Frans B. M., editor. Tree of Origin: What Primate Behavior Can Tell Us about Human Social Evolution. Harvard University Press. 2001. p. 232.


“However, ecological communities, unlike multicellular organisms, cannot be characterised by a pronounced closed boundary delimiting the internal milieu of the community from its external environment. Internal milieu of ecological communities represents an external environment for all types of correlated associations of lower levels of organisation, e.g. multicellular organisms. Thus, by maintaining their own internal milieu, ecological communities stabilise the external environment for all organisms of the biosphere. Correlated interaction of individuals in ecological communities is, therefore, the most complex work performed by living objects in the biosphere.

“Viability of cells is maintained by a strictly specified set of macromolecules and organelles. Viability of a multicellular organism is maintained by a strictly specified set of internal organs. Elimination of any of them or their substitution for [=by] alien structures adversely affects the state of the organism and may even cause its death. In very much the same manner, normal functioning of an ecological community can be maintained only by a strictly specified set of species characterised by strictly specified population densities of their individuals. Elimination of an aboriginal species or introduction of an alien one disturbs the normal functioning of the community and, consequently, impairs its internal milieu. This leads to a decrease in competitiveness of this particular community. As a result, the latter is forced out from the population of communities by a normal community which contains all the necessary aboriginal species and does not include any alien ones.

“Consequently, not all the species that are able to adapt to an external environment are able to survive in the biosphere. Only those species that are able to perform certain specific work on the stabilisation of the environment in the framework of some ecological community have a chance to persist. It is the correlation of an individual of a given species with other individuals in a community that determines the meaning of the notion norm for this particular species.” Gorshkov, Victor and Vadim Gorshkov and Anastassia Makarieva. Biotic Regulation of the Environment. Springer Verlag. 2000. p. 53.


"The question 'what is life?' has been posed in one form or another since the beginning of modern science. Is living matter basically the same as nonliving, only more complicated, or is something else required? Descartes placed living matter firmly within the ken of the laws of physics, or more specifically, mechanics. Since then, generations of vitalists, including the embryologist Hans Driesch, the philosopher Henri Bergson, and the physiologist J.S. Haldane, have found it necessary to react against the mechanical conception of life by positing an additional entelechy, or elan vital, which is outside the laws of physics and chemistry.

"The vitalists were right not to lose sight of the fundamental phenomenon of life that the mechanists were unable to acknowledge or to explain. But we no longer live in the age of mechanical determinism. Contemporary physics grew out of the breakdown of Newtonian mechanics at the beginning of the present century, both at the submolecular quantum domain and in the universe at large. The full implications for biology have yet to be worked out; although some major thinkers like Whitehead already saw the need to explain physics in terms of a general theory of the organism, thus turning the hierarchy of explanation upside down. Whitehead's view is not accepted by everyone, but, at least, it indicates that the traditional boundaries between scientific disciplines can bo longer be upheld, if one is to really understand nature. Today, physics has made further inroads into the 'organic' domain, in its emphasis on nonlinear phenomena far from equilibrium, on coherence and cooperativity which are some of the hallmarks of living systems. The vitalist/mechanist opposition is of mere historical interest, for it is the very boundary between living and nonliving that is the object of our enquiry, and so we can have no preconceived notion as to where it ought to be placed.

"As a first tentatve answer to the question of 'what is life,' we propose that life is a process of being an organizing whole. By 'whole,' we do not mean an isolated, monadic entity. Instead, it is an open system that structures or organizes itself by simultaneously 'enfolding' the external environment and spontaneously 'unfolding' its potential into highly reproducible or dynamically stable forms." "Biological Organization, Coherence, and Light Emission from Living Organisms," Mae-Wan Ho and Fritz-Albert Popp, Stein, Wilfred & Francisco Varela, Ed., Thinking About Biology, Addision-Wesley, 1993, p. 183-4.


"Ecologists, geobiologists, and plant pathologists, awe-struck by the diversity and complexity of species interactions, are frustrated by the paucity of information available about natural communities. Given the fact of differential growth rates, it can be demonstrated mathematically that in a constant environment and in the absence of interrelationships among organisms, some one species should always predominate and outgrow all the others. Observations of natural populations, especially in freshwater environments, show the opposite to be true: rarely does a single species exclude all others. Why stable dynamic equilibria of many hundreds of species in the various niches of the marine, freshwater, and terrestrial environments persist is not entirely understood. In spite of the nearly infinite biological potential for reproduction, balance is maintained. No matter if one frog lays 10,000 eggs or one mold disseminates 1,000,000 spores in a season; in the following season, only one frog lives and only one mold disseminates spores.

"Natural selection acts relentlessly throughout all stages of the life cycles of all organisms, yet all organisms are dependent on others for the completion of their life cycles. Never, even in spaces as small as a cubic meter, is a living community of organisms restricted to members of only a single species. Diversity, both morphological and metabolic, is the rule. Most organisms depend directly on others for nutrients and gases. Only photo-and chemoautrophic bacteria produce all their organic requirements from inorganic constituents; even they require food, gases such as oxygen, carbon dioxide, and ammonia, which, although inorganic, are end products of the metabolism of other organisms. Heterotrophic organisms require organic compounds as food; except in rare cases of cannibalism, this food comprises organisms of other species or their remains. Many heterotrophs are extraordinarily particular about their food sources; for example, some opisthobranchs choose only certain species of algae for their food and will starve rather than attempt to eat other, closely related algae. The lines between nutritional fussiness and dependency, parasitism, symbiosis, and other associations of different species are very fine; such interrelationships are always modulated by the environment. Many terms that distinguish different kinds of symbiosis have been defined--for example, mutualism, pathogenicity, commensalism, parasitism, parasymbiosis, phoresy, and biotrophism. So far as they desscribe only interspecific ecological relationships, they are misemphases--they obscure the genetic nature of the associations." Margulis, Lynn, Symbiosis in Cell Evolution, W.H. Freeman, 1981, pp. 162-4.


"The house of a caddis is strictly not a part of its cellular body, but it does fit snugly round the body. If the body is regarded as a gene vehicle, or survival machine, it is easy to see the stone house as a kind of extra protective wall, in a functional sense the outer part of the vehicle. It just happens to be made of stone rather than chitin. Now consider a spider sitting at the centre of her web. If she is regarded as a gene vehicle, her web is not a part of that vehicle in quite the same obvious sense as a caddis house, since when she turns round the web does not turn with her. But the distinction is clearly a frivolous one. In a very real sense her web is a temporary functional extension of her body, a huge extension of the effective catchment area of her predatory organs." Dawkins, Richard. The Extended Phenotype: The Long Reach of the Gene. Oxford University Press. 1989. P. 198.


"Plants put carbon dioxide into the soil, eroding crystalline rocks with chemical skill; they manufacture hydrocarbons, gels of silicic acid, nitrates, phosphates, and calcium ions. They rid the atmosphere of carbon dioxide, staving off the greenhouse effect. From the planetary point of view they are the only real good guys, heroes and patient employees of theliving Gaia, beings without claws, teeth, or blood. They sit calmly, silently, filled with green optimism, enjoying their self-sacrifice.

"But I think that the only reason we cling to this bucolic view of plant life is that we've never been green plants and hence don't know what their everyday life is like. We don't know the real ways of these humble producers of oxygen, these quiet and diligent little pumps in the planetary thermostat. When I really look at a meadow, I'm not sure that it isn't filled with battle screams, piercing cries of hate, terror, and pain, individuals and tribes fighting for nutrition, for light, for space, for carbon dioxide, for bacteria, for fungi; that it doesn't echo with the howls of the winners and losers, the songs of the nascent and the hymns of the dying--non-audible, vegetable cries, I'm not sure that the tender velvety mesh of branches, roots, bulbs, and stems is not really an interminable wrestling hold; that there isn't perpetual chemical warfare going on among roots, among root-stocks, and among seeds; that there isn't some limitless hyena-ism of the stronger ones against the weaker ones, sick ones, humiliated ones--all of which is obscured in our delusion of a great symbiotic tranquility, hidden behind the veil of a harmonic biocenosis....

"As a struggling gardener I detest the combative and vicious activity of plants. But as a negligible human individuum I have great admiration for the brave behavior of couch grass and timothy and thistles, which carry on and proceed with a victorious song through abandoned, half-neglected, and senescent gardens, stomping over the decaying bodies of the feeble, intellectual, pleasing cultivars. I have a high regard for the perfect athletic training and fitness of dandelions, nettles, wall cress, and bindweed, and I recognize certain traits of sorrels and plantains as admirable virtues, even though I have to fight them in my lawn." Harper's Magazine, May 1993, p. 26. Excerpt from Holub, Miroslav, Symbiotic Tranquility, translated by David Young.


“Stability of biological objects is maintained due to detection of defective objects with a lowered degree of organisation and their substitution for [=by] copies of normal objects retaining the initially high level of organisation. Normal objects must have time to produce their copies before they decay. The process of detection and elimination of decay objects requires energy and matter expenditures that are consumed by living beings from the environment. Thus, life can only exist on the basis of continuous metabolic processes of energy and matter exchange that take place within living objects. Detection of decay of the level of organisation of one biological object is ensured by competitive interaction of living objects. All these processes constitute the essence of stabilising selection. Any level of internal correlation of individuals in a populatin can be maintained over indefinitely long periods of time by stabilising selection.

“Individuals in a population are not correlated with each other. Competitive interaction between them is aggressive and occurs irrespective of abundance or shortage of resources. Each individual is characterised by a certain probability of losing the initial level of organisation (decay probability). A stationary population number is maintained due to reproduction of normal individuals retaining their competitiveness at the maximum level. In the absence of population and competitive interaction, any type of internal correlation of individuals decays and never arises again spontaneously. All the aforesaid refers equally to all types of biological correlation from molecular level up to ecological communities.” Gorshkov, Victor and Vadim Gorshkov and Anastassia Makarieva. Biotic Regulation of the Environment. Springer Verlag. 2000. pps. 49-50.


“As with all correlated associations, there cannot be aggressive competitive interaction between individuals of different species, i.e. under normal ecological conditions interspecific competition is completely absent from ecological communities. Interspecific competition may only take place in disturbed communities during the period of their recovery.” Gorshkov, Victor and Vadim Gorshkov and Anastassia Makarieva. Biotic Regulation of the Environment. Springer Verlag. 2000. pps. 46.


“[Bacteria are invariably the most abundant organisms in topsoils, with typical counts of 109–1010/g.] Fungi come next (104–106/g), but their much larger size and their often extensive networks of filamentous mycelia mean that they dominate microbial biomass in some ecosystems, particularly in forests.”

“Mycorrhizae are very common harvest mutualisms of plants and fungi, with some 90% of all plant species, and every conifer, being symbiotic with at least one or more kinds of fungi.” Smil, Vaclav. The Earth’s Biosphere. The MIT Press. 2003. p. 170, p. 221.


“We would like to propose another one by suggesting that when organisms niche construct, it is not just the organisms that evolve, because they are also likely to cause a more general coevolution in organism-environment systems by their niche construction. In arguing thus, we do not advocate the mere redescription of environmental change as evolution, which would constitute a purely semantic substitution. Instead we maintain that niche-constructed components of the environment are both products of the prior evolution of organisms and, in the form of modified natural selection pressures, causes of the subsequent evolution of organisms, and that as both products and causes of evolution, these environmental components need to be incorporated in evolutionary theory more fully than they are at present. It is in this sense that we see organisms and their environments as comprising coevolving systems.” Susan Oyama, Paul Griffiths & Russell Gray. Cycles of Contingency: Developmental Systems and Evolution. MIT Press. 2001. “Niche Construction, Ecological Inheritance, and Cycles of Contingency in Evolution.” Kevin Laland, F. John Odling-Smee & Marcus Feldman. p. 125.


“These are the metaphors of development, which carries the implication of an unfolding or unrolling of an internal program that determines the organism’s life history from its origin as a fertilized zygote to its death, and the metaphor of adaptation, which asserts that evolution consists in the shaping of species to fit the requirements of an autonomous external environment. That is, both in developmental and in evolutionary biology, the inside and the outside of organisms are regarded as separate spheres of causation with no mutual dependence. The burden of the essay is that these metaphors mislead the biologist because they fail to take account of the interactive processes that link the inside and the outside.” Lewontin, Richard. 2001. “Gene, Organism and Environment: A New Introduction.” Susan Oyama, Paul Griffiths & Russell Gray. Cycles of Contingency: Developmental Systems and Evolution. MIT Press. P. 55.


“...the standard definition equates evolution with genetic changes, rather than viewing evolution more expansively as a multileveled process in which genes, gene complexes, genomes, organisms, and the natural environment interact with one another and evolve together in a dynamic relationship of mutual and reciprocal causation, including (in the current jargon) ‘upward’ causation, ‘downward’ causation, and even ‘horizontal’ causation (i.e. between organisms). The emergence of ‘multilevel selection theory’ in biology during the past few years has been an important step in the right direction.” Corning, Peter. Nature’s Magic: Synergy in Evolution and the Fate of Mankind. Cambridge University Press. 2003. P. 169.


“The Synergism Hypothesis represents an extension of this line of reasoning. I call it ‘Holistic Darwinism,’ because the focus is on the selection of wholes, and the combinations of genes that produce those wholes. Simply stated, cooperative interactions of various kinds, however they may occur can produce novel combined effects–synergies–that in turn become the causes of differential selection. The ‘parts’ that are responsible for producing the synergies (and their genes) then become interdependent ‘units’ of evolutionary change. In other words, it is the ‘payoffs’ associated with various synergistic effects in a given context that constitute the underlying cause of cooperative relationships–and complex organization–in nature. The synergy produced by the ‘whole’ provides the functional benefits that may differentially favor the survival and reproduction of the ‘parts.’ Although it may seem like backwards logic, the thesis is that functional synergy is the underlying cause of cooperation (and organization) in living systems, not the other way around. To repeat, the Synergism Hypothesis is really, at heart, an ‘economic’ theory of complexity in evolution.” Corning, Peter. Nature’s Magic: Synergy in Evolution and the Fate of Mankind. Cambridge University Press. 2003. P. 117.


“... synergy is of central importance in virtually every scientific discipline, though it very often travels incognito under various aliases (mutualism, cooperativity, symbiosis, win-win, emergent effects, a critical mass, coevolution, interactions, threshold effects, even non-zero-sumness).” Corning, Peter. Nature’s Magic: Synergy in Evolution and the Fate of Mankind. Cambridge University Press. 2003. P. 5.


“The biosphere’s evolution is unimaginable without symbioses. We see them in the very formation of eukaryotic cells, in the intricate coevolutionary patterns in coral reefs–where about fifty fish and shrimp species act as cleaners of ectoparasites, often entering even into the gill chambers and mouth of the host fish–and in flowering plants and their pollinators. Without endosymbioses there would be no cattle husbandry and beef empires, and termites, those miniature tropical cows, could not process a large share of the biosphere’s litter fall.” Smil, Vaclav. The Earth’s Biosphere: Evolution, Dynamics, and Change. MIT Press. 2002. P. 225


“In theory, organisms can be decomposed into arrays of features (traits or characters), while environments can be decomposed into arrays of factors. A feature of an organism is only an adaptation if and when it is matched to a specific selection pressure arising from an environmental factor at a particular location, it is the product of national selection, and that it increases the fitness of the organism at that address and moment, for example, if it permits more efficient acquisition of a food resource. We interpret Bock (1980) as treating adaptation as a dynamic and historical process: current utility, that is, synergy between a feature and a factor, is not sufficient to label the feature an adaptive trait. Niche construction occurs when an organism modifies the functional relationship between itself and its environment by actively changing one or more of the factors in its environment either by physically perturbing these factors at its current address or by relocating to a different address, thereby exposing itself to different factors.” Oyama, Susan, Paul Griffiths, and Russell Gray, editors. Cycles of Contingency: Developmental Systems and Evolution. MIT Press. 2001. Laland, Kevin, John Odling-Smee, and Marcus Feldman. “Niche Construction, Ecological Inheritance, and Cycles of Contingency in Evolution.” P. 118.


“... organisms not only adapt to environments, but in part also construct them. They may also do so across a huge range of temporal and spatial scales stretching, for example, from a hole bored in a tree by an insect, to the contribution of cynobacteria to the earth’s 21 percent oxygen atmosphere, as a consequence of millions of years of photosynthesis. Niche construction starts to take on a new significance when it is acknowledged that, by changing their world, organisms modify many of the selection pressures to which they and their descendants are exposed, and that this may change the nature of the evolutionary process.” Oyama, Susan, Paul Griffiths, and Russell Gray, editors. Cycles of Contingency: Developmental Systems and Evolution. MIT Press. 2001. Laland, Kevin, John Odling-Smee, and Marcus Feldman. “Niche Construction, Ecological Inheritance, and Cycles of Contingency in Evolution.” P. 119.


“The first consequence [of niche construction on evolution] is that traits whose fitness depends on sources of selection that are alterable by niche construction (recipient traits) coevolve with traits that alter sources of selection (niche-constructing traits). This results in very different evolutionary dynamics for both traits from what would occur if each had evolved in isolation. Selection resulting from niche construction may drive populations along alternative evolutionary trajectories, may initiate new evolutionary episodes in an unchanging external environment, and may influence the amount of genetic variation in a population, by affecting the stability of polymorphic equilibria.

“Moreover, because of the multigenerational properties of ecological inheritance, niche construction can generate unusual evolutionary dynamics. This is because when ecological inheritance is involved, the evolution of the recipient trait depends on the frequency of the niche-constructing trait over several generations. For instance, timelags were found between the onset of a new niche-constructing behavior, and the response of a population to a selection pressure modified by this niche construction. These timelags generated an evolutionary inertia, where unusually strong selection is required to move a population away from an equilibrium, and a momentum, such that populations continue to evolve in a particular direction even if selection pressures change or reverse.” Oyama, Susan, Paul Griffiths, and Russell Gray, editors. Cycles of Contingency: Developmental Systems and Evolution. MIT Press. 2001. Laland, Kevin, John Odling-Smee, and Marcus Feldman. “Niche Construction, Ecological Inheritance, and Cycles of Contingency in Evolution.” Pps. 121-2.

“They comprise ‘facultative’ or ‘open’ developmental processes that are based on specialized information-acquiring subsystems in individual organisms, such as brain-based learning in animals or the immune system in vertebrates. We regard these subsystems as particularly interesting forms of phenotypic plasticity because they are capable of additional, individually based information acquisition, again relative to particular environments. Unlike other developmental influences on the phenotype, these systems are adaptive traits selected precisely because of their information-gathering quality. This allows learned knowledge to guide niche construction in many animal species.” Oyama, Susan, Paul Griffiths, and Russell Gray, editors. Cycles of Contingency: Developmental Systems and Evolution. MIT Press. 2001. Laland, Kevin, John Odling-Smee, and Marcus Feldman. “Niche Construction, Ecological Inheritance, and Cycles of Contingency in Evolution.” P. 123.


“Instead we maintain that niche-constructed components of the environment are both products of the prior evolution of organisms and, in the form of modified natural selection pressures, causes of the subsequent evolution of organisms, and that as both products and causes of evolution, these environmental components need to be incorporated in evolutionary theory more fully than they are at present. It is in this sense that we see organisms and their environments as comprising coevolving systems.” Oyama, Susan, Paul Griffiths, and Russell Gray, editors. Cycles of Contingency: Developmental Systems and Evolution. MIT Press. 2001. Laland, Kevin, John Odling-Smee, and Marcus Feldman. “Niche Construction, Ecological Inheritance, and Cycles of Contingency in Evolution.” P. 125.


“... to varying degrees, organisms choose their own habitats, choose and consume resources, generate detritus, construct important components of their own environments (such as nests, holes, burrows, paths, webs, pupal cases, dams, and chemical environments), and destroy other components.”

...
“Niche construction is not the exclusive prerogative of large populations, keystone species or clever animals; it is a fact of life. All living organisms take in materials for growth and maintenance, and excrete waste products. It follows that, merely by existing, organisms must change their local environments to some degree.” Oyama, Susan, Paul Griffiths, and Russell Gray, editors. Cycles of Contingency: Developmental Systems and Evolution. MIT Press. 2001. Laland, Kevin, John Odling-Smee, and Marcus Feldman. “Niche Construction, Ecological Inheritance, and Cycles of Contingency in Evolution.” P. 117.


“The Synergism Hypothesis represents an extension of this line of reasoning. I call it ‘Holistic Darwinism,’ because the focus is on the selection of wholes, and the combinations of genes that produce those wholes. Simply stated, cooperative interactions of various kinds, however they may occur, can produce novel combined effects - synergies - that in turn become the causes of differential selection. The ‘parts’ that are responsible for producing the synergies (and their genes) then become interdependent ‘units’ of evolutionary change. In other words, it is the ‘payoffs’ associated with various synergies effects in a given context that constitute the underlying cause of cooperative relationships - and complex organization - in nature. The synergy produced by the ‘whole’ provides the functional benefits that may differentially favor the survival and reproduction of the ‘parts.’ Although it may seem like backwards logic, the thesis is that functional synergy is the underlying cause of cooperation (and organization) in living systems, not the other way around. To repeat, the Synergism Hypothesis is really, at heart, an ‘economic’ theory of complexity in evolution.” Corning, Peter. Nature’s Magic: Synergy in Evolution and The Fate of Humankind. Cambridge University Press. 2003. p. 117.


“More important, our respect for the ‘cognitive’ abilities of various animals continues to grow. Innumerable studies have documented that many species are capable of sophisticated cost-benefit calculations, sometimes involving several variables, including the perceived risks, energetic costs, time expenditures, nutrient quality, resource alternatives, relative abundance, and more. Animals are constantly required to make ‘decisions’ about habitats, foraging, food options, travel routes, nest sites, even mates. Many of these decisions are under tight genetic control, with ‘preprogrammed’ selection criteria. But many more are also, at least in part, the products of past experience, trial-and-error learning, observation, and even, perhaps, some insight learning. Corning, Peter. Nature’s Magic: Synergy in Evolution and The Fate of Humankind. Cambridge University Press. 2003. p. 163.


“There is no contradiction or competition between self-organization and natural selection. Instead, it is a cooperative ‘marriage’ in which self-organization allows tremendous economy in the amount of information that natural selection needs to encode in the genome. In this way, the study of self-organization in biological systems promotes orthodox evolutionary explanation, not heresy.” Camazine, S., et al. Self-Organization in Biological Systems. Princeton University Press. 2001. p. 89. Quoted in Corning, Peter. Nature’s Magic: Synergy in Evolution and The Fate of Humankind. Cambridge University Press. 2003. p. 288.


“The reductionist hypothesis does not by any means imply a ‘constructionist’ one: The ability to reduce everything to simple fundamental laws does not imply the ability to start from the laws and reconstruct the universe... The constructionist hypothesis breaks down when confronted with the twin difficulties of scale and complexity... Anderson, P.W. “More is Different: Broken Symmetry and the Nature of the Hierarchical Structure of Science.” (1972) Science, 177: 393-6. Quoted in Corning, Peter. Nature’s Magic: Synergy in Evolution and The Fate of Humankind. Cambridge University Press. 2003. p. 296.


“Up to now, physicists looked for fundamental laws true for all times and all places. But each complex system is different; apparently there are no general laws for complexity. Instead one must reach for ‘lessons’ that might, with insight and understanding, be learned in one system and applied to another. Maybe physics studies will become more like human experience.” Goldenfeld, N., and L.P. Kadanoff. “Simple Lessons from Complexity.” (1999) Science, 284: 87-89. Quoted in Corning, Peter. Nature’s Magic: Synergy in Evolution and The Fate of Humankind. Cambridge University Press. 2003. p. 323.


“Recall that power is defined as energy per unit time. Energy, in turn, is expressed as force times distance, or mass times the square of velocity. Mass, distance, force, speed, energy, and duration are therefore all potential components of power. An entity’s power increases if any or all of the first four of these components increases, or if the sixth (duration) is reduced. Ecologically, this means that powerful entities are large, fast, wide-ranging, rapidly metabolizing units capable of exerting strong forces, storing and regulating resources, and responding appropriately to a wide variety of circumstances. Power makes for prolific producers and demanding consumers with a wide reach.” Vermeij, Geerat. Nature: An Economic History. Princeton University Press. 2004. P. 124.


“In all economies, I suggest, efficiency becomes important when power is low and output cannot be increased in absolute terms. This occurs when energy or raw materials are sufficiently scarce that reducing the cost of acquiring them is the only way of not losing ground. Increases in power, however, are sufficiently beneficial that considerations of efficiency are secondary, especially if productivity also benefits the supply of raw necessities. In such cases, absolute performance is far more important than efficiency. Thus it pays to be efficient for subordinate members of an economy, and it pays to increase in performance for those in power.” Vermeij, Geerat. Nature: An Economic History. Princeton University Press. 2004. P. 125.


“High speed, rapid acceleration, and keen vision are among the capacities that in animals are made possible by the dedication of a large proportion of body mass to muscles and other organs rich in mitochrondria and very high in energy demand.” Vermeij, Geerat. Nature: An Economic History. Princeton University Press. 2004. P. 134.


“I would argue, for example, that internal fertilization is a means of exposing eggs and sperm and their bearers to more efficient selection, with the result that offspring will be fitter on average.” (Comparison to earlier, water-born fertilization) Vermeij, Geerat. Nature: An Economic History. Princeton University Press. 2004. P. 143.


“... the sexual selection related to mate choice powerfully amplifies top-down consumer-related selection. My point here is that it also makes the process of selection more effective in that it reduces the chance, and increases the role of competition with respect to offspring performance.

“Perhaps the most sweeping manifestation of concentrated, coordinated power to emerge from simple, locally communicating, semiautonomous components is intelligence. When many components acting in parallel use the same few rules to accept or reject available choices, the whole adapts, or learns; it develops a better hypothesis of its environment. The emergent collective intelligence is thus a largely reactionary capacity, an ability to predict, to organize information in ways that benefit the whole.” Vermeij, Geerat. Nature: An Economic History. Princeton University Press. 2004. P. 144.

“G. Evelyn Hutchinson pointed out long ago that many protists are at home in both fresh- and saltwater, a distribution that is rare among more complex animals except among physiologically specialized vertebrates. In effect, these organisms observe few boundaries; for them, the world is a far more homogeneous place than is the world as perceived by most animals and plants.” Vermeij, Geerat. Nature: An Economic History. Princeton University Press. 2004. P. 171.


“Ways of classifying spatial structure vary according to the size, movements, and sensory apparatus of organisms. Economic geography on the scale familiar to humans thus emerged as the sizes of living things increased, and as the specialization that accompanies trade-offs in competition came to be expressed at larger spatial scales. Where millimeter-scale or smaller variations might have mattered most in the unicellular economies of Archean eon, spatial structure on larger scales became important for larger life forms in the succeeding Proterozoic and especially the Phanerozoic eons.” Vermeij, Geerat. Nature: An Economic History. Princeton University Press. 2004. P. 172.


“The general decrease in performance observed with increasing latitude, increasing water depth, decreasing salinity, greater sediment depth, decreasing rainfall, higher altitude, and other gradients has evidently been stable through out the history of life. This is not the case, however, with the gradient between sea and land. Whereas the dry land began as a less productive environment than the sea, the tables turned when land plants reached the size of trees about 370 million years ago. Not only did this mean a reversal in the gradient of top economic performance, but it also changed the pattern of evolutionary invasion between these two physically contrasting environments.” Vermeij, Geerat. Nature: An Economic History. Princeton University Press. 2004. P. 179.


“It is not surprising that warm-blooded animals, which maintain high constant body temperatures during times of activity in the face of wide variation in the temperature of their surroundings, show no obvious latitudinal patterns of adaptation.” Vermeij, Geerat. Nature: An Economic History. Princeton University Press. 2004. P. 177.


“No later than 300 Ma in the Late Carboniferous, terrestrial productivity and perhaps the competitive performance of economic dominants began to exceed those in the adjacent coastal ecosystems of the sea. Globally, opportunity on the land was greater than in the sea, but so was resistance from marine incumbents and competitive pressure among high-energy species. These relationships did not prevail everywhere, of course. To this day, deserts and polar regions on land remain much less productive than nearby inshore waters. Resistance from terrestrial competitors normally prevents marine species from colonizing the dry land, but on small islands they may have been weak enough to allow a few animals to colonize from the sea.” Vermeij, Geerat. Nature: An Economic History. Princeton University Press. 2004. P. 182.


“Temperature regulation, extensive movement by individuals, and other economic characteristics of advanced top consumers are ultimately made possible by favorable circumstances controlled by geological processes beyond the control of organisms, but once they have evolved, and provided they can withstand or rapidly recover from the inevitable disturbances that affect economies from time to time, they provide the economy with an increasingly strong and persistent feedback and control mechanism that increasingly generates and tests innovations and new emergent structures regardless of external conditions.” Vermeij, Geerat. Nature: An Economic History. Princeton University Press. 2004. P. 201.


“In human history as well as in the history of life as a whole, we can discern a general shift from external, bottom-up disruptions to crises created within economies themselves. Extinctions driven by climates, volcanic eruptions, and above all by celestial impacts will surely occur again, but relentless and cumulative selection has perhaps increasingly protected survivors from previous catastrophes from subsequent bottom-up disruptions. In a parallel way, climate-related famines have been largely absent in the last 150 years of human history. By contrast, extinctions due to other, mostly powerful, species may have become increasingly common through geological time. In the same way, economic disruptions stemming from human activities may have become more frequent and more destructive. The cause for this shift is the same in the human and nonhuman realm: intense competition, fed by an increasingly prolific and reliable supply system, has produced more powerful agents and larger, more productive economies, which have correspondingly acquired greater abilities to disrupt and destroy as well as to spread wealth.” Vermeij, Geerat. Nature: An Economic History. Princeton University Press. 2004. P. 241.


“Within limits imposed by external conditions and by existing technology, economic systems tend to increase in productivity, diversity, and opportunity, powered by positive feedbacks to yield increasingly powerful top competitors, which collectively restrict less powerful entities to parts of the economy where power, productivity, and the intensity (or stakes) of competition are lower. They also increase the rate of supply and the predictability of resources, with the result that the realm of regulation expands while that of uncertainty and external dependence recedes.” Vermeij, Geerat. Nature: An Economic History. Princeton University Press. 2004. P. 246-7.


“This pre-Cambrian universal microbial loop of the plankton, which for the most part failed to produce a surplus usable by larger consumers, was replaced near the beginning of the Cambrian by an ecosystem in which animals living in the plankton as well as on the seafloor converted excess production into larger bodies. There was, in other words, a revolutionary transformation from a subsistence economy with little top-down control and modestly developed anticonsumer defenses among the primary producers, to a more complex economy productive enough to support large populations of larger, actively metabolizingg consumers, which began to exercise strong evolutionary control on their food organisms. Thanks to this top-down influence, planktonic acritarchs beginning in the Tommotian time during the Early Cambrian developed spines as defenses against consumers. Moreover, consumers initiated or greatly amplified positive feedbacks between consumption and the nutrient supply for primary producers. With the advent of these animals, therefore, the biosphere entered what we might call the consumer age. The economic regime of the Proterozoic eon gave way over an interval of perhaps tens of millions of years to the new order of the Phanerozoic eon.” Vermeij, Geerat. Nature: An Economic History. Princeton University Press. 2004. P. 261-2.


“With their appearance [fungi] and with that of land plants, the rate of chemical weathering and soil formation on land may have risen by a factor of ten, contributing not only to a huge increase in productivity on land but also to an enormous enrichment of the nutrient base in the oceans.” Vermeij, Geerat. Nature: An Economic History. Princeton University Press. 2004. P. 268.


“Production by plants, herbivory by animals, and decomposition by a diverse array of microbes and fungi and animals went hand in hand, all contributing to land vegetations in which nutrients move rapidly and through many organisms in a self-made microclimate that is particularly amenable to plant growth and consumer sustenance.” Vermeij, Geerat. Nature: An Economic History. Princeton University Press. 2004. P. 276.


“The origin and evolution of skeletons, which affected at least eight phylum-level clades independently during the latest Neoproterozoic and Early Cambrian, therefore can be ascribed in large part to the emergence of predators whose modus operandi includes breaking and entering.” Vermeij, Geerat. Nature: An Economic History. Princeton University Press. 2004. P. 277.


“Ancient predators moved slowly and probably detected victims at short distances or upon contact; many more derived ones were fast and could recognize prey from far away.” Vermeij, Geerat. Nature: An Economic History. Princeton University Press. 2004. P. 277.


“By the Late Devonian, cephalopods with coiled shells had surpassed the straight and curved ones in diversity, indicating a general rise in locomotor performance through time.” Vermeij, Geerat. Nature: An Economic History. Princeton University Press. 2004. P. 284.


“Even groups that led sedentary lives in the Paleozoic gave rise to clades of motile animals in the Mesozoic and Cenozoic.” Vermeij, Geerat. Nature: An Economic History. Princeton University Press. 2004. P. 285.


“As is the case with rapid and powerful methods of predation, the derived, rapid, sustained locomotion of top predators and the increased emphasis on locomotion in many victim species were superimposed on older, less energy-intensive means retained by animals with smaller energy budgets. To some, these trends exemplify only an increase in the range of functional possibilities, practically a statistical necessity if overall diversity is increasing. To me, however, the generally increasing performance of the most powerful members of successive ecosystemss represents a general raising of the bar, not just for the top predators that lead the way, but for many of the species with which they interact.” Vermeij, Geerat. Nature: An Economic History. Princeton University Press. 2004. P. 286.


“Power-enhancing innovations arise preferentially in the most productive economies and spread outward in space and forward in time.” Vermeij, Geerat. Nature: An Economic History. Princeton University Press. 2004. P. 289.


“... mammals and birds seem to obey the rule that the number of co-occurrring species increases exponentially with area among islands in an archipelago. Insects, plants, parasites, and marine invertebrates are much more lawless. Numbers of their species vary greatly even among islands or habitats of the same area. There are no well-defined upper limits to diversity, meaning that many potential ways of making a living are not realized.” Vermeij, Geerat. Nature: An Economic History. Princeton University Press. 2004. P. 294.


“Perhaps from the very beginning of metabolism, production and other forms of economic work have depended on the ability of entities–molecules and unicells at first, multicellular organisms and societies later–to store energy and material resources for subsequent use. If a resource is used as soon as it is acquired, any interruption in supply of that resource means serious economic disruption for the entity in question.” Vermeij, Geerat. Nature: An Economic History. Princeton University Press. 2004. P. 109.


“In many aquatic ecosystems, three more or less distinct categories of primary producers exist, which differ in their competitive method. At the weedy extreme are phytoplankton, which can efficiently and rapidly take up nutrients and compete for light with attached seaweeds and plant-animal partnerships. The addition of nutrients through upwelling or through human agency typically results in plankton blooms. The second level of weediness is represented by annual attached seaweeds, which in the absence of grazers quickly overgrow, shade out, and inhibit recruitment of perennial species. Experiments by Boris Worm in the Baltic Sea have demonstrated that the nutrient enrichment that has characterized the marine ecosystems of this region and of many other coastal waters around the world has favored annual seaweeds at the expense of longer-lived rockweeds, kelps, and red algae. On reefs, the addition of nutrients and the removal of grazers similarly favors ephemeral fleshy algae over photosynthesizing corals and encrusting coralline algae. Perennials, the third and least weedy category of primary producers, persist in the face of intense grazing by virtue of sophisticated chemical and architectural defenses, which tend to be incompatible with rapid growth. Where grazers are present under a regime of high nutrient supply, as in reefs along continental coastlines and on many surf-swept shores around the world, all these types of primary producer coexist, the weeds being held in check by grazers; but where grazers are removed, the perennials are imperiled, and the weedy species take over.” Vermeij, Geerat. Nature: An Economic History. Princeton University Press. 2004. P. 108


.The distinction between opportunists and more permanent entities seems to be very general. Parasites that kill their host must find another before the death of their host kills them as well.” Vermeij, Geerat. Nature: An Economic History. Princeton University Press. 2004. P. 109.


“...predators tend to outperform their victims in sensation, locomotion, and the use of force, but typically not in such passive attributes as large size, toxicity, and skeletal strength.” Vermeij, Geerat. Nature: An Economic History. Princeton University Press. 2004. P. 111.


“Great works of nature and of humanity all have something in common: they exemplify power. The competitively dominant producers provide food, create structure, offer shelter and living space for others, modify the environment of life, and even in death nourish their surroundings, chiefly to their own advantage but also to the benefit of many other members of their economy. The dominant consumers regulate when, where, and how the economic units with which they interact make their livings, and determine the adaptive responses that producers and fellow consumers deploy to defend themselves and the resources they control.” Vermeij, Geerat. Nature: An Economic History. Princeton University Press. 2004. P. 122.


“Microorganisms use sunlight and organic energy sources as well but, in addition, use many other chemical energy sources, some of which are toxic to plants and/or animals. Perhaps the most remarkable of these are reduced inorganic compounds such as hydrogen sulfide, methane, hydrogen gas, carbon monoxide, ammonia, and ferrous ion. Furthermore, organic compounds–including hydrocarbons, halogenated organic compounds, and lignin–many of which are toxic or refractory to decomposition by plants and animals, can be used by one or more microbial groups as carbon sources for growth. Staley, James T. “A Microbiological Perspective of Biodiversity” in Staley, James & Anna-Louise Reysenbach, Ed. Biodiversity of Microbial Life. Wiley-Liss. 2002. Pps. 10-11.


“... plants and animals have succeeded in evolving into niches not available to microorganisms. The sessile plants have successfully colonized terrestrial environments on Earth by taking advantage of their large light-harvesting structures that emerge above ground. In so doing, they are exposed to the desiccating effects of the atmosphere with which typical photosynthetic bacteria and algae cannot cope. Like the algae, however, the plants still rely on the cyanobacterial chloroplast to carry out their photosynthesis. In turn, these large plants have created new niches that have led to the evolution of macroscopic animals that rely on plant, animal, and microbial organic matter as their energy source. It is also interesting to note that plants have not displaced microorganisms from their niches. In fact, they and the animals have provided additional niches for microbial symbionts.” Staley, James T. “A Microbiological Perspective of Biodiversity” in Biodiversity of Microbial Life. Edited by James Staley & Anna-Louise Reysenbach. Wiley-Liss. 2002. P.11.


“In contrast [to microbes which have a monopoly on life without air], plants and animals and many microorganisms are restricted to the use of oxygen as an electron acceptor in aerobic respiration.” Staley, James T. “A Microbiological Perspective of Biodiversity” in Biodiversity of Microbial Life. Edited by James Staley & Anna-Louise Reysenbach. Wiley-Liss. 2002. P. 11.


“Because they are of micron-size, microorganisms fit very nicely into microphysical habitats and microchemical gradients where energy sources and electron acceptors are available.” Staley, James T. “A Microbiological Perspective of Biodiversity” in Biodiversity of Microbial Life. Edited by James Staley & Anna-Louise Reysenbach. Wiley-Liss. 2002. Pps. 11-12.


“Not only is the bacterial species concept more typological and less evolutionary than plants and animals but it is much broader and more inclusive. For example, from a molecular standpoint, a typical species like Escherichia coli has as much or more diversity than all of its primate host species.” Staley, James T. “A Microbiological Perspective of Biodiversity” in Biodiversity of Microbial Life. Edited by James Staley & Anna-Louise Reysenbach. Wiley-Liss. 2002. P. 19.


“No doubt many microbial specialists still remain unknown to microbiologists becasue we have not been clever enough to understand how they make their living and, therefore, have not yet designed an artificial environment in a test tube that will permit them to grow.” Staley, James T. “A Microbiological Perspective of Biodiversity” in Biodiversity of Microbial Life. Edited by James Staley & Anna-Louise Reysenbach. Wiley-Liss. 2002. P.20.


“Ontogeny is a condition-sensitive, bifurcating process that allows and even promotes polymodal adaptation.” West-Eberhard, Mary Jane. Developmental Plasticity and Evolution. Oxford University Press. 2003. P. 10.


“Yet if we accept the dual nature of the phenotype–the undeniable fact that the phenotype is a product of both genotype and environment, and the equally undeniable fact that phenotypes evolve, there is no escape from the conclusion that evolution of a commonly recognized sort can occur without genetic change.” West-Eberhard, Mary Jane. Developmental Plasticity and Evolution. Oxford University Press. 2003. P. 17.


“I believe that there is a connection between the neglect of environmental influence in development and the lack of an adequate theory of biological organization.” West-Eberhard, Mary Jane. Developmental Plasticity and Evolution. Oxford University Press. 2003. P. 19.


“... the environment is not only an agent of selection but also a determinant of the range of phenotypes exposed to selection.” West-Eberhard, Mary Jane. Developmental Plasticity and Evolution. Oxford University Press. 2003. P. 27.

“Environment means the world outside a trait or individual of focal reference. The external environment, meaning the environment external to an individual, is sometimes broken down for special purposes into the physical environment, the biotic environment, the social environment, and so forth. The internal environment, meaning the environment within an individual, includes such factors as gene products, cells or growing tissues of different kinds, body temperature, and so on.” West-Eberhard, Mary Jane. Developmental Plasticity and Evolution. Oxford University Press. 2003. P. 32.


“The phenotype includes all traits of an organism other than its genome.” West-Eberhard, Mary Jane. Developmental Plasticity and Evolution. Oxford University Press. 2003. P. 31.


“Plasticity (responsiveness, flexibility) is the ability of an organism to react to an internal or external environmental input with a change in form, state, movement, or rate of activity. It may or may not be adaptive (a consequence of previous selection). Plasticity is sometimes defined as the ability of a phenotype associated with a single genotype to produce more than one continuously or discontinuously variable alternative form of morphology, physiology, and/or behavior in different environmental circumstances.” West-Eberhard, Mary Jane. Developmental Plasticity and Evolution. Oxford University Press. 2003. P. 33.


“Of these two properties [plasticity and modularity], plasticity is probably the more fundamental, for the ability to replicate, which distinguishes organic from inorganic nature, requires molecules which are interactive and precisely responsive–adaptively plastic. So plasticity must have been an early universal property of living things. The universality of modularity is a secondary, or ‘emergent’ result of the universality of plasticity. Any organism whose size, whether due to accretion or growth, is large enough to create internal environmental differences, such as those between the inner and the outer regions of a clump of material, has the potential for regional internal differentiation. As differentiation evolves to produce specialized parts and an internal division of labor, internal heterogeneity gives rise to conditional switches between developmental pathways. The result is a structure characterized by somewhat discrete parts–modularity. Thus, given plasticity as a universal property of living matter, modularity follows.” West-Eberhard, Mary Jane. Developmental Plasticity and Evolution. Oxford University Press. 2003. P. 34.


“Modularity is an aspect of phenotype organization at all levels, from the amino acid residues that compose a protein, through the separation of functions within and between cells, the segmentation of body parts, and other aspects of animal morphology, to the organization behavior and of societies with divisions of labor among individuals.” West-Eberhard, Mary Jane. Developmental Plasticity and Evolution. Oxford University Press. 2003. P. 62.


“A switch point refers to a point in time when some element of a phenotype changes from a default state, action, or pathway to an alternative one–it is activated, deactivated, altered, or moved. It is a useful concept because it can apply to any phenotypic change at any level of organization. A switch point is the locus of operation of the mechanisms of responsiveness and the influence of the genetic and environmental factors that affect response thresholds.” West-Eberhard, Mary Jane. Developmental Plasticity and Evolution. Oxford University Press. 2003. P. 67.


“A switch implies some change in state, for example, between on and off, under certain conditions. If a process were constantly on or off regardless of conditions, there would be no operative switch. So condition sensitivity is an implicit quality of all switches. The mark developmental decision points that depend on conditions. Conditions in this case may refer to the internal environment, the social environment, or the external environment.” West-Eberhard, Mary Jane. Developmental Plasticity and Evolution. Oxford University Press. 2003. P. 68.


“What distinguishes behavior from morphological plasticity, then, is neither condition sensitivity nor freedom from genetic influence on component elements. Rather, it is the greater time delay between gene expression and gene-product use, and the number and reversibility of permutations or reorganizations of elements that can occur during the lifetime of an individual. Phenotypic recombination, or reorganization of the phenotype during development or evolution, resulting in the assembly of new combinations of traits, is common during the ontogeny of morphology, especially at the molecular level. It is one form of pleiotropy, for the protein products of a single gene may be incorporated into several or many phenotypic traits at different levels of organization. But ontogenetic phenotypic recombination of behavioral subunits is far more extensive. This has been succinctly stated by Trewavas and Jennings in contemplating the differences between plants, which are noted for their physiological and morphological plasticity, and animals, noted for their behavioral plasticity: ‘The adaptiveness of animals lies in the brain, in the almost endless number of combinations in which the different tissues can be made to work together to produce different types of behavior.’” West-Eberhard, Mary Jane. Developmental Plasticity and Evolution. Oxford University Press. 2003. P. 77. [Subquote from Trewavas, A. J. and Jennings, D.H. 1986. Introduction. In: Plasticity in Plants, D.H. Jennings and A.J. Trewavas (eds.). Symposia of the Society for Experimental Biology, No. 40. Company of Biologists Limited, Cambridge, pp. 1-4.]


“The coexpressed traits whose expression or use is governed by a single switch are pleiotropic effects of the genes that influence the switch. As a result, they may show high phenotypic and genetic correlations due to their coordinated expression and selection as a functional set. In effect, the coexpressed traits are developmentally, rather than chromosomally linked.” West-Eberhard, Mary Jane. Developmental Plasticity and Evolution. Oxford University Press. 2003. P. 77.


“Developmental switches create genetic correlations within traits and break genetic correlations between traits.” West-Eberhard, Mary Jane. Developmental Plasticity and Evolution. Oxford University Press. 2003. P. 77.


“Similarly, under sexual selection the genetic correlations of a Fisherian runaway process involving male signals and female preference derive not from chromosomal linkage but from the highly coordinated and interdependent interactions of male and female. To the degree that they are genetically correlated, signal and response in effect develop as a single socially coordinated unit.” West-Eberhard, Mary Jane. Developmental Plasticity and Evolution. Oxford University Press. 2003. P. 78.


“Fentress succinctly expressed the relation between modularity and connectedness in behavior: ‘If interactions were the only feature we would end up with so much homogenous soup, whereas if extreme compartmentalization were the rule there would be no way to obtain organized action.’” West-Eberhard, Mary Jane. Developmental Plasticity and Evolution. Oxford University Press. 2003. P. 82. [Subquote from Fentress, J.C. 1983. A view of ontogeny. In: Structure, Development and Function. J. Eisenberg and D. Kleiman (eds.). Special Publications American Society of Mammalogists 7:24-64.]


“... one can emphasize the modular nature of a subindividual trait such as the vertebrate skull, or the fact that bony components of skulls are continuously variable and finely accommodated during interactive growth that cannot be described in terms of rigid isolated pathways for each part.” West-Eberhard, Mary Jane. Developmental Plasticity and Evolution. Oxford University Press. 2003. P. 84.


“[choice is] differential responsiveness to different alternatives.” West-Eberhard, Mary Jane. Developmental Plasticity and Evolution. Oxford University Press. 2003. P. 97.


“The nature-nurture dichotomy disappears with the realization that the developing phenotype responds to both internal and external stimuli in much the same way.” West-Eberhard, Mary Jane. Developmental Plasticity and Evolution. Oxford University Press. 2003. P. 99.


“Possession of a particular trait rather than an alternative trait can be either genetically or environmentally determined, but regulation–the mechanism or the process–can never be determined by genes or environment alone, because the mechanism is an aspect of structure, and structure is always a product of both genetic and environmental influence. There is no exception to this universal law of dual environmental-genetic influence.” West-Eberhard, Mary Jane. Developmental Plasticity and Evolution. Oxford University Press. 2003. Pps. 99-100.


“When dealing with plastic traits, then, one cannot ignore the dual role of the environment in determining the strength of selection and the course of evolution: the environment is not only the agent of selection in the sense of being the arena where phenotypes are evaluated in a game of survival and reproductive success. It is also an agent of development, which by interacting differently with different available genotypes sets the phenotypes in the positions where they will be seen by selection.” West-Eberhard, Mary Jane. Developmental Plasticity and Evolution. Oxford University Press. 2003. P. 101.


“...environmentally induced novelties may have greater evolutionary potential than do mutationally induced ones. They can be immediately recurrent in a population; are more likely than are mutational novelties to correlate with particular environmental conditions and be subjected to consistent (directional) selection; and, being relatively immune to selection, are more likely to persist even though initially disadvantageous.” West-Eberhard, Mary Jane. Developmental Plasticity and Evolution. Oxford University Press. 2003. P. 498.


“The development of precise neural connections requires nerve activity. In the case of the visual system, such activity is normally provided by an environmental factor–light. In mammalian fetuses, which develop in uterine darkness, there is a kind of head-start program that enables visual centers to develop precise connections without light. During a critical period of visual development, when the retinal cells are forming patterned connections in the lateral geniculate nucleus of the brain, retinal ganglion cells mimic the effect of light by producing spontaneous, synchronously generated bursts of action potentials. Not only do they stimulate the requisite nerve activity, but they do so in pulses followed by periods of inactivity, a pattern that optimizes coordinated connections and allows axons from the two eyes to sort out in a fashion approximating the topographically separate organization that characterizes the adult visual system. By simulating the environmental information provided by light, this allows neural development to proceed prenatally, in the dark of the uterus.” West-Eberhard, Mary Jane. Developmental Plasticity and Evolution. Oxford University Press. 2003. P. 111.


“A fully provisioned insect egg is 1000 to 10,000 times the volume of the original germ cell.” West-Eberhard, Mary Jane. Developmental Plasticity and Evolution. Oxford University Press. 2003. P. 114.


“In social and symbiotic organisms, there is a level above the individual in the hierarchy of influences on trait expression: trait expression can be manipulated by other individuals. That is, interchangeability can be achieved by changes in the social environment. In stingless bees, the evolution of increased genetic influence on caste determination has occurred in a lineage with primarily nutritional determination. This was achieved via a social manipulation of development that in effect created a genocopy of the ancestral, conditional trait. In stingless bees, with nutrition-dependent caste determination, workers build dimorphic cells, with queen-producing cells much larger and more heavily provisioned than worker-producing cells. In the Melipona species, with increased genotypic determination of caste, the brood manipulation performed by workers resembles that of laboratory scientists who wish to expose genotypic influence in a condition-sensitive trait. As if controlling environmental variables, workers make brood cells of nearly uniform size, and this is associated with increased uniformity in the distribution of provision among cells, thereby creating more nearly uniform rearing conditions.” West-Eberhard, Mary Jane. Developmental Plasticity and Evolution. Oxford University Press. 2003. P. 128.


“Spatial proximity plays a role in developmental and functional integration at every level of organization. At the molecular level, coordinately transcribed segments of DNA occur together or are brought together by devices such as RNA splicing and transposons. At the cellular level, migration and aggregation or ‘condensation’ precede coordinated differentiation of cells. At the organ level, contiguous tissues of different embryological origin form integrated structures such as the eye, the mandible, the stomach, or a limb. At supraindividual levels of organization, in the evolution of social life, the first essential organizing step is spatial contiguity, or group formation, just as in the evolution of multicellular organisms the first step was likely cell aggregation, either through migration and mutual attraction or by staying together following multiplication (population viscosity).” West-Eberhard, Mary Jane. Developmental Plasticity and Evolution. Oxford University Press. 2003. P. 135.


“The causal chain of adaptive evolution begins with development. Development, or ontogenetic change induced by genomic and environmental factors, causes phenotypic variation within populations. If the phenotypic variation caused by developmental variation in turn causes variation in survival and reproductive success, this constitutes selection. Then, if the phenotypic variation that causes selection has a genetic component, this causes evolution, or cross-generational change in phenotypic and genotypic frequencies. Selection depends upon phenotypic variation and environmental contingencies only; it does not require genetic variation. But genetic variation is required for selection to have a cross-generational effect–an effect on evolution.” West-Eberhard, Mary Jane. Developmental Plasticity and Evolution. Oxford University Press. 2003. P. 141.


“Given the causal chain of events in adaptive evolution, all that is required for adaptive evolution to occur is intraspecific recurrence and heritability of a developmental novelty.” West-Eberhard, Mary Jane. Developmental Plasticity and Evolution. Oxford University Press. 2003. P. 142.


“But evolved change in phenotype frequency need not involve change in the threshold of a switch. It is possible for the response to selection to be a change in the ability to pass a threshold.” West-Eberhard, Mary Jane. Developmental Plasticity and Evolution. Oxford University Press. 2003. P. 149.


“The leading event is a phenotypic change with particular, sometimes extensive, effects on development. Gene-frequency change follows, as a response to the developmental change. In this framework, most adaptive evolution is accommodation of developmental-phenotypic change. Genes are followers, not necessarily leaders, in phenotypic evolution.” West-Eberhard, Mary Jane. Developmental Plasticity and Evolution. Oxford University Press. 2003. P. 158.


“Unlike genetic recombination, in which most new combinations are lost during meiosis in every generation unless tightly chromosomally linked, novel combinations produced by phenotypic recombination can be preserved by developmental linkage–preservation and spread of novel phenotypic combinations due to selection on regulation that favors their coexpression or sequence. This–developmental rather than chromosomal linkage–is how new adaptive trait combinations are formed during evolution.” West-Eberhard, Mary Jane. Developmental Plasticity and Evolution. Oxford University Press. 2003. Pps. 172-3.


“The evolutionary effect of phenotypic plasticity is a subject of debate. Some argue that it can accelerate evolution due to environment matching of alternative forms. Others maintain that plasticity retards evolution because it allows the phenotype to adjust non-genetically and therefore damps the genetic response to selection. Still others have vacillated between these two views or discussed both effects, showing that either can occur, depending on circumstances.

“Phenotypic plasticity can have either result, depending on the effect of plasticity on the distribution of phenotypes, and on whether or not a quantitative trait or plasticity in switching between alternatives is involved. When a condition-sensitive switch produces recurrent expression of an alternative phenotype with environmental matching, plasticity can accelerate directional evolution of a recurrently expressed conditional alternative. When a hyperplastic mechanism such as learning, or a continuously variable reaction norm, produces a wide range of phenotypes, selection cannot act on a single recurrent trait or mode, and plasticity is expected to retard directional evolution.” West-Eberhard, Mary Jane. Developmental Plasticity and Evolution. Oxford University Press. 2003. P. 178.


“Combinatorial evolution is not just moving the furniture. It can increase phenotypic complexity, multiplying the potential for further variation and evolutionary change. So increasing the phenotype repertoire of the genome, by increasing the potential for further phenotypic recombination, is a self-accelerating process that greatly augments the production of selectable variation.” West-Eberhard, Mary Jane. Developmental Plasticity and Evolution. Oxford University Press. 2003. P. 200.


“As long as there is a behavioral decision mediated by learning, learning potentially affects the recurrent expression of particular behaviors, the action of selection, and the course of evolution.” West-Eberhard, Mary Jane. Developmental Plasticity and Evolution. Oxford University Press. 2003. Pps. 337-8.


“On this continuum of complexity, learning is among the most highly condition-sensitive and also highly polygenic developmental mechanisms.” West-Eberhard, Mary Jane. Developmental Plasticity and Evolution. Oxford University Press. 2003. P. 338.


“It is easy to see room for genetic variation in all of these evolvable components of the ability to learn. Individual organisms vary genetically in their motivational levels whenever there are genetic differences in such things as hormone systems, or sensory acuity or ability to see relevant stimuli in the environment. They may vary genetically in aspects of morphology (e.g., muscle size, beak length) that make certain exploratory maneuvers easier, or more effective than others. They may vary genetically in their ‘tastes’ or precise sensations of what is delicious or disgusting, and they may vary in their ability to observe the details of successful maneuvers and remember them or match them to particular tasks. In other words, differences in learning ability have to do with motivation, including hormones and social interactions, motivation-maneuver matching, rewards, and sensory apparatus–not just with the memory centers of the brain.” West-Eberhard, Mary Jane. Developmental Plasticity and Evolution. Oxford University Press. 2003. P. 342.


“A common result of simple learning is to create individual differences in behavior. Learned individual differences are the result of multidimensional plasticity in continuously variable traits whose magnitudes (e.g., frequency or intensity of performance) can be influenced by experience. This establishes idiosyncratic combinations or interrelations of traits such that different individuals have different complex phenotypes with each one at a low frequency in the population (hence the individuality of the differences). The greater the number of variable traits involved, the more highly idiosyncratic individual differences can be.” West-Eberhard, Mary Jane. Developmental Plasticity and Evolution. Oxford University Press. 2003. P. 344.


“Individuals are often alert to the resource-acquisition activities of conspecifics, and stealing (cleptoparasitism) and ‘socially facilitated’ flocking to newly discovered supplies (both food and mates) are common in insects and vertebrates.” West-Eberhard, Mary Jane. Developmental Plasticity and Evolution. Oxford University Press. 2003. P. 350.


“The ability to selectively forget is a hallmark of a continuing ability to learn, as distinct from imprinting or irreversible learning during a critical period.” West-Eberhard, Mary Jane. Developmental Plasticity and Evolution. Oxford University Press. 2003. P. 351.


“Alternative phenotypes are different traits expressed in the same life stage and population, more frequently expressed than traits considered anomalies or mutations, and not simultaneously expressed in the same individual.” West-Eberhard, Mary Jane. Developmental Plasticity and Evolution. Oxford University Press. 2003. P. 378.


“Switch-mediated alternatives are a convenient place to examine the links between development and evolution. They occur within individuals at all levels of phenotypic organization from alternatively spliced molecules to alternative behavioral tactics, so they can be observed by any biologist in any field from molecular biology to ethology.” West-Eberhard, Mary Jane. Developmental Plasticity and Evolution. Oxford University Press. 2003. P. 380.


“Switches between alternative phenotypes are often sensitive to stress in the biotic and physical environment, status in social or sexual competition, presence of predators and parasites, and seasonal change and spatial environmental heterogeneity that encourage the cyclical or opportunistic adoption of different modes of life.” West-Eberhard, Mary Jane. Developmental Plasticity and Evolution. Oxford University Press. 2003. P. 380.


“Some alternatives are phenotype dependent in that the alternative adopted depends upon relative ability of individuals having different characteristics to acquire resources (e.g., food, shelter, water, or mates) in competition with others having other phenotypic characteristics.” West-Eberhard, Mary Jane. Developmental Plasticity and Evolution. Oxford University Press. 2003. P. 388.


“In nonsocial phenotype-dependent competition, individuals may sort themselves into behavioral alternatives or dietary specializations in accord with phenotypic variation in ability to pursue different tactics of acquisition of limited resources. In Galapagos finches, trophic preferences and, consequently, food-handling tactics are influenced by beak size, especially during times of food shortage.” West-Eberhard, Mary Jane. Developmental Plasticity and Evolution. Oxford University Press. 2003. P. 390.


“Alternative phenotypes, then, differ from other modular traits in the potential to be expressed independently of each other, as mutually exclusive traits.” West-Eberhard, Mary Jane. Developmental Plasticity and Evolution. Oxford University Press. 2003. P. 393.


“Assessment of mates, for example, is not part of a switch between alternative phenotypes, but it is similar to other kinds of social assessment, such as the assessment of dominance in social insects, that does influence the switch between alternative worker and queen phenotypes.” West-Eberhard, Mary Jane. Developmental Plasticity and Evolution. Oxford University Press. 2003. P. 442.


“Assessment–evaluation of environmental circumstances, competitors, or mates–occurs whenever a particular response correlates consistently with some environmental variable. Choice between two or more actions, pathways, objects, or individuals occurs when there is a differential response to stimulus differences associated with the alternatives, that is, if an organism responds differentially to different stimuli.” West-Eberhard, Mary Jane. Developmental Plasticity and Evolution. Oxford University Press. 2003. P. 442.


“When ritualized resolution of dominance disputes is advantageous, clear signals of rank are expected to evolve. Signal antithesis, or sharp contrast between signals of dominance and signals of subordinance achieved by adoption of opposite postures or movements, occurs in a wide variety of animals. Darwin considered the ‘principle of antithesis’ to be a fundamental rule of animal communication and proposed that its function is to facilitate unambiguous assessment. A similar principle is a general property of signal amplification in physical and biological systems (such as neural nets and logical thought), where polar opposites, although they sacrifice information, facilitate decision.” West-Eberhard, Mary Jane. Developmental Plasticity and Evolution. Oxford University Press. 2003. P. 454.


“The various gadgets and communicative devices that we call sexual signals are very much like the internal signaling events of development. Interactions during courship stimulate sequential events: first external attractive stimuli, then internal interactions during copulation, with many circuitous and complex physiological responses eventually leading to fertilization. In one sense, sexual interaction is an aspect of adult reproductive development, one where essential environmental input comes from a conspecific individual of the opposite sex.” West-Eberhard, Mary Jane. Developmental Plasticity and Evolution. Oxford University Press. 2003. P. 457.


“Sexual behavior is also interesting from a developmental point of view because it draws attention to the manipulability of environmentally sensitive responses. The susceptibility of behavior and development to environmental influence means that they are eminently subject to influence by other organisms if natural selection favors behaviors that cause them to pervert development for their own selfish ends. In this respect, sexual manipulations of female reproductive physiology by male conspecifics are just one of a very large category of developmental manipulations by outsiders, such as the manipulation of caste by adult social insects in their interactions with larvae, the induction of galls by a multitude of plant feeding insects, the selfish deformation of host phenotypes by parasites, the mimicry by social parasites in some insects and birds of host stimuli known or likely to affect acceptance and resource acquisition, and the acculturation and education of human infants, children, and adults.” West-Eberhard, Mary Jane. Developmental Plasticity and Evolution. Oxford University Press. 2003. P. 458.


“The remarkable assessment of shells by hermit crabs is discussed above. Hermit crabs also have the ability to alter their size if shell assessment indicates that the size of their otherwise suitable shell is too small to accommodate growth. When that occurs, the crab actually decreases its body size at the next molt.” West-Eberhard, Mary Jane. Developmental Plasticity and Evolution. Oxford University Press. 2003. P. 462.


“Learning simplifies the proximate process of assessment and decisions by making an integrated evaluation of numerous environmental and phenotypic variables that may affect the success of a tactic, ending with one overreaching criterion: whether or not, taken together, they resulted in a reward. The complex set of factors that are thereby collapsed into one could include variable morphology and behavior involved in searching, distinguishing, and handling some resource, and variable environmental features and cues that are encountered during the search. If the combination of selective searching, handling, idiosyncratic morphology, and reinforced cue is successful in obtaining a reward, the whole combination, having been rewarded, will be repeated under a regime where learning governs behavior. If something works (attains a reward), it is repeated. Each component of the successful maneuver need not be separately assessed by the organism. But at the population level, each will be assessed, due to effects on fitness, by selection.” West-Eberhard, Mary Jane. Developmental Plasticity and Evolution. Oxford University Press. 2003. P. 463.


“Learning does sometimes create a large number of individualized alternatives, as in the highly individualized foraging tactics in some populations of birds. Multiple alternatives in a single functional context mean that selection is less able to improve the form of particular alternatives. But with multiple alternatives, selection on assessment is strong, and assessment may be more complex when multiple variable options are involved. The expected result is accelerated evolution in plasticity and assessment per se. This may give rise to a self-accelerating process, where multiple alternatives bring improved assessment ability, and improved assessment ability further multiplies alternatives in a mutually reinforcing spiral of change.

“The pivotal event at the point of upward inflection in the evolution of human brain size may have been some breakthrough in the evolution of flexibility, causing a self-accelerating process such as that just described, where multiple learned alternatives switch the focus of selection from a small number of evolved specializations, to a large number of learned alternatives, and where environmentally (in this case, socially) complex variables increase selection on plasticity and assessment ability per se. In highly social organisms, social competition screens access to virtually all crucial resources (food, space, protection, and mates). Dominance at feeding sites, for example, is a good predictor of winter survival in song sparrows, and socially dominant social insect females are the only ones that lay eggs, to the exclusion of hundreds and sometimes thousands of potential competitors. Probably as a result of this, traits used in social competition are notable for their exaggeration. An exaggerated trait like the human brain in such an eminently social (and socially competitive) animal seems likely explained at least in part by feats of social maneuvering and assessment.” West-Eberhard, Mary Jane. Developmental Plasticity and Evolution. Oxford University Press. 2003. P. 463-4.


“Since manipulative signals evolve unrestrained by their correlation with any underlying quality, they can be elaborated and improved without limits other than their cost under natural selection. Choice, then, may screen for three aspects of quality:

1. Phenotypic quality, which rewards accurate assessment due to superior performance of the chosen individual during the chooser’s lifetime (e.g., as a helpful mate or a productive queen)
2. Genetic quality under natural selection, which rewards accurate assessment due to superior quality of descendants or other relatives in the nonsocial environment (e.g., in food getting, predator escape, and resistance to parasites and pathogens)
3. Genetic quality under social selection per se, which includes ability to excel in the social environment through effective signals.

“In the first two aspects, selection favors close correlation between the indicator signal and some underlying trait, and choice that detects the truth of the indicator. The signal itself has no value except as an indicator. In the third, selection favors the best manipulative signalers, and choice that distinguishes the best signals, due to the advantage of signaling superiority of descendants. It is the latter type of choice that can lead to a genetic correlation between signal ability and discrimination ability, and so-called runaway change.” West-Eberhard, Mary Jane. Developmental Plasticity and Evolution. Oxford University Press. 2003. P. 467.


“...many other prominent evolutionary biologists including Spencer, Severtzoff, Beurlen, J.S. Huxley and G.G. Simpson, saw evolution as ‘liberating the organism from the determining influence of the environment.’ I maintain instead that, far from being liberated from environmental influence, organisms evolve so as to incorporate environmental elements and exploit them as essential components of normal development.” West-Eberhard, Mary Jane. Developmental Plasticity and Evolution. Oxford University Press. 2003. P. 499. [Subquote from Rensch, B. Evolution Above the Species Level. Columbia University Press. 1960. P. 298.]


“The environment can contribute to the origin of phenotypic novelties in two ways, given its role in the determination of regulation and form. In regulation, environmental factors such as temperature, day length, and ingested substances can serve as signals or cues at switch points in development. In phenotype construction, environmental materials serve as building blocks, or integral elements of form.” West-Eberhard, Mary Jane. Developmental Plasticity and Evolution. Oxford University Press. 2003. P. 500.


“All obligatory mutualisms or symbioses, such as the union of a fungus and an alga to form a lichen, represent reciprocal entrenchment of environmental factors in development.” West-Eberhard, Mary Jane. Developmental Plasticity and Evolution. Oxford University Press. 2003. P. 500.


“When phenotypes construct niches, they become more than simply ‘vehicles’ for their genes, as they may now also be responsible for modifying some of the sources of natural selection in their environments that subsequently feed back to select their own genes. However, relative to this second role of phenotypes in evolution, there is no requirement for the niche-constructing activities of phenotypes to result directly from naturally selected genes before they can influence the selection of genes in populations. Animal niche construction may depend on learning and other experiential factors, and in humans it may depend on cultural processes.” Odling-Smee, F. John, Kevin Laland & Marcus Feldman. Niche Construction: The Neglected Process in Evolution. Princeton University Press. 2003. P. 21.


“Niche construction occurs when an organism modifies the feature-factor relationship between itself and its environment by actively changing one or more of the factors in its environment, either by physically perturbing factors at its current location in space and time, or by relocating to a different space-time address, thereby exposing itself to different factors.” Odling-Smee, F. John, Kevin Laland & Marcus Feldman. Niche Construction: The Neglected Process in Evolution. Princeton University Press. 2003. P. 41.


“Moreover, niche construction is likely to generate indirect epistatic interactions between genes via resources in the external environment. For example, flamingos are pink not because they synthesize this color, but rather because they consistently choose environments containing their crustacean prey, and this habitat choice has generated selection for extraction of the carotenoid pigment.” Odling-Smee, F. John, Kevin Laland & Marcus Feldman. Niche Construction: The Neglected Process in Evolution. Princeton University Press. 2003. P. 114.


“Obviously organisms cannot break the second law of thermodynamics. Instead they participate with their local environments in two-way interactions that create coupled organism-environment systems that do permit organisms to stay alive without violating the second law. These two-way interactions account for the origins of obligate niche construction. To gain the resources they need and to dispose of their detritus, organisms cannot just respond to their environments. They must also act on their local environments and by doing so change them, in the process converting free energy to dissipated energy. Hence, evolution is contingent on the capacity of organisms to use their environments in ways that allow them to gain sufficient energy and material resources from their environments, and to emit sufficient detritus into their environments, to stay alive and reproduce. Variability in these processes offers the potential for the process of natural selection to operate.

“It follows that biological evolution must have consequences for environments as well as for organisms.” Odling-Smee, F. John, Kevin Laland & Marcus Feldman. Niche Construction: The Neglected Process in Evolution. Princeton University Press. 2003. Pps. 168-9.


“Here they point out that the impact of organisms is greatest when the resource flows or abiotic ecosystem components that they modulate are utilized by many other species. It follows that some of the most significant consequences of niche construction in ecosystems are found in soils, sediments, rocks, in hydrology, and in fire ecology, and even in wind resistance.” Odling-Smee, F. John, Kevin Laland & Marcus Feldman. Niche Construction: The Neglected Process in Evolution. Princeton University Press. 2003. P. 217.

“The selection pressure modified by the source population’s niche construction may be indifferent to which species is carrying the genes that are now favored.” Odling-Smee, F. John, Kevin Laland & Marcus Feldman. Niche Construction: The Neglected Process in Evolution. Princeton University Press. 2003. P. 220.


“Waechtershaeuser’s controversial scenario covers a large portion of the spectrum of the origin of biochemistry and life. The origin of life was chemoautotrophic, and took place in or near hydrothermal vents at the bottom of the primordial oceans. Its energy source is the oxidative formation of pyrite from hydrogen sulfide and ferrous ions. This energy source is large enough to pull an autocatalytic carbon dioxide–fixation cycle and the first ensuing metabolic cycles. The products of the autocatalytic CO2 fixation reaction are organic anions, which are adsorbed onto the positively charged pyrite surfaces. The adsorption-induced compartmentation is the most primitive mechanism for retaining the organic anions thus produced in close vicinity. Chemical reactions between the adsorbed organic anions result in the establishment of the first metabolic cycle, the archaic form of the reductive citrate cycle (RCC). This pyrite-pulled autocatalytic cycle can be reconstructed from the extant RCC. Inheritable variations occur by branch products with dual catalytic feedback into both the reproduction cycles and their own branch pathways. Nucleic acids, the genetic apparatus, and template-directed syntheses appeared at a later stage. Cellularization is initiated by the formation of lipophilic zones on the pyrite surfaces, followed by the expansion of the lipophilic layer to produce a cell.” Lahav, Noam. Biogenesis: Theories of Life’s Origin. Oxford Univ. Press. 1999. P. 281.


“The investigation of animal traditions has been an active area of research in recent years, and it has become clear that behavioral traditions, mediated through social learning, affect all aspects of bird and mammal life–their food preferences, courtship behavior, communication, parental care, predator avoidance, and choice of a home. Inheriting behavior through social learning is not uncommon.” Jablonka, Eva & Marion Lamb. Evolution in Four Dimensions: Genetic, Epigenetic, Behavioral, and Symbolic Variation in the History of Life. MIT Press. 2005. P. 171.


“So there are excellent reasons to believe that symbiont transmission is an inheritance mechanism. Hosts copy their associates to their offspring with great reliability. Moreover, as we have seen, it is a mechanism of great evolutionary significance. For symbiotic association enables host lineages to invade new adaptive zones. In turn, that is because the formation of symbiotic associations is probably the only evolutionary process that generates in animals adaptive saltational changes at any appreciable frequency, even on evolutionary time scales (plants, with their more modular organization, are less constrained). Organisms that acquire, for the first time in their lineage’s history, a new symbiotic associate may acquire a whole new capacity ready-made, though doubtless one that is subject to coevolutionary fine-tuning. They are hopeful monsters. On human time scales, such events must be vanishingly rare. But mutualisms are fairly common. Over evolutionarily significant periods such associations must be formed quite often. So symbiosis is significant partly because it is one way for lineages to cross fitness trenches and overcome historical constraints. A bivalve shift from, say, filter feeding to sulphide metabolism might well be blocked by historical constraints. No metazoan has evolved for itself these biochemical pathways. Perhaps the only way an animal can invade these sulphide-rich, oxygen-poor environments is by acquiring an appropriate symbiont.” Sterelny, Kim. “Symbiosis, Evolvability, and Modularity” pps. 490-513. In Schlosser, Gerhard & Guenter Wagner, Ed. Modularity in Development and Evolution. University of Chicago. 2004. P. 513.


“Although many animals live largely solitary lives, some live in groups. Groups vary from anonymous collections of individuals such as fish shoals to the highly structured societies of the social insects, in which specialized castes of sterile workers maintain the nest and help the queen raise her young. Important selection pressures that favor group living include advantages from predator evasion and resource acquisition. By living in groups animals may reduce their chances of being captured by a predator through dilution, hiding in the herd, the benefit of increased vigilance from many eyes and ears, and group defense. They may locate, capture, or defend food more successfully.” Pusey, Anne. “Social Systems” pps. 315-341. In Bolhuis, Johan & Luc-Alain Giraldeau, Ed. The Behavior of Animals: Mechanism, Function and Evolution. Blackwell. 2005. P. 341.


“... rather than being fundamentally different, both behavioral and developmental plasticity encompass broad and overlapping ranges of a continuum of plasticity. Both should be considered in the study of phenotypic plasticity.” Sih, Andrew. “A Behavioral Ecological View of Phenotypic Plasticity” Pps. 112-123. DeWitt, Thomas & Samuel Scheiner, Ed. Phenotypic Plasticity: Functional and Conceptual Approaches. Oxford University Press. 2004. P. 114.


“The usual idea is that behavioral plasticity differs from developmental plasticity in both the speed and reversibility of response. At one extreme, behavior might, in some cases, be infinitely plastic; that is, capable of immediate and infinitely reversible changes in response to spatially or temporally varying environments. At the other extreme, developmental plasticity might be relatively slow to unfold and often irreversible. As noted in previous reviews, the differences between these extreme ends of the spectrum are important both for the evolutionary process and for the likely outcome of evolution.” Sih, Andrew. “A Behavioral Ecological View of Phenotypic Plasticity” Pps. 112-123. Phenotypic Plasticity: Functional and Conceptual Approaches. Edited by Thomas DeWitt & Samuel Scheiner. Oxford University Press. 2004. P. 113.


“Where niche construction affects multiple generations, it introduces a second general inheritance system in evolution, one that works via environments. This second inheritance system has not yet been widely incorporated by evolutionary theory.” Odling-Smee, F. John, Kevin Laland & Marcus Feldman. Niche Construction: The Neglected Process in Evolution. Princeton University Press. 2003. P. 13.

“Many nongenetic resources are reliably passed on across the generations. Variations in these resources can be passed on, causing changes in the life cycle of the next generation. The concept of inheritance is used to explain the stability of biological form from one generation to the next. In line with this theoretical role, developmental systems theory applies the concept of inheritance to any resource that is reliably present in successive generations, and is part of the explanation of why each generation resembles the last. This seems to us a principled definition of inheritance. It allows us to assess the evolutionary potential of various forms of inheritance emprically, rather than immediately excluding everything but genes and a few fashionable extras.” Griffiths, Paul & Russell Gray. “The Developmental Systems Perspective: Organism-Environment Systems as Units of Development and Evolution” Pps. 409-427. In Pigliucci, Massimo & Katherine Preston, Ed. Phenotypic Integration: Studying the Ecology and Evolution of Complex Phenotypes. Oxford Univ. Press. 2004. P. 411.


“Organisms and their ecological niches are co-constructing and co-defining. Organisms both physically shape their environments and determine which factors in the external environment are relevant to their evolution, thus assembling such factors in what we describe as their niche. Organisms are adapted to their ways of life because organisms and their way of life were made for (and by) each other.” Griffiths, Paul & Russell Gray. “The Developmental Systems Perspective: Organism-Environment Systems as Units of Development and Evolution” Pps. 409-427. In Phenotypic Integration: Studying the Ecology and Evolution of Complex Phenotypes. Edited by Massimo Pigliucci & Katherine Preston. Oxford Univ. Press. 2004. P. 418.


“Developmental systems include much that is outside the traditional phenotype. This raises the question of where one developmental system and one life cycle ends and the next begins.” Griffiths, Paul & Russell Gray. “The Developmental Systems Perspective: Organism-Environment Systems as Units of Development and Evolution” Pps. 409-427. In Phenotypic Integration: Studying the Ecology and Evolution of Complex Phenotypes. Edited by Massimo Pigliucci & Katherine Preston. Oxford Univ. Press. 2004. P. 423.


“We suggest, then, that a repeated assembly is a developmental system in its own right, as opposed to a part of such a system or an aggregate of several different systems when specific adaptations exist, presumably due to trait-group selection, which suppress competition between the separate components of the assembly.” Griffiths, Paul & Russell Gray. “The Developmental Systems Perspective: Organism-Environment Systems as Units of Development and Evolution” Pps. 409-427. In Phenotypic Integration: Studying the Ecology and Evolution of Complex Phenotypes. Edited by Massimo Pigliucci & Katherine Preston. Oxford Univ. Press. 2004. P. 424.


“In fact, evolved lineages are ‘addicted’ to innumerable aspects of the environment with which they have coevolved, although most of these aspects are reproduced so reliably that this does not give rise to significant variation, and so is overlooked.” Griffiths, Paul & Russell Gray. “The Developmental Systems Perspective: Organism-Environment Systems as Units of Development and Evolution” Pps. 409-427. In Phenotypic Integration: Studying the Ecology and Evolution of Complex Phenotypes. Edited by Massimo Pigliucci & Katherine Preston. Oxford Univ. Press. 2004. P. 426.


“All four ways [genetic, epigenetic, behavioral & symbolic] of transmitting information introduce, to different degrees and in different ways, instructive mechanisms into evolution.” Jablonka, Eva & Marion Lamb. Evolution in Four Dimensions: Genetic, Epigenetic, Behavioral, and Symbolic Variation in the History of Life. MIT Press. 2005. P. 344.


“As epigenetic systems became more elaborate, they became more effective information-transmitting systems and, as we argued in chapter 4, they enabled the evolution of multicellular organisms with many cell types. Epigenetic and genetic inheritance systems (including interpretive mutations) continued to play the major role in the evolution of plants, fungi, and simple animals, as well unicellular organisms. However, once more complex animals with a central nervous system had evolved, behavior and behaviorally transmitted information became important. Through behavioral transmission, animals had the potential to adapt in ways that were impossible or unlikely through transgenerational epigenetic inheritance or gene mutations. With animals’ increasing reliance on socially learned information came complex social structures and relations, and group traditions. Eventually, in the primate lineage, symbolic communication emerged and led to the explosive cultural changes we see in humans, where symbols have taken the leading role in evolution. As has happened throughout evolutionary history, a higher-level inheritance system now guides evolution through the lower-level systems, including the genetic system.” Jablonka, Eva & Marion Lamb. Evolution in Four Dimensions: Genetic, Epigenetic, Behavioral, and Symbolic Variation in the History of Life. MIT Press. 2005. P. 342.


“Information is transferred from one generation to the next by many interacting inheritance systems. Moreover, contrary to current dogma, the variation on which natural selection acts is not always random in origin or blind to function: new heritable variation can arise in response to the conditions of life. Variation is often targeted, in the sense that it preferentially affects functions or activities that can make organisms better adapted to the environment in which they live. Variation is also constructed, in the sense that, whatever their origin, which variants are inherited and what final form they assume depend on various ‘filtering’ and ‘editing’ processes that occur before and during transmission.” Jablonka, Eva & Marion Lamb. Evolution in Four Dimensions: Genetic, Epigenetic, Behavioral, and Symbolic Variation in the History of Life. MIT Press. 2005. P. 319.


“Although the pathway from hormones to behavior can be complex, some insights can be gained by classifying hormonal effects into two main categories: organization effects versus activational effects. Oranization effects are usually thought to act early in development by organizing brain anatomy and neurochemistry, and other aspects of morphology or physiology that set the stage for later hormonal effects on behavior. Organization is thus traditionally associated with effects that are fixed for life (e.g., primary sexual differentiation through sex-specific gonadal development), or at least for some significant amount of time. In contrast, activational effects of hormones are usually thought to act later in life; e.g., adult mating behavior might be activated by a hormonal surge. Both organizational and activational effects can come into play in a given system, although their relative importance likely varies across systems. Moore et al. proposed a ‘relative plasticity hypothesis’ that posits that organizational effects of hormones early in development produce fixed alternative phenotypes, while activational effects later in life govern plastic alternative phenotypes. Both effects can be important in one system.” Sih, Andrew, Alison Bell, J. Chadwick Johnson & Robert Ziemba. “Behavioral Syndromes: An Integrative Overview.” Quarterly Review of Biology. Sept 2004, V79, i3, P241. P. 269. [Subquote is from Moore, M.C., D. K. Hews & R. Knapp. “Hormonal Control and Evolution of Alternative Male Phenotypes: Generalizations of Models for Sexual Differentiation.” American Zoologist. 1998. V38:133-151]


“Interestingly, large-scale studies and meta-analyses suggest that out of the Big Five [Five axes of human personalities–neuroticism, extroversion, agreeableness, openness, and conscientiousness], the best predictor of overall positive life outcomes is conscientiousness.” Sih, Andrew, Alison Bell, J. Chadwick Johnson & Robert Ziemba. “Behavioral Syndromes: An Integrative Overview.” Quarterly Review of Biology. Sept 2004, V79, i3, P241. P. 273.


“Behavior analysts consider behavior to be the product of current variables and learning history; therefore, both can be considered independent variables.” Hixson, Michael. “Behavioral Cusps, Basic Behavioral Repertoires, and Cumulative-hierarchical Learning.” The Psychological Record. Summer 2004. V54 i3 P. 387-403.


“In the same vein, the notion of environment is perhaps best conceived as a Russian doll, a nested series of structures organized from ‘outside’ to ‘inside.’ Mothers serve as the environment for the fetus. Organs serve as environments for one another–scaffolding, supporting, blocking and shaping one another into a final configuration. And individual cells are powerfully influenced by their neighbors.” Elman, Jeffrey, Elizabeth Bates, Mark H. Johnson, Annette Karmiloff-smith, Domenico Parisi & Kim Plunkett, editors. Rethinking Innateness: A Connectionist Perspective on Development. 1998. MIT Press. P. 245.


“The evidence for plasticity that we have reviewed so far pertains entirely to variations that occur (or can occur under special circumstances) during brain development, before the adult endpoint is reached. It is widely believed (and undoubtedly true) that there is much less plasticity in the adult brain. However, this does not mean that plasticity has come to an end. At the very least, we know that some form of local structural change occurs whenever anything new is learned....

“... it now seems clear that the adult brain is capable of fairly large-scale structural and functional change–less plasticity than we find in the developing brain, but impressive nonetheless.” Elman, Jeffrey, Elizabeth Bates, Mark H. Johnson, Annette Karmiloff-smith, Domenico Parisi & Kim Plunkett, editors. Rethinking Innateness: A Connectionist Perspective on Development. 1998. MIT Press. P. 280.


“The main conclusion we come to is that part of the evolution of ontogenesis has involved taking advantage of interactions at increasingly higher levels. We shall suggest that organisms have evolved from ontogenetic development based on mosaic systems (molecular level interactions), to regulatory systems (cellular level interactions), to nervous systems (systems level interactions), to an increasing dependence on behavioral/cultural factors (environment-organism interactions). Each of these steps in the evolution of ontogenetic systems increases the time taken for the development of an individual of the species. In the case of our own species, this process has played a particularly crucial role.” Elman, Jeffrey, Elizabeth Bates, Mark H. Johnson, Annette Karmiloff-smith, Domenico Parisi & Kim Plunkett, editors. Rethinking Innateness: A Connectionist Perspective on Development. 1998. MIT Press. Pps. 322-3.


“By making organisms the objects of force whose subjects were the internal heritable factors and the external environment, by seeing organisms as the effects whose causes were internal and external autonomous agents, Mendel and Darwin brought biology at last into conformity with the epistemological meta-structure that already characterized physics since Newton and chemistry since Lavoisier. This change in world view was absolutely essential if biology was to progress by making contact with physical science and by becoming quantitative and predictive. The mechanistic reductionism and the clear separation of internal and external were as necessary in the nineteenth century for the creation of a scientific biology as Newton’s ideal bodies and perfect determinism were for the physics of the seventeenth. But we must not confuse the historically determined necessity of a particular epistemological stance at one stage in the development of a science with a perfect model that will guarantee all future progress. On the contrary, the very progress made possible by certain revolutionary formulations may lead eventually to results that are in contradiction with those earlier formulations and which can be resolved only by their reexamination.” Lewontin, Richard. 2001. “Gene, Organism and Environment: A New Introduction.” Susan Oyama, Paul Griffiths & Russell Gray. Cycles of Contingency: Developmental Systems and Evolution. MIT Press. Pps. 59-60.


“This view of evolution [the usual description of evolution], however, has certain paradoxical features. One is that all extant species are said to be already adapted to their environments. A good deal of evolutionary biology is taken up with demonstrating that their features represent optimal solutions to environmental problems. What then is the motive power of further evolution? The solution proposed by Van Valen is that the environment is constantly moving and that species are simply running to keep up. In that case, it is the autonomous forces of environmental change that govern the rate of evolution, and we would be well advised to study the laws of envionmental rather than organismic change if we want to understand what has been happening.” Lewontin, Richard. 2001. “Gene, Organism and Environment: A New Introduction.” Susan Oyama, Paul Griffiths & Russell Gray. Cycles of Contingency: Developmental Systems and Evolution. MIT Press. P. 63.


“Horizontal gene transfer is not a new fact, but it is more dominant an evolutionary factor than we previously thought it to be.” Woese, Carl. 2002. “Perspective: Microbiology in Transition.” Pps. xvii-xxxi. James Staley and Anna Louise Reysenbach, Editors. Biodiversity of Microbial Life. Wiley-Liss. P. xxvii.


“Microbiologists have for some time accepted the gene shuffling that occurs among bacteria via phages, plasmids, and the like. Yet in all of these cases, we have continued to speak of organismal lineages, be they eukaryotic, bacterial, or archaeal–and justifiable so–because foreign genetic contributions appear to provide only a minor perturbation on what is otherwise a shared history common to the bulk of the genes in the genome. However, the levels of horizontal gene transfer genomicists now see are not negligible. The further the organismal lineage is retrodicted, the more it becomes eroded by lateral gene transfer, the fewer the number of genes that share a common history in the long term.” Woese, Carl. 2002. “Perspective: Microbiology in Transition.” Pps. xvii-xxxi. James Staley and Anna Louise Reysenbach, Editors. Biodiversity of Microbial Life. Wiley-Liss. P. xxvii.


“... instead of every antigen having a single ‘handle’ (called a determinant or epitope by immunologists) for the antibody to grasp, they all have many such determinants, each of which is different and thus can be bound by a different type of antibody. These determinants correspond to small patterns of molecular structure on the surface of the antigen.” Cziko, Gary. Without Miracles: Universal Selection Theory and the Second Darwinian Revolution. 1995. MIT Press. P. 43.


“Not being content with a single-step selection process, we can instead take the best of the variations, vary them, and then select the best of the new generation, repeating the process over and over again. This, of course, is constructive cumulative selection. This process of selecting and fine-tuning the occasional accidentally useful emergent system turns out to be so powerful that we should not be surprised that the adaptive processes of biological evolution, antibody production, learning, culture, and science all employ it, and that its power is now being explicitly exploited in the design of organisms, drugs, and computer software by one of evolution’s most complex and adaptive creations–the human species.” Cziko, Gary. 1995. Without Miracles: Universal Selection Theory and the Second Darwinian Revolution. MIT Press. Pps. 309-10.


"Cells are complex, with millions of individual proteins, and you might wonder whether diffusive motion is sufficient to allow interaction between the proper partners amidst all the competition. At the scale of the cell, diffusive motion is remarkably fast, so once again our intuition may play us false. If you release a typical protein inside a bacterial cell, within one-hundredth of a second, it is equally likely to be found anywhere in the cell. Place two molecules on opposite sides of the cell, and they are likely to interact within one second. As articulated by Hess and Mikhailov: 'This result is remarkable: It tells us that any two molecules within a micrometer-size cell met each other every second.'" Goodsell, David. Bionanotechnology: Lessons from Nature. Wiley-Liss. 2004. P. 13.


"Before the first atomic structures of biological molecules were determined, the physicist H. R. Crane postulated that two design concepts would be required for macromolecular recognition in self-assembling systems. First, 'for a high degree of specificity the contact or combining spots on the two particles must be multiple and weak.' This may not seem obvious: We might think that it is better to use one very strong interaction to hold two parts together. Using one or a few strong interactions will provide stability. However, it will not provide specificity. The same arrangement of a few strong combining sites might be found on many other molecules, increasing the risk of improper pairings. Instead, an array of many weak interactions is better. Then, all of the interactions are necessary to add up to the proper binding strength.

Second, 'one particle must have a geometrical arrangement which is complementary to the arrangement on the other.' The shape of the interacting surface must form a tight fit, bringing the 'multiple, weak interactions' into the proper alignment." Goodsell, David. 2004. Bionanotechnology: Lessons from Nature. Wiley-Liss. P. 122.


"Flexibility at all levels is used to enhance the function of bionanomachines. This includes harnessing of thermal motion for chemical catalysis, use of induced fit for recognition, design of different conformational states for use in regulation, and incorporation of selective flexibility to link several separate functionalities. Goodsell, David. 2004. Bionanotechnology: Lessons from Nature. Wiley-Liss. P. 133.


"Potassium channels allow passage of potassium ions but block passage of sodium ions and chloride ions, which are also common in the cellular environment. The blocking of chloride ions is not difficult because they are negatively charged and potassium ions are positively charged. By adding a few negative charges at the entry to the channel, chloride will be repelled and will not pass through the channel. But blockage of sodium ions is a far more difficult task. Both sodium and potassium ions carry a positive charge, so an approach based on charge will not work. A simple filter based on size also will not work, because sodium ions are slightly smaller than potassium ions (0.095 nm for sodium and 0.133 nm for potassium). The trick used in natural potassium channels is to take advantage of the water environment of biological systems. In solution, ions are surrounded by a strongly associated shell of water molecules. The potassium channel is designed with a pore that is small enough to pass the ion but not the shell of waters. The channel contains several rings of oxygen atoms, formed by amino acids surrounding the channel, that mimic the shell of waters. As ions enter the narrow channel, they shed their waters but enter into an environment that is just as favorable, surrounded by the channel oxygen atoms. The ion may then exit at the other side, picking up a new shell of water molecules as it leaves the channel. The process is driven by a concentration gradient.

Potassium ions flow freely through the channel at rates of up to one hundred million ions per second. But it is also remarkably selective. The selectivity is provided by the shape of the channel. The oxygen atoms are designed to fit exactly to potassium ions, forming strong interactions from all sides of the channel. Sodium ions, on the other hand, are too small to form stable interactions with all of the surrounding channel oxygen atoms. The water shell of sodium is slightly smaller than that around potassium, so if it sheds its shell it will take an energetic loss, because it cannot form interactions with all of the oxygen atoms in the channel. This difference in energy provides the specificity, allowing only one sodium ion to pass for every ten thousand potassium ions." Goodsell, David. 2004. Bionanotechnology: Lessons from Nature. Wiley-Liss. Pp. 205-7.


"Thus, in the Newtonian picture, systems get states; environments do not; environments rather become identified with dynamical laws, i.e., with the rules governing the diachronic succession of states

This is a fateful situation. Once we have partitioned the ambience into a system and its environment, and (following Newton) once we have encoded system into a formalism whose only entailment is a recursion rule governing state succession, we have said something profound about causality, and indeed about Natural Law itself. In brief, we have automatically placed beyond the province of causality anything that does not encode directly into a state-transition sequence. Such things have become acausal, out of the reach of entailment in the formalism, and hence in principle undecodable from the formalism." Rosen, Robert. Life Itself: A Comprehensive Inquiry into the Nature, Origin, and Fabrication of Life. Columbia University Press. 1991. P. 102.


"The Second Law thus asserts that a closed system cannot autonomously tend to an organized state. Or, contrapositively, a system autonomously tending to an organized state cannot be closed.

This reformulation for the Second Law is suggestive, because it indicates a way of extending the notion of organization, from state of a system, to system itself. For if the closed system autonomously tends to a disorganized state of equilibrium, then 'the closed system' can be thought of a[s] setting a standard for organization (or better, for disorganization) among systems, just as an equilibrium state sets such a standard for states. We can therefore say that a system is organized if it autonomously tends to an organized state." Rosen, Robert. 1991. Life Itself: A Comprehensive Inquiry into the Nature, Origin, and Fabrication of Life. Columbia University Press. Pp. 114-5.


Re final causality: "Thus it is that finality is allied to the notion of possibility, while the other causal categories involve necessity." Rosen, Robert. 1991. Life Itself: A Comprehensive Inquiry into the Nature, Origin, and Fabrication of Life. Columbia University Press. P. 140.


"Biologists today have come to see in Darwinian evolution a way of distinguishing themselves again, of making themselves separate, without the vitalistic traps. Basically, the argument is now that it is evolution which is unpredictable, non-mechanical, immune to the entailments, the causality, the determinism which mechanism made them espouse. By the single, simple act of redefining biology, to assert that it is about evolution rather than about organism, we can in effect have our mechanistic cake, and eat our vitalistic one to. Biologists continue to espouse a most narrow form of mechanism as far as what goes on within organisms is concerned. But if biology is about evolution, these mechanistic shackles can be devalued; conceptually assigned a subordinate role. One can (at least apparently) embrace evolution without having to deny mechanism; but we can thereby devalue it." Rosen, Robert. 1991. Life Itself: A Comprehensive Inquiry into the Nature, Origin, and Fabrication of Life. Columbia University Press. P. 256.


"Roughly speaking, folding serves to bring constituent residues that are remote in primary structure into close spatial proximity. Thus, in standard chemical terms, atoms and reactive residues are brought into, and held in, close spatial proximity, even though they seem far apart in terms of primary structure."

"Heuristically, this is exactly what an 'active site' is presumed to be. What I am going to argue now is that, although these 'active sites' embody in themselves many of the properties of traditional chemical molecules, they are not molecules. Not being held together by internal chemical bonds of their own, they cannot be isolated as independent 'substances'; as such, they are not fractionable in these terms from the bigger molecule which manifests them. They have sources from which they emerge, and sinks down which they disappear, but they are neither the products of conventional chemical reactions, nor are they used up thereby. Nevertheless, they actively participate in conventional molecular reactions, though which they can be characterized in functional terms. The reactants that interact with them can see them; indeed, that is all these reactants can see. But we have rendered them invisible to ourselves by our very way of intrinsically characterizing chemical structure. As such, they cannot be directly coded for via any purely syntactic scheme.

Indeed, this second problem, of going from primary structure to active site, manifests in a molecular microcosm the genotype-phenotype dualism we have already described above." Rosen, Robert. 1991. Life Itself: A Comprehensive Inquiry into the Nature, Origin, and Fabrication of Life. Columbia University Press. P. 272. [Later, made distinction between enzyme and protein while maintaining that protein comes along with enzymatic activity as "unavoidable contaminant" as he made reference to a know organic chemist.]


"'In the steady state systems, the flow of energy through the system from a source to a sink will lead to at least one cycle in the system.' This statement, a better candidate than Kauffman's for a fourth law of thermodynamics, connects life to nonlife. Building up complexity over time, energy-driven cycles embody a natural memory and record of their past states. Today Morowitz compares cell metabolisms among bacteria, looking for shared biochemical pathways--some of which are likely to have arisen before DNA or highly stable means of replication. 'Metabolism,' Morowitz puts it, 'recapitulates biogenesis.' The chemical cycles of modern cells, in other words, may contain traces not only of their bacterial ancestors but of the thermodynamic cycles from which bacteria themselves evolved." Schneider, Eric & and Dorion Sagan. Into the Cool: Energy Flow, Thermodynamics, and Life. University of Chicago Press. 2005. P. 94. Subquotes are from Morowitz, Harold. 1968. Energy Flow in Biology: Biological Organization as a Problem in Thermal Physics. P. 33. Ox Bow Press.


"As an example he asks us to consider the leaves of the carnivorous plant Utricularia. Plants of this genus grow in shallow freshwater lakes. The leaves and stems of Utricularia are covered with communities of gorgeous symmetrical microbes known as diatoms. In and among the diatoms are microscopic crustaceans known as zooplankton which feed on the daitoms. To close the circle, Utricularia catches and devours the zooplankton that graze on the diatoms that grow on its leaves.

As Ulanowicz points out, an increase 'in any one of these three populations, say, the zooplankton, would contribute to the growth of its downstream partners. That is, more zooplankton would be available to the planktivorous ... Utricularia, that would grow to provide more substrate for the diatoms that nourish the zooplankton, etc.' Each member in the self-reinforcing Utricularia network is thus acting, for all intents and purposes, as a catalyst." Schneider, Eric & and Dorion Sagan. 2005. Into the Cool: Energy Flow, Thermodynamics, and Life. University of Chicago Press. P. 101. Subquote is from Ulanowicz, R. E. 1997. Ecology: The Ascendant Perspective. Columbia University Press. P. 258.


"There is no a priori connection between dissipation and structuring. The reason the two tend to be coupled, the reason evolutionary phenomena in the progressive sense are possible at all, is that the forces of nature are for the most part associative ones. In a universe where cosmic expansion maintains a disequilibrium between potential and thermal forms of energy, this means that putting smaller entities together to form larger entities will generate entropy through the conversion of potential energy to heat. Hence, the potential energy wells into which natural processes tend to flow are correlated with the buildup of structure ... Dissipation is the driving force of the universe's building up or integrative tendency. Entropic dissipation propels evolutionary structuring; nature's forces give it form." Wicken, J. 1987. Evolution, Thermodynamics, and Information: Extending the Darwinian Program. Oxford University Press. P. 72. Quoted in Schneider, Eric & and Dorion Sagan. 2005. Into the Cool: Energy Flow, Thermodynamics, and Life. University of Chicago Press. P. 106.


"Corliss's octopus's gardens [discovery of deep-sea hot springs with their own ecosystems] are only one reason, the first of 'four expermimental discoveries' that Dyson suggests came in relatively quick succession to present us with a new picture of life's origin. A second is the discovery, deep underground, of bacteria living in the cold and the dark, in the pores of rocks removed in cores from as far below the surface as it has been possible to dig...."

"The third line of evidence surrounds 'strikingly lifelike phenomena observed in the laboratory, when hot water saturated with soluble iron sulfides is discharged into a cold water environment. The sulphides precipitate as membranes and form gelatinous bubbles. The bubbles look like possible precursors of living cells The membrance surfaces adsorb organic molecules from solution, and the metal sulphide complexes catalyze a variety of chemical reactions on the surfaces....'"

"Dyson's fourth discovery that contributes to the new picture of life that we like, and consider compelling, while of course not considering it proven [gradient driven cycles as precursors to metabolism], is that most ancient bacteria lineages are thermophilic; they are, in other words, comfortable and able to grow in hot, almost boiling water." Schneider, Eric & and Dorion Sagan. 2005. Into the Cool: Energy Flow, Thermodynamics, and Life. University of Chicago Press. Pp. 180-1. Subquotes are from Dyson, Freeman. 1999. Origins of Life. Cambridge University Press. Pp. 37, 26.


"Ulanowicz points out that above a certain point increasing interconnectivity increases fragility of the system. Having all the system interconnected 100% is as fragile as having just a single connection. A connectivity of about 50% seems optimal. Kauffman showed that at system interconnectivity about 50%, systems congeal into interconnected clumps, with clumps of nodes interacting as one. When systems congeal into larger and larger groups, they lose their diversity and the stability associated with it." Schneider, Eric & and Dorion Sagan. 2005. Into the Cool: Energy Flow, Thermodynamics, and Life. University of Chicago Press. P. 204. Ulanowicz reference is 1997. Ecology: The Ascendant Perspective. Columbia University Press. Kauffman reference is 1995. At Home in the Universe. Oxford University Press. P. 56.


"The pattern of growth of the first cells dividing from a fertilized animal egg resembles that of an early ecosystem colonization. The cells of the initial blastula phase of the embryo reproduce quickly. The cells look identical. But as the embryo develops, cells differentiate and die. The animal's various limbs, organs, and tissues represent an increase in diversity similar to the growing biodiversity seen in a developing ecosystem. Then as in an ecosystem, growth tapers off. An integrated, energy-efficient mature form appears. Adult organisms and mature ecosystems have achieved high levels of energy use and gradient reduction."

"Might animals be in some sense legacies of ancient episodes of cell growth and ecological succession? Are ancient patterns of microbial growth, from rapid initial phase to efficient final network, 'frozen' in animal development? Are adults mobile, latter-day 'climax' communities?"

"Our hunch is yes. Just as evolution is largely ecology writ large, so the organism seems to be ecology writ small. Clearly work needs to be done in this area, but perhaps individual organisms can be understood as spatially and temporally condensed versions of ecological processes." Schneider, Eric & and Dorion Sagan. 2005. Into the Cool: Energy Flow, Thermodynamics, and Life. University of Chicago Press. P. 256.


"Yet while in ecosystems energy and material flow in the same direction, in economic systems money and energy cycle opposite one another: money is exchanged for energy, goods, and work, with money flowing toward these items. Today hundreds of billions of dollars are paid for energy: oil and gas are exported to China, the United States, and Europe, while dollars flow toward the energy-rich states. Money, tradable for energy, work, and products behaves like energy changing form as it organizes flows through nonhuman natural systems." Schneider, Eric & and Dorion Sagan. 2005. Into the Cool: Energy Flow, Thermodynamics, and Life. University of Chicago Press. P. 276.


“Soil is a multiphase system consisting of solid, liquid and gaseous phases. It represents an enormous matrix with extremely high absorption and sequestration potential and it is highly efficient in buffering physical and chemical influences.” Larcher, Walter. Physiological Plant Ecology: Ecophysiology and Stress Physiology of Functional Groups, 4th Edition. Springer Verlag. 2003. P. 9.


“Examples of ecological interactions are: facilitation, when mature plants shield juvenile forms from strong irradiation, overheating or excessive cooling; competition, when plants compete for space, light, nutrients and water; chemical communication when plants, microorganisms and animals release signaling substances. Depending on the types of interaction(s) between organisms, the development and persistence of a single species in a community is either enhanced or inhibited, which all together controls the stability of the ecosphere as a whole.” Larcher, Walter. 2003. Physiological Plant Ecology: Ecophysiology and Stress Physiology of Functional Groups, 4th Edition. Springer Verlag. P. 10.


“Bioactive plant substances are mostly intermediary or end products of secondary metabolism; therefore, they are also referred to as secondary plant substances. They are biosynthesized from precursors arising from primary metabolism. The most important synthetic pathways are those leading from carbohydrate and fat metabolism via acetyl-coenzyme-A, mevalonic acid and isopentenylpyrophosphate to terpenoids and steroids, from sugar and amino-acid metabolism via shikimic acid and the acetate polyketide pathway to phenol bodies and their derivatices (e.g., phenylpropanes, flavonoids, tannins, numerous lichen substances), and from amino acids to alkaloids.” Larcher, Walter. 2003. Physiological Plant Ecology: Ecophysiology and Stress Physiology of Functional Groups, 4th Edition. Springer Verlag. P. 19.


“Some of the more common and functionally important categories [of synergy] include synergies of scale, threshold effects, phase transitions, emergent phenomena, functional complementarities, augmentation or facilitation (e.g., catalysts), joint environmental conditioning, cost-and-risk-sharing, information sharing, collective decision making, a division of labor, animal-tool symbioses, and convergent fortuitous combinations.” Earlier he notes synergy has “... traveled under many different aliases: emergent effects, cooperativity, symbiosis, a division of labor, epistasis, threshold effects, phase transitions, coevolution, heterosis, dynamical attractors, holistic effects, mutualism, complementarity–even interactions and cooperation.” Corning, Peter. Holistic Darwinism: Synergy, Cybernetics, and the Bioeconomics of Evolution. University of Chicago. 2005. P. 106, 15.


“... functional synergy explains the evolution of cooperation in nature, not the other way around. In other words, functional groups (in the sense of functionally integrated teams of cooperators of various kinds) have been important units of evolutionary change at all levels of biological organization; functional group selection is thus a ubiquitous aspect of the evolutionary process.” Corning, Peter. Holistic Darwinism: Synergy, Cybernetics, and the Bioeconomics of Evolution. University of Chicago. 2005. P. 24.


“As Maynard Smith has noted, extreme non-specificity is the rule among mutualists, whereas parasitism is highly specific.” Corning, Peter. Holistic Darwinism: Synergy, Cybernetics, and the Bioeconomics of Evolution. University of Chicago. 2005. P. 25.


“One of the most extraordinary examples is the single-celled eukaryotic protist, Mixotricha paradoxa. In fact, each cell represents an association of at least five different types of organisms. In addition to the host cell, there are three surface symbionts, including large spirochetes, small spirochetes, and bacteria. The function of the large spirochetes, if any, is not clear; they may even be parasites. However, the hairlike small spirochetes, which typically number about 250,000 per cell, provide an unusually effective propulsion system for the host through their highly coordinated undulations, the control mechanism for which is still obscure. Each of these spirochetes, in turn, is closely associated with another surface symbiont, a rod-shaped anchoring bacterium. Finally, each Mixotricha host cell contains an endosymbiont, an internal bacterium that may serve as the functional equivalent of mitochondria, removing lactate or pyruvate and producing ATP.

“What makes this partnership all the more extraordinary is the fact that Mixotricha is itself an endosymbiont. It is found in the intenstine of an Australian termite, Mastotermes darwinensis, where it performs the essential service of breaking down the cellulose ingested by its host. Indeed, these and other symbionts may constitute more than half the total weight of the termite.

“Perhaps the most impressive form of multiple symbioses, though, can be found in coral communities. A single coral reef may encompass millions of organisms from dozens of different plant and animal species, many of which are symbiotic with one another as well as with the coral outcropping itself. The coral provides oxygenated water and shelter. The plants and animals consume the oxygen, plankton, and organic debris and deposit calcium to build the coral. In addition, there are many kinds of symbioses between the creatures that are associated with the corals–among others, clams and algae, crabs and sea anemone, fish and sea anemone, shrimp and sea anemone and sea urchins and fish. The functions associated with these relationships include nutrition, protection from predators, mobility, mutual defense, and parasite removal.” Corning, Peter. Holistic Darwinism: Synergy, Cybernetics, and the Bioeconomics of Evolution. University of Chicago. 2005. Pp. 104-5.


“At the behavioral level, in other words, there is a proximate selective agency (in Ernst Mayr’s terminology) at work that is analogous to natural selection. Moreover, this ‘mechanism’ is very frequently the initiating cause of the ultimate changes associated with natural selection.

“This is where the phenomenon of functional synergy (and the subcategory of symbiosis) fits into the evolutionary picture: It is the immediate, bottom-line payoffs of synergistic innovations in specific environmental contexts that are the cause of the biological/behavioral/cultural changes that, in turn, lead to synergistic, longer term evolutionary changes in the direction of greater complexity, both biological and cultural/technological.” Corning, Peter. Holistic Darwinism: Synergy, Cybernetics, and the Bioeconomics of Evolution. University of Chicago. 2005. P. 109.


“The relationship between synergistic effects and the evolution of complexity should now be more apparent. The process of complexification in evolution has been closely linked to the production of novel, more potent forms of synergy. That is, the differentiation and/or integration of various parts, coupled with the emergence of cybernetic regulation and the development of hierarchical controls, has been driven by the ‘mechanism’ of functional synergy; synergistic effects of various kinds have been a primary cause of the observed trend toward more complex, multifunctional, multileveled, hierarchically organized systems. Furthermore, the same causal agency is applicable both to biological complexification and to the evolution of complex human societies–though both the sources of innovation and the selective processes involved differ in some important respects.

“Returning to another point raised earlier, we can now also see why it may be said that, at least in the process of evolutionary complexification, wholes have been more important units of selection than parts. It is wholes of various sorts that produce the synergies that then become the objects of positive selection. Thus, synergistic relationships of various kinds, and at various levels of organization, have been important units of evolution. To repeat, the Synergism Hypothesis is a theory about the causal role of relationships. Synergistic combinations, whether they arise through an integration of various parts (symbioses) or through the differentiation and specialization or elaboration of an existing whole, may provide a competitive advantage.” Corning, Peter. Holistic Darwinism: Synergy, Cybernetics, and the Bioeconomics of Evolution. University of Chicago. 2005. Pp. 110-1.


“With the emergence and increasing scope of cybernetic self-control, a subtle but important dividing line was crossed in evolution; self-organization was augmented by self-determination.” Corning, Peter. Holistic Darwinism: Synergy, Cybernetics, and the Bioeconomics of Evolution. University of Chicago. 2005. P. 116.


“In any event, the evolutionary emergence of self-determination over the course of time has had two implications: One is that self-determining processes have gained increasing ascendancy over the blind processes of autocatalysis, mutations, and natural selection. And the second is that, as noted earlier, the partially self-determining organisms that are the products of evolution have come to play an increasingly important causal role in evolution; they have become co-designers of the evolutionary process.” Corning, Peter. Holistic Darwinism: Synergy, Cybernetics, and the Bioeconomics of Evolution. University of Chicago. 2005. P. 117.


“In recent years it has become clear that the learning capabilities of animals go well beyond the simplistic behaviorist paradigm. They include specific learning predispositions, selective attention, stimulus filtering and selection, purposive trial-and-error learning, observational learning, and even capabilities for cost-benefit estimate, risk-assessments and discriminative choice-making.

“Thus it may be appropriate to deploy the notion of teleonomic selection (or neo-Lamarckian selection) to characterize the proximate ‘mechanism’ of value-driven, self-controlled behavioral changes.” Corning, Peter. Holistic Darwinism: Synergy, Cybernetics, and the Bioeconomics of Evolution. University of Chicago. 2005. P. 118.


“In a nutshell, the story of energy in evolution has little to do with entropy; it has more to do with progressive improvements in bioenergetic technologies. This can be seen clearly in the development of photosynthesis, a highly sophisticated nanotechnology for exploiting a virtually unlimited energy resource with fantastic profit potential.” Corning, Peter. Holistic Darwinism: Synergy, Cybernetics, and the Bioeconomics of Evolution. University of Chicago. 2005. P. 349.


“... these increasingly complex forms of energy capture and metabolism were the result of synergistic functional developments that provided adaptive economic advantages. They were not the result of thermodynamic instabilities, fluctuations, or bifurcations.” Corning, Peter. Holistic Darwinism: Synergy, Cybernetics, and the Bioeconomics of Evolution. University of Chicago. 2005. P. 350.


“Furthermore, many bioenergetic processes are remarkably efficient and entail very little entropy. Internal conversion of chemical energy (ATP) to mechanical work within animal muscles, for instance, ranges from about 66 to 98 percent efficient. Likewise, there is almost no entropy associated with the light-dependent reactions in photosynthesis.” Corning, Peter. Holistic Darwinism: Synergy, Cybernetics, and the Bioeconomics of Evolution. University of Chicago. 2005. P. 352.


“We define control information as the capacity (know-how) to control the acquisition, disposition, and utilization of matter/energy in purposive (teleonomic) processes.” Corning, Peter. Holistic Darwinism: Synergy, Cybernetics, and the Bioeconomics of Evolution. University of Chicago. 2005. P. 367.


“... if energy is ‘the capacity to do work,’ control information is the capacity to control the capacity to do work.” Corning, Peter. Holistic Darwinism: Synergy, Cybernetics, and the Bioeconomics of Evolution. University of Chicago. 2005. P. 368.


“Tiny parasitic wasps called Biosteres longicaudatus lay their eggs in the larvae of Caribbean fruit flies, which they find by following the strong smell of rotting fruit where the larvae mature. Three simple chemical compounds from the fruit (acetaldehyde, ethanol, and acetic acid) are particularly enticing to the wasps. These chemical markers, themselves products of microbial fermentation, are formed as bacteria and fungi feed on the fruit and decompose it. In this case, then, the feeding of one group of organisms (microbes) on another (fruit) yields a chemical signal that leads a third group (wasps) to the location of a fourth (fly larvae). Only with this elaborate assistance are the wasps able to reproduce.” Agosta, William. 2001. Thieves, Deceivers and Killers: Tales of Chemistry in Nature. Princeton University Press. Pp. 90-1.


“Limpets are small marine mollusks with soft bodies covered by a single low rounded shell. They have a muscular foot they use to hold fast to a surface and to move about in their intertidal habitat, feeding at high tide on green plants, seaweed, and other algae. When the tide begins to ebb, limpets cling firmly to a rock or other surface, drawing their shell down tightly to resist being washed out to sea and shield themselves from desiccation on exposrue at low tide. Their way of life is ancient: Limpet-like creatures first appeared over half a billion years ago in the early to middle Cambrian period.

“These particular California limpets are called Tectura paleacea and are adapted in shape and lifestyle to an uncommonly limited habitat. Most limpets live on rocks, some even maintaining a depression in a rock surface as a home to which they habitually return as the tide goes out. These Tectura limpets, however, spend their lives on blades of surfgrass, grazing on the plant’s surface layers. Surfgrass grows luxuriantly in the lower intertidal zone along the California coast, where it covers rocks with splashes of bright green and creates a safe haven for many small creatures. It is a member of the eel-grass family, which takes its name from its long narrow leaves. To accommodate themselves to life on the leaves, these tiny limpets have a parallel-sided shell, perhaps 6 millimeters long and 2 millimeters wide. These dimensions permit the shell to fit lengthwise on a blade of surfgrass quite precisely from one edge to the other. If disturbed, a limpet can clamp down snugly and remain immobile on its leaf.

“A bed of surfgrass protects limpets and other small mollusks because large predators find the thin fluttering leaves relatively inaccessible. However, one local resident that preys persistently on these little creatures is the lovely six-rayed star, a small pinkish starfish about 3 centimeters in diameter. Six-rayed stars hunt by moving along a surfgrass blade, waving their long, mobile tube feet here and there as they search out small prey to ensnare and stuff into their mouths. Unlike other mollusks in the surgrass, the Tectura limpets show no unusual reaction to an approaching six-rayed star. They neither run nor fight, but simply pull their shell down onthe leaf and remain motionless as a hunting starfish crawls over them. Usually the starfish ignores them and continues its quest for food.

“Starfish ignore the limpets because they fail to distinguish them from the background surfgrass. To the starfish’s chemical sense, limpet and surfgrass are indistinguishable because both ‘smell’ of chemical compounds called flavonoids. Surfgrass synthesizes these flavonoids, probably as a defense against herbivores, and limpets then ingest them as they nibble on the plant. Flavonoids do not repel the limpets, but become a crucial defense for them. The limpets incorporate flavonoids in their shells, but not their soft bodies, where they serve as a chemical disguise. A six-rayed star gliding along a blade of surfgrass detects flavonoids in both surfgrass and limpet shell and is unaware of the limpet’s presence. The subterfuge is quite effective. Tectura limpets are only a minor component of six-rayed stars’ diet despite the two animals’ frequent encounters.” Agosta, William. 2001. Thieves, Deceivers and Killers: Tales of Chemistry in Nature. Princeton University Press. Pp. 99-100.


“Far from Antarctica in the Caribbean Sea, there is another amphipod, Pseudamphithoides incurvaria (PI), with a comparable chemical defense. However, PI does not appropriate an entire organism, but only small bits of one. Its defense lies somewhere between Hyperiella’s kidnapping a living sea butterfly and lacewing larvae’s removing woolly wax from their aphid prey.

“PI originally attracted attention owing to two unusual habits. It feeds on seaweed, and although many seaweed-eating amphipods have broader tastes, PI nibbles at only one species. It feeds only on a flat-bladed brown seaweed called Dictyota bartayresii. Specialist feeders are less common among marine organisms than on land, but PI seeks out this one species even when other Dictyota seaweeds are more abundant.

“Dictyota species are rich with unpleasant-tasting chemicals to discourage grazing fishes. Amphipods and other small creatures often find safety in among such unpalatable seaweeds, where fishes are infrequent visitors. The chemicals in Dictyota bartayresii are not unpleasant to PI, and in fact the amphipod uses them to identify the seaweed it eats. Conceivably, PI could also sequester these distasteful compounds for its own protection; perhaps surprisingly, it does not.

“Instead of sequestering the seaweed’s compounds as a defense, PI appropriates the seaweed itself. The amphipod constructs a millimeter-sized domicile, joining together little bits of seaweed to fashion a structure something like the shell of a clam, with the two halves hinged by a threadlike secretion. PI is 1-2 millimeters long and fits nicely inside this seaweed structure, with its head and several forward pairs of legs sticking out so that it can swim. In this way, the amphipod remains mobile while safe and secure within its seaweed home. This is an effective defense. In a laboratory experiment, fish quickly snapped up naked defenseless amphipods but rejected those inside their domiciles.” Agosta, William. 2001. Thieves, Deceivers and Killers: Tales of Chemistry in Nature. Princeton University Press. Pp. 109-10.


“Quorum sensing also triggers events more elaborate than the production of light. One of the most remarkable of these involves rod-shaped microbes known as myxobacteria, such as Myxococcus xanthus, that flourish in cultivated soil all over the world. These bacteria live individually in the soil as long as food is in good supply. If water or nutrients begin to fail, about one hundred thousand cells come together, progressing through the soil to a gathering point. Here the cells develop an elaborate structure known as a fruiting body, within which they undergo a remarkable transformation. Over the next twenty-four hours, they turn themselves into spores. Unlike the free-living cells, these spores are seedlike thick-walled structures that are resistant to heat, starvation, and lack of water. Although the individual cells are microscopic, the mature fruiting body they create is just large enough to be seen with the naked eye as a colored speck. Not all of the aggregated cells become spores, as many of them are sacrificed in constructing the fruiting body.

“In taking this drastic action, the bacterial cells collectively desert a locale where nutrients have become scarce. Now a packet of spores, they await transportation to a new home. The wind, an animal, or perhaps flowing water will pick up the fruiting body and deposit it elsewhere. The spores of course do not guide their journey, but if by chance they land in an appropriate environment, they then revert to their free-living form. If nourishment is plentiful, they may establish a flourishing new colony of bacteria.

“Transforming free-living myxobacteria into a fruiting body requires at least four different chemical signals. Two of these are well enough understood that we can describe them briefly. The first is a quorum-sensing pheromone that promotes the initial aggregation of individual cells. When a cell no longer finds adequate nutrients, it secretes a mixture containing several common amino acids. This mixture spreads through the soil, broadcasting its message in all directions: ‘I am here, and I am starving.’ As long as only a few cells are sending this message, the pheromone’s concentration in the soil remains low. If many cells begin to signal a lack of food, it naturally rises. The colony members sense this concentration in their surroundings. While it is low, they take no action: Most cells still have adequate nourishment. Aggregation commences only when the pheromone level indicates the number of starving cells is sufficient to assemble a complete fruiting body. The signal now declares not only that nourishment is scarce but also that the number of protesting cells is great enough to take meaningful action. By aggregating only when assured they can form a fruiting body, the bacteria increase the probability of successful relocation.

“Once the cells come together, they begin to produce a second pheromone, which activates spore formation. Unlike the first signal, this pheromone is a small protein that remains attached to each cell’s surface. Since it does not spread through the soil, cells must be in direct contact to distribute its message. During aggregation, each rod-shaped cell moves about, adjusting its position so the cells fit together snugly, end to end and side by side. As the cells become aligned, the signal passes from one cell to the next, ultimately reaching the entire mass. Only then do they begin the transformation into spores.

“The requirement that cells be in intimate contact to transmit the second pheromone ensures that spore formation commences only after they have arranged themselves in a compact mass. Closely packed cells generate a fruiting body filled with closely packed spores. The arrangement is critical because the likelihood of successful relocation depends on the number of spores the fruiting body contains and how efficiently they are packaged. Although the two remaining chemical signals are not yet well understood, we already know enough to appreciate these microbes’ impressive communal effort to perpetuate their species.” Agosta, William. 2001. Thieves, Deceivers and Killers: Tales of Chemistry in Nature. Princeton University Press. Pp. 126-8.


“In establishing their relationship, bacteria and plants engage in an extensive chemical dialog. Rhizobia live not only with plants but are free-living soil bacteria as well. Free in the soil, rhizobia do not fix nitrogen, although there are other soil bacteria that do. When free rhizobia find themselves near a legume root, they may detect amino acids, sugars, and other attractants released from the plant’s tiny root hairs. Drawn to this nourishment, the rhizobia move toward the root. Once the bacteria are nearer, they pick up another root hair signal that has a more profound effect. The exact chemical nature of this second signal varies among legumes, but in all known cases, the signals are related to chemicals known as flavonoids, which include many common plant pigments. A plant’s particular flavonoid signal is one factor in determining its associated rhizobia, although there is no one-to-one correlation of species in the interaction between plant and rhizobium. Some organisms, both plants and rhizobia, associate with several different partners, and others with only one.

“When the flavonoid signal reaches the rhizobia, it induces them to produce and secrete a compound composed of sugarlike units that is called Nod (for nodulation or nodule-forming) factor. Nod factor spreads through the soil and is soon detected by the root that sent out the flavonoid. Here its message to the plant is to begin building a root nodule, which in time the rhizobia will inhabit. Nod factor induces the cell division in the root necessary to form a nodule and at the same time causes the root hairs to grow, branch, and become somewhat deformed. As this is happening, the rhizobia are moving closer, soon coming into direct contact with the root hairs. Carbohydrates borne on the bacterial surface now signal the root hairs to develop tiny tubules called infection threads. These carbohydrates then enable the rhizobia to pass into these infection threads. Once the rhizobia enter the threads, they are inside the plant. While plant cells are proliferating in the root to create a nodule, rhizobia begin proliferating within the infection threads.

“Subsequent events are visible under a microscope, but information about the signals involved is vague. Very likely there is an extended exchange of chemical messages both between bacterial and plant cells and also among the bacteria themselves, because the ensuing events demand close coordination. The rhizoba, increased in number through division, move down the tunnel-like infection thread. On reaching its end, they induce a weakening in plant cell walls, probably through the agency of another chemical secretion, and make their way into cells of the developing nodule. Once inside, the rhizobia undergo a fundamental transformation. They increase in size and differentiate into what are called bacteroids, cells that no longer undergo cell division but begin to fix nitrogen. The plant cells maintain the bacteroids, providing them with nutrients and nitrogen to fix, and carefully controlling the local acidity and other conditions–the price the plant must pay to benefit from nitrogen fixation. As the bacteroids generate ammonia, the plant cells assimilate it for their own use.” Agosta, William. 2001. Thieves, Deceivers and Killers: Tales of Chemistry in Nature. Princeton University Press. Pp. 130-1.


“A promising material of a quite different sort comes from the edible blue mussels that are common along seashores around the world. To avoid being tossed about in the water, blue mussels anchor themselves to a rock or other holdfast with fibers known as byssal threads. These coarse, dark-colored strands, popularly called a mussel’s beard, are strong modified tendons. Like other tendons, byssal threads are composed largely of a widespread structural protein called collagen, but they are significantly sturdier than human tendons and much more elastic. These differences are important. Mussels live along coasts in the intertidal zone, where waves batter them endlessly. To withstand the constant assault, their attachment must be both secure and flexible or they risk being torn loose by the surf and swept away.

“Byssal threads combine strength and flexibility in a novel way. A thread is elastic near the mussel’s foot but it is stiff at its other end where it attaches to the anchoring holdfast. This permits it to act as shock absorber close the mussel, and at the same time act as a tough tether at the holdfast. In between, the thread’s properties vary gradually, as it becomes progressively firmer and less elastic from the mussel to the holdfast.” Agosta, William. 2001. Thieves, Deceivers and Killers: Tales of Chemistry in Nature. Princeton University Press. P. 143.


“Similar apparently self-medicating behavior involves the scarlet macaw, a large, brightly colored parrot species found in the rainforest of southeastern Peru. These birds are fond of the poisonous unripe fruit of the sandbox tree, tearing it open with their powerful beaks to feast on its flesh and seeds. They survive eating the poisonous fruit only because they also eat a clay they find on high river banks that neutralizes the fruit’s toxin. The macaws eat this clay regularly and feed it to their chicks, who clearly relish the treat and clamor for more.” Agosta, William. 2001. Thieves, Deceivers and Killers: Tales of Chemistry in Nature. Princeton University Press. P. 153.


“The larvae that hatch from Cotesia eggs remain inside their caterpillar host, exploiting it as a secure haven from the outer world and a convenient food supply. They feed on the caterpillar from within until they are mature and ready to pupate. Then they emerge from its body and immediately begin spinning small white cocoons, which they attach by one end to the caterpillar’s back. It is not uncommon for a tobacco hornworm, still alive, to be festooned with fifty or more Cotesia cocoons, each resembling a diminutive grain of rice fastened to the caterpillar. Each cocoon contans a developing pupa that should ultimately come forth as a new adult wasp.

“This arrangement is ideal for the wasps, provided the caterpillars can be prevented from destroying the wasps’ offspring. Like other creatures, tobacco hornworms have potent defenses against foreign invasion. Unless the wasps somehow disable the hornworms’ defenses, wasp eggs and larvae are doomed to a quick death. Furthermore, wasps must disarm the hornworms without killing them. If the caterpillars die before the larvae mature and emerge, the larvae will die with them. For the same reason, the wasp larvae must also avoid killing their host as they consume its body fluids. The wasps need to keep the hornworms alive but defenseless.

“How do the wasps do this? Many kinds of parasitic wasps employ their venom to neutralize a caterpillar’s defenses, adding a dose of toxic proteins as they deposit their eggs. A female Cotesia uses her venom to neutralize a caterpillar’s defenses, adding a dose of toxic proteins as they deposit their eggs. A female Cotesia uses her venom, but for her, this is only the beginning. Cotesia congregata is one of several dozen kinds of wasps that inject a virus along with their venom when laying eggs, and this virus is responsible for many of the striking effects that follow. A virus has genes and proteins of its own and is much more complex than any single chemical substance. With a generous stretch of definition we can treat it as a large special chemical, providing we note one characteristic of viruses that chemical compounds lack: Given an appropriate host, a virus can replicate itself efficiently inside a host cell, destroying the cell as it creates many new virus particles.

“In addition to genes for its own replication, the virus that female Cotesia wasps deposit along with their eggs has genes for synthesizing toxic proteins that impair hornworms in several ways. The most important of these is to disable the caterpillars’ defenses against external attack. Thirty minutes after Cotesia has laid her eggs, the virus that accompanied them has spread throughout the caterpillar’s body and gained entry into its cells. Most importantly, it has penetrated those immune cells that identify and eliminate foreign invaders. A few hours later, these cells undergo a rapid transformation that can readily be observed under a microscope. They begin by losing bits of their membrane and cellular contents; soon thereafter they clump together and die. These immune cells constituted the caterpillar’s major defense against invasion, and now they are gone. A simple experiment demonstrates how vital these cells are. If Cotesia eggs taken directly from a gravid wasp and washed free of any virus adhering to them are artificially inserted into an unparasitized caterpillar, they do not survive. Normal immune cells immediately recognize them as foreign, and quickly attack and kill them. A healthy caterpillar in this case has no trouble riding itself of wasp eggs before they hatch.

“The virus’s next significant assault on the hornworms arrests their normal development. Wasp larvae can grow and mature only so long as their hosts continue life as feeding caterpillars. However, left to their natural schedule, caterpillars will be ready to bury themselves in the ground and pupate before the wasp larvae are mature. For the wasps to succeed, this must not happen. The wasps must artificially extend the caterpillars’ larval life and so prevent their metamorphosis. The Cotesia virus provides toxins that prevent pupation by interfering with the hormones that control it. Long after the wasps have emerged and long after the normal time for metamorphosis, parasitized caterpillars remain developmentally retarded. These ill-fated caterpillars will never pupate. Decorated with the wasps’ tiny cocoons, they may linger as long as two weeks before dying.” Agosta, William. 2001. Thieves, Deceivers and Killers: Tales of Chemistry in Nature. Princeton University Press. Pp. 204-6.


“Although scientists have observed these remarkable ants at work for decades, only in early 1999 was it recognized that the story involves not two, but four different organisms. It appears that fungus gardens harbor an unwanted guest. Like our own vegetable gardens, the ants’ gardens should be attractive targets for hungry, destructive intruders. In this case, the intruder is a specialized fungus that overruns the garden fungus and seriously endangers the ants’ food supply.

“This virulent parasite is probably an ancient pest, and the ants long ago devised an efficient response to its threat. To protect their gardens, the ants carry on their bodies antibiotic producing bacteria that stop the parasite in its tracks. It is striking that the bacterium the ants carry is a species of Streptomyces, the same genus that affords many of our own antibiotics. Our development of Streptomyces antibiotics in the mid-twentieth century was a milestone that helped revolutionize clinical medicine, but fungus-growing ants had made the same discovery long before, probably millions of years before we existed.” Agosta, William. 2001. Thieves, Deceivers and Killers: Tales of Chemistry in Nature. Princeton University Press. Pp. 216-7.


“It has been suggested that the computational devices of the CNS are organized according to a ‘Russian doll’ (‘nested’) hierarchic principle. Thus, it has been surmised that computation can be performed at various hierarchic levels in the Central Nervous System (CNS). Broadly speaking these levels can be listed as follows:

̵ “System of cellular networks, made by assemblies of cellular networks working as an integrated computational system (e.g., the CNS). The result of the integration process is a multi-facet functional response of the system, i.e., a so-called high level ‘syndromic response’ of the system.
̵ “Cellular network, made by assemblies of neurons and/or glial cells capable of carrying out one function (or more than one function in the case of polymorphic networks) in a system of cellular networks such as the CNS. It is suggested that a term more precise than ‘polymorphic networks’ could be ‘polyfunctional networks’ since these networks under specific pervading influences (e.g., a highly diffusible VT [volume transmission] signal such as CO2) can change their functional output.
̵ “Local circuit, made by portions of a neuron (or neurons) that, under given conditions, function as an independent integrative unit....”
̵ “System of molecular networks, made by the assemblies of molecular networks involved in carrying out a complex cellular function and work as an integrated computational system. Thus, also at the cellular level there is the production of a ‘syndromic response’ (i.e., a multi-facet high level cellular response).
̵ “Molecular network, made by molecules that function as a metabolic and/or signalling pathway in a cell. The molecular network is especially involved in carrying out one function but often it can also operate as a polyfunctional network, since also these networks (as the cellular networks, but at a different level of miniaturization) under specific pervading influences can change their functional output.
̵ “Macro-molecular complex, made by functional groups in a large molecule (or, e.g., protomers in a multimeric protein) that allow the macromolecular complex to carry out its function.

“The first two levels can be considered as ‘macro-scale levels’, the third is the ‘meso-scale level’, the last three ones as ‘micro-scale levels’. The impact of the elaborations at any of these levels on the overall brain function will be dependent on the hierarchic level at which they have been carried out, the location of this computing device in the mass of the CNS and on the temporal aspects that characterize these elaborations.” Agnati, Luigi, L. Santarossa, S. Genedani, E Canela, G. Leo, R. Franco, A. Woods, C. Lluis, S. Ferre & K. Fuxe. 2004. “On the Nested Hierarchical Organization of CNS: Basic Characteristics of Neuronal Molecular Networks.” From Erdi, P et al. Cortical Dynamics, Lecture Notes in Computer Science. Pp. 24-54. Springer Verlag. P. 26.


“Local circuits can be defined as any portion of the neuron (or neurons, especially short-axon neurons (i.e., Golgi II type neurons) that, under given conditions, functions as an independent integrative unit. This phenomenon depends on the fact that in local circuits membrane domains belonging to the same and/or different cells are so close to each other to make possible prompt and highly effective chemical and electrotonic interactions between molecular circuits present in the plasma membranes facing each other. These computational capabilities are very likely of the highest importance since local circuits may indeed prove to be the neural substrate of higher brain functions.” Agnati, Luigi, L. Santarossa, S. Genedani, E Canela, G. Leo, R. Franco, A. Woods, C. Lluis, S. Ferre & K. Fuxe. 2004. “On the Nested Hierarchical Organization of CNS: Basic Characteristics of Neuronal Molecular Networks.” From Erdi, P et al. Cortical Dynamics, Lecture Notes in Computer Science. Pp. 24-54. Springer Verlag. Pp. 27-8.


“If we accept the view of the CNS as a nested hierarchical complex system, it is possible to search for schemes of functional organization at the various miniaturization levels. It is suggested that basically the same schemes for communication and elaboration of the information are in operation at the various miniaturization levels. This functional organization suggests a sort of ‘fractal structure’ of the CNS. As matter of fact, according to fractal geometry, fractal objects have the property that as we magnify them, more details appear but the shape of any magnified detail is basically the same as the shape of the original object. It is, therefore, suggested to introduce the term ‘fractal logic’ to describe networks of networks where at the various levels of nested organization the same principles (logic) to perform operations are used.” Agnati, Luigi, L. Santarossa, S. Genedani, E Canela, G. Leo, R. Franco, A. Woods, C. Lluis, S. Ferre & K. Fuxe. 2004. “On the Nested Hierarchical Organization of CNS: Basic Characteristics of Neuronal Molecular Networks.” From Erdi, P et al. Cortical Dynamics, Lecture Notes in Computer Science. Pp. 24-54. Springer Verlag. Pp. 29-30.


“A fringe is an area of overlap between two networks and it leads to facilitation or occlusion.” Agnati, Luigi, L. Santarossa, S. Genedani, E Canela, G. Leo, R. Franco, A. Woods, C. Lluis, S. Ferre & K. Fuxe. 2004. “On the Nested Hierarchical Organization of CNS: Basic Characteristics of Neuronal Molecular Networks.” From Erdi, P et al. Cortical Dynamics, Lecture Notes in Computer Science. Pp. 24-54. Springer Verlag. P. 31.


“Volume Transmission (VT): is ‘one to many’ communication. The signal released from the source into a medium (extracellular fluid) reaches its targets either along preferential pathways or in a three-dimensional fashion.

“Wiring Transmission (WT): is a ‘point to point’ communication. The signal released from the source reaches its target following ‘wired pathways’ (e.g., axons and synaptic contacts).” Agnati, Luigi, L. Santarossa, S. Genedani, E Canela, G. Leo, R. Franco, A. Woods, C. Lluis, S. Ferre & K. Fuxe. 2004. “On the Nested Hierarchical Organization of CNS: Basic Characteristics of Neuronal Molecular Networks.” From Erdi, P et al. Cortical Dynamics, Lecture Notes in Computer Science. Pp. 24-54. Springer Verlag. P. 32.


“Channels or edges are transmission lines among Ns [Nodes]. They can be active or passive (i.e., the migration of the signal along the channel can be due to an active transport or it can occur thanks to pre-existing energy gradients).” Agnati, Luigi, L. Santarossa, S. Genedani, E Canela, G. Leo, R. Franco, A. Woods, C. Lluis, S. Ferre & K. Fuxe. 2004. “On the Nested Hierarchical Organization of CNS: Basic Characteristics of Neuronal Molecular Networks.” From Erdi, P et al. Cortical Dynamics, Lecture Notes in Computer Science. Pp. 24-54. Springer Verlag. P. 39.


“Von Newmann, in his pioneering book ‘The Computer and the Brain’, stated that both logics and mathematics are historical, accidental forms of expression and the brain could use a communication code that has no meaning for us. As pointed out in the Introduction, a holistic approach is needed taking into account the ‘animating principles’ that make from many different nested hierarchic levels a single complex system. According to Bacon’s view a basic step to this aim is the investigation of the logic behind the phenomenon under study. In our opinion, a logic is needed capable of describing organization and operations of the elements within each hierarchic level of the network and to combine the different levels. The development of a ‘fractal logic’ capable of dealing with systems of different miniaturization levels, organized in a nested hierarchic fashion and operating according to the same rules at each level has been suggested.” Agnati, Luigi, L. Santarossa, S. Genedani, E Canela, G. Leo, R. Franco, A. Woods, C. Lluis, S. Ferre & K. Fuxe. 2004. “On the Nested Hierarchical Organization of CNS: Basic Characteristics of Neuronal Molecular Networks.” From Erdi, P et al. Cortical Dynamics, Lecture Notes in Computer Science. Pp. 24-54. Springer Verlag. P. 48.


“Arguments based on both in vitro and in silico models suggest that biogeochemical cycles will readily evolve on planets with life, along with many of the putative fundamental processes described in this book. Artificial life models illustrate the potential for these emergent cycling systems to have a positive Gaian effect. The well-known potential for exponential growth in unconstrained ecological systems suggests that these emergent systems will often regulate their environments around low-nutrient states (biotic plunder) rather than at states which optimize productivity. This provides a context in which to understand why human-caused entrophication is often a problem, if the natural state of most systems tends towards nutrient scarcity then it is not surprising that raising nutrient levels dramatically can sometimes have unwelcome effects. In the context of biotic plunder it makes sense to define Gaia in relation to prolonged habitability of a planet but not as a process which maximizes biological productivity at any one point in time.” Wilkinson, David. 2006. Fundamental Processes in Ecology: An Earth Systems Approach. Oxford University Press. P. 123.


“A related idea that was developed during the 1990s is that of ecological engineering, this is a more ecological idea–compared to the evolutionary approach taken by niche construction. It points to the way in which some organisms greatly alter their environment both for themselves and other species; either by their physical presence (e.g. trees) or their behaviour (e.g. beavers or humans). Unlike niche niche construction, with it mathematical underpinning from population genetics, ecological engineering is grounded in natural history observation.” Wilkinson, David. 2006. Fundamental Processes in Ecology: An Earth Systems Approach. Oxford University Press. P. 132.


“The Earth System is obviously very complex and we are currently altering it in many ways. A Gaian approach is a way of trying to organize a lot of information in a way that allows one to ask interesting, and hopefully useful, questions. In particular, it forces us to think hard about feedbacks and gives microbes the central place they deserve in ecology. In the context of the processes described in this book the ecologically most important group are the prokaryotes followed by the single-celled eukaryotes and then the fungi and plants. The least important group is the animals. The striking thing about this ranking is it is almost exactly opposite to the amount of attention given to these groups by ecologists!” Wilkinson, David. 2006. Fundamental Processes in Ecology: An Earth Systems Approach. Oxford University Press. Pp. 140-1.


“It is now clear to many scientists that it is impossible to understand a planet such as the Earth without considering multiple feedbacks between life and the abiotic environment.” Wilkinson, David. 2006. Fundamental Processes in Ecology: An Earth Systems Approach. Oxford University Press. P. 141.


“Asking about the role of learning in the development of some bit of behavior is not the same as asking about its phylogenetic history. But using innate to mean both ‘unlearned’ and ‘shared by evolutionary relatives’ obscures this fact. Similarly, whether or not behavior can be affected by any particular experience is quite independent of its survival value. Appearance early in life is not the same as imperviousness to outside influences. And so on. Once these nature-nurture questions are disambiguated, it should be clear that they are different questions, with different evidential bases as we shall see below. They are not alternative ways of glimpsing a single underlying nature; rather, they reveal the diverse, sometimes conflicting meanings of ‘nature.’

“It is sometimes said that the division between nature and nurture needs healing. Similar remarks are made about the body and the mind. In neither case, though, are there two parts that need rejoining, like a broken dish. Both oppositions mislead by implying that their terms are of the same type, and that these terms are in complementary relation, defining some larger whole, the way complementary angles make up a right angle – that is, that behavior is partly innate and partly acquired and a person is composed of a body and a mind. Once the metaphor of a partitioned whole is accepted, all sorts of oddities follow. An anthropologist may argue that a behavior is cultural, not biological. Or, trying to convey a sense of unreasoning compulsion, a drug user may insist that the craving is physical, not just mental. A legal scholar may suggest that stepparents’ biologically ‘programmed’ tendency to; abuse their stepchildren ‘may operate as hard-to-resist impulse,’ and thus make the act seem less reprehensible than abuse by natural parents.” Oyama, Susan. 2000. Evolution’s Eye: A Systems View of the Biology-Culture Divide. Duke University Press. P. 156.


“However we gerrymander the outlines of evolutionary ‘nature,’ there will always be some residual chunk of acquired ‘nurture’ hovering mysteriously in thin air, without a ‘biological base’ to support it. But if natures are the result of the continuous nurture of developmental construction, we ought to object when we are told that nature interacts with nurture (or biology with culture, etc.), just as we do when we read about material body-stuff interacting with immaterial mind-stuff.” Oyama, Susan. 2000. Evolution’s Eye: A Systems View of the Biology-Culture Divide. Duke University Press. P. 157.


“When nature is identified by some criterion, it is easy to conclude that it is intractable or fixed, that it must be. This is probably the most common inference about ‘biology,’ and it is often unjustified.

“In this style of reasoning, it is usually universal nature that is supposed to be fixed. Martin Daly and Margo Wilson correctly point out that it is not only biologically oriented theorists who make claims about universal human nature; even ‘the staunchest antinativists’ generalize psychological principles to the entire species. Daly and Wilson follow Symons in saying that the real point of contention between evolutionists and their opponents is the specificity of mechanisms, not their fixity, and that the nature-nurture controversy is a red herring. This is an important point, but part of the concept of human nature is that it is universal and at least relatively fixed. Insofar as the nature-nurture opposition is fueled by concerns about fixity, it is not so easily set aside. If it were not for the widespread conviction that ‘nature’ is fixed, in fact, nature-nurture questions would surely not have generated so much heat over the years. Oyama, Susan. 2000. Evolution’s Eye: A Systems View of the Biology-Culture Divide. Duke University Press. P. 157.


“Although we frequently invoke the distinction between ‘ultimate causes’ (conditions prevailing over evolutionary time) and immediate ‘proximate causes,’ we disagree on just how to keep them apart. One problem is that the distinction tends to collapse: Ultimate causes are transmuted into proximate ones, often in the guise of genetic programs.” Oyama, Susan. 2000. Evolution’s Eye: A Systems View of the Biology-Culture Divide. Duke University Press. P. 161.


“This opposition between reason and instinctive passion is evident in some of the works cited above. With the growth of sociobiological theory, however, a fascinating, if subtle, change has occurred: Long considered our best defense against the beast within us, rational deliberation is being appropriated to do that animal nature’s work. As we have seen, certain theorists suppose us to be forever doing the bidding of our selfish, fitness hungry genes. Their machinations conveniently unconscious, these calculating prodigies are said to produce, and explain, our behavior. Regardless of what we think we are doing, we are really serving our genes’ interests. It seems that the biological beast has commandeered the very rationality that used to keep it in check.” Oyama, Susan. 2000. Evolution’s Eye: A Systems View of the Biology-Culture Divide. Duke University Press. P. 164.
 

“It is now generally accepted that the integrative analysis of the function of multiple gene products has become a critical issue for the future development of biology. Such integrative analysis will rely on bioinformatics and methods for systems analysis. It is thus likely that over the coming years and decades biological sciences will be increasingly focused on the systems properties of cellular and tissue functions. These are the properties that arise from the whole and represent biological properties. These properties are sometimes referred to as ‘emergent’ properties since they emerge from the whole and are not properties of the individual parts.” Palsson, Bernhard. 2006. Systems Biology: Properties of Reconstructed Networks. Cambridge University Press. P. 2.


“Metabolism, information processing, and cellular fate processes represent some of the major categories of genetic circuits. Considerable unity in biology is likely to result in conceptualizing biological functions as genetic circuits. From this standpoint, gene therapy may no longer be viewed as replacing a ‘bad’ gene, but instead fixing a ‘malfunctioning’ genetic circuit. Evolution may be viewed as the ‘tuning’ or ‘honing’ of circuits to improve performance and chances of survival. Classifying organisms based on the types of genetic circuits they possess may lead to ‘genomic taxonomy.’” Palsson, Bernhard. 2006. Systems Biology: Properties of Reconstructed Networks. Cambridge University Press. P. 4.


“All reactions inside a cell are governed by thermodynamics. The relative rate of reactions, forward and reverse, is therefore fixed by basic thermodynamic properties. Unlike stoichiometry, thermodynamic properties do change with physicochemical conditions such as pressure and temperature. The thermodynamic properties of associations between macromolecules can be changed by altering the sequence of a protein or the base-pair sequence of a DNA binding site. The thermodynamics of transformation between small molecules in cells are fixed but condition dependent....”

“In contrast to stoichiometry and thermodynamics, the absolute rates of chemical reactions inside cells are highly manipulable. Highly evolved enzymes are very specific in catalyzing particular chemical transformations. Cells can thus extensively manipulate the rates of reactions through changes in their DNA sequence.” Palsson, Bernhard. 2006. Systems Biology: Properties of Reconstructed Networks. Cambridge University Press. P. 15.


“Therefore, what are called silent phenotypes in biology may be mathematically synonymous to multiple equivalent network states. Palsson, Bernhard. 2006. Systems Biology: Properties of Reconstructed Networks. Cambridge University Press. P. 19.


“In higher eukaryotes, the complexity of promoter and enhancer regions of the genome is usually much higher, and these regions can contain binding sites for tens of different regulatory proteins. The higher the number of molecules participating in transcriptional regulation, the larger the combinatorial possibilities are, and thus a larger number of functional states can be derived as the number of components grows.” Palsson, Bernhard. 2006. Systems Biology: Properties of Reconstructed Networks. Cambridge University Press. P. 58.


“... the relative fraction of transcription factor coding genes tends to be higher for organisms that encounter more varied environmental conditions during their lifetime, indicating that there are limits to the range of transcriptional states that can be achieved with a fixed number of transcription factors.” Palsson, Bernhard. 2006. Systems Biology: Properties of Reconstructed Networks. Cambridge University Press. P. 61.


“Cells in multicellular organisms communicate in three principal ways:

• one cell sends a soluble signal that diffuses to the target cell,
• cells can manipulate the composition of the extracellular matrix,
• cells can communicate with very specific direct cell-to-cell mechanisms.”
Palsson, Bernhard. 2006. Systems Biology: Properties of Reconstructed Networks. Cambridge University Press. P. 74.


“At this point, we already know that the chemistry of life is determined not only by reactions under thermodynamic control, but by a large series of reactions under kinetic control. Thermodynamic control gives products as a kind of ‘free lunch’; to ask the question of how and why products under kinetic control were formed, is another way of questioning the origin of life. As will be revealed later on in this book, and as already clear to most readers, macromolecular sequences are not under thermodynamic control – the primary structure of lysozyme is not as it is because of being the most stable combination of 129 amino-acid residues. In fact the aetiology of macromolecular sequences is the bottle neck of research on the origin of life. It is fine to get excited about hydrothermal vents, coupling reactions on clay, reductions by hydrogen sulfide – but with these reactions alone one does not go far. As a ‘Gedankenexperiment’ one can offer the researchers in the origin of life all kinds of low-molecular-weight compounds in any quantity they want, including ATP and mononucleotides, lipids and amino acids, and ask them to make life – or simply to describe how life comes about. They would not know how to even start. Things would be different only if – as a continuation of the previous Gedankenexperiment – an unlimited source of enzymes and nucleic acids were to become available.” Luisi, Pier Luigi. 2006. The Emergence of Life: From Chemical Origins to Synthetic Biology. Cambridge University Press. Pp. 56-7.


“Clearly, there are good reasons for long chains: only a long chain permits the dilution in the same string of many active residues and, simultaneously, their mutual proximity due to the forced folding; in turn, this folding and the corresponding conformational rigidity is due to the very large number of intramolecular interactions, which is only possible in long chains; the consequence of the length is an elaborate three-dimensional architecture that brings forth a particular micro-environment and reactivity of the active site; the large size is also responsible for the overall physicochemical properties, such as solubility in water or affinity to the membrane, conformational changes and cooperativity. These are properties that can only emerge from a long chain. Luisi, Pier Luigi. 2006. The Emergence of Life: From Chemical Origins to Synthetic Biology. Cambridge University Press. P. 59.


“Enzymes and nucleic acids are not simply polymers, they are copolymers.” Luisi, Pier Luigi. 2006. The Emergence of Life: From Chemical Origins to Synthetic Biology. Cambridge University Press. P. 60.


“Also, it is well known that in aqueous solution the reaction leading to chain condensation starting from amino acids is thermodynamically unfavorable, even when starting from the corresponding amides. The same thermodynamic difficulty holds for the condensation of mononucleotides into polynucleotides. Thus, an energy input is necessary in order to make chains.” Luisi, Pier Luigi. 2006. The Emergence of Life: From Chemical Origins to Synthetic Biology. Cambridge University Press. P. 62.


“Self, in the connotation of this chapter and in the field of life science in general, defines a process that is dictated by the ‘internal rules’ of the system.” Luisi, Pier Luigi. 2006. The Emergence of Life: From Chemical Origins to Synthetic Biology. Cambridge University Press. P. 86.


“When surfactant molecules solubilize in water, often the process is slow at the very beginning, and gets faster with time: the more surface bilayer is formed, the more the process speeds up, because there is more and more active surface where the next steps of aggregation can take place. The same behavior is observed in crystallization; in other words, an autocatalytic process: the product of the reaction (organized surface bilayer or crystals) speeds up further self-organization. Actually, the point can be made, that generally self-organization in chemical system is attended by some kind of autocatalytic behavior.” Luisi, Pier Luigi. 2006. The Emergence of Life: From Chemical Origins to Synthetic Biology. Cambridge University Press. P. 91.


“The biological world is by definition full of self-organized structures, and here only a few examples are given. Usually, a complex interplay between thermodynamic and kinetic control is at work to guarantee the complexity of the biological structures. In addition, many such syntheses in vivo take place on a matrix – pre-existing fibers or membrane structures or organelles – so that steric factors also play a role in the assemblage. These steric factors can also be seen as determinants for the kinetic control.” Luisi, Pier Luigi. 2006. The Emergence of Life: From Chemical Origins to Synthetic Biology. Cambridge University Press. P. 100.


“Another complex macromolecular aggregate that can reassemble from its components is the bacterial ribosome. These ribosomes are composed of 55 different proteins and by 3 different RNA molecules, and if the individual components are incubated under appropriate conditions in a test tube, they spontaneously form the original structure. It is also known that even certain viruses, e.g., tobacco mosaic virus, can reassemble from the components: this virus consists of a single RNA molecule contained in a protein coat composed by an array of identical protein subunits. Infective virus particles can self-assemble in a test tube from the purified components.” Luisi, Pier Luigi. 2006. The Emergence of Life: From Chemical Origins to Synthetic Biology. Cambridge University Press. P. 102.


“In order to summarize the various aspects of self-organization, the following classification can be proposed:

1. Self-organization systems under thermodynamic control (spontaneous processes with a negative free-energy change), such as supramolecular complexes, crystallization, surfactant aggregation, certain nano-structures, protein folding, protein assembly, DNA duplex.
2. Self-organization systems under kinetic control (biological systems with genomic, enzymatic and/or evolutionary control), such as protein biosynthesis, virus assembly, formation of beehive and anthill, swarm intelligence.
3. Out-of-equilibrium systems (non-linear, dynamic processes), such as the Zabotinski-Belousov reaction, and other oscillating reactions; bifurcation, and order out of chaos; convection phenomena; tornadoes, vortexes.
4. Social systems: (human enterprises that form out of self-imposed rules), such as business companies, political parties, families, tribes etc.; armies, churches.” Luisi, Pier Luigi. 2006. The Emergence of Life: From Chemical Origins to Synthetic Biology. Cambridge University Press. Pp. 109-10.


“Francis Crick, in his book ‘The astonishing hypothesis,” stresses the concept that there is nothing particularly new or exotic in the notion of emergence, as chemistry is full of it. He gives, as one of many, the example of benzene. The aromatic character of the benzene molecule is obviously not present in the atomic components, but is a property arising in the ensemble of the particular atomic configuration – an emergent property.” Luisi, Pier Luigi. 2006. The Emergence of Life: From Chemical Origins to Synthetic Biology. Cambridge University Press. P. 114.


“Taking instead extremely simple examples, consider the geometric emergence shown in Figure 6.3 [Accompanying a diagram of a progression from points to line segments to angles to surface to cube]: it is clear that the notion of angle has no meaning at the hierarchic level of the lines; likewise, there is no notion of surface at the hierarchic level of angles: and this flat world of surfaces does not have the property of volume. Thus, at each increasing step of complexity a novel feature, an emergent property that is not present in the lower hierarchic level, is found.” Luisi, Pier Luigi. 2006. The Emergence of Life: From Chemical Origins to Synthetic Biology. Cambridge University Press. Pp. 115-6.


“As pointed out by Wimsatt, it is possible to be an emergentist and reductionist at the same time, accepting the reductionistic view in terms of structure, and the emergentistic view with regard to properties.” Luisi, Pier Luigi. 2006. The Emergence of Life: From Chemical Origins to Synthetic Biology. Cambridge University Press. P. 117.


“We have also learned that self-replication is not a prerogative only of nucleic acids, but it can be shared by different kinds of chemical families; see the formose reaction, the self-replicating peptides, and the self-reproducing micelles and vesicles.” Luisi, Pier Luigi. 2006. The Emergence of Life: From Chemical Origins to Synthetic Biology. Cambridge University Press. P. 153.


“Micellar catalysis is a broad field, and caution is needed when using this term. In fact, whereas the broad term ‘catalysis’ is justified when referring to an increase of the velocity of reaction, this does not always mean that the velocity constant is increased (namely that there is a decrease of the specific activation energy). Rather, the velocity effect can be due to a concentration effect operated by the surface of the micelles.” Luisi, Pier Luigi. 2006. The Emergence of Life: From Chemical Origins to Synthetic Biology. Cambridge University Press. P. 188.


“There are indeed objective difficulties still facing the construction of a minimal cell. We have seen for example that in the best case death by dilution is one limit we probably have to live with. Generally, the constructs realized in the laboratory until now represent still poor approximations of a fully fledged biological cell. The gap between this and real biological cells is such, that the possible bioethical hazards of the field of the minimal cell can for the moment be discounted.

“Yet, just the conceiving and the study of these forms of ‘limping life,’ represent in my opinion the most interesting part of this on-going research. In fact, these approximations to life, such as a cell that produces proteins and does not self-reproduce; or one that does self-reproduce for a few generations and then dies out of dilution; or a cell that reproduces only parts of itself; and/or one characterized by a very poor specificity and very poor metabolic rate ... all these may and probably are intermediates experimented with by nature to arrive at the final destination, the fully-fledged biological cell. Thus, the realization in the laboratory of these partially living cells may be of fundamental importance to understand the real essence of cellular life, as well as the historical evolutionary pathway by which the final target may have been reached. It is true, however, that construction of a semi-synthetic cell by using extant enzymes and nucleic acids is not the solution to the origin of life. For that, we have to find ways by which such functional macro-molecules are produced in a prebiotic world – and we have seen that this is not yet understood.” Luisi, Pier Luigi. 2006. The Emergence of Life: From Chemical Origins to Synthetic Biology. Cambridge University Press. P. 265.


"In the miracle of life, material substance takes on complex, self-organizing order. Life is not merely the product of the past but a program to make a future, a novelty in the universe, structure shaped for needs....

"Although everything about life is in a sense miraculous, its achievements usually excite little wonder. One does not much admire the architecture of the weeds that are so well designed as to defy efforts to eradicate them....

"The number of admirable, more or less inexplicable traits that one might cite is limited not by the inventiveness of nature but by the ability of investigators to study and describe them--and those that are known would fill many large volumes. The ants, for example, are cited many times in this book, and few other families have received so much attention as these fascinating social insects. Yet the wealth of potentially intriguing information has hardly been tapped. There has been intensive study of only about 100 species of approximately 8,800 that have been described and probably 20,000 existent...

"The liver, a much simpler organ [than the brain], has about 500 functions, including manufacture of bile and other digestive fluids; storage, conversion, and release of carbohydrates; the storage of iron and vitamins; the regulation of fat, cholesterol, and protein metabolism; the manufacture of materials used in the coagulation of blood (some 30 substances); the removal of bacteria from the blood; and the destruction of excess hormones and many toxic substances. And almost all of these functions are performed by cells of a single type....

"Hearing is a simpler sense [than sight], but some species have developed it quite remarkably. Owls can use a hundredth of a millisecond difference in the time a sound reaches one ear or the other to fix the direction of a mouse. One ear of the barn owl is tuned to lower frequencies to locate a sound in the horizontal plane, the other to higher frequencies for the vertical plane.

"The echolocation system of bats is more elaborate. The bat not only registers the infinitesimal echo of its squeak from a mosquito but can also determine accurately its distance and direction. This requires a very high frequency–up to 220 kilohertz. The bat must overcome the fact that the signal it sends out, lasting as little as 1/2,000 second, is millions to billions of times stronger than the returning echoes. To prevent the echo from being totally swamped, there is an insulating pad behind the bat's inner ear, and muscles stiffen the eardrum up to 100 times per second synchronously with the squeaks. The brain is geared to ignore strong auditory messages while registering weak ones. Bats are also sensitive to a change of interval between click and echo indicating movement of the target, and they pick out echoes timed to their own signals to distinguish them from those of other bats. The membrane of the inner ear is thickened to impede perception of the clicks but to permit perception of a shifted echo. There is even an offset system between the two ears to increase contrast and permit more accurate direction finding. The brain of the mustached bat (can distinguish a difference of 1/700 of a note. Many species have a constant-frequency signal, to tell the direction of a prey, and sharp falling signal, to tell distance. This apparatus enables the bat to fix range within a centimeter or two at a distance of several meters, to detect the shape of a tiny target, and flit among a network of threads a tenth of a millimeter in diameter.

"Yet this wonderful adaptation is less useful than might seem because prey may perceive the chirps much farther away than the bat can hear the echo. Moths, lacewings, crickets, and other insects have cells tuned to bats' wavelengths and take evasive action when one approaches . Some moths, hearing the signals, produce ultrasonic clicks of their own, apparently to jam the bat's sonar. Bats have sometimes reacted by turning off their echolocation and hunting, as owls do, by sight and sound." Wesson, Robert. Beyond Natural Selection. MIT Press, 1991, pp. 54, 59-60, 63-4.


"There are countless problematic adaptations of parasites, of which there are millions of species; there are probably more parasitic than nonparasitic animal species. In many cases, especially of internal parasites, there is no readily imaginable halfway house between free living and parasitic dependence. It is also difficult to adapt to two or more hosts as different as snails, cockroaches, and mammals. But among arthropods alone, some 1,000 species, mosquitoes, fleas, ticks, and so forth, are disease vectors. Many parasites, especially worms, go through bewildering metamorphoses through a sequence of as many as four hosts.

"The brainworm that reproduces in sheep uses ants to get back into a sheep. The worms get into ants by infecting snails that eat sheep feces. The snails expel tiny worm larvae in a mucus that ants enjoy, and some dozens of worms take up residence in an ant. But this would do them no good if the ant behaved normally; too few ants would be eaten by sheep. Consequently, while most of the worms make themselves at home in the ant's abdomen, one finds its way to the ant's brain and causes the ant to climb up a grass stem and wait to be eaten by a sheep. Ironically, the worm that programs the ant is cheated of happiness in the sheep's intestine; it becomes encysted and dies.

"The whole procedure seems unnecessary. Why do the worm eggs defecated by the sheep not simply hatch and climb up a grass stem to await being eaten by a sheep instead of making the hazardous trip through snail and ant? Beyond Natural Selection, Robert Wesson, MIT Press, 1991, pp. 72-3.


"Stability seems to permit a self-compounding proliferation of types. It is not that the rain forest is intrinsically blessed with so many niches; life itself creates them....

"Structure is not closely related to habits. Animals may change their way of life with little visible change of morphology. For example, cichlid fish of East African lakes have, in their explosive speciation, taken to many diverse diets, from predation to scraping algae from rocks, while making only minor organic alterations. Iguanas on the Galapagos Islands must have taken to eating seaweed strewn on the beach and then ventured into the ocean in search of more such food, but the marine iguanas look much like their land-bound cousins. The water ouzel or dipper, a small bird that finds insects on the bottom of brooks, looks like an ordinary land bird. Although it uses its wings to swim, it, like the marine iguana, has failed to acquire webbed feet.

"Sea otters are thoroughly aquatic in habit; they seldom haul out onto land, sleep in kelp beds, dive to respectable depths, and swim long distances. They mate, give birth, and raise their pups in the water. But they look much like land animals, as seals do not. Wasps of several families find their living entirely under water and use their wings to swim, but they have all the appearances of land dwellers. Water spiders remain submerged, with an air bubble, for many days, build webs in the water, and swim out to capture prey, yet they are very similar to their landbound relatives. Evolution is not continually fine-tuning structures....

"It is easy to give accumulated mutations credit for countless incredible adaptations, but this makes it the more surprising that the process has failed to endow animals with many seemingly accessible capacities. For example, no multicellular animal is known to have the ability to digest the most abundant organic substance, cellulose. The necessary enzyme, cellulase, cannot be difficult to manufacture. Bacteria, fungi, and protozoa have it, but it does not fit in the metazoan genome. Termites and herbivores rely on protozoa or bacteria in their guts; the symbiont digests the vegetable material, and the animal digests the symbiont.

"It is also odd that birds and mammals, often beset by parasites such as lice, ticks, and worms, have developed practically no chemical protection, in marked contrast to the multitude of defenses evolved by plants. On the other hand, it is puzzling that plants have never invented anything like an immune system to ward off invading pathogens. It is curious that no animals, whatever their incredible and often inexplicable instincts and adaptations, have hit on the simple strategy of cultivating plants, except only fungus ants and recently humans. In view of the fact that animals frequently store or bury seeds, it would seem easier to attain something like agriculture than many an adaptation already cited....

"Animals often do much less than they might to defend themselves. A tarantula lives by seizing and killing insects, but when a spider-hunting wasp comes around, the tarantula may passively allow it to seek the spot to insert its paralyzing sting. Except for the muskoxen, which stand in a circle to defend weaker members of a herd, and African buffalo, which will charge a menacing lion, ungulates hardly cooperate against enemies. Even hornless zebras could easily repel lions if they joined forces. Adult wildebeest, although powerful and equipped with potent horns, make little effort to protect their young or themselves against hyenas.

"Nature is often wasteful. Avocados have a hundred flowers for one fruit matured. Marsupials may produce a dozen times more embryonic babies than they have teats to nourish. Another negative 'adaptation' is the practice of many wasps and some bees and ants of eating their eggs. Founder-queen ants convert body stores into food for their first brood by laying sterile eggs, which are crushed and fed to the larvae; these trophic eggs are the equivalent of milk. But in many social hymenoptera, workers or queens eat eggs laid by nestmates or by themselves, feasting on their own substance. The habit is metabolically wasteful; three eggs are necessary to provide the nourishment to produce one." Beyond Natural Selection, Robert Wesson, MIT Press, 1991, pp. 85, 87, 89-90, 94-5.


"We suggest that living organisms are physical systems with genetically and epigenetically determined individual characteristics, which utilize energy that is flowing through the environment in a relatively stochastic manner. A general characterization of dissipative structures is that they are physical systems in which at least one stochastic and one determinate factor interact. The interaction of finite epigenetic information, determined by egg and sperm, with a sufficient, stochastic flow of energy establishes the stochastic-determinate dynamics that permits an organism to survive. The organisms's epigenetic information allows certain forms of energy to be utilized for homeostasis (maintenance), ontogeny (growth and differentiation), or homeorhesis (reproduction). The energy taken up is used to produce metabolic wase products, heat, biochemical changes, and complex structures. Each of these processes involves a series of metabolic pathways for converting matter and dissipating energy. As properties of a single cohesive ontogenetic sequence, these pathways for dissipation are causally linked....

"The metaphysical view of species as individuals is being widely adopted by biologists, because it provides a cogent metaphysics to appreciate species as evolutionary units. A temporal sequence of transforming individuals implies an inherent time asymmetry in the process of transformation. If we view biological evolution as a historically constrained process, we must reject the metaphysics of immutable classes. This means we must reject theories in which ecological constructs ('niches,' 'adaptive zones') serve as analogues of quantum states and the biological entities occupying them are contingencies determined by the energy flowing from the sun to the earth. Rather, we must view those ecological constructs as contingent energy flow pathways determined by the constraints on energy dissipation inherent in the historical order of the 'individuals' undergoing ontogeny, reproduction, population change, speciation, or community evolution." Brooks, Daniel & Wiley Evolution as Entropy; Toward a Unified Theory of Biology. University of Chicago, 1986, pp. 38-41.
 

“Integrating the protein or other molecule under study in the fabric of its natural environment can, in effect, put the ‘bio’ back into biochemistry. Integrative biochemistry stresses the critical nature of interactions among large and small constituents of the cell.” Hochachka, Peter & George Somero. Biochemical Adaptation: Mechanism and Process in Physiological Evolution. 2002. Oxford University Press. Pp. 12-3.


“How many genes, then, are required to encode proteins needed for core biochemical functions If we consider the yeast as a representative single-celled eukaryote, then about 6,000 genes appear to be required to generate the suite of functions allowing a single-celled eukaryote to survive.” Hochachka, Peter & George Somero. Biochemical Adaptation: Mechanism and Process in Physiological Evolution. 2002. Oxford University Press. P. 14.


“Consider the genomes of the nematode Caenorhabditis elegans and the insect Drosophila melanogaster. The genome of the former contains about 19,000 genes and the genome of the latter comprises about 14,000 genes. Assuming that about 6,000 of these genes are the same as in yeasts (albeit we pair this assumption with the caveat that the biology of yeast obviously involves an unknown number of yeast-specific genes) we can ask what the additional approximately 8,000-13,000 genes are used for.” Hochachka, Peter & George Somero. Biochemical Adaptation: Mechanism and Process in Physiological Evolution. 2002. Oxford University Press. P. 15.


“The control networks that have evolved are hugely complex by comparison with single-celled eukaryotes such as yeasts. We hypothesize that the need for these kinds of functions in metazoans explains in part why these species possess so many more genes than are found in unicellular eukaryotes. More formally, the hypothesis is that genes whose products are involved in such processes as interorgan communication, in cell-cell communication, in development and differentiation, in general sensing and signal transduction, in immune defense systems, and in host defense against pathogens and parasites, are fundamental to the evolution of physiological diversity. We believe that this is a key element in resolving one major aspect of the unity–diversity duality of biological systems. Several thousand or so genes in unicellular and multicellular organisms seem to be involved in so-called ‘core processes’ central to cell-level survival and representative of the ‘unity’ of biochemical design. So-called ‘none-core’ functions, such as those listed immediately above, are what a substantial fraction of the remainder of the protein-encoding regions of the large genomes of complex eukaryotes represents–these are the genes that account for physiological diversity.” Hochachka, Peter & George Somero. Biochemical Adaptation: Mechanism and Process in Physiological Evolution. 2002. Oxford University Press. Pp. 15-6.


“The above analyses are notable and instructive; they indicate that when evolutionary pressures driving biochemical and physiological processes reach some inherent limit, organisms are then required to turn to novel mechanisms (e.g., utilizing global physical parameters such as operating cell temperatures), if they are to achieve either further upward or further downward expansion of metabolic scope. The evolution of high aerobic metabolic scopes so beautifully illustrated in the tunas can be viewed in terms of the assembly of conservative, probably ancestral, characters with more adaptable physiological components (biological innovations including features such as regional tissue-specific endothermy). How these two categories of characters are assembled in any given tuna lineage specifies the metabolic scope of that lineage. Moving in the other direction, the evolution of expanded hypometabolic capacities, in diving animals such as aquatic turtles (ectothermic example) or pinnipeds (endothermic example) can similarly be viewed in terms of the assembly of conservative, probably ancestral, characters (such as bradycardia and peripheral hypoperfusion with associated metabolic consequences) with more adaptable physiological components (biological innovations such as regional tissue-specific hypothermia).” Hochachka, Peter & George Somero. Biochemical Adaptation: Mechanism and Process in Physiological Evolution. 2002. Oxford University Press. P. 93.


“Like oxygen respiration, denitrification allows a complete oxidation of the organic substrate to CO2 and H2O. For instance, when Bacilus licheniformis grows with glucose and nitrate under anaerobic conditions, the substrate is degraded via glycolysis and the Krebs cycle, while NADH2 and FADH2 serve as electron donors for the respiratory chain. Nitrate, however, does not simply replace oxygen; special types of cytochromes and membrane-bound enzyme systems are utilized, which systematically reduce nitrate to nitrite and further to nitrogen in at least four distinguishable steps.

“It is now evident that at least two, and probably more, of the four possible reductive steps are coupled to ATP formation in denitrifying bacteria. As may be expected from thermodynamic consideration, this crucial observation implies an ATP yield per mole of glucose similar to that for normal oxidative metabolism.

“From these considerations, it is clear that the three most fundamental features of oxygen-based respiration are also expressed in nitrate-based respiration:

1. the free energy drop of glucose oxidation is large and negative and the process, therefore, is thermodynamically very favorable;
2. the process leads to the complete degradation of glucose to CO2 and H2O without the concomitant accumulation of large amounts of partially catabolized anaerobic end products; and
3. the process is relatively efficient in terms of ATP yield per mole of carbon substrate because of a tight-coupling between electron transfer and phosphorylation.

“That is why anaerobic respiration, based on nitrate as a terminal electron acceptor, is more similar to oxygen-based (aerobic) respiration that it is to fermentation and is why it must by definition be clearly distinguished from the latter. The great pioneer in this area, Louis Pasteur, first and simply defined fermentation as life in the absence of oxygen. But today, a century after his pathbreaking work, fermentations are more precisely defined as those metabolic processes that occur in the dark and do not involve respiratory chains with either oxygen or nitrate as terminal electron acceptors.” Hochachka, Peter & George Somero. Biochemical Adaptation: Mechanism and Process in Physiological Evolution. 2002. Oxford University Press. Pp. 104-5.


“The design rules for fermentative metabolism in bacteria are few in number and are widely expressed in the microbial world. Firstly, the fermentation process always involves the partial oxidation of substrate, although there is a tremendous diversity in choice of substrate. Almost any organic compound can be fermented by some microorganism somewhere. Secondly, the oxidative reaction or reactions must always be balanced by subsequent reductive reactions in order to allow sustained function; organic compounds usually serve as electron and proton acceptors in the reductive reactions leading to the formation of organic anaerobic end products. The end products typically accumulate to some extent and are released to the outside. Thirdly, because the free energy changes associated with substrate conversion to end products are always modest, the ATP yield per mole of substrate fermented is always relatively low. One or two moles ATP per mole substrate fermented is not unusual. Fourthly, some fermentative reactions must be retained not for energy purposes per se but for the generation of key metabolite intermediates which are required for biosyntheses and growth; these may be directly related to anaerobic energy-producing pathways or may be unrelated to them; in the latter case, different substrates may be fermented to satisfy these different needs. Finally, for a unicellular system, it is reasonable and economical not to synthesize all the time all of the enzymes it is able to make but to make only those that are needed under specific and current physiological conditions.” Hochachka, Peter & George Somero. Biochemical Adaptation: Mechanism and Process in Physiological Evolution. 2002. Oxford University Press. Pp. 105-6.


“When we review the many ways in which water interacts with inorganic ions and organic molecules through noncovalent bonding, we find a wide array of instances in which the differential solubilities of solutes are of fundamental importance. Here, differential solubility refers to that fact that inorganic ions, small organic solutes, and constituent groups of macromolecules (for instance, different amino acid side-chains) vary in their solubilities in water. Some chemicals are virtually infinitely miscible in water: the amount of solute in solution can be increased to nearly 100%. Other solutes, notably the acyl chains of fatty acids and the nonpolar side-chains of some amino acids, are only very weakly soluble in water. Many organic molecules are amphipathic: they contain both highly soluble and poorly soluble groups. The occurrence of differential solubility among the chemicals found in the cellular water is not some type of evolutionary accident that was dictated by the particular types of chemicals available to early cells. Rather, natural selection has exploited the principle of differential solubility to fabricate an intracellular milieu and a set of proteins, lipids, and nucleic acids having solubility relationships that are critical for the development of cellular structures and the support of physiological processes. The pivotal importance of differential solubilities indeed is observed at all size scales of biochemistry, from the largest to the smallest constituents of the cell.” Hochachka, Peter & George Somero. Biochemical Adaptation: Mechanism and Process in Physiological Evolution. 2002. Oxford University Press. Pp. 221-2.


“One of the great insights arising from biochemical research, starting in the 1930s and extending to present times, is that almost all cell work functions–biosynthetic work, ion pumping work, mechanical work–are coupled to the hydrolysis of adenosine triphosphate or ATP. When coupled with the requirement that at steady state cells, tissues, organs, and organisms must be in energy balance, this means that at steady state ATP demand pathways must be balanced with ATP supply pathways both at low and at high work rates. The energetic hub of living cells thus can be described as an ATP cycle with steady-state requirements for flux through the ATP demand pathways of the cycle to be balanced by flux through the ATP supply pathways.” Hochachka, Peter & George Somero. Biochemical Adaptation: Mechanism and Process in Physiological Evolution. 2002. Oxford University Press. P. 20.


“The simplest mechanism for generating ATP is phosphagen mobilization. In vertebrate tissues such as muscle containing creatine phosphate (PCr) this mobilization is catalyzed by creatine phosphokinase (CPK), a process which requires no O2 ...” Hochachka, Peter & George Somero. Biochemical Adaptation: Mechanism and Process in Physiological Evolution. 2002. Oxford University Press. P. 20.


“Fermentation, or the partial (O2 independent) catabolism of substrates to anaerobic end products, is a second means of forming ATP. In animals, the commonest fermentative pathway is that of anaerobic glycolysis.” Hochachka, Peter & George Somero. Biochemical Adaptation: Mechanism and Process in Physiological Evolution. 2002. Oxford University Press. P. 20.


“The third means for generating ATP requires O2. In animal fermentations, an organic molecule (e.g., pyruvate) serves as a terminal proton and electron acceptor, forming an organic end product (e.g., lactate). In contrast, O2 is required as a terminal acceptor for the complete oxidation of substrates such as glucose, glycogen, fatty acids, or amino acids.” Hochachka, Peter & George Somero. Biochemical Adaptation: Mechanism and Process in Physiological Evolution. 2002. Oxford University Press. P. 22.


“The pathways by which such complete oxidations are achieved are much more complex than most fermentation pathways.” Hochachka, Peter & George Somero. Biochemical Adaptation: Mechanism and Process in Physiological Evolution. 2002. Oxford University Press. P. 22.


“Thus, such polymerization reactions [protein shape reactions and hydrophobic interactions such as membrane formation] are termed entropy-driven processes, in recognition of the role played by changes in water organization during the assembly event. It bears emphasizing again that water can play a dominant role in the energy changes that occur during a biochemical process even though water is not involved in the formation or rupture of covalent bonds. The enthalpy and entropy changes that accompany reorganization of water molecules may be the essential driving force of the process.” Hochachka, Peter & George Somero. Biochemical Adaptation: Mechanism and Process in Physiological Evolution. 2002. Oxford University Press. P. 223.


“The differential solubilities exhibited by biomolecules thus should be appreciated as one of the most important aspects of the effects of water on living systems. Differential solubility is a critical principle in much of biochemical evolution, and it is a principle that is manifested in a number of contexts of adaptation to the environment. This is seen particularly clearly in the evolution of proteins in the face of different chemical and physical conditions. The amino acids selected to construct a particular protein reflect a finely tuned process that results in the generation of an appropriate three-dimensional structure and a correct balance between structural stability and flexibility–a balance termed marginal stability–that is essential for protein function. The marginal stability of the protein will be seen to be the consequence of complementary adaptations in the protein itself (intrinsic adaptations) and in the medium bathing the protein (extrinsic adaptations). Together, these adaptations generate a set of conditions in which the solubilities of protein side-chains and peptide backbone linkages are appropriate for the physical and chemical conditions in which the protein must function.” Hochachka, Peter & George Somero. Biochemical Adaptation: Mechanism and Process in Physiological Evolution. 2002. Oxford University Press. P. 223.
 

“One clear theme of evolutionary history is the cumulative nature of biological diversity. Individual species (of nucleated organisms at least) may come and go in geological succession, their extinctions emphasizing the fragility of populations in a world of competition and environmental change. But the history of guilds–of fundamentally distinct morphological and physiological ways of making a biological living–is one of accrual. The long view of evolution is unmistakably one of accumulation through time, governed by rules of ecosystem function. The replacement series implied by the Generations of Abraham approach fails to capture this basic attribute of biological history.

“Another great theme is the coevolution of Earth and life. Both organisms and environments have changed dramatically through time, and more often than not they have changed in concert. Shifts in climate, in geography, and even in the composition of the atmosphere and oceans have influenced the course of evolution, and biological innovations have, in turn, affected environmental history. Indeed, the overall picture that emerges from our planet’s long history is one of interaction between organisms and environments. The evolutionary epic recorded by fossils reflects, as much as anything else, the continuing interplay between genetic possibility and ecological opportunity.

“This long view of biological history provides what may be the grandest theme of all. Life was born of physical processes at play on the young Earth. These same processes–tectonic, oceanographic, and atmospheric–sustained life through time as they shaped and reshaped our planet’s surface. And, eventually, life expanded and diversified to become a planetary force in its own right, joining tectonics and physical chemistry in the transformation of air and oceans.” Knoll, Andrew H. Life on a Young Planet: The First Three Billion Years of Evolution on Earth. 2003. Princeton University Press. P. 5.


“As large animals, we can be forgiven for holding a worldview that celebrates ourselves, but, in truth, this outlook is dead wrong. We have evolved to fit into a bacterial world, and not the reverse.” Knoll, Andrew H. Life on a Young Planet: The First Three Billion Years of Evolution on Earth. 2003. Princeton University Press. P. 19.


“Size and shape surely favor eukaryotes, but morphology provides only one of several yardsticks for measuring ecological significance. Metabolism–how an organism obtains materials and energy–is another, and by this criterion, it is the prokaryotes that dazzle with their diversity.” Knoll, Andrew H. Life on a Young Planet: The First Three Billion Years of Evolution on Earth. 2003. Princeton University Press. Pp. 19-20.


“The metabolic pathways of prokaryotes sustain the chemical cycles that maintain Earth as a habitable planet.” Knoll, Andrew H. Life on a Young Planet: The First Three Billion Years of Evolution on Earth. 2003. Princeton University Press. P. 21.


“More generally, wherever carbon passes through oxygen-free environments, bacteria are essential to the carbon cycle; eukaryotes are everywhere optional.

“The fundamental importance of prokaryotes extends to other biologically important elements, as well. Indeed, in the biogeochemical cycles of sulfur and nitrogen, all the principal metabolic pathways that cycle these element are prokaryotic.” Knoll, Andrew H. Life on a Young Planet: The First Three Billion Years of Evolution on Earth. 2003. Princeton University Press. P. 22.


“The cycles of carbon, nitrogen, sulfur, and other elements are linked together into a complex system that controls the biological pulse of the planet. Because organisms need nitrogen for proteins and other molecules, there could be no carbon cycle without nitrogen fixation. Nitrogen metabolism itself depends on enzymes that contain iron; thus, without biologically available iron, there could be no nitrogen cycle ... and, hence, no carbon cycle. Biology on another planet may or may not include organisms that are large or intelligent, but wherever it persists for long periods of time, life will feature complementary metabolisms that cycle biologically important elements through the biosphere.” Knoll, Andrew H. Life on a Young Planet: The First Three Billion Years of Evolution on Earth. 2003. Princeton University Press. P. 23.


“In terms of energy yield, aerobic respiration is the favored pathway for breaking down organic molecules, so wherever oxygen is present, O2-respiring organisms will dominate this leg of the carbon cycle. Within sediments, however, organisms use oxygen faster than it can be supplied from overlying waters. As a result, oxygen declines and, at some distance below the surface, disappears completely. (In lakes and coastal marine environments, oxygen can drop to zero within a few millimeters of the sediment surface.) Under these conditions, other metabolic pathways kick in. Nitrate respiration is next in line in terms of energy yield, but nitrate is generally in short supply, so these bacteria aren’t major players in the carbon cycle. More important are sulfate-reducing bacteria. Sulfate is a major ion in seawater, enabling oxygen-depleted marine sediments to host large populations of sulfate reducers. Only where sulfate has been depleted, deep within marine sediments and at the bottom of the metabolic ladder, do we find fermenting bacteria and methanogenic archaeans. Lakes are a bit different. Because sulfate is only a minor constituent of fresh water, methanogens are more important than sulfate reducers in these settings.” Knoll, Andrew H. Life on a Young Planet: The First Three Billion Years of Evolution on Earth. 2003. Princeton University Press. Pp. 100-1.


“Perhaps the most important differences between eukaryotes and other cells concern the way in which the cell’s contents are stabilized. Archaeans and bacteria enclose their cytoplasm in a rigid wall. In contrast, eukaryotes evolved an internal scaffolding called the cytoskeleton, and that, as Robert Frost once wrote, has made all the difference. Built from tiny filaments of actin and other proteins, the cytoskeleton is a remarkably dynamic structure, continually able to form and re-form in ways that change the cell’s shape.” Knoll, Andrew H. Life on a Young Planet: The First Three Billion Years of Evolution on Earth. 2003. Princeton University Press. Pp. 132-3.


“Today, coloniality is widespread among cnidarians, from the Portuguese man-of-war that floats on the sea surface (its float, stinging tentacles, and reproductive structures are all anatomically complete individuals) to the massive reef corals and delicate sea fans that proliferate on the ocean floor. In the absence of well-developed organ systems, cnidarians achieved complexity by differentiating individuals within colonies, and this may have been the case for vendobionts, as well.” Knoll, Andrew H. Life on a Young Planet: The First Three Billion Years of Evolution on Earth. 2003. Princeton University Press. P. 169.


“Sponges form one great limb of the animal tree; all other animals fall on the other. More complicated animals, in turn, can also be divided into two major branches, the Cnidaria and the Bilateria.... Cnidarians comprise the jellyfish, corals, sea pens, and other taxa that provide structural analogues for many Ediacaran fossils; bilaterian animals, known mainly from trackways in Ediacaran sediments, today include an astonishing range of species from flatworms to whales.

“As a group, cnidarians are distinctly more complicated than sponges–they have more types of cells, including muscle cells and a simple nerve network. Moreover, in cnidarians (and bilaterian animals), extracellular proteins bind cells into coherent sheets call epithelia that divide the animal body into compartments. Unlike sponges, therefore, cnidarians can form discrete tissues.

“All cnidarians conform to a simple body plan–a hollow bowl or cylinder, with armlike tentacles around the opening (mouth). Two tissue layers that differentiate early in development line the inner and outer surfaces of the body, sandwiching gelatinous material in between (the ‘jelly’ of jellyfish). The outer tissue, called ectoderm, contains muscle cells, nerves, and cnidocytes, specialized cells armed with tiny poison-tipped harpoons, coiled and ready for action (If you have ever been stung by a jellyfish, you have firsthand experience of cnidocytes.) The inner endoderm bristles with cells that secrete digestive enzymes. Cnidarians do not build complex organs that integrate several tissues like the heart or stomach of a mammal. However, ... they gained complexity in another way–by differentiating functionally specialized individuals within colonies.” Knoll, Andrew H. Life on a Young Planet: The First Three Billion Years of Evolution on Earth. 2003. Princeton University Press. P. 183.


“Remaining animal species–all 10 million of them, including humans–belong to the Bilateria. Bilaterian animals differ from the Cnidaria in three fundamental ways. ... a single plane of symmetry divides the bilaterian body into left and right sides from head (more or less differentiated in most bilaterians) to tail. Moreover, three rather than two cell layers differentiate early in development–an ectoderm that contributes skin and nerve cells, an endoderm that gives rise to the digestive system, and an intervening layer called the mesoderm that differentiates into muscles and the reproductive system, among other things. Like cnidarians, bilaterian animals form tissues. Unlike cnidarians, however, bilaterians combine tissues into complex organs, once again opening up new and diverse functional possibilities.

“Cnidarians may have invented animal predation, but bilaterians perfected it. With organ systems came rapid swimming; muscular appendages to grasp and hold prey; mouths lined by mandibles, teeth, or rasping organs; sophisticated sensory organs including well-focused eyes; and, especially, brains able to coordinate the complex interactions of all these systems.

“Increased predation intensified the need for protection. Some animals avoid predators by hiding. Others secrete poison. A third solution, discovered independently by many different groups, is armor–mineral-impregnated skeletons that protect against teeth and claws.” Knoll, Andrew H. Life on a Young Planet: The First Three Billion Years of Evolution on Earth. 2003. Princeton University Press. Pp. 184-5.


“Cambrian body plan evolution may have taken 50 million years, but those 50 million years reshaped more than 3 billion years of biological history.” Knoll, Andrew H. Life on a Young Planet: The First Three Billion Years of Evolution on Earth. 2003. Princeton University Press. P. 193.


“Nonetheless, on the Proterozoic Earth, before animals evolved sophisticated circulatory systems, oxygen levels must have determined the effective sizes of animals.” Knoll, Andrew H. Life on a Young Planet: The First Three Billion Years of Evolution on Earth. 2003. Princeton University Press. P. 218.


“Guided by developmental genetics, expanding animal populations began to accumulate the biological features we associate today with arthropods and brachiopods, echinoderms and chordates. And with emerging body plans came differing functional possibilities that partitioned the metazoan world and shaped the connections among species. Algae diversified, as well, in a Cambrian Explosion that cut across kingdoms.

”Physical events may thus have provided the opportunity for Cambrian diversification. But the evolutionary paths actually traveled by Cambrian animals reflect the interplay between development and ecology. Predators and prey locked into an evolutionary arms race, while grazers and algae began to shape the limits of each other’s existence. More than ever before, biological interactions and not just the physical environment determined the shape of life. And as the world filled ecologically, evolutionary opportunities for further new body plans dwindled. In the seas, the hand that animal evolution would play for the next 500 million years had been dealt.

“Beneath this new ecological edifice, of course, Earth’s age-old ecological circuitry continued unchanged. As they did 3 billion years earlier, bacteria continued to cycle biologically important elements through ecosystems, sustaining the biosphere that made animal life possible.” Knoll, Andrew H. Life on a Young Planet: The First Three Billion Years of Evolution on Earth. 2003. Princeton University Press. Pp. 222-3.


“If there is one lesson that paleontology offers to evolutionary biology, other than the documentation of biological history itself, it is that life’s opportunities and catastrophes are tied to Earth’s environmental history. We can only understand macroevolution–the comings and goings of species and higher taxa through time–if we link the microevolutionary processes studied by geneticists with Earth’s dynamic environmental history. The great physical events that framed early animal evolution–global glaciation, the rise of oxygen-filled oceans, and extraordinary perturbations of the carbon cycle–are among our planet’s most profound environmental events. We ignore them at our peril.” Knoll, Andrew H. Life on a Young Planet: The First Three Billion Years of Evolution on Earth. 2003. Princeton University Press. P. 223.


“The complexities involved in defining immunocompetence are well exemplified by infections with schistosomes, which are important parasites of humans and other animals. These parasites require components of the host immune system to complete their development. They thus succeed in immunocompetent hosts but fail to thrive in immunodeficient hosts. This, by implication, identifies the immunocompetent as immunodeficient, thus underscoring the difficulties of finding a global definition of immunocompetence. Accordingly, immunocompetence is a relational property that transcends the boundaries of the organism.” Ulvestad, Elling. Defending Life: The Nature of Host-Parasitic Relations. Springer. 2007. Pp. 67-8.


“A variety of scientific observations support the claim that organisms, which appear well demarcated from their surroundings, are actually inhomogeneous entities. They sometimes consist of cells derived from other organism, in which case the organism is a chimera; or their cells may have been altered during development as happens with cancerous cells or cells of the adaptive immune system, in which case the organism is a mosaic. It is thus clear that our intuitive notions of organismal being are imprecise.” Ulvestad, Elling. Defending Life: The Nature of Host-Parasitic Relations. Springer. 2007. Pp. 72-3.


“Hence, instead of viewing immunity as beginning with stimulation of the innate system and ending with the response, immunity should be imagined as extending into the environment in which the organism lives as well as backwards to environments encountered by its ancestors.” Ulvestad, Elling. Defending Life: The Nature of Host-Parasitic Relations. Springer. 2007. P. 80.


“In their study of life-history evolution Jokela and Haukioja presented a simplified model in which they singled out developmental modules as consisting of a hierarchy of traits, tactics and strategies. There are modules at each level, one nested within another. At the highest level of the hierarchy they placed the organism’s developmental strategy. This depicts the totality of plastic responses that the organism can perform during its interactions with environmental stimuli. At the bottom level of the hierarchy they placed the traits, which are the characteristics that directly interacted with the environment. In between the strategies and the traits are the tactics, which consist of interacting traits that coevolve as a response to the same selection pressures. The developmental tactics signify the various modes by which the organism exhibits tolerance to external and internal stressful perturbations.” Ulvestad, Elling. Defending Life: The Nature of Host-Parasitic Relations. Springer. 2007. P. 128.


“The genesis of life’s embodied drive, the active urge to transcend limits, goes al the way back to life’s origin. Self-maintaining cells are actively engaged in exploring environmental resources; without this activity life could not be. The concept of embodied drive is teleological. But in contrast to vitalism, in which living entities received their teleological characteristics from an external goal-conceiving agent, embodied drive signifies an immanent goal-directed property.” Ulvestad, Elling. Defending Life: The Nature of Host-Parasitic Relations. Springer. 2007. P. 132.


“Programmed cell death was initially considered to be a phenomenon confined to multicellular animals, but the phenomenon has now been described also in unicellular organisms like bacteria and yeast. It is as yet not clear whether cells of the domain Archaea undergo programmed cell death but cells from the two other domains of life, Eubacteria and Eukaryota, do have this mechanism to control life. Since apoptosis as defined in multicellular eukaryotes involves organellar disassembly, and since organelles are not found in prokaryotes, the term apoptosis cannot properly be used to describe the programmed cell death in prokaryotes.

“The processes of autophagy as well as regulations of cell proliferation, differentiation, and apoptosis are dependent upon protein synthesis. When for example yeast are treated with cycloheximide which inhibits protein synthesis, induction of apoptosis is hindered, indicating an active role of the cell in the death process. A similar inhibition of apoptosis has been described also in bacteria and cells from multicellular animals. Hence, organisms, both uni- and multicellular, must continuously inhibit self-destruction to stay alive. There are thus three developmental alternatives for a cell – it can divide, differentiate or die.” Ulvestad, Elling. Defending Life: The Nature of Host-Parasitic Relations. Springer. 2007. Pp. 134-5.


“However, if organism is understood as laid out in this book, as a composite entity made up from lower level individuals that once coalesced to form higher level individuals, autoimmunity can be put on par with immunity, the difference being that immunity designates contemporary conflicts whereas autoimmunity is the re-enacting of ancient conflicts between lower level evolutionary individuals.” Ulvestad, Elling. Defending Life: The Nature of Host-Parasitic Relations. Springer. 2007. P. 191.


“The hypothesis stating that chronic diseases are caused by the re-enacting of ancient conflicts between evolutionary individuals emphasizes the role of conflict modification and deregulation of conflict modifiers throughout development, and is built on three major assumptions. The first assumption is that conflict modifying mechanisms emerged and evolved as a consequence of evolutionary transitions, especially the transitions from prokaryotes to eukaryotes and from eukaryotes to multicellular animals, and that harmonizing of the layered and entwined conflict modifying mechanisms was necessary at the higher transitory level. The second assumption is that some conflict modifiers, owing to their central function for cellular life, should have been retained throughout phylogeny. A third major assumption is that deregulation of the conflict modifiers should lead to malfunctioning.” Ulvestad, Elling. Defending Life: The Nature of Host-Parasitic Relations. Springer. 2007. Pp. 193-4.


“Subterranean prokaryotes, be they in deep vadose zones, in rocks, or in consolidated sediments, may metabolize ten to fourteen orders of magnitude more slowly than their counterparts in soils or shallow lake sediments. Such organisms are masters of starvation survival, but it is hardly appropriate to combine their collectively large biomass with that of, in aggregate, much smaller but incomparably more active cells in root trips, leaves, or vascular cambium. But even a conservative estimate of all prokaryotic biomass and its subsequent halving would still mean that the protoplasm of prokaryotes is as large as that of plants.” Smil, Vaclav. The Earth’s Biosphere: Evolution, Dynamics, and Change. 2003. MIT Press. P. 196.


“Even the highest combined estimate of terrestrial and oceanic values means that the global zoomass adds up to less that 0.3% of standing phytomass.” Smil, Vaclav. The Earth’s Biosphere: Evolution, Dynamics, and Change. 2003. MIT Press. P. 186.


“My best estimate is that at the beginning of the twentieth century, the zoomass of wild mammals was at least as large as the anthropomass of 1.6 billion humans, but by 2000, human biomass was an order of magnitude larger.” Smil, Vaclav. The Earth’s Biosphere: Evolution, Dynamics, and Change. 2003. MIT Press. P. 186.


“Published estimates of terrestrial invertebrate and vertebrate biomass range between 500 and 1,000 Mt C, with wild mammals contributing less than 5Mt C. Vertebrate zoomass also includes domestic animals, whose biomass is dominated by bovines, and calculations based on Food and Agriculture Organization animal counts and on conservative averages of their live weights result in 100-120 Mt C, or at least twenty times the wild mammalian total.” Smil, Vaclav. The Earth’s Biosphere: Evolution, Dynamics, and Change. 2003. MIT Press. P. 186.


“Traditional biology has tended to concentrate attention on individual organisms rather than on the biological continuum. The origin of life is thus looked for as a unique event in which an organism arises from the surrounding milieu. A more ecologically balanced point of view would examine the protoecological cycles and subsequent chemical systems that must have developed and flourished while objects resembling organisms appeared.” Morowitz, Harold. Beginnings of Cellular Life: Metabolism Recapitulates Biogenesis. 1992. Yale University Press. P. 54. Quoted in Thompson, Evan. Mind in Life: Biology, Phenomenology, and the Sciences of Mind. 2007. Harvard University Press. P. 118.


“In 1985, Staley and Konopka reviewed data on scientists’ ability to bring microbes from the environment into laboratory cultivation. The ‘great plate-count anomaly’ they identified was this: the vast majority of microbial cells that can be seen in a microscope and shown to be living with various staining procedures cannot be induced to produce colonies on Petri plates or cultures in test tubes. It is estimated that only 0.1-1.0% of the living bacteria present in soils can be cultured under standard conditions; the culturable fraction of bacteria from aquatic environments is ten to a thousand times lower still.” National Research Council. The New Science of Metagenomics: Revealing the Secrets of Our Microbial Planet. 2007. National Academies Press of the National Academy of Science. P. 25.


“... in metagenomics, necessity not only is the mother of invention but will be the grandmother of a paradigm shift. It will refocus us one level higher in the biological hierarchy. It will shift the emphasis from individuals to interactions, from parts to processes – a change that would be timely and highly desirable even if it were not also technologically necessary. Not coincidentally, this shift will parallel the new focus of organismal genomics on interactions between cellular components and how they are coordinated within the complex systems called organisms. This new focus is called systems biology. Metagenomics will be the systems biology of the biosphere.” National Research Council. The New Science of Metagenomics: Revealing the Secrets of Our Microbial Planet. 2007. National Academies Press of the National Academy of Science. Pp. 30-1.


“Today genome is used to describe all the DNA present in a haploid set of chromosomes in eukaryotes, in a single chromosome in bacteria, or all the DNA or RNA in viruses. The suffix ome is derived from the Greek for ‘all’ or ‘every.’ In the past several years, many related neologistic omes have come into use to describe related fields of study that encompass other aspects of large-scale biology. Some of them are:
• The proteome, the total set of proteins in an organism, tissue, or cell type; proteomics is the associated field of study.
• The transcriptome, the total set of RNAs found in an organism, tissue, or cell type.
• The metabolome, the entire complement of metabolites that are generated in an organism, tissue, or cell type.
• The interactome, the entire set of molecular interactions in an organism.” National
Research Council. The New Science of Metagenomics: Revealing the Secrets of Our Microbial Planet. 2007. National Academies Press of the National Academy of Science. P. 14.


“Darwinian evolutionary theory provides a theoretical basis for the description of evolution. However, it is also true that there are several exceptional life and life-like systems, that are difficult to accommodate with this theoretical framework; notably, human societies and the system of prebiotic chemical reactions that were precursors to the emergence of life.” Kawamura, Kunio. “Civilization as a Biosystem Examined by the Comparative Analysis of Biosystems.” Biosystems. 2007. 90: 139-150. P. 139


“Historically, systems biology has two roots. The best known root is in molecular genetics, high-throughput genomics, and functional genomics. The other root is in mathematical biology, metabolic control analysis, and flux balance analysis.

“So-called top-town systems biology derives more from the former root. It typically measures all mRNAs or all proteins of an organism under a set of experimental conditions, determines how their abundance changes with conditions and detects correlations between the changes in mRNAs. Taking the picture of a tree through which the wind blows as an illustration, the method observes the apparently random movement of the individual leaves, yet detects by a more precise analysis that part of the movement of some leaves is identical and different from the correlated movement of other sets of leaves. It is then postulated that the two sets of leaves are each attached to different branches of the tree, and that the two sets of mRNA correspond to different regulons. This top-down systems biology can be carried out in the virtual absence of explicit pre-existing hypotheses. It could largely be hypothesis-free empirical science. Entirely new hypotheses about interactions can emerge however.

“Bottom-up systems biology relates more to the mathematical biology root. It starts from components and some of their known interactions and then examines which new properties might emerge from these. In the example of the tree, it would accept that some of the structure of the tree is already known, e.g., in terms of the stem and some leaves, and would ask how the stem and the leaves could support each other so as to become viable. The idea might come up that the one provides the water required by the other, the other providing the free energy for the former. This would then be refined by modeling and tested by experimentation.” Westerhoff, H.V. “Systems Biology: New Paradigms for Cell Biology and Drug Design.” Systems Biology: Applications and Perspectives. 2007. Springer Verlag. P. 51.


“... choice being differential responsiveness to different alternatives ...” West-Eberhard, Mary Jane. Developmental Plasticity and Evolution. Oxford University Press. 2003. P. 97.


“Today, it is widely recognized that enzyme catalysis involves very specialised molecular recognition, and that this accounts for a major part of the efficiency of enzyme catalysis. Molecular recognition is due to the complementarities of non-covalent forces. The active site of the enzyme stabilises the transition state through desolvation, electrostatic fores, van der Waals forces, proximity (entropy trap), steric effects and other mechanisms. Additionally, molecular recognition is enforced by partially covalent interactions such as hydrogen bonding and general acid-base catalysis.” Arnaut, Luis, S. Formosinho & H. Burrows. Chemical Kinetics: From Molecular Structure to Chemical Reactivity. Elsevier. 207. Pp. 376-7.


“The typical viral abundance of 1010 per liter in surface water is five to twenty-five times the usual bacterial counts. The size disparity (an average of 0.2 fg C per virus and 20 fg C per bacterial cell) between the two types of organisms means that the total mass of oceanic viruses is most likely less than 300 Mt C.” Smil, Vaclav. The Earth’s Biosphere: Evolution, Dynamics, and Change. 2003. MIT Press. P. 197.


“But if we view life on the largest scale, from the first replicating molecules, through simple cells, multicellular organisms, and up to human societies, the means of transmitting information have changed. It is these changes that we have called the ‘major transitions’: ultimately, they are what made the evolution of complexity possible.” Smith, John Maynard, and Eörs Szathmary. The Origins of Life. Oxford University Press. 1999. P. 3.


“This approach to evolution has led us to recognize several ‘major transitions’, starting with the origin of life and ending with the origin of human language–the most recent change in the way in which information is transmitted between generations. Or perhaps it is not the most recent: we may today be living through yet another major transition, with unpredictable consequences.” Smith, John Maynard, and Eörs Szathmary. The Origins of Life. Oxford University Press. 1999. P. 3.


“This is the concept we refer to as the developmental test–the hierarchical concept that a growing cell in a developing organism is continuously performing tests of its environment. According to this concept, it is on the basis of the results of such tests that the appropriate genes are turned on to conduct the appropriate developmental processes. When we think of this testing concept, we see that it is a very general hierarchical control concept.” Bonner, James. “Hierarchical Control Programs in Biological Development.” Pp. 49-70. Pattee, H.H., Editor. Hierarchy Theory: The Challenge of Complex Systems. George Braziller, Inc. 1973. P. 65.


“Therefore, most biologists today hold strongly to the strategy of looking at the molecular structures for the answers to the question of ‘how it works.’

“Nevertheless, it is surprising and discouraging to find so many biologists who, finding this strategy productive, mistake it for a theory of life. Some biology departments have even gone so far as to exclude study of theories of life, as if the detailed facts of molecular biology had somehow demonstrated that theory is not relevant for biology. I was once asked by a leading molecular biologist, quite seriously, ‘If we can find all the facts, why do we need a theory?’ This attitude is especially inappropriate now that molecular biologists are moving on to developmental biology and neurobiology where the integrated function is removed from the detailed structure by even more hierarchical control interfaces. One could not imagine a mathematician trying to understand the nature of computation in terms of how real computer components are designed and wired together. In fact, deep understanding of the nature of computation has come only from theories of computation, which are largely free of the details of real machines.” Pattee, H.H. “The Physical Basis and Origin of Hierarchical Control.” Pp. 71-108. Pattee, H.H., Editor. Hierarchy Theory: The Challenge of Complex Systems. George Braziller, Inc. 1973. Pp. 79-80.


“Remember, we are looking for a physical reason why an ordinary molecule can become the controlling factor in forming a chemical bond or in the expression of a whole developmental program. A control molecule is not a typical molecule even though it has a normal structure and follows normal laws. In the collection where it exerts some control it is not just a physical structure–it functions as a message, and therefore the significance of this message does not derive from its detailed structure but from the set of hierarchical constraints which we may compare with the integrated rules of a language. These rules do not lie in the structure of an element. We are asking for the physical basis of the hierarchical rules of the collection that turn these ordinary molecules into special messages.” Pattee, H.H. “The Physical Basis and Origin of Hierarchical Control.” Pp. 71-108. Pattee, H.H., Editor. Hierarchy Theory: The Challenge of Complex Systems. George Braziller, Inc. 1973. P. 81.


“Bonner found that to represent the developmental process by a program it was necessary to use the concept of the developmental test. According to this concept, the developing organism performs tests of the environment or surrounding cells, and the outcome of the tests is to turn off or on the genes appropriate for the developmental response. Now clearly such ‘tests’ must classify interactions. First, there must be a selection of what is tested. For example, such tests would not measure the positions of all the amino acids in the environment–that would hardly be significant for the cell even if it were practical. Second, there must be a selection of what range of results of a test will trigger a control response. Thus, out of the innumerable detailed physical interactions of the cells and their surroundings, there is a classification into significant and insignificant interactions, which I would say amounts to selective neglect of details in favor of only a very limited number of crucial conditions.” Pattee, H.H. “The Physical Basis and Origin of Hierarchical Control.” Pp. 71-108. Pattee, H.H., Editor. Hierarchy Theory: The Challenge of Complex Systems. George Braziller, Inc. 1973. P. 90.


“The scientific goal of systems biology is not merely to create precision models of cells and organs, but also to discover fundamental and structural principles behind biological systems that define the possible design space of life.” Kitano, Hiroaki. “Towards a theory of biological robustness.” Molecular Systems Biology. 3:137 18 September 2007. doi: 10:1038/msb4100179. Pps. 1-7. P. 1.


“Phenotypic plasticity enables organisms to develop functional phenotypes despite variation and environmental change via phenotypic accommodation–adaptive mutual adjustment among variable parts during development without genetic change. Phenotypic accommodation occurs regardless of the cause of variation, whether genetic or environmental, normal or pathological.” West-Eberhard, Mary Jane. Developmental Plasticity and Evolution. 2003. Oxford U.P. P. 51.


“There is abundant evidence that the two-legged goat effect is important in evolution, in the phenotypic accommodation of novel traits and of potentially disruptive variants that occur during development. Several authors have written of the phenotypic accommodation of evolutionary novelties, calling it by various names: compensation, functional adaptation, epigenetic regulation, and epigenetic accommodation.” West-Eberhard, Mary Jane. Developmental Plasticity and Evolution. 2003. Oxford U.P. P. 55.


“The growth in the number of phyla recognized between the mid-nineteenth century and today, from four to over thirty, occurred chiefly because those studies revealed distinctive differences in invertebrate bodyplans. For the most part, relatively simple biomechanical principles underlie the architectures of invertebrates.” Valentine, James. On the Origin of Phyla. 2004. University of Chicago Press. P. 40.


“Evolutionary transitions from unicellular protistans to multicellular organisms have occurred many times; Buss estimated the minimum number as twenty-three. The cells of multicellular organisms should retain many of the features of their unicellular forebears. Protista display a vast array of cell structures and complexities, most of which differ in significant ways from those found in animal cells, so that those protistan groups are not likely to be animal ancestors. Animals share some common attributes that suggest that they have originated only once, most likely from an ancestor within or allied to the protistan phylum Choanoflagellata.” Valentine, James. On the Origin of Phyla. 2004. University of Chicago Press. P. 201.


“Theories are excellent servants but very bad masters.” Thomas Henry Huxley. Quoted in Valentine, James. On the Origin of Phyla. 2004. University of Chicago Press. P. 427.


“The bodyplans of most crown phyla can plausibly be interpreted as indicating adaptations to life in benthic environments.” Valentine, James. On the Origin of Phyla. 2004. University of Chicago Press. P. 429.


“A broad generalization, with many exceptions, would be that at lower taxonomic levels the Early Cambrian radiation involved chiefly benthic detritus feeders, suspension feeders utilizing bacteria, and their predators, while the Ordovician radiation was particularly enriched by many clades of suspension feeders that chiefly ate protistants and, probably, larvae. The early diversity patterns do not suggest a biosphere replete with previous occupants that were preempting much of the ecospace available to the radiating clades.” Valentine, James. On the Origin of Phyla. 2004. University of Chicago Press. P. 459.


“It seems that ecological constraints should play the more important role in the diversification of lower taxa, while developmental constraints should play the more important role in the diversification of novel morphologies and therefore of higher taxa. To the extent that morphological change is driven by speciation, ecology might be the more important constraining factor. When morphology changes in response to major adaptive opportunities, though, constraints might be more likely to arise from development.” Valentine, James. On the Origin of Phyla. 2004. University of Chicago Press. P. 462.


“The early history of complexity within metazoans, then, appears to read something like the following. Multicellularity arose probably before 600 Ma, perhaps only tens of millions of years earlier. The early metazoans may have had two or three cell morphotypes and are likely to have been benthic. Bodyplans of the vendobionts required tissue sheets, which evidently evolved sometime before or near 570 Ma; vendobionts were probably of diploblastic grade, but whether they were organized like the surviving radiates is uncertain, to say the least. Their complexity cannot be estimated except to speculate that they may have been less complex than living radiates. Diploblastic organisms that were organized like living radiates, consisting of forms with perhaps seven to ten cell morphotypes, probably also arose before or near 570 Ma. Meanwhile, benthic bilaterians with mesodermal tissues also appeared, probably establishing forms with fifteen or more cell morphotypes, to judge by living paracoelomates, that were patterned by a large suite of developmental genes. Many of the early bilaterians may have been hemocoelic from the first, in the sense that they retained a fluid-filled blastocoel to complement muscles associated with the body wall that functioned chiefly in locomotion. Circumpharyngeal muscles evolved in forms of this grade to aid in feeding, and in some cases muscle fibers extended along the gut. As these forms attained larger body sizes, schizocoelic organ coeloms may have evolved to serve as renal and gonadal ducts and other spaces. Nerve nets became consolidated into cords as the need for integrated control of differentiated and iterated tissues and organs increased. Some of these forms were capable of disturbing the bottom sediments, and their traces entered the fossil record.” Valentine, James. On the Origin of Phyla. 2004. University of Chicago Press. Pp. 494-5.


“One branch of the deuterostomes remained benthic, and while those phyla, Echinodermata and Hemichordata, are interesting, they do not stand out as complex groups. The other branch took to the water column and developed swimming behaviors based on a notochord, radiating into the clades of Chordata, some of which are spectacularly successful and quite complex, and probably in some cases they recolonized the benthos.” Valentine, James. On the Origin of Phyla. 2004. University of Chicago Press. P. 507.


“Yet Darwin had also to acknowledge that according to his theory of variation under natural selection, by which he claimed to account for the modification of organisms along lines of descent, each organism on a line exists solely to be itself, to fulfill a project coterminous with the bounds of its own existence. It neither carries forward the life-course of its antecedents nor anticipates that of its descendants, for what it passes on to the future, by way of its own reproduction, is not its life but a suite of hereditary characteristics that may be recombined or reassembled in the formation of other projects for other lives. In this Darwinian conception, evolution is absolutely not a life-process. Whereas evolution takes place across generations, life is expended within each generation – in the task of passing on the heritable components, nowadays known as genes, needed to get it restarted in the next. As historian of science Charles Gillespie has rightly observed, the logic of this argument drives a wedge between Lamarckian and Darwinian understanding of the evolutionary process, for what Darwin did ‘was to treat the whole range of nature which had been relegated to becoming, as a problem in being, an infinite set of objective situations reaching back through time’. It follows that the continuity of evolution is not a real continuity of becoming but a reconstituted continuity of discrete individuals in genealogical sequence, each of which differs minutely from predecessors and successors. As I put it in an earlier work, ‘the life of every individual is condensed into a single point; it is we who draw the connecting lines between them, seeing each as a moment of a continuous process’.” Ingold, Tim. Lines: A Brief History. 2007. Routledge. Pp. 113-4. [Gillespie, C.S. ‘Lamarck and Darwin in the history of science.’ From Glass, Temkin and Straus (Eds.) Forerunners of Darwin: 1745-1859. Johns Hopkins University Press. P. 291.]


The causal theory of evolution has to include a hypothesis that suggests how innovation is generated. Darwin and his descendants have not formulated a generative synthesis. Their hypothesis only circumscribes the demographic fate of novelties.” Reid, Robert. Biological Emergences: Evolution by Natural Experiment. 2007. MIT Press. P. 15.


“Since I know of no word that covers all the biological and sociological aspects of this issue I have to invent ‘symbiostasis.’ At one end of the association spectrum, sociobiology recognizes the development of change-resistant dynamic social stabilities–social homeostasis. At the other end of the spectrum, where endosymbiosis resides, dynamic biochemical and physiological stabilities are involved.” Reid, Robert. Biological Emergences: Evolution by Natural Experiment. 2007. MIT Press. P. 133.


“While adaptations are inflexible, adaptability is the quality of an individual organism to adjust itself effectively in response to internal and external environmental change.” Reid, Robert. Biological Emergences: Evolution by Natural Experiment. 2007. MIT Press. P. 141.


“A more striking example of a bird that exposes itself to stressfully extreme environments is the Arctic cormorant. One would think that temperature homeostasis would be utmost importance to it. Yet subdermal fat insulation and the secretion of preening oils have regressed in that cormorant species. Not only do they get colder faster, but also their plumage is more wettable, and they have to hang out their wings to dry in freezing temperatures after a dive. On the plus side, reduced insulation means reduced buoyancy, and cormorants can dive after prey to greater depths with less effort. Owing to the anomalous properties of water, the deep temperature of Arctic seas is not much colder than that in more temperate zones. The potential trouble arises from having to expose a wet body surface to dry off in subzero air, where the sacrifice of body heat is unavoidable. Yet diving for about nine minutes a day satisfies the cormorants’ usual nutritional and thermoregulatory needs. In the absence of competition from other birds, they are able to tap a major resource of high-energy, fatty food. Their adaptability sustains them even in the absence of apparently crucial ‘adaptations’ for living in the Arctic.” Reid, Robert. Biological Emergences: Evolution by Natural Experiment. 2007. MIT Press. Pp. 153-4.


“But to achieve a reasonably faithful copy a living system has to be unstable enough to come apart and go back together again, making it vulnerable to physicochemical influences, error-prone, and thus raw material for natural experiments.” Reid, Robert. Biological Emergences: Evolution by Natural Experiment. 2007. MIT Press. P. 159.


“...Newman and Muller’s theme is worth re-emphasis: simple, primitive, multicellular organisms were more plastic, and responsive to epigenetic influences than complex organisms with mechanisms that buffer morphogenesis and homeostasis. Epigenetic causes were not gene determined, but were physiogenic, and thus contingent – they may or may not have acted; it depended on the circumstances. Consistent behaviors and contingencies would have led to consistently altered morphogenesis, and only then would the linkage between phenotype and genotype be established. Then the genome would have been able to co-opt the morphological outcome of development. Ontogeny does not recapitulate phylogeny, it creates it. Thus, they conclude that evolvability, at least in terms of large innovations like the emergence of different body forms decreases with time. Genetic determination obstructs it.” Reid, Robert. Biological Emergences: Evolution by Natural Experiment. 2007. MIT Press. P. 210.


“... the jack-of-all-trades qualifications of hominids allowed them to escape genetic co-option of behavior.” Reid, Robert. Biological Emergences: Evolution by Natural Experiment. 2007. MIT Press. P. 211.


“Although the distinctive body plans of the marine animal phyla may have appeared very rapidly in the early Cambrian, their tenacious stability has depended largely on the establishment of strongly canalized homeorhesis. But along with it came some reduction of evolvability. Even the simple anatomies of polyps and flatworms have been canalized to the point of intransigence. Paradoxically, although it took longer for the basic fishy vertebrate plan to emerge, vertebrate developmental evolution kept on progressing in fits and starts for more than 400 million years, while most Cambrian animals, with the other obvious exception of arthropods and the lesser example of mollusks, stayed stuck in the mud.

“This supports Brian Hall’s contention that the neural crest is a major generative condition for the emergence of vertebrates and their continued evolution. This distinctive embryonic ectodermal structure appeared early in the craniate lineage. Before it appeared, some migratory cells, especially the neuroblasts, helped to modify body plan. But the evolutionary versatility of the neural crest justifies Hall’s claim that it is an emergent, fourth germ layer. Along with duplications of the whole genome in the early vertebrates, and further duplication and differentiation of genes that regulate development and physiology, the neural crest provided powerful experimental tools for emergent evolution. During the evolution of fish, amphibians and reptiles there were anatomical experiments, often involving numbers of vertebrae, the limb transposition early noted by Goodrich, and the arrangement of fin-rays and digits. Among the reptiles, for example, contrast the forms of turtles, plesiosaurs, ichthyosaurs, dinosaurs, pterosaurs, and snakes. These could be generated by changes in homeotic gene expression. They could also be effected by changes in cellular interactions, such as the migration of neural crest cells, and by heterochronic shifts. But behavior must also have been important in determining what changes would be relevant to the animals’ way of life.” Reid, Robert. Biological Emergences: Evolution by Natural Experiment. 2007. MIT Press. Pp. 216-7


“Once the foundational multicellular association had formed and emerged to the level of complexity of a gastruloid, developmental evolution became possible. It initially involved differential adhesion, and experiments with body spaces, and simple structural patterns that were responses to extrinsic and intrinsic epigenetic stimuli. Ultimately epigenesis came to involve genes and their regulation. This was then made more variable by repetitive differentiation of molecules and cell types, coupled with reorganization, integration and regression.” Reid, Robert. Biological Emergences: Evolution by Natural Experiment. 2007. MIT Press. P. 219.


“Simple multicellular organisms had the emergent qualities of being hard to eat and slow to starve. Without much differentiation, they also had an easily realizable potential to eat larger things, store more food, locomote more efficiently, and commit themselves more effectively to reproduction.” Reid, Robert. Biological Emergences: Evolution by Natural Experiment. 2007. MIT Press. P. 256.


“Jablonka and Lamb note that epigenetic inheritance systems had a double role in the transition to complex multicellular organisms:

‘First, they enabled the emergence of a new unit of structure and function, the phenotypically distinct cell lineage. Second, they allowed the formation of the stable interdependences between epigenetically distinct cell lineages, which resulted in the evolution of integrated organism from loose groups of cells.’”

Reid, Robert. Biological Emergences: Evolution by Natural Experiment. 2007. MIT Press. Pp. 256-7.


“Bell asserts that the absence of sexual reproduction kept living organisms in a primitive unicellular state for about 2 billion years. Furthermore, natural experiments in multicellularity may often have been tried during that time, but failed because of the lack of the repair facilities that emerged with meiosis. Thus, the tradeoff between faithful reproduction and experimental flexibility held early progressive evolution back until a saltatory boost arrived in the form of sex. For most of the time in question prokaryotic unicells could complexify themselves by gene acquisition through a variety of routes, and could reproduce asexually. Although some engaged in conjugation, which falls within a loose definition of sexual mating, sex in eukaryotes involves chromosomes. Chromosome packaging was an immediately advantageous feature for mitotic asexual reproduction, and it potentiated sexual reproduction as well. Membrane adhesion molecules, and the pre-existent experience of conjugation were other generative features. The natural experiment of sexual reproduction succeeded because of the prior lack of reconditioning mechanisms–there was nothing to prevent it at that stage. Once in place, repair mechanisms could be refined, and a new, efficient level of change-resistant dynamic stability (i.e. homeorhesis) established.” Reid, Robert. Biological Emergences: Evolution by Natural Experiment. 2007. MIT Press. P. 257.


“Intron dissemination, repetitive differentiation, molecular drive, self assembly, anticipation, and other aspects of complexification can occur without causal reference to adaptiveness–in other words, ‘out of the sight of natural selection.’” Reid, Robert. Biological Emergences: Evolution by Natural Experiment. 2007. MIT Press. P. 260.


“At different times in the history of evolution symbiosis, association, epigenetic differentiation, physiological adaptability, behavioral freedom, have interacted to send out waves of progressive change that generated new major emergences. ‘Bootstrapping’ says it more succinctly. Orthogenetic/allometric shifts in the central nervous system have been an integral part of several independent animal lineages, with the most dramatic found in the primates. While chronological priority is easy to establish, it is impossible to rank the causes of emergent evolution in order of importance for evolutionary progress.” Reid, Robert. Biological Emergences: Evolution by Natural Experiment. 2007. MIT Press. Pp. 286-7.


“Emergence is the spontaneous appearance of novel qualities through the interactions and constraints of generative conditions, consisting of the dynamic structure of the original, and properties of its environment. Thus stated, emergence includes a wide range of physical events from the Big Bang to the physicochemcial reactions that produce liquid water from hydrogen and oxygen at appropriate temperatures and pressures. It also allows for the introduction of a catalytic factor. And it assumes physicochemical and biological constraints on natural experimentation.” Reid, Robert. Biological Emergences: Evolution by Natural Experiment. 2007. MIT Press. P. 290.


“Holons, or modules, at the anatomical level evolve according to similar principles, first multiplying and then differentiating.” Reid, Robert. Biological Emergences: Evolution by Natural Experiment. 2007. MIT Press. P. 302.


“Not only does hierarchical organization provide reliability and stability but modularized structure also allows systems of great complexity, which also retain the ability to evolve. Both are key attributes of life.” Rollo, David. Phenotypes: Their Epigenetics, Ecology, and Evolution. Chapman and Hall. 1994. P. 8. Quoted in Reid, Robert. Biological Emergences: Evolution by Natural Experiment. 2007. MIT Press. P. 302.


“In ‘What are the biotic hierarchies of integration and linkage?’, Vrba calls for an ‘expanded evolutionary theory; and baldly states that it is dishonest to claim that the Modern Synthesis can be stretched and modified to infinity. At this point I have no wish to engage in semantic quibbling, but should explain that she uses the word ‘structure’ in the special sense of a biological emergent phenomenon. Structuralists would use the expression ‘dynamic structure’ which includes developmental, and physiological functions, as well as anatomy. The generative conditions at any hierarchical level is usually based on some kind of structure–molecule, cell, organ, etc. Although Vrba knows that behavior has a downward causal effect on both physiology and anatomical development it stretches the word ‘structure’ to include behavior, the physiogenic interpenetration of organism and environment, and the interaction between the organism with its own kind, or other organisms in its environment.” Reid, Robert. Biological Emergences: Evolution by Natural Experiment. 2007. MIT Press. P. 304. Reference is to Elisabeth Vrba from Integration and Evolution in Vertebrates. Edited by Wake and Roth. 1989. Wiley. P. 382.


“Levels of organization from molecules to ecosystems are hierarchically ordered.” Reid, Robert. Biological Emergences: Evolution by Natural Experiment. 2007. MIT Press. P. 310.


“The properties of a mere aggregate are independent of variations in its components, since the latter do not interact. The nature of the whole can be discovered by testing the effects of intersubstitution or rearrangement of parts, the effects of addition or subtraction of parts, and the effects of decomposition or reaggregation of parts. If none of these have any effect on the properties of the whole, it is an aggregate. If the whole has non-linear emergent properties arising from interactions between the components, some or all of the three tests will cause indentifiable change in the original system. This approach demonstrates that mere aggregates are rare, even outside biological systems.” Reid, Robert. Biological Emergences: Evolution by Natural Experiment. 2007. MIT Press. P. 316. Referring to article by William Wimsatt. “Aggregativity: Reductive heuristics for finding emergence.” 1997. Phil. Sci. 64: S372-S384.


“In categorizing emergent evolution into saltatory and critical-point, and intrinsic/extrinsic events, it must not be forgotten that evolution is both progressive and adaptational. Progressive evolution involves the emergence of new levels of complexity/self-organization/adaptability. It is followed by a phase of diversification, involving orthogenesis/allometry, and specialization of habit in relation to habitat. I only need to confirm that all categories of emergence are involved in progressive and adaptational evolution, with a larger component of intrinsic/saltatory emergence in progress, and a larger component of extrinsic/critical-point emergence in adaptation.” Reid, Robert. Biological Emergences: Evolution by Natural Experiment. 2007. MIT Press. P. 326.


“As time passes, stases become stronger and more resistant to the further modification. The most familiar are homeorhesis in the epigenetic arena, homeostasis in the physiological arena, and ecostasis in the environment at large. Symbiostasis is the parallel stabilization of associative relationships and it demonstrates that evolution can progress despite stasis. Stasis is actually in a constant state of flux–the Red Queen is always running, and minor natural experiments lead to minor adaptations, without achieving any progress, although the Ultras call it ‘evolution.’” Reid, Robert. Biological Emergences: Evolution by Natural Experiment. 2007. MIT Press. Pp. 326-7.


“The quintessential feature of progressive physiological evolution is the adaptability to keep on doing the same things when external conditions change, and to do different things when external conditions stay the same–and anything in between. This underpins anatomical and behavioral specialization for specific habits and habitats. Thus, placental mammals can get themselves into strange situations, and persist until emergent morphological features and new behaviors are integrated. The stability of their internal milieu, in particular the constancy of body temperature, is especially significant for the developing embryo. The placenta allows maternal homeostasis to be shared intimately with the developing fetus until birth at a mature stage.” Reid, Robert. Biological Emergences: Evolution by Natural Experiment. 2007. MIT Press. Pp. 332-3.


“But adaptational changes will not usually create adaptability, since they substitute one condition for another, and are static rather than flexible. Evolution goes backwards when adaptations make an adaptable system regress to an inflexible specialized system.” Reid, Robert. Biological Emergences: Evolution by Natural Experiment. 2007. MIT Press. P. 335.


“As I noted in ‘Evolution by Association,’ gut bacteria also effect ‘normal’ gut development and digestive and immunological functions in mice. Just as interesting are the free-living bacteria that stimulate the sea lettuce, Ulva, to make ‘lettuce-leaf’ thalli instead of the thready form that they have in axenic (sterile) culture. Nitrogen-fixing bacteria stimulate the formation of root nodules in their host plants. Brian Hall classes these kinds of influences under ‘interspecific epigenetics.’” Reid, Robert. Biological Emergences: Evolution by Natural Experiment. 2007. MIT Press. P. 344.


“Just as there is no organism without an environment, there can be no environment without an organism.... An environment is something that surrounds or encloses, but for there to be a surrounding there has to be something at the center to be surrounded.” Lewontin, Richard. The Triple Helix: Gene, Organism, and Environment. Harvard U. P. P. 48. Quoted in Reid, Robert. Biological Emergences: Evolution by Natural Experiment. 2007. MIT Press. P. 345.


“The evolutionary significance of repetitive differentiation as ‘varied repeats’ has finally been appreciated by molecular biologists. The concept illustrates how natural experiments can take place out of sight of natural selection, and how the simplest kind of self-replicating system can spontaneously become complex and potentially self-organizing through multiple feedback controls. And it applies to the duplication of discrete codons, exons, introns, genes, chromosomes, karyotypes, cells, tissues, organs, segments, organisms, populations, and societies.” Reid, Robert. Biological Emergences: Evolution by Natural Experiment. 2007. MIT Press. P. 354.


“Hierarchical layering is both spatial and temporal in organisms. During development the branching and interaction of cell lineages follow algorithms that are susceptible to heterochronous variation. In the mature organism the spatial layers (molecules, cells, organs, whole organism) interact constantly. They will be further influenced by temporal changes that are either random or cyclical.” Reid, Robert. Biological Emergences: Evolution by Natural Experiment. 2007. MIT Press. P. 377.


“In practical terms hierarchically ordered complexity may be governed by physiological communication such as hormonal and nervous systems, i.e., both ‘wireless broadcast’ and ‘hard-wired.’ These are subject to emergent changes.” Reid, Robert. Biological Emergences: Evolution by Natural Experiment. 2007. MIT Press. P. 377.


“In some animals, experiments in behavior will tend at first to be genetically assimilated. Then they will tend to escape to greater degrees of individual freedom. Progress in behavioral evolution, if unconstrained, will increasingly influence the nature of functional-morphological emergences. (E.g., insect size is physically constrained by the exoskeleton, which limits the size of the nervous system, which restricts them to stereotyped behavior patterns.)” Reid, Robert. Biological Emergences: Evolution by Natural Experiment. 2007. MIT Press. Pp. 377-8.


“Social interactions will produce effective wholes beyond the organismal entity.” Reid, Robert. Biological Emergences: Evolution by Natural Experiment. 2007. MIT Press. P. 378.


“The simple answer is that these ideas [emergence, complexity theories] begin to present alternatives to a prevailing theory that for seven decades has focused the attention of self-styled evolutionists on minor, non-evolutionary fluctuations of dynamically stable systems. That theory has generated no useful predictions about or insights into progressive evolution. It is ‘armoured against it.’ The central role that Julian Huxley gave evolutionary progress has been written out of the neo-Darwinist drama.” Reid, Robert. Biological Emergences: Evolution by Natural Experiment. 2007. MIT Press. P. 385.


“There are several generative causal arenas: symbiosis/association; epigenetic/developmental processes; physiology and behavior.” Reid, Robert. Biological Emergences: Evolution by Natural Experiment. 2007. MIT Press. P. 392.


“Major emergences increase adaptability by having multifunctional features.” Reid, Robert. Biological Emergences: Evolution by Natural Experiment. 2007. MIT Press. P. 404.


“Progressive emergent evolution in animals means greater freedom to choose how and when to act. That animals should have such greater freedom increases their individual roles in generating further evolutionary change.” Reid, Robert. Biological Emergences: Evolution by Natural Experiment. 2007. MIT Press. P. 404.


“Equilibria may be organismal (i.e., physiological) or ecological (involving behavior, the physicochemical environment, and intraspecific and interspecific relationships).” Reid, Robert. Biological Emergences: Evolution by Natural Experiment. 2007. MIT Press. P. 404.


“As was noted in the introduction to this chapter, the biological synthesis contains both the component of progressive evolution, which involves discontinuous, complexification on a biological time scale, and the component of dynamic stability (i.e., the selection syndrome), which has dominated the history of life on a geological time scale.” Reid, Robert. Biological Emergences: Evolution by Natural Experiment. 2007. MIT Press. P. 405.


“For most neo-Darwinists, adaptive radiation, or any kind of large-scale evolution, is no more than slow, cumulative adaptational divergence. From the emergentist’s point of view, the typological, essentialistic organism, long despised by Ernst Mayr and his disciples, must make a comeback. The multifunctional emergent properties of an archetype are what make specialization of divergent adaptive lines possible.” Reid, Robert. Biological Emergences: Evolution by Natural Experiment. 2007. MIT Press. P. 412.


“I want reductionism and neo-Darwinism and natural selection to be seen for what they actually are, and then find a different synthesis. Such a synthesis would be interdisciplinary as well as dialectical, since it must involve more than the conciliation of a set of apparent contradictions. Post-Lamarckism, structuralism, complexity theory, the lucky-strike paradigm of neo-catastrophism, evo-devo, and symbiosis studies all focus on important elements of evolutionary causation. But their individual adherents, whether modern mutineers or postmodern privateers, lack the resolve to escape the vortex of Darwinism. If they do not all hang together in a new synthesis they will all hang separately, to be scavenged by the Modern Synthesis, stuck in the hold, and forgotten.” Reid, Robert. Biological Emergences: Evolution by Natural Experiment. 2007. MIT Press. P. 422.


“Holistic evolutionary studies should discover the lateral relationships between traditional disciplines–the three ring circus of epigenetics/form, physiology/behavior/function, symbiosis/society under the big top of an ecology that does not forever strain to abstract the environment to numbers. Within them there are hierarchical relationships–functional morphology relates up to behavior and down to biological molecules. Intolerant reductionism has no place in an emergence program; nor does a hylozoism that forces the characteristics of higher emergent levels onto lower ones. New rules emerge at each new level of progressive evolution, and their identification requires knowledge of the organism and its relationships.” Reid, Robert. Biological Emergences: Evolution by Natural Experiment. 2007. MIT Press. P. 424.


“Now we know that the cambrian explosion was the spontaneous evolution of external body parts in all phyla, where the internal body plans of all phyla are already in place.” Parker, Andrew. In the Blink of an Eye: How Vision Sparked the Big Bang of Evolution. 2003. Basic Books. P. 37.


“The skin of the chameleon or cuttlefish is packed with chromatophores – colour cells. These are simply cells packed (usually) with pigment. Each colour cell contains just one type of pigment that causes one colour. But the cell is elastic – it can change its shape. Under nervous control, it can become flat and thin, lying parallel with the surface of the animal, or short and squat. And the pigment is spread evenly throughout the cell in each case. Looking at the animal, the short, squat cells reveal only a small area of pigment, and the visual effect is negligible. But the thin, flat cells reveal much more of their pigment, and can be seen by the naked eye. Compare these two possible forms of the colour cell, considered off and on, with a coin. A coin is easily observed when lying flat, but it is more difficult to see edge on.

“Chameleon and cuttlefish skin is actually packed with colour cells of various hues. In comparison with a TV screen, individual cells can be considered sub-dots, collectively forming dots that can independently cause any colour. By being turned on and off, or be becoming an intermediate phase, the different sub-dots contribute to a dot that is capable of assuming any colour of varying brightness. At high magnification, imagine the skin as an assortment of juxtaposed and coloured coins. When some coins are turned on their sides, different overall colours are achieved. And this works – it really is extremely effective. One would hope so, too, considering the evolutionary trouble involved and the physical costs of such a mechanism. Significant electrical wiring, brain space, production of pigment and specialised cells, muscles, and sensors are required. With these costs in mind we can begin to consider the importance of light as an evolutionary factor and behavioural concern.” Parker, Andrew. In the Blink of an Eye: How Vision Sparked the Big Bang of Evolution. 2003. Basic Books. Pp. 92-3.


“So animals have to accept, or in evolutionary terms adapt to, the sunlight that strikes them. There are two routes an animal can take – the path to camouflage or the path to conspicuousness.” Parker, Andrew. In the Blink of an Eye: How Vision Sparked the Big Bang of Evolution. 2003. Basic Books. P. 94.


“Unfortunately for some other moths, their camouflage code is all too often cracked. But the moths are prepared for this. In the event that their cover is blown, they opt for conspicuousness as a last resort. The camouflage of these moths is confined to their upper wings – the only wings visible during rest. But when danger comes too close for comfort, their lower wings are quickly displayed, along with their warning colouration. Predators are confused by these unexpected blazes of bright colour and, in theory, the moths buy some time to escape.” Parker, Andrew. In the Blink of an Eye: How Vision Sparked the Big Bang of Evolution. 2003. Basic Books. P. 97.


“The hard parts described so far all evolved at one point in time. This evolution was the Cambrian explosion – all animal phyla suddenly evolved their hard parts simultaneously between 543 and 538 million years ago. As mentioned already, hard parts can have functions other than to provide protection against predators, but it would appear extremely coincidental for all phyla to evolve hard parts at precisely the same time to provide strength or as a barrier against osmotic stress. Multicelled animals from different phyla had been around, in soft-bodied form, for 100 million years or so beforehand.” Parker, Andrew. In the Blink of an Eye: How Vision Sparked the Big Bang of Evolution. 2003. Basic Books. P. 253.



“Also of interest in the proto-trilobites were curved, shallow ridges on the head, in the region that eyes were housed in Cambrian trilobites. But eyes themselves, like grasping limbs and spiny mouthparts, were absent in the Precambrian forms.

“The proto-trilobites of the Precambrian were grazers, feeding on algal mats and probably dead animal matter lying on the sea floor. It seems the voracious predators that emerged with the Cambrian had rather peaceful beginnings. If anything, the proto-trilobites would have been prey themselves – the tables may really have turned at the Cambrian border. In general the Precambrian was rather an experimental stage for predation, occupied mainly by peace-loving vegetarians that were willing enough to accept any occasional animal matter they stumbled upon. For they were developing a taste for meat.” Parker, Andrew. In the Blink of an Eye: How Vision Sparked the Big Bang of Evolution. 2003. Basic Books. Pp. 258-9.


“The first true trilobite was also a predator. Fallotaspis, Neocobboldia and Shizhudiscus, all trilobites with eyes, were also icons of the beginning of the Cambrian, around the time the Cambrian explosion began. Their limb shapes indicate that these trilobites were predators; their spiny shields affirm that they were also prey. They probably attacked each other – the archetypal attacks on Earth, since their bodies were armoured in only rudimentary form. Their skins had become less soft than those of the Precambrian proto-trilobites, but they were still not fully hardened, as were exoskeletons of trilobites that appeared a few million years later. They were, however, highly active animals. They could swim rapidly, they could manoeuvre in mid-water ... and they were predators with spiny, robust limbs. They were bad news for Precambrian-style, soft-bodied forms everywhere. Life was about to be stirred up.

“So the beginning of the Cambrian was also the beginning of active predation.” Parker, Andrew. In the Blink of an Eye: How Vision Sparked the Big Bang of Evolution. 2003. Basic Books. P. 259.


“Consider dividing geological time into two parts – pre-vision and post-vision. The boundary separating these parts stands at 543 million years ago. Considering vision as the most powerful stimulus on earth, the way the world functions today is the same way it functioned ten million years ago, 100 million years ago and 537 million years ago, after the Cambrian explosion. Similarly, the world was without vision 544 million years ago just as it was 600 million years ago. In the interval of life’s history of these two parts, a light switch was turned on. For the second half it remained on, although during the first half it was always off.” Parker, Andrew. In the Blink of an Eye: How Vision Sparked the Big Bang of Evolution. 2003. Basic Books. P. 268.


“Competition and predation would not have been major selective pressures in the Precambrian, but they were taking a foothold. The Ediacaran animals of the Precambrian were gradually developing brains. They were developing ways to pick up environmental cues, or news items, and process that information. They were also evolving the ability to chew, and were gradually developing a rudimentary form of rigidness in their limbs. Precambrian trace fossils or footprints suggest that legs could support bodies off the ground.” Parker, Andrew. In the Blink of an Eye: How Vision Sparked the Big Bang of Evolution. 2003. Basic Books. P. 269.


“In other words, the evolution of smell and taste over geological time was linear – it involved a series of numerous but gradual transitional stages.” Parker, Andrew. In the Blink of an Eye: How Vision Sparked the Big Bang of Evolution. 2003. Basic Books. P. 283.


“The evolution through geological time of chemical and mechanical receptors cannot be compared with the evolution of light detection. There is no event in the evolution of receptors of other senses that can match, or even come close to, the evolution of the lens. Chemical and mechanical detectors certainly would have become more efficient throughout the Cambrian explosion, but not to the extent that they would have changed the entire behavioural system of animals. There is no case of a receptor suddenly changing in efficiency ‘a hundredfold’, like the change from a light-sensitive patch to an eye capable of producing visual images. Here lies the fundamental difference between light detectors and the receptors of other stimuli – those of other stimuli still work at their intermediate stages of complexity and efficiency. The evolution of receptors for stimuli other than vision can theoretically show a linear progression, but a light perceiver with an inadequate lens has little advantage over one with no lens. The theoretical intermediate stages of a lens increase light perception only slightly, but when a complete, fully focusing lens is formed, the increase suddenly becomes vast.” Parker, Andrew. In the Blink of an Eye: How Vision Sparked the Big Bang of Evolution. 2003. Basic Books. Pp. 283.4.


“Tooby and Cosmides’ logic seems sound, but, empirically, human populations have exploded in the last ten thousand years; we are now vastly more successful than we were in the Pleistocene. Another variant of the adaptationist’s dilemma! One reason is that humans themselves now create rapid, large-scale environmental change comparable to the climate changes of the last glacial. For example, agriculture changes the environment for wild plants and animals and the foragers who would depend on them for subsistence. Even though weeds, pests and diseases evolve to take advantage of the new anthropogenic environments, we readapt even faster, generating further deterioration. So long as we generally find human-modified environments more congenial than our competitors, predators, and parasites, we can thrive, if only by using cultural adaptations to stay one step ahead of onrushing pests. Humans succeed by winning arms races with species that attack our resources and us. They evolve too slowly; we outwit them by cultural counteradaptations, staying a step ahead in the race.” Richerson, Peter & Robert Boyd. Not by Genes Alone: How Culture Transformed human Evolution. 2005. University of Chicago Press. P. 146.


“Better to think of genes and culture as obligate mutualists, like two species that synergistically combine their specialized capacities to do things that neither one can do alone. Humans by themselves cannot convert grass into usable food. Cows by themselves cannot drive away lions and wolves. The cow-human mutualism works to the advantage of both. However, such mutualisms are never perfect. Humans will always be tempted to take more milk at the expense of calves, and cows will always be subject to natural selection that favors shorting the humans to feed their offspring. Each caters to the whimsical biology of the other so long as there is a net payoff to the cooperation. Humans chauvinistically see themselves as controlling domestication. A cow might as well flatter herself on how clever she is to elicit so much work on her behalf from her humans. The relationship between genes and culture is similar. Genes, by themselves, can’t readily adapt to rapidly changing environments. Cultural variants, by themselves, can’t do anything without brains and bodies. Genes and culture are tightly coupled but subject to evolutionary forces that tug behavior in different directions.” Richerson, Peter & Robert Boyd. Not by Genes Alone: How Culture Transformed human Evolution. 2005. University of Chicago Press. P. 194.


“... the symbiosis between genes and culture in the human species has led to an analogous major transition [like the transition from prokaryotes to eukaryotes] in the history of life – the evolution of complex cooperative human societies that radically transformed almost all the world’s habitats over the last ten thousand years.” Richerson, Peter & Robert Boyd. Not by Genes Alone: How Culture Transformed human Evolution. 2005. University of Chicago Press. P. 195.


“Size and complexity are, of course, relative terms, but in relation to the size and complexity into which some forms of life have evolved, the vast majority of the biomass on Earth, even today, is microscopically small and no more complex than the solitary eukaryotic cell.

“Physiology favors simplicity, and simplicity is aided by small size. The ratio of surface to volume decreases inversely as size increases. The simplest living functions (physiological processes) depend critically on exchange of materials across the boundaries of the system (external membrane). Not only does the high surface to volume ratio of small compartments favor exchange of materials, the ability of those materials to migrate to and from the center of the cell by diffusion, the simplest mode possible, depends on having a cell radius small enough for diffusion to be a practical mechanism for movement.

“Ultimately, some advantages are gained by increased complexity. Multicellular organisms can achieve greater mobility and enhanced capacity to deal with a specific range of environmental fluctuations, but multicellularity requires specializations for distributions of materials, ingestion and excretion, and coordination of different body parts. This requires greater hereditary information for coding development and physiological coordination, consumes more energy, requires more space, and draws more resources from the environment. The density of such organisms is thereby reduced. Also, while advantages accrue for adaptation to specific niches, flexibility is diminished so that overall fitness to a broad range of changing conditions over time remain with the simpler structures and functions that require less coding, smaller size, and less elaborate cellular engineering.” Schulze-Makuch, Dirk and Louis Irwin. Life in the Universe: Expectations and Constraints. Second Edition. 2008. Springer. P. 46.


“In Darwin’s great vision, evolution is fundamentally a process of branching, of divergence–new forms and physiologies arise as the descendants of a common ancestor grow ever more different from one another. Lynn Margulis, however, argued for the emergence of evolutionary novelty as branches fused.” Knoll, Andrew. Life on a Young Planet: The First Billion Years of Evolution on Earth. 2005. Princeton University Press. P. 124. Reference is to Margulis, Lynn. Symbiosis in Cell Evolution. 1981. W.H. Freeman.


“Clearly, we are a long way from resolving all mysteries of eukaryotic cell origins. But hypotheses like those of Martin and Mueller, and of Hartman and Fedorov, cap a strengthening view of early evolution in which nature appears not so much ‘red in tooth and claw’ as ‘green in mergers and acquisitions’.... Knoll, Andrew. Life on a Young Planet: The First Billion Years of Evolution on Earth. 2005. Princeton University Press. P. 137. References are to: Martin, W., and M. Mueller. 1998. “The hydrogen hypothesis for the first eukaryote.” Nature. 392: 37-41. Hartman, H., and A. Federov. 2002. “The origin of the eukaryotic cell: A genomic investigation.” Proceedings of the National Academy of Sciences, USA. 99: 1420-1425.


“Culture is interesting and important because its evolutionary behavior is distinctly different from that of genes. For example, we will argue that the human cultural system arose as an adaptation because it can evolve fancy adaptations to changing environments rather more swiftly than is possible by genes alone. Culture would never have evolved unless it could do things that genes can’t!” Richerson, Peter & Robert Boyd. Not by Genes Alone: How Culture Transformed human Evolution. 2005. University of Chicago Press. P. 7.


“The concept of heritability can thus be generalized into that of transmittability which is the heredity of differences whatever the mechanism of transmission involved.” Danchin, E., L. Giraldeau & F. Cezilly. Behavioural Ecology. 2008. Oxford University Press. P. 699.


“In eukaryotes, genetic information is only transmitted vertically from parents to offspring. Vertical tansmission of culture is also present. However, culture is also transmitted horizontally, among individuals of the same generation (as in fashion in humans), and obliquely among non-kin individuals of different generations (as in teaching in humans). No such possibilities exist in genetic transmission.” Danchin, E., L. Giraldeau & F. Cezilly. Behavioural Ecology. 2008. Oxford University Press. P. 709.


“... we need better descriptions of the relationship between the properties of evolving organisms and their coevolving environments. To achieve that, however, we shall have to recognize that evolution depends not on one, but on two general selective processes: natural selection and niche construction.” Odling-Smee, F. John, Kevin Laland & Marcus Feldman. Niche Construction: The Neglected Process in Evolution. Princeton University Press. 2003. P. 385.


“... the significance of evolutionary theory to the human sciences cannot be fully appreciated without a more complete understanding of how organisms, and human beings in particular, modify significant sources of natural selection in their environments, thereby codirecting subsequent biological evolution.” Odling-Smee, F. John, Kevin Laland & Marcus Feldman. Niche Construction: The Neglected Process in Evolution. Princeton University Press. 2003. P. 242.


“Reciprocal cooperation has been described in birds, mammals, and in some fish species, and it is also a fundamental property of human interactions.” Danchin, E., L. Giraldeau & F. Cezilly. Behavioural Ecology. 2008. Oxford University Press. P. 547.


“Hamilton’s rule was a major breakthrough and has deeply influenced our understanding of social behaviour. One merit of this rule is that it provides a simple and intuitive evolutionary explanation of altruistic traits: genes that cause a fitness cost to their altruistic bearers can be rewarded if they contribute to enhance the replication of genes related by descent in recipients.” Danchin, E., L. Giraldeau & F. Cezilly. Behavioural Ecology. 2008. Oxford University Press. P. 559.


“Indeed, the same factors that enhance cooperation among relatives may also increase local competition for space and food between relatives, a form of competition called kin competition.” Danchin, E., L. Giraldeau & F. Cezilly. Behavioural Ecology. 2008. Oxford University Press. P. 559.


“The cost of mobility is crucial to explain the emergence of altruism and the persistence of high levels of altruism requires strong costs of mobility.” Danchin, E., L. Giraldeau & F. Cezilly. Behavioural Ecology. 2008. Oxford University Press. P. 559.


“Group augmentation is an alternative to kin selection that can explain the evolution and persistence of altruism among unrelated individuals. Clutton-Brock suggested that group augmentation operates in most cooperatively breeding vertebrates and invertebrates because indirect benefits of altruism increase with group size. A larger group size is indeed often associated with a higher foraging success, predation avoidance, dispersal, or reproduction.” Danchin, E., L. Giraldeau & F. Cezilly. Behavioural Ecology. 2008. Oxford University Press. Pp. 561-2.


“Buss, Maynard Smith and Szathmary, and Michod each argued that the hierarchical organization of life (genes, chromosomes, cells, multicellular organisms, and societies) resulted from major evolutionary transitions driven by cooperation: cooperation among genes on the same chromosome, cooperation among cells within a multicellular organism, and cooperation among individuals within a cooperative group.” Danchin, E., L. Giraldeau & F. Cezilly. Behavioural Ecology. 2008. Oxford University Press. P. 566.


“Cooperation thus appears as a major evolutionary force that allows the emergence of integrated units capable of self replication and where conflicts between lower level units can be repressed.” Danchin, E., L. Giraldeau & F. Cezilly. Behavioural Ecology. 2008. Oxford University Press. P. 573.


“Whereas Darwin laid down the principle of speciation by natural selection, Buss, Maynard Smith and Szathmary, and Michod have all turned the evolution of cooperation into a central question for the study of the increasing complexity of life.” Danchin, E., L. Giraldeau & F. Cezilly. Behavioural Ecology. 2008. Oxford University Press. P. 574.


“All creatures with limbs, whether those limbs are wings, flippers, or hands, have a common design. One bone, the humerus in the arm or the femur in the leg, articulates with two bones, which attach to a series of small blobs, which connect with the fingers or toes. This pattern underlies the architecture of all limbs.” Shubin, Neil. Your Inner Fish: A Journey into the 3.5-billion-year History of the Human Body. 2008. Pantheon Books. P. 30.


“For our distant ancestors to go from single-celled creatures to bodied ones, as they did over a billion years ago, their cells had to utilize new mechanisms to work together. They needed to be able to communicate with one another. They needed to be able to stick together in new ways. And they needed to be able to make new things, such as the molecules that make our organs distinct. These features – the glue between cells, the ways cells can ‘talk’ to each other, and the molecules that cells make – constitute the toolkit needed to build all the different bodies we see on earth.” Shubin, Neil. Your Inner Fish: A Journey into the 3.5-billion-year History of the Human Body. 2008. Pantheon Books. P. 119.


“There are obvious advantages of becoming a creature with a large body: besides avoiding predators, animals with bodies can eat other, smaller creatures and actively move long distances. Both of these abilities allow the animals to have more control over their environment.” Shubin, Neil. Your Inner Fish: A Journey into the 3.5-billion-year History of the Human Body. 2008. Pantheon Books. P. 137.


“The number of odor genes has increased over time, from relatively few in primitive creatures such as jawless fish, to the enormous number seen in mammals. We mammals, with over a thousand of these genes, devote a huge part of our entire genetic apparatus just to smelling. Presumably, the more of these genes an animal has, the more acute its ability to discern different kinds of smells.” Shubin, Neil. Your Inner Fish: A Journey into the 3.5-billion-year History of the Human Body. 2008. Pantheon Books. P. 145.


“Humans devote about 3 percent of our genome to odor genes, just like every other mammal. When geneticists looked at the structure of the human genes in more detail, they found a big surprise: fully three hundred of these thousand genes are rendered completely functionless by mutations that have altered their structure beyond repair.” Shubin, Neil. Your Inner Fish: A Journey into the 3.5-billion-year History of the Human Body. 2008. Pantheon Books. P. 146.


“... so why have so many of our odor genes been knocked out? Yoav Gilad and his colleagues answered this question by comparing genes among different primates. He found that primates that develop color vision tend to have large numbers of knocked-out smell genes. The conclusion is clear. We humans are part of a lineage that has traded smell for sight. We now rely on vision more than on smell, and this is reflected in our genome. In this trade-off, our sense of smell was deemphasized, and many of our olfactory genes became functionless.” Shubin, Neil. Your Inner Fish: A Journey into the 3.5-billion-year History of the Human Body. 2008. Pantheon Books. P. 147.


“Monkeys that live in trees would benefit because color vision enabled them to discriminate better among many kinds of fruits and leaves and select the most nutritious among them. From studying the other primates that have color vision, we can estimate that our kind of color vision arose about 55 million years ago. At this time we find fossil evidence of changes in the composition of ancient forests. Before this time, the forests were rich in figs and palms, which are tasty but all of the same general color. Later forests had more of a diversity of plants, likely with different colors. It seems a good bet that the switch to color vision correlates with a switch from a monochromatic forest to one with a richer palette of colors in food.” Shubin, Neil. Your Inner Fish: A Journey into the 3.5-billion-year History of the Human Body. 2008. Pantheon Books. Pp. 153-4.


“The biological ‘law of everything’ is that every living thing on the planet had parents.” Shubin, Neil. Your Inner Fish: A Journey into the 3.5-billion-year History of the Human Body. 2008. Pantheon Books. P. 174.


“The centripetal nature of autocatalysis becomes evident as soon as we realize that any change in B is also likely to involve a change in the amounts of material and energy that flow to sustain B. In our Utricularia example, for instance, if the periphyton is starved for phosphorus and any change (or immigrant species) enables the film of algae to increase its activity by taking in more phosphorus, that change will be rewarded by the loop. From this, we perceive a tendency to reward and support those changes that bring ever more resources into B. As this circumstance pertains to all the other members of the feedback loops as well, any autocatalytic cycle becomes the center of a centripetal vortex, pulling as many resources as possible into its domain.” Ulanowicz, Robert. A Third Window: Natural Life beyond Newton and Darwin. 2009. Templeton Foundation Press. Pp. 70-1.


“... whenever two or more autocatalytic loops draw from the same pool of resources, it is their autocatalytic centripetality that induces competition between them. By way of example, we notice that, whenever two loops partially overlap, the outcome could be the exclusion of one of the loops.” Ulanowicz, Robert. A Third Window: Natural Life beyond Newton and Darwin. 2009. Templeton Foundation Press. P. 73.


“One should never lose sight of the fact that the autocatalytic scheme is predicated upon mutual beneficence or, more simply put, upon mutuality. Although facilitation in autocatalysis proceeds in only one direction, its outcome is, nevertheless, mutual in the sense that an advantage anywhere in the autocatalytic circuit propagates so as to share that advantage with all other participants. That competition derives from mutuality and not vice versa represents an important inversion in the ontology of actions.” Ulanowicz, Robert. A Third Window: Natural Life beyond Newton and Darwin. 2009. Templeton Foundation Press. P. 75.


“In order to facilitate legitimate analogies without invoking the specter of rigid top-down control, I have suggested that those ensemble living systems that exhibit organic-like behaviors, but are more flexible than organisms, be referred to as organic systems. That is, organic systems exhibit some degree of top-down selection and system coherence, but such influence is less strict and programmatic than what one encounters in organisms, where development of the system follows an inflexible script that usually includes the construction of an integument to surround itself.

“It appears, then, that top-down influence is a defining characteristic of higher-level systems, but reductionism appears to work well among the lower, less complicated levels of the physical realm.” Ulanowicz, Robert. A Third Window: Natural Life beyond Newton and Darwin. 2009. Templeton Foundation Press. Pp. 96-7.


“At its [process ecology’s] very core lie three fundamental postulates:

I. The operation of any system is vulnerable to disruption by chance events.
II. A process, via mediation by other processes, may be capable of influencing itself.
III. Systems differ from one another according to their history, some of which is recorded in their material configurations.” Ulanowicz, Robert. A Third Window: Natural Life beyond Newton and Darwin. 2009. Templeton Foundation Press. P. 115.


“The ecological scenario, however, differs from conventional evolutionary theory on three major points. First, selection in process ecology is distinctly an internal phenomenon, in that a major agency of selection (autocatalysis) acts entirely within the system boundaries. Darwin, to the contrary, was determined to place selection outside that which is undergoing selection (the organism). Second, under process ecology, systems are wont to exhibit a preferred direction proper to their own behavior. This concurs with observations elsewhere of directionality in nature. For example, Schneider and Sagan, Schneider and Kay, Salthe, and Chaisson all ascribe a preferred thermodynamical direction to the universe. Most neo-Darwinists, to the contrary, remain intent on exorcising any hint of directionality from their discourses. Third, process ecology holds mutuality to be essential and competition to be derivative of it, in stark contrast to the fundamental position of competition in conventional Darwinian narrative.” Ulanowicz, Robert. A Third Window: Natural Life beyond Newton and Darwin. 2009. Templeton Foundation Press. Pp. 128-9.


“We noted that chance, self-reference, and history all played roles in this simplest of artificial processes [Polya process - one each of red and blue balls in urn, upon drawing one out put it back in with another ball of same color; hovers around different ‘limits’]. That is, the three postulates we have formulated appear to go hand-in-glove with the very idea of process.” Ulanowicz, Robert. A Third Window: Natural Life beyond Newton and Darwin. 2009. Templeton Foundation Press. P. 129.


“We take the side of science in spite of the patent absurdity of some of its constructs, in spite of its failure to fulfill many of its extravagant promises of health and life, in spite of the tolerance of the scientific community for unsubstantiated just-so stories, because we have a prior commitment, a commitment to materialism. It is not that the methods and institutions of science somehow compel us to accept a material explanation of the phenomenal world, but, on the contrary, that we are forced by our a priori adherence to material causes to create an apparatus of investigation and a set of concepts that produce material explanations, no matter how counter-intuitive, no matter how mystifying to the uninitiated, ...” Lewontin, Richard. “Billions and billions of demons.” 1997. New York Review of Books. 44(1): 28-32, January 9. P. 31. Quoted in Ulanowicz, Robert. A Third Window: Natural Life beyond Newton and Darwin. 2009. Templeton Foundation Press. P. 135.
 

“Robert Rosen recalls the physicist’s approach, which denies that the mind can be the object of legitimate scientific study, since it cannot be identified with objective reality....

“He also remarks that biologists adopt a more narrow concept of objectivity: it should be independent not only from perceptive agents, but also from the environment: to explain wholes from parts, that is ‘objective,’ but parts in terms of wholes, that is not.  To put it another way: closed causal loops are forbidden in the ‘objective’ world.”  Erdi, Peter.  Complexity Explained.  Springer.  2008.  P. 132.
 

“A metabolic network is a directed and weighted tri-partite graph, whose three types of nodes are metabolites, reactions and enzymes, and two types of edges represent mass flow and catalytic regulation;”  Erdi, Peter.  Complexity Explained.  Springer.  2008.  P. 221.
 

“Most microorganisms display what in higher animals is termed attention.  A stentor or amoeba dislodged from a surface actively seeks a new site of attachment.  While engaged in this search it ignores other stimuli such as changes in temperature or chemical signals that produce an immediate reaction in a free-living individual.  Indeed, it is probably necessary for something like attention to exist, since it is usually impossible for a cell to react simultaneously to two or more kinds of stimuli.”  Bray, Dennis.  Wetware: A computer in Every Living Cell.  2009.  Yale University Press.  P. 18.
 

“Proteins provide the equivalent of muscles, skeleton, digestive system, and lungs.  They create networks of communication and logical machines–the substrate for the cell’s computations.  Where higher organisms have a brain and spinal cord, single cells have networks of interacting proteins.”  Bray, Dennis.  Wetware: A computer in Every Living Cell.  2009.  Yale University Press.  P. 226.
 

“Major locations of the cell have something analogous to a postal address.  Proteins destined to work in the nucleus, for example, contain distinctive sequences of amino acids rich in positively charged amino acids known as ‘nuclear import signals.’  These signatures are recognized by receptors in the nuclear membrane and the molecules conveyed forthwith into the nucleus.  Other targeting sequences exist for organelles such as mitochondria and for the many kinds of internal membrane found in eukaryotic cells.

“RNA molecules provide perhaps the most remarkable example.  Messenger RNA molecules are made in the nucleus.  They then move into the cytoplasm, where they are directed to specific locations according to sequences of bases at one end of the molecule.  These sequences do not code for amino acids and are not used to make protein; instead, they act as ZIP codes.  Their precision can be amazing, some RNAs finding their way to the ends of growing nerve cells, or to the synapses of a large pyramidal cell.

“Evidently something more than simple diffusion must be responsible.  A molecule the size of RNA would take weeks to diffuse from one end of a large nerve cell to the other.  What in fact happens is that motor proteins seize the RNA molecules and then carry them along microtubules.  Specific adapter proteins are needed to recognize the RNA, read its destination, and then attach it to a suitable motor protein heading in the desired direction.  Once the RNA cargo has reached the correct region of the cell, other proteins cause it to detach from the motor.  It begins its appointed task of making a protein.”  Bray, Dennis.  Wetware: A computer in Every Living Cell.  2009.  Yale University Press.  P. 229.
 

“As has been explored through computer simulations and some laboratory experiments, autocatalytic cycles can complexify over time to achieve a condition of catalytic closure in which all components of a complex chemical system, including the catalysts, are produced by at least one reaction of the network.  Such complexification occurs when matter/energy fluxes exceed certain critical values, resulting in the emergence of macroscopic structures that more effectively dissipate energy (entropy) than microscopic processes.  Hurricanes, Benard cells, the Belousov-Zhabotinskii reaction, living cells, and ecosystems are all examples of dissipative structures that arise by processes of self–(or more accurately system-) organization.  Many lines of empirical evidence demonstrate that self-organization is a phenomenon, and not just a mathematical concept, of cellular organization.  Patterns of cellular and subcellular order and complexity reflect constraints of chemistry and natural laws, including those being studied by complex systems dynamics.”  Weber, Bruce.  “What is Life?  Defining Life in the Context of Emergent Complexity.”  Origin of Life in the Evolving Biosphere.  (2010) 40:221-229.  February 19, 2010.  P. 223.
 

“Three kinds of emergence can be distinguished in complex systems.  First-order emergence is just the synchronic supervenience of the macroscopic on the microscopic, as in wave propagation in fluid; second-order emergence is diachronic self-organization of energy dissipative systems, such as a snowflake or the Belousov-Zhabotinskii reaction; third-order emergence is diachronic with biasing across iterations or generations, as in biological development and evolution.”  Weber, Bruce.  “What is Life?  Defining Life in the Context of Emergent Complexity.”  Origin of Life in the Evolving Biosphere.  (2010) 40:221-229.  February 19, 2010.  P. 224.
 

“Though thermodynamics provides the driving force for self-organization in complex chemical systems, it is the kinetic mechanisms that afford the pathways of emergence.  In the transition to living systems there is a shift to an extreme expression of kinetic control in which thermodynamic requirements play a supporting rather than a directing role.  Replication is an instance of this extreme kinetic control.  From this emerges the teleonomic character of living entities.  Non-living chemical reactions, driven by thermodynamics, explore the state space in an ergodic fashion; in contrast, living systems explore a combinatorially large space of possibilities through evolutionary processes.”  Weber, Bruce.  “What is Life?  Defining Life in the Context of Emergent Complexity.”  Origin of Life in the Evolving Biosphere.  (2010) 40:221-229.  February 19, 2010.  P. 226.
 

“In complex systems, such as those that gave rise to living systems, not only is the whole defined by closure conditions (physical and catalytic) but there is redundancy and parallelism.  Thus, even weakly incipient functional patterns of structure and interaction can persist due to greater stability and/or efficiency. With functionality comes pressure for improved structures/stability/efficiency, through an on-going process of selection and self-organization.  Therefore, in thinking about the origin of life we should not expect one function to be perfected, say replication, before others appear.  Rather, we should expect that there was an inherent holism in the process by which cellular life arose.  Rather than expect that we can develop a single narrative trajectory for the emergence of life we should explore all possible routes of chemistry and proto-biochemistry to develop a range of plausible scenarios, as well as keeping in view the range of phenomena associated with living systems.”  Weber, Bruce.  “What is Life?  Defining Life in the Context of Emergent Complexity.”  Origin of Life in the Evolving Biosphere.  (2010) 40:221-229.  February 19, 2010.  Pp. 226-7.
 

“There is no doubt, however, that many animals, even though they can be assigned to different groups, share a sort of ‘syntax of the body,’ in which it is possible to discern a main axis, with the mouth (and possibly the brain) at one of the two extremities.”  Minelli, Alessandro.  Forms of Becoming: The Evolutionary Biology of Development.  2009.  Princeton University Press.  P. 38.
 

“The zootype is the topographical plan according to which the different organs are distributed along the main body axis of all animals–or, to be more precise, along the main body axis of all animals with bilateral symmetry....”

“In these animals, the front is the extremity with which the animal always enters new locations, and the top is the side opposite the one the animal, if it moves on the ocean floor or on the ground, uses to remain in contact with the substrate.  In these animals, therefore, we recognize a main body axis, which seems to be ‘the same’ in all of them, and not only because in our descriptions we use an identical vocabulary (front, back, top, bottom, etc.), but precisely because, along this axis, different positions are marked by the borders of the areas in which the same hox genes are expressed.  All bilateral animals would therefore seem to have essentially the same set of hox genes and in all bilateral animals these genes would be expressed in the same early phase of embryo development.  Finally the proteins codified by these genes would be distributed along the anteroposterior axis of all these animals in a characteristic and basically unmodified fashion, thus defining basically invariable positions within all Bilateria.  In other words it is precisely the presence of these genes and the typical spatial distribution of their products that form the basic plan for the animal’s organization.  And this is what has been called the zootype.”  Minelli, Alessandro.  Forms of Becoming: The Evolutionary Biology of Development.  2009.  Princeton University Press.  Pp. 47-8.
 

“We also must resign ourselves to the fact that many other living beings, both plants and animals, have a more richly endowed genome than ours.”  Minelli, Alessandro.  Forms of Becoming: The Evolutionary Biology of Development.  2009.  Princeton University Press.  Pp. 50-1.
 

“A single organ endowed with a complex structure can involve the expression of a great number of genes: in the case of a Drosophila’s eye the estimate is about 2,500, which would correspond to about 18 percent of the total number present in the insect’s genome.  Naturally, of the many genes that may have a role in the realization of an organ, only a small fraction are expressed solely in this organ,...”  Minelli, Alessandro.  Forms of Becoming: The Evolutionary Biology of Development.  2009.  Princeton University Press.  P. 51.
 

“Taking development seriously means to finally stop viewing it as the process that prepares the animal or plant for its adult existence ...”  Minelli, Alessandro.  Forms of Becoming: The Evolutionary Biology of Development.  2009.  Princeton University Press.  P. 89.
 

“The metamorphoses that these larvae undergo are, in some cases, even more catastrophic than those that affected the butterfly’s caterpillar or Drosophila’s larva.  In the case of the sea urchin, the larva is a small gelatinous and transparent thing exhibiting bilateral symmetry.  The larvae contain a little group of cells that for a while seems to remain at rest, excluded from the vital functions (locomotion, nutrition, interactive life) of the larvae, but that at a certain point begins to grow, soon revealing the characteristic five-ray symmetry characteristic of the sea urchin.  This predecessor of the future adult grows rapidly, to the detriment of the larval structures, which are soon reduced to a residue that is destined to disappear completely.  One could almost say that the adult has used the larva like a parasite (or, better, a parasitoid) uses its victim.”  Minelli, Alessandro.  Forms of Becoming: The Evolutionary Biology of Development.  2009.  Princeton University Press.  Pp. 149-50.
 

“It is not easy, therefore to foresee the degree of difficulty represented in nature’s passing from one form to another.  No one would have imagined that it is easy for a scolopendra to pass from twenty-one to twenty-three pairs of legs, or vice versa, whereas a trunk with twenty-two pairs seems really out of reach.  Nobody would have imagined that mammals can easily evolve necks of different length by modifying only the shape, but not the number, of their cervical vertebrae.

“Evolutionary transitions from one form to the other are a little like the movements of chess pieces. Only by knowing the rules of the game can we understand which squares a knight can reach by moving from its current position, and which squares, instead, can be reached by a bishop or a rook in a certain number of moves.”  Minelli, Alessandro.  Forms of Becoming: The Evolutionary Biology of Development.  2009.  Princeton University Press.  Pp. 205-6.
 

“... the Sun has increased by 30% in luminosity over 5 X 109 years, while the CO2 cover has decreased more that 10-fold, and considerable amounts of methane may have been introduced by early life.  The curious and fortuitous fact (known as the ‘faint young Sun paradox’) is that the combination of the changes of the atmosphere, of CO2 and probably CH4 especially, and of the Sun have been compensatory in total energy capture by the surface, so that over the whole period of existence of the cool planet, Earth, the surface temperature has been fixed within narrow limits of 300 + 30 K.”  Williams, R.J.P. & J.J.R. Frausto da Silva.  The Chemistry of Evolution: The Development of our Ecosystem.  2006.  Elsevier.  P. 6.
 

“We shall have to distinguish clearly, therefore, between thermodynamic stability of a compound, meaning that it cannot change unless exposed to changed conditions, and kinetic stability, meaning that it should change spontaneously but is prevented from doing so by a barrier.  The very nature of the different atoms decides both their thermodynamic and kinetic properties in compounds.”  Williams, R.J.P. & J.J.R. Frausto da Silva.  The Chemistry of Evolution: The Development of our Ecosystem.  2006.  Elsevier.  P. 37.
 

“Some of the most stable light nuclei are based on multiples of mass 4, two protons and two neutrons of almost equal mass, e.g. carbon, atomic mass 12 (6 of each) and oxygen, atomic mass 16 (8 of each), while heavier elements require a larger ratio of neutrons to protons, e.g. Fe, 26 protons and 30 neutrons.”  Williams, R.J.P. & J.J.R. Frausto da Silva.  The Chemistry of Evolution: The Development of our Ecosystem.  2006.  Elsevier.  P. 37.
 

“The non-metals and the non-metal/non-metal compounds concerned here are formed stoichiometrically through covalent bonds between atoms and are very different from salts.  Such bonds are a means of satisfying the electron demand by nuclei to reach a noble gas complement through sharing electrons in pairs between atoms so that they form molecular structures with shapes....”

“These combinations are relatively inert, like Ne, so that they show kinetic, not thermodynamic, stability even in the presence of oxygen and water with which they should react. (It is the resistance to reaction that has allowed the chemistry of organisms to appear.)”  Williams, R.J.P. & J.J.R. Frausto da Silva.  The Chemistry of Evolution: The Development of our Ecosystem.  2006.  Elsevier.  P. 43.
 

“For the non-metals, the variations in combination arise from the kinetic stability of many compounds.  The obvious examples are the two oxides of carbon, CO and CO2.  In CO, carbon has retained some electrons to itself while sharing with others.  The oxide of nitrogen NO, equivalent combining ratio 2, contrasts with the hydride NH3 combining ratio 3; the hydride of sulfur H2S is very different in combining ratio from that in the two oxides SO2 and SO3.  We refer in these different kinetically or thermodynamically stable combinations to the oxidised states of elements when oxygen (or halides) is involved, or to the reduced states of elements when hydrogen is involved, and where H2O is treated as neutral.”  Williams, R.J.P. & J.J.R. Frausto da Silva.  The Chemistry of Evolution: The Development of our Ecosystem.  2006.  Elsevier.  P. 47.
 

“In discussing evolution of the inorganic chemicals and geochemistry, we must always remember that in the (buried) non-equilibrated state there is a huge reserve of energy in the Earth, which could be transferred to surface (biological) chemistry at any time with possible disastrous consequences.”  Williams, R.J.P. & J.J.R. Frausto da Silva.  The Chemistry of Evolution: The Development of our Ecosystem.  2006.  Elsevier.  P. 54.
 

“A temperature of 300 K is essential in two respects: water is kept as a liquid and the rate of change of organic chemicals is very slow in the absence of catalysts.  The second point implies that, ... biological change is almost invariably under the control of the catalysts.”  Williams, R.J.P. & J.J.R. Frausto da Silva.  The Chemistry of Evolution: The Development of our Ecosystem.  2006.  Elsevier.  P. 62.
 

“To be most useful in catalysis, usually by metal ions, the catalyst should have oxidation potentials close to those of the organic reaction to be catalysed.  When the environment became oxidising, a quite different set of redox potentials of compounds arose and quite different metal catalysts were necessary.  The levels of redox potentials of metal ions are managed by the organic ligands which bind them.  Organic and inorganic chemistry in life had to develop together.”  Williams, R.J.P. & J.J.R. Frausto da Silva.  The Chemistry of Evolution: The Development of our Ecosystem.  2006.  Elsevier.  P. 70.
 

“Experience shows that there are also other observable conditions of materials besides this variety of stable equilibrium states.  One is a frozen metastable state such as we observe in organic chemicals, many in biological cells, in air, or when we isolate 100% NH3 at any temperature as mentioned above.  They should change but they do not.  All organic chemicals should react with oxygen and should change but they do not.  All organic chemicals should react with oxygen and all NH3 should decompose (be oxidised) to some extent.  Metastable states are in stationary energised states, not in equilibrium, trapped by kinetic barriers to change.”  Williams, R.J.P. & J.J.R. Frausto da Silva.  The Chemistry of Evolution: The Development of our Ecosystem.  2006.  Elsevier.  P. 82.
 

“Study of ordered, even energised, structure alone, as in much of molecular biology, cannot describe living organisms since that study is mostly of static molecular structure, order, in isolated molecules (not of their states) and not of the essential controlled flow within boundaries, organisation.”  Williams, R.J.P. & J.J.R. Frausto da Silva.  The Chemistry of Evolution: The Development of our Ecosystem.  2006.  Elsevier.  P. 84.
 

“The distinction (between bi-directional arrows that are straight for equilibrium reactions vs curved to represent cyclic steady state with separated flows) we are making is very important since the rates of going from one side of the equation to the other in an equilibrium condition are equally altered by catalysts – they cross the same barrier.  In effect, catalysts are substances which increase both forward and back reaction rates but are not changed overall in themselves so that the equilibrium composition does not change.  In a cyclic steady state away from equilibrium added catalysts can change one rate, say forward, relative to the other, say backward, when the composition of the whole cyclic steady state changes.  We shall be mainly concerned in this book with the evolution towards a catalysed cyclic steady state, that of the total Earth ecosystem and therefore with rates of both forward and back reactions separately in which different catalysts can be used.  It is ‘element neutral’ and non-polluting if fully cyclic.”  Williams, R.J.P. & J.J.R. Frausto da Silva.  The Chemistry of Evolution: The Development of our Ecosystem.  2006.  Elsevier.  P. 86.
 

“The general chemical effect of energy absorption is to create charge separation, ie. Separation of oxidised and reduced materials.  To all intents and purposes, therefore, the expanded ecological evolution which has occurred on the Earth’s surface can only be due to its increasing absorption of energy causing redox separation as is seen between organisms (reduced) and the environment (oxidised).”  Williams, R.J.P. & J.J.R. Frausto da Silva.  The Chemistry of Evolution: The Development of our Ecosystem.  2006.  Elsevier.  P. 98.
 

“It is very important to observe that each chemical can have an energy and information content related to its bonds, its concentration and the fields to which it is subjected.”  Williams, R.J.P. & J.J.R. Frausto da Silva.  The Chemistry of Evolution: The Development of our Ecosystem.  2006.  Elsevier.  P. 112.
 

“For information to be used in an organism there needs to be a source in cells of releasable chemical or physical messengers and responsive receivers, receptors, which recognise by binding, as well as energy supplies in order to store and respond.  Information is a quality embedded in these relationships.”  Williams, R.J.P. & J.J.R. Frausto da Silva.  The Chemistry of Evolution: The Development of our Ecosystem.  2006.  Elsevier.  P. 112.
 

“... we shall describe cellular evolution as being at all times within an energised advancing environment.  Now the organisms evolved (a) in chemical content and use of chemicals, (b) in the ways they obtained and used energy, (c) in the space they occupied, and (d) in their organisation.”  Williams, R.J.P. & J.J.R. Frausto da Silva.  The Chemistry of Evolution: The Development of our Ecosystem.  2006.  Elsevier.  P. 127.
 

“By using the word chemotype, as opposed to genotype, we are therefore using an all-embracing thermodynamic concept based in part upon the concentrations of elements in the energised genome, the proteome, the metabolome and the metallome.  As stated we are then forced to describe also the spaces (volumes) which are under consideration, the energy which is put into both compounds and concentrations since many of the elements are not in equilibrium with their surroundings, as well as the internal organisation, and any relationship to the environment.”  Williams, R.J.P. & J.J.R. Frausto da Silva.  The Chemistry of Evolution: The Development of our Ecosystem.  2006.  Elsevier.  P. 131.
 

“Now, in any cellular system, the very selective catalysts in the cell, the enzymes, act like local field gradients in that they direct internal reaction paths along selected routes.  These routes may have controlled inputs of energy and controlled rates due to feedback.  All these properties are products of binding interactions, effectively local field constraints.  It is these enzymes together with filaments and membranes which ‘structure’ the internal flow of synthesis and degradation.”  Williams, R.J.P. & J.J.R. Frausto da Silva.  The Chemistry of Evolution: The Development of our Ecosystem.  2006.  Elsevier.  P. 155.
 

“The non-metals [C, H, O, N, S, P] above were trapped in kinetically stable organic compounds, while free concentrations of metal ions are trapped as such by pumping into or out of cells and there they frequently equilibrate with partners internally or externally.  Their concentrations as free ions are very specially controlled in compartmental kinetic traps described in Chapter 5.  A very important but obvious use is in structures, e.g. of Mg/K in DNA/RNA, of Ca, Mg and Zn in some proteins, and of Ca in polysaccharides and membrane surfaces, but their most striking value is in catalysis and controls.  Without metal ion properties cellular life could not exist.”  Williams, R.J.P. & J.J.R. Frausto da Silva.  The Chemistry of Evolution: The Development of our Ecosystem.  2006.  Elsevier.  P. 170.
 

“Again and again, we have to consider if these uses of elements in various mechanisms and pathways were the only possible ways for the system we call life to evolve, given environmental availability.  The matching of function with the known chemical potentialities of the elements is extremely suggestive that there was but one effective way.”  Williams, R.J.P. & J.J.R. Frausto da Silva.  The Chemistry of Evolution: The Development of our Ecosystem.  2006.  Elsevier.  P. 173.
 

“In fact, the almost fixed ionic composition of cell cytoplasm of the vast majority of organisms, ancient and modern, is a remarkable feature of evolution.”  Williams, R.J.P. & J.J.R. Frausto da Silva.  The Chemistry of Evolution: The Development of our Ecosystem.  2006.  Elsevier.  P. 174.
 

“We shall note again and again the progression in evolution from recognition and rejection of a poison, e.g. Na+, Ca+, Mn2+, Cu2+(Cu+), and Cl-, to its later functional value, often of its gradients.  In conclusion, we stress that the control of concentrations of about 12 metal ions is an essential requirement of all organisms and is a thermodynamic feature different in different chemotypes.  Williams, R.J.P. & J.J.R. Frausto da Silva.  The Chemistry of Evolution: The Development of our Ecosystem.  2006.  Elsevier.  P. 176.
 

“As the environment and possible use of it and energy became more varied, different chemotypes evolved to reduce the need for extra complexity in one cell and increase complexity in the sum of the many interactive chemotypes.”  Williams, R.J.P. & J.J.R. Frausto da Silva.  The Chemistry of Evolution: The Development of our Ecosystem.  2006.  Elsevier.  P. 195.
 

“As the partial pressure of molecular oxygen increased further some 2 X 109 years ago then O2 itself became a very useful cellular source of energy in the oxidation of reduced materials, e.g. of debris.  These materials included not only sources of hydrogen from organic carbon compounds but also the reduced compounds of nitrogen and sulfur.  The new organisms are true aerobes.  Looking at all oxidative processes, and remembering that cellular chemistry is essentially reductive, we observe that initial oxidations are of environmental chemicals.  Evolution then generated cellular oxidation using these oxidised chemicals of the environment ultimately as energy aids to reductive growth, by oxidation of some of their own reduced chemicals and those of their debris faster than the same steps 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. 253.
 

“As already stated, all prokaryotes faced a problem with the introduction of oxidation reactions since one of their major compartments had to be reducing in nature.  Due to oxidation of the environment their cytoplasm, as noted before, also faced the problem of new metal ions dangerously competitive with internal Mg2+ and Fe2+ functions.  Yet, as explained, it is useful for cells to use oxidation to gain extra energy and to use certain novel metal enzymes to assist in these reactions.  Considerable risks to basic processes are also present, for example reduction of N2 to NH3, which must be cytoplasmic, is extremely sensitive to oxygen.  We find then that many bacteria (and other organisms) that use oxygen do not carry out protein synthesis without an external supply of directly usable nitrogen.  Quite interestingly we also find bacteria using oxidised products such as sulfate, ferric ions or nitrate as distinct species.  Effectively these bacteria are all mutually beneficial, separate chemical ‘compartments’.  Note again the highly convoluted membranes of many bacteria, which could help to localise reactions in effectively isolated compartments and which become real physically separate compartments in eukaryotes, but the limited size of a bacterial cell and the constraint of the walls are severe restrictions on more extensive development of such internal spaces.”  Williams, R.J.P. & J.J.R. Frausto da Silva.  The Chemistry of Evolution: The Development of our Ecosystem.  2006.  Elsevier.  Pp. 263-4.
 

“The demand to cope with and then make use of the increasingly available chemistry of oxygen, while maintaining the necessity of central reductive chemistry of the cytoplasm, increased the number of compartments essential for efficient energy and material management in a single cell.  The limited size and structure of the earlier prokaryotes, anaerobic or aerobic, left little space for such development in one cell, while all eukaryotes are large cells, 10 to 100 μm, allowing several compartments.  Their large size and a new strong but flexible membrane enabled them to dispense with a limiting cell wall and to digest large molecules, particles and even bacteria.  We conclude that this together with the greater number of compartments of eukaryotes, and hence, as we shall show, greater energy and chemical effectiveness, allowed the eukaryotes to evolve and survive alongside aerobic prokaryotes in an oxygen atmosphere despite slower reproductive and adaptive rates and hence a larger possibility of being attacked.”  Williams, R.J.P. & J.J.R. Frausto da Silva.  The Chemistry of Evolution: The Development of our Ecosystem.  2006.  Elsevier.  P. 280.
 

“In conclusion, the differential distribution of elements in different compartments is very marked but is little known.”  Williams, R.J.P. & J.J.R. Frausto da Silva.  The Chemistry of Evolution: The Development of our Ecosystem.  2006.  Elsevier.  P. 297.
 

“A central feature of evolution is the extension of organisation to larger and larger volumes, so that slowly the surface geosphere and the biosphere are interacting to become one thermodynamic whole – the ultimate aim of a steady state of optimal energy retention and degradation.”  Williams, R.J.P. & J.J.R. Frausto da Silva.  The Chemistry of Evolution: The Development of our Ecosystem.  2006.  Elsevier.  Pp. 298-9.
 

“The use of the calcium ion is ideal for its purpose as a messenger in that a gradient of some 104, inside close to 10-7 M, outside 10-3 M, was established at the very beginning of prokaryote life of necessity.  [There was little or no need for the use of Ca2+ as a messenger in prokaryotes since their short life made reproduction dominant over the complexity of response to environmental challenges.]  Free Ca2+ concentrations in vesicles are often 10-3 M, and much is stored there is rapid exchange so that Ca2+ can be released from these vesicles as an amplification of input from outside.  Now the rates of calcium binding to a target are very fast, say 10-9 s.  So for a binding constant of 106 M-1 the off-rate from the target is 10-3 s, a millisecond, which is long enough and the binding of Ca2+ is strong (energetic) enough to bring about a protein conformation change inside cells.  This rate, a millisecond, then became a fundamental restriction on all eukaryote biological transformation due to the properties of the calcium ion and proteins....

“Of the ions that could cause conformation changes, only Mg2+ is in high enough concentration and binds strongly enough, but it undergoes rather slow exchange and has too small a gradient across a membrane to be of much use as a signal....

“An important point to note here and elsewhere in the description of cell activity is that the particular nature of calcium biochemistry, including the availability of the element and its necessary rejection from the prokaryote cell, when linked to stimulated input and interaction with specific internal proteins of selected properties, made it uniquely suitable for the function as an elementary ionic fast in/out messenger.  It was then capable of signalling to cell changes once cell size and organisation increased beyond the elementary level of a cell with one small, rapidly reproduced, internal compartment.  No other element has the same inherent and environmental properties.  The genetic machinery of eukaryotes had to discover the value of this calcium chemistry and to code the proteins involved with it. It is not just a matter of random mutation but of opportunity meeting necessity as this was an inevitable advance if optimal energy capture and use in chemistry was to be secured within organisation of a large, environment sensitive organism.”  Williams, R.J.P. & J.J.R. Frausto da Silva.  The Chemistry of Evolution: The Development of our Ecosystem.  2006.  Elsevier.  Pp. 303-5.
 

“... much of evolution can be followed through gene sequences, but this discussion often appears as if it is an analysis of random events which dominates the selection of the ‘fittest’ species.  This leaves the impression that there is no rational explanation of the general development of life and to the limits of biological evolution towards ecological fitness.  Our stance does not question that this description of the random origin of species is correct, we believe it is, but we consider that the species-embracing chemotypes and their divisions, which include very large groups of species in well-separated classes of organisms, have developed differently in an inevitable logical sequence forced by equilibrium thermodynamic environmental, and largely kinetically controlled life chemistry.”  Williams, R.J.P. & J.J.R. Frausto da Silva.  The Chemistry of Evolution: The Development of our Ecosystem.  2006.  Elsevier.  P. 307.
 

“These new structures [glycosylated proteins forming with sugars meshes in the extracellular mesh] and certain other new extracellular proteins which have little fixed fold, ‘random’ structures, allow the properties associated with dynamic properties of the whole organism.  The understanding of their functions is not so much related to chemical as to physical properties such as elasticity, ability to withstand direct stress and strain.  Note that many of these developments occur in the extensive endoplasmic reticulum or other vesicles before exocytosis.  We stress that they all originate from increase in oxidation and the use of particularly a novel element copper, in this extracellular oxidation.

“In plants and fungi, the extracellular matrices are more generally of polysaccharides, although they are present in animals too.  The polysaccharides are modified celluloses, etc. and are often cross-linked by calcium ions.”  Williams, R.J.P. & J.J.R. Frausto da Silva.  The Chemistry of Evolution: The Development of our Ecosystem.  2006.  Elsevier.  Pp. 336-7.
 

“Now, when we come to consider modes of information exchange by messengers between cells in multi-cellular organisms we have to recognise that they must be chemically different from those already in use in the cytoplasm of all cells and from Ca2+ utilised by all eukaryote cells to give information about the nature of the immediate external environment of a given cell which is now the extracellular fluid with a fixed Ca2+ concentration.  These signalling systems remain essential for the multi-cellular organisms but have to be coupled to several novel chemical messengers for long-range, cell-cell communication, in which a selective message is sent out from one particular cell or organ to another in the extracellular fluids.  The choice of these messengers was limited to organic molecules since all simple inorganic ions which can perform message functions – diffuse and then bind – have been used earlier in evolution mostly internally, e.g. organic phosphates, iron, and magnesium and so on, and there are many cell types which must receive different messengers....

“The two types of messengers are: (i) hormones (morphogens) for long-term management and (ii) transmitters which could cause a rapid response in metabolism through coupling to pre-existing local outside/inside message systems.”  Williams, R.J.P. & J.J.R. Frausto da Silva.  The Chemistry of Evolution: The Development of our Ecosystem.  2006.  Elsevier.  Pp. 345-6.
 

“Plants, as we have seen in Chapter 8, cannot gain easy access to all the elements even for their own lifestyle, nor can they scavenge their own debris.  Consequently, plant life had to be supported by better collectors and scavengers to complete the biological cycle....

“As plant life has developed to what may be close to an optimal condition of light capture, animal and fungal life had increased to keep pace with the needs of plants and the opportunities of debris consumption.”  Williams, R.J.P. & J.J.R. Frausto da Silva.  The Chemistry of Evolution: The Development of our Ecosystem.  2006.  Elsevier.  Pp. 366-7.
 

“We can see, with hindsight again, that this use [the development of nerve cell chemistry] of elementary chemistry, conduction by chemically innocuous ions – and electrolytic physical currents-connected to previously devised flux of Ca2+ and chemical binding agents was inevitable, given the pressures to increase scavenging.  Once the demands of osmotic and electrical neutrality of the first prokaryote cells forced energy to be used to create physical gradients of these ions, Na+, K+ and Cl-, evolution was almost bound to use them sooner or later in messages as organisation increased in size.  It waited upon organisational need in large scavengers for them to be used coordinatively, since in single cells this kind of communication had no advantage.  The choice of calcium and then of organic transmitters at synaptic terminals was also virtually inevitable since they must be small (for fast diffusion), charged or polar so as to be retained in vesicles or held outside cells, bind relatively strongly and must not be substrates of the main metabolism.  Note that the order of the use of messengers in evolution follows the order of organisational complexity: (a) single small cells, prokaryotes, Mg2+, Fe2+ and internal organic transcription factors especially phosphates; (b) larger single eukaryote cells with added calcium internal/external messengers connecting to extra-internal organic factors, especially phosphates; (c) multi-cell eukaryotes with added organic molecules external to and going between cells but stored in the organism, as well as the above Ca2+ and internal transmitters, and finally (d) all of these messengers were combined together with Na/K ionic transmission in advanced animals.”  Williams, R.J.P. & J.J.R. Frausto da Silva.  The Chemistry of Evolution: The Development of our Ecosystem.  2006.  Elsevier.  P. 372.
 

“While there is this dependence in humans on energy, elements and compounds from external organisms there is also a direct dependence upon ‘internal’ organisms.  It is said that the human body has at least as many cells coded with non-human DNA as with human DNA.  Many of the internal organisms living symbiotically in the human body are needed for digestion and protection: that is essential bacteria and unicellular eukaryotes.  The ‘wrong foreign’ organisms (and viruses) internally are the causes of many diseases, but it is clear that every human being is internally an ‘ecosystem’ of required internal organisms and is also dependent upon a vast external ecosystem of organisms, plants and animals, which in turn depend upon other organisms down to prokaryotes: anaerobic and aerobic.”  Williams, R.J.P. & J.J.R. Frausto da Silva.  The Chemistry of Evolution: The Development of our Ecosystem.  2006.  Elsevier.  P. 397.
 

“The term Chemotype is not just analytically descriptive but includes concentrations, energy content, space limitations and organisation, and is therefore a comprehensive thermodynamic description.  We have shown that evolution is not constrained by the changing information in coded molecules, which had to follow rather than lead change, but depends upon an ever wider ability of organisms in the ecosystem to sense, obtain information about, and then exploit both changing environmental materials and energy sources not just internally but, finally, also externally.  The whole system is an inevitable, not a random, development and is a cooperative ecosystem of energy stored in chemicals both in cells and 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. 421.
 

“We return now to our physical/chemical view of evolution.  In the above molecular descriptive correlation between the organisms and genetic information seven important physical/chemical changes with time are missing: (i) the exposure to the observed gradual switch to an increasing presence in the environment of oxidised chemicals; (ii) the sequential increase and use of the chemical and energy stores in chemicals in organisms; (iii) the way increasing energy is put selectively into changing patterns of cellular reactions against a fixed background of biopolymer synthesis in different organisms; (iv) the gradual introduction of new compartments, the extension of cellular organisation in space with time; (v) the increasing complexity of the management of the changing flow of chemicals in the organisms; (vi) the increasing total uptake and degradation of energy in the ecosystem as organisms increasingly synthesise chemicals and establish chemical gradients which are then degraded, all approaching a total cyclic steady state, and (vii) the increasing ability to do work as seen in the switch from single molecular machines in the simplest cells to the cooperative activities of many such machines in more complicated single cells, to the synchronised activities of macro-machines in multi-cellular organisms, and finally to large macro-machines devised by mankind and operating external to cells in and on the environment.”   Williams, R.J.P. & J.J.R. Frausto da Silva.  The Chemistry of Evolution: The Development of our Ecosystem.  2006.  Elsevier.  Pp. 426-7.
 

“We believe we have demonstrated that this is a general rule for systems which absorb energy: they optimalise the rate of thermal entropy production.  The rule is in accord with the second law of equilibrium thermodynamics but relates to kinetic, not equilibrium thermodynamic, factors.  It follows that evolution must have an inevitable direction toward a cyclic steady-state condition which simultaneously optimalises use of the materials and degradation of the energy of the environment in this process.”  Williams, R.J.P. & J.J.R. Frausto da Silva.  The Chemistry of Evolution: The Development of our Ecosystem.  2006.  Elsevier.  P. 427.
 

“Life is then seen as a catalyst of energy degradation, thermal entropy production.”  Williams, R.J.P. & J.J.R. Frausto da Silva.  The Chemistry of Evolution: The Development of our Ecosystem.  2006.  Elsevier.  P. 428.
 

“We turn now to a more detailed account of the four major directional thermodynamic characteristics of the evolution of the ecosystem which incorporate the seven features of change which we noted above.  They are:

 

(1)             the chemical composition changes in the environment and in organisms;

(2)             the increase in energy utilised by the organisms;

(3)             the increasing use of space by organisms including eventually the space outside the bodies of the organisms;

(4)             the changing pattern of organisation required to manage (1)–(3).”

 Williams, R.J.P. & J.J.R. Frausto da Silva.  The Chemistry of Evolution: The Development of our Ecosystem.  2006.  Elsevier.  P. 429.
 

“During the long period since the Earth was formed the ecosystem has lost available quantities of carbon and some nitrogen, but much of both elements has been retained inside life and in the case of carbon much is also locked in coal, oil and gas as well as in carbonates.  There is then a compensation in that these stores and life itself have prevented greater loss of CO2 (and N2) from the atmosphere.  Insofar as man is bringing back stored carbon into circulation as CO2, he is in fact restoring the cycling of this element in line with the drive of evolution.  That this produces an upward fluctuation in temperature may be a disaster for human population, a problem for this one species, but may not be so for the slow advance of the ecosystem as an energy-capturing system.”  Williams, R.J.P. & J.J.R. Frausto da Silva.  The Chemistry of Evolution: The Development of our Ecosystem.  2006.  Elsevier.  Pp. 430-1.
 

“Understanding of physics and chemistry, needed to develop increased external organisation, led to the very fast development of new chemistry, new compartmental structures, new energy sources and uses, new transport and message systems and new information storage by mankind, e.g. in computers, but the basic nature of this development is no more than a remarkably fast and large addition to all previous steps in evolution.”  Williams, R.J.P. & J.J.R. Frausto da Silva.  The Chemistry of Evolution: The Development of our Ecosystem.  2006.  Elsevier.  P. 438.
 

“As we have stressed, as organisation in cell communities evolved; earlier chemotypes did not disappear but the old and the new assisted each another in an ecosystem.  Hence, evolution of different biological genotypes changed by chance variation in time while competing, but organisms moved forward within different chemotypes (of multiple species) increasingly together and interactively.”  Williams, R.J.P. & J.J.R. Frausto da Silva.  The Chemistry of Evolution: The Development of our Ecosystem.  2006.  Elsevier.  P. 439.
 

“Looking at evolution of organisation of cells from its beginning to the present in what is considered to be separate organisms, at first of single cells, we see that from the earliest times to the present day organisation and specialisation within a whole, internal cells and cells in different organisms, have increased.  The organisation needs structures in the two senses of stationary frameworks and dynamic potential energy constraints.  For maintenance of flow, and more so for growth with communication in the organisations, more and more energy is trapped in devices (made eventually from elementary chemicals) which are useful to the whole.”  Williams, R.J.P. & J.J.R. Frausto da Silva.  The Chemistry of Evolution: The Development of our Ecosystem.  2006.  Elsevier.  Pp. 439-40.
 

“... we believe we have demonstrated that three of the thermodynamic characteristics of chemotypes (components with their concentrations, the space they use, and their organisation) have evolved systematically and inevitably following the equally inevitable changes of the environment.  The other possible variables, external energy input, temperature and pressure, which characterise a dynamic flow system, have remained approximately fixed.”  Williams, R.J.P. & J.J.R. Frausto da Silva.  The Chemistry of Evolution: The Development of our Ecosystem.  2006.  Elsevier.  P. 442.
 

“Using our approach we cannot allow separation of cognitive from metabolic activity as an excuse for removing human kind from general evolution as some biologists appear to wish to do since we are analysing by continuous chemical thermodynamics.  Human beings present as great a change in evolution of chemotypes in 10,000 years as in the preceding four billion and in one sense they were predictable with hindsight.  They seem to represent the last steps of the expansion of cooperation from energised chemistry inside organisms to that outside them.”  Williams, R.J.P. & J.J.R. Frausto da Silva.  The Chemistry of Evolution: The Development of our Ecosystem.  2006.  Elsevier.  P. 449.
 

“One major point is that development is based on access to new chemicals and new energy sources together with new space and organisation and the necessary communication systems, that is in exactly the same way as all previous biological evolution, to aid survival while generating heat.”  Williams, R.J.P. & J.J.R. Frausto da Silva.  The Chemistry of Evolution: The Development of our Ecosystem.  2006.  Elsevier.  P. 449.
 

“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. (2007) 44, 167-181.  P. 175.
 

“I propose that most or all major evolutionary transitions that show the ‘explosive’ pattern of emergence of new types of biological entities correspond to a boundary between two qualitatively distinct evolutionary phases.  The first, inflationary phase is characterized by extremely rapid evolution driven by various processes of genetic information exchange, such as horizontal gene transfer, recombination, fusion, fission, and spread of mobile elements.  These processes give rise to a vast diversity of forms from which the main classes of entities at the new level of complexity emerge independently, through a sampling process.  In the second phase, evolution dramatically slows down, the respective process of genetic information exchange tapers off, and multiple lineages of the new type of entities emerge, each of them evolving in a tree-like fashion from that point on.  This biphasic model of evolution incorporates the previously developed concepts of the emergence of protein folds by recombination of small structural units and origin of viruses and cells from a pre-cellular compartmentalized pool of recombining genetic elements.  The model is extended to encompass other major transitions.  It is proposed that bacterial and archaeal phyla emerged independently from two distinct populations of primordial cells that, originally, possessed leaky membranes, which made the cells prone to rampant gene exchange; and that the eukaryotic supergroups emerged through distinct, secondary endosymbiotic events (as opposed to the primary, mitochondrial endosymbiosis).”  Koonin, Eugen.  2007.  “The Biological Big Bang model for the major transitions in evolution.”  Biology Direct.  V. 2, Article 21, Aug 20, 2007.  Abstract.
 

“A more and more developed subfield in the study of biological complexity and self-organization is the emergence of life.  It was neglected by the first molecular biologists, but it is now treated with renewed interest, and has become the subject of various controversies.  One important question concerns the possibility of life (or proto-life) before the appearance of natural selection: is it possible to extend back the action of natural selection to the pre-biotic era, or did the emergence of life reflect a phase transition in progressively complexifying and self-organizing pre-biotic systems?  Some suggest that evolution by ‘pre-Darwinian’ selection may be characterized by self-organization and robustness principles.  If natural selection arose long after the appearance of life, is it possible to say when this event occurred?  And, perhaps even more importantly, what do laws of self-organization and robustness tell us about the definition of life?”  Barberousse, Anouk, M. Morange & T. Pradeu, Ed.  2009.  Mapping the Future of Biology: Evolving Concepts and Theories.  Introduction.”  Pp. 1-13.  Springer.  P. 7.
 

“Traditional approaches in biology are challenged by new ones: genetics by epigenetics and developmental systems (DS) theory; the molecular description of the genetic program by self-organization models; the explanatory power of natural selection by the capacity of biological systems to self-organize; and the Darwinian model by apparent Lamarckian revivals.”  Morange, Michel.  Articulating Different Modes of Explanation: The Present boundary in Biological Research.”  2009.  Pp. 15-26.  Barberousse, Anouk, M. Morange & T. Pradeu, Ed.  Mapping the Future of Biology: Evolving Concepts and Theories.  Springer.  P. 15.
 

“As we have seen, one major problem is that molecular explanations and self-organization models do not operate at the same level: the former aims to characterize very precisely what happens in cells and organisms; the latter to provide general guiding principles for the organization of the system.  A further difficulty is that the dichotomy introduced by Ernst Mayr between molecular and evolutionary explanations is rejected by those proposing self-organization models.  For the latter, this dichotomy has no ‘raison-de’etre’, the principle of self-organization being at the root of both the development of organisms and their evolution.”  Morange, Michel.  Articulating Different Modes of Explanation: The Present boundary in Biological Research.”  2009.  Pp. 15-26.  Barberousse, Anouk, M. Morange & T. Pradeu, Ed.  Mapping the Future of Biology: Evolving Concepts and Theories.  Springer.  P. 18.
 

“The number of studies devoted to molecular noise has exploded over the last years.  Most of these have simply been aimed at describing the nature of molecular noise, its amplitude, and its origin.  Some work is though already focused on describing how the organisms manage molecular noise, how the architecture of the networks limits its consequences, and conversely how the organisms can exploit it to generate transient diversity likely to improve their adaptation to varying conditions, or to give rise to complex structures during development.  An explanation may be at hand for the origin of phenotypic plasticity, which is so important in evolution.  Such studies dissipate the clouds under cover of which some models of self-organization have given noise a pre-eminent role.  The truth is simpler: molecular noise exists, and organisms have learnt to deal with it, and possibly exploit it.”  Morange, Michel.  Articulating Different Modes of Explanation: The Present boundary in Biological Research.”  2009.  Pp. 15-26.  Barberousse, Anouk, M. Morange & T. Pradeu, Ed.  Mapping the Future of Biology: Evolving Concepts and Theories.  Springer.  P. 21.
 

“In contrast, it is probably not a coincidence that the models of self-organization today take center stage in the scenarios of the origin of life.  The scarcity of ‘hard facts’, the difficulty of linking together molecular physico-chemical explanations and evolutionary models, in the context of the prebiotic soup – whatever its precise nature is – leave considerable room for models of self-organization.”  Morange, Michel.  Articulating Different Modes of Explanation: The Present boundary in Biological Research.”  2009.  Pp. 15-26.  Barberousse, Anouk, M. Morange & T. Pradeu, Ed.  Mapping the Future of Biology: Evolving Concepts and Theories.  Springer.  P. 22.
 

“But scientists tend to remain in ignorance of the criticism addressed to the falsificationist model of Karl Popper – with a distinction drawn between a central core of knowledge and a protective belt, and of the difficulty of extending this notion beyond physics.  The simple lesson that has been learned is that the main objective for scientists should be to falsify a well established theory or to introduce a new paradigm.  Scientists’ abuse of the notion of paradigm has already been underlined.  The degenerate form of epistemological knowledge that has permeated science is used as an argument for intolerance and rejection.

“In a similar way, some epistemological debates absorb all the attention of scientists while masking more interesting issues.  Such is the case of the reductionist/holistic debate on the future of molecular biology, to which one should add the place and significance of ‘emergent’ phenomena.  Our intent is not to deny the intellectual interest of these debates, but serious bias does arise if this question is the sole focus of discussion of what happens today in the field of biological research.  To reduce the present state of biology to a transition from a reductionist to a holistic vision of biological phenomena does not acknowledge the richness of the studies being presently done.  It prevents us from seeing that what is at stake is a search for a way to link different explanatory schemes.  The most active works pursued today in systems biology does [sic] not seek to replace the molecular description by a holistic one, but rather to link a molecular description to another one – in terms of the structural and dynamic properties of networks – located at a different level of organization.”  Morange, Michel.  Articulating Different Modes of Explanation: The Present boundary in Biological Research.”  2009.  Pp. 15-26.  Barberousse, Anouk, M. Morange & T. Pradeu, Ed.  Mapping the Future of Biology: Evolving Concepts and Theories.  Springer.  P. 23.
 

“And what does chance signify for atheistic evolutionists?  Why is natural selection its antithesis?  If information for the Christian writers is a vehicle for Logos, what does it channel for atheistic evolutionists?  Why are readers encouraged by atheistic evolutionists to read selection intentionally, and then scolded when they do so?”  Oyama, Susan.  “Compromising Positions: The Minding of Matter.”  2009.  Pp. 27-45.  Barberousse, Anouk, M. Morange & T. Pradeu, Ed.  Mapping the Future of Biology: Evolving Concepts and Theories.  Springer.  P. 39.
 

“Talk of ‘approximation’ is natural when the description is closely shadowing a real system (at least in intention), and there is little role for the deliberate and rich imaginative construction of non-actual features.  Talk of ‘modeling’ is most natural when the scientist’s immediate focus is the fictional system itself, relations to the real system are secondary, and the differences between the two are substantial.  Talk of ‘idealization’ can be natural within either of these kinds of activity.”  Godfrey-Smith, Peter.  “Abstractions, Idealizations, and Evolutionary Biology.”  2009.  Pp. 47-55.  Barberousse, Anouk, M. Morange & T. Pradeu, Ed.  Mapping the Future of Biology: Evolving Concepts and Theories.  Springer.  P. 49.
 

“Complexity depends on reconciling two competing demands of differentiation and shared evolutionary identity. The generation of benefit requires differentiation; the division of benefit requires identity.  It pays cells to stick together because of collective synergies in survival and in gathering resources.  But this phenotypic power of complex animal and plant life depends on specialisation and the division of labour, and hence on cellular differentiation.”  Sterelny, Kim.  “Novelty, Plasticity and Niche Construction: The Influence of Phenotypic Variation on Evolution.”  2009.  Pp. 93-109.  Barberousse, Anouk, M. Morange & T. Pradeu, Ed.  Mapping the Future of Biology: Evolving Concepts and Theories.  Springer.  P. 107.
 

“The historical record supports the expectation that different mechanisms for ensuring robustness marked off different evolutionary epochs, and my reading of the literature suggests three epochal divides.  If we start by assuming the early existence of autocatalytic systems of some form – systems with built-in mechanisms for more-making – the arrival of nucleic acid molecules might be taken to mark the first major discontinuity.  Such molecules, which almost certainly appeared on the scene long before the advent of anything like a primitive cell, introduced a significant advance over earlier mechanisms for auto-catalysis, precisely because they made possible the replication (a particular kind of more-making) of molecules with arbitrary sequences.  But the presence of nucleic acid molecules does not yet imply the presence of genes.  That requires the arrival of a translation mechanism between nucleic acid sequences and peptide chains, and of necessity, it must come later, for it requires the combination of already existing nucleic acid molecules AND protein structures, but that innovation – in effect, the advent of genes – ushered in an entire new order of evolutionary dynamics.  During the next epoch – the few hundred million years over which cellularity evolved – change seems to have depended primarily on the horizontal flow of genetic bits between porous entities (or proto-cells) that are not yet sufficiently sealed off to qualify as candidates for natural selection.  Carl Woese argues that cellular evolution, precisely because it needed so much componentry, ‘can occur only in a context wherein a variety of other cell designs are simultaneously evolving ... [and] globally disseminated.’  He writes, ‘The componentry of primitive cells needs to be cosmopolitan in nature, for only by passing through a number of diverse cellular environments can it be significantly altered and refined.’  Similarly, he also concludes ‘Early cellular organization was necessarily modular and malleable’.

“Only with the sealing off of these composite structures and the maintenance of their identity through growth and replication – i.e., after a few hundred million years of extremely rapid evolution – did individual lineages become possible, and this marks the third major discontinuity.  With individual lineages (and the predominance of vertical gene transfer), the operation of the entirely new, albeit far slower, kind of selection that we call Natural Selection. Woese calls this the Darwinian threshold.”  Fox Keller, Evelyn.  “Self-Organization, Self-Assembly, and the Origin of Life.”  2009.  Pp. 131-140.  Barberousse, Anouk, M. Morange & T. Pradeu, Ed.  Mapping the Future of Biology: Evolving Concepts and Theories.  Springer.  Pp. 133-4.
 

“In particular, the four-part periodization I describe here, in which evolutionary history is divided by three thresholds, the nucleic, the genetic and the Darwinian, bears an obvious resemblance to the tripartite periodization proposed by Bruce Weber and David Depew.  They too see natural selection as a phenomenon emerging out of prior (more basic) selective processes, and they distinguish these as two different dynamics, the first of which they characterize as ‘physical selection’ (or selection of the ‘stable’), and the second, as ‘chemical selection’ (or selection of the ‘efficient’).”  Fox Keller, Evelyn.  “Self-Organization, Self-Assembly, and the Origin of Life.”  2009.  Pp. 131-140.  Barberousse, Anouk, M. Morange & T. Pradeu, Ed.  Mapping the Future of Biology: Evolving Concepts and Theories.  Springer.  P. 135.
 

“Their faith [in the expectedness of the origin of life such as Kauffman’s] is reminiscent of Ross Ashby’s, who, 34 years earlier, had argued, ‘In the past, when a writer discussed the topic, he usually assumed that the generation of life was rare and peculiar, and he then tried to display some way that would enable this rare and peculiar event to occur. ...  The truth is the opposite – every dynamic system generates its own form of intelligent life, is self-organizing in this sense.’  Ashby’s intuition now seems almost commonplace.  In recent years, this refusal of what Christian de Duve calls ‘the gospel of contingency’ has become so widespread as to prompt Eors Szathmary to refer to the currently accepted wisdom as ‘the gospel of inevitability’.”  Fox Keller, Evelyn.  “Self-Organization, Self-Assembly, and the Origin of Life.”  2009.  Pp. 131-140.  Barberousse, Anouk, M. Morange & T. Pradeu, Ed.  Mapping the Future of Biology: Evolving Concepts and Theories.  Springer.  P. 137.
 

“A third problem [with assumptions about the possibilities for the origin of life] is the tendency to bifurcate the range of possibilities for the emergence of life under suitable physical conditions into two extreme forms: on the one hand, near-inevitabiity (the ‘deterministic’ position), and on the other hand, the result of a single, highly improbably event, ‘a happy accident’, ‘almost a miracle’, a ‘decisive event [that] occurred only once’.  Clearly, these are not the only two options, and the effect of such an artificial bifurcation seems to me unfortunate in the extreme.”  Fox Keller, Evelyn.  “Self-Organization, Self-Assembly, and the Origin of Life.”  2009.  Pp. 131-140.  Barberousse, Anouk, M. Morange & T. Pradeu, Ed.  Mapping the Future of Biology: Evolving Concepts and Theories.  Springer.  P. 138.
 

“Actually, much of what is treated under the rubric of autocatalysis does not involve true catalysis.  A catalyst is something that speeds up a reaction without itself being changed.  The phenomenon under discussion might more accurately be termed autofacilitation because that which accelerates is itself changed.”  Ulanowicz, Robert.  A Third Window: Natural Life beyond Newton and Darwin.  2009.  Templeton Foundation Press.  Note on P. 170 which refers the point to a personal communication with Terrence Deacon.
 

“Chemical energy is, in fact, an electrostatic storage of energy in relatively unstable bonds.”  Williams, R.J.P. & J.J.R. Frausto da Silva.  The Chemistry of Evolution: The Development of our Ecosystem.  2006.  Elsevier.  Pp. 78-9.
 

“It must be emphasized that when physiologists talk about causal loops and circular causal chains, they never mean to say that two particular events A and B in such a chain cause each other.  Rather, what is meant is that a particular event A of a generic type X at a certain time t1 causes a particular event B of a different generic type Y at a later time t2, which in turn causes a particular event C of the first mentioned generic type X at a still later time t3.  Edin, Benoni.  “Assigning biological functions: making sense of causal chains.”  Synthese.  2008.  161:203-218.  P. 207.
 

“Similarly, some authors insist that the capacity for Darwinian evolution is an essential feature of life, yet any single organism during its lifetime is clearly not undergoing evolution.  Thus, the condition of ‘being alive’ needs to be distinguished from the ‘properties of a living system.’”  Schulze-Makuch, Dirk and Louis Irwin.  Life in the Universe: Expectations and Constraints.  Second Edition.  2008.  Springer.  P. 14.
 

“There does not appear to exist a single characteristic property that is both intrinsic and unique to life.  Rather we have to argue that life meets certain standards, or that it qualifies by the collective presence of a certain set of characteristics.”  Schulze-Makuch, Dirk and Louis Irwin.  Life in the Universe: Expectations and Constraints.  Second Edition.  2008.  Springer.  P. 7.
 

“The weakness in defining life as a collection of attributes is that any given attribute fails the exclusivity test–examples of entities that clearly are not alive can be found that exhibit one or more of these traits.”  Schulze-Makuch, Dirk and Louis Irwin.  Life in the Universe: Expectations and Constraints.  Second Edition.  2008.  Springer.  P. 8.
 

“In fact, it is fair to say that consensus has crystallized around a basic outline of the major events in the origin of life, consisting approximately of the following, not necessarily in this exact order: (1) Under conditions of an energy-rich neutral to reducing atmosphere, monomeric organic compounds were created from elementary molecules like H2, N2, CO2, NH3 ,HCN, and formaldehyde.  To an unknown degree, the reservoir of monomers was probably supplemented by cometary bombardment, which delivered organic compounds to the Earth’s surface from an alien origin.  (2) Monomers formed polymers and interchanged both atomic components and energy in a growing web of chemical interchange.  (3) Films, micelles, or other protomembranous boundaries began to encapsulate the chemically interactive monomers and polymers, concentrating reactants and sequestering products.  (4) A statistical recurrence of effective and efficient metabolites became prevalent, facilitated probably by inorganic catalysts like transition metals or heterogeneous surface minerals.  (5) Reliably producible ‘infopolymers’ led to crude, and probably initially inexact, mechanisms of replication.  (6) Refinement of replicative mechanisms enabled the emergence of ribonucleic acid (RNA) as a dominant macromolecular regulator of metabolism, with catalytic properties as well as the capacity to replicate itself.  This inaugurated what has been termed the RNA world.  (7) Proteins assumed increasingly sophisticated structural and enzymatic properties, coincident with the emergence of RNA-directed protein synthesis.  (8) Deoxyribonucleic acid (DNA emerged as a stable repository for genetic information, rendering RNA an intermediate in the flow of information, as cellular life of constant form and function achieved the capacity to perpetuate itself indefinitely.

“To be sure, there is a gulf of uncertainty about and between most of the steps above.  How largely chaotic if not random interactions among simple organic monomers (step 2) could transition into reliably channeled metabolic pathways (step 4), for example, is an unresolved puzzle.  One of the greatest ‘unknowns’ is how the first RNA or oligonucleotide was formed.  The link between the simplest early genetic codes (step 7) and the sophisticated steps of protein translation as it occurs in modern organisms (step 8) seems totally elusive.  Furthermore, there is heated debate about the sequence itself – whether, for instance, sequestration and primitive metabolism (step 3) preceded or followed development of the capacity for replication (step 6).  But most of the steps enumerated above have been at least convincingly modeled, and many have been demonstrated experimentally.  While the steps individually, therefore, enjoy a broad degree of support, there is no consensus on the details or environments in which they unfolded during the early days of the Earth.  Schulze-Makuch, Dirk and Louis Irwin.  Life in the Universe: Expectations and Constraints.  Second Edition.  2008.  Springer.  P. 26.
 

“Increased heterogeneity of reservoir contents [during origin of life] enables a more complicated web of interactions.  As protopolymers elongate, they acquire limited catalytic and autocatalytic functions, by virtue of assuming secondary and tertiary conformations.”  Schulze-Makuch, Dirk and Louis Irwin.  Life in the Universe: Expectations and Constraints.  Second Edition.  2008.  Springer.  P. 31.
 

“A consideration of what we know about the origin of life on Earth provides a list of constraints that is frustratingly short.  Indeed, plausible arguments have been made that life could have emerged on Earth in different habitats at the full range of planetary temperatures using a variety of energy sources.  Schemes for protometabolism, minimal cells, and primeaval coding mechanisms are numerous, with credible models and, in many cases, proof-of-concept data to back them up.”  Schulze-Makuch, Dirk and Louis Irwin.  Life in the Universe: Expectations and Constraints.  Second Edition.  2008.  Springer.  P. 40.
 

“Mathematical biologist Jack Cowan loves to describe the difference between biophysicists and theoretical biologists.  A university president once said to him: ‘You both use a lot of math and physics to do biology–you must be doing the same thing.  Why shouldn’t I merge your departments?’

“‘I’ll tell you the difference,’ Cowan said, ‘take an organism and homogenize it in a Waring blender.  The biophysicist is interested in those properties that are invariant under that transformation.’”  Wimsatt, William.  Re-Engineering Philosophy for Limited Beings: Piecewise Approximations to Reality.  2007.  Harvard University Press.  Pp. 174-5.
 

"... closeness of phylogenetic relationship is only one of at least four bases for comparing two species. Three others are similarity of reproductive strategy, similarity of ecological adaptation, and similarity of major sensory channels used in communication. The chimpanzee, our closest relative and a species surely worthy of study, differs from humans living under natural conditions in having a much smaller territorial or home range, doing much less hunting, dramatically displaying ovulatory status, and exhibiting little or no pair bonding. Mammals that hunt, such as lions, exhibit much more human-like patterns of sharing behavior–and some elements of teaching behavior–than do any higher primates. Ring-necked doves and prairie voles have proved to be superb models of the physiology of pair bonding, which is nonexistent in any great ape. Foxes are pair-bonding, hunting mammals and a potentially good model for certain aspects of human parent-offspring relations, but have been studied only a little, mainly in field settings." Konner, Melvin. The Evolution of Childhood: Relationships, Emotion, Mind. 2010. Harvard University Press. Pp. 24-5.
 

"These nine levels (‘of causation in the explanation of behavior’) can be aggregated into three overarching kinds of causes.

"Levels 1 to 3: Remote or Evolutionary Causation

"1. Phylogenetic constraints. Because an organism is of a certain broad taxonomic type, it is constrained to some extent in the way it can solve the problems posed by its environment, even under fairly aggressive selection; its deep evolutionary history is relevant.

"2. Ecological/demographic causes. Because the organism faced a certain set of adaptive problems in a particular environment, its fitness was in effect maximized for that environment; studying it in that environment should be illuminating.

"3. Genome. The result of the first two causes, the individual’s genome falls within a certain spectrum of variation for its species, population, or sex. It is the result of the phylogenetic and ecological/demographic causes, and in turn the cause of all further possibilities in the life cycle, although not all further outcomes.

"Levels 4 to 6: Intermediate or Developmental Causation

"4. Embryonic/maturational processes. Given the normal expectable environment or ontogenetic niche of the species, the genome does not merely start the events of ontogeny, but guides them; birth (hatching, pupation) may be an important event, but ontogenetic mechanisms operate throughout life.

"5. Formative early-environment effects. These ‘critical’ or ‘sensitive’ period effects, which constitute important developmental directions set by the environment, are either facultative adaptations (developmental options shaped by natural selection) or maladaptive consequences of deprivations.

"6. Ongoing environmental effects. These are factors such as nutrition, stress, and reinforcement contingencies that operate similarly at different life stages, in a time frame of days to years; in principle they are more reversible than formative early effects, although major trauma at any stage of life can be irreversible.

"Levels 7 to 9: Proximate or Functional Causation

"7. Longer-term physiology. Though mainly hormonal, longer-term physiology also accounts for other metabolic effects (energy flow, muscle fatigue, toxic substances), in a time frame of minutes to days, as outcomes of gene expression in response to environmental contingencies.

"8. Short-term physiology. Behavioral output is mediated by short-term physiology, mainly through neural circuits and their sensorimotor ‘peripherals,’ on a time course of milliseconds to minutes, which are the immediate internal causes of behavior.

"9. Elicitors or releasers. The immediate external causes of behavior, elicitors are the events in the stimulus envelope that precipitate the behavior; ethologists call this the releasing mechanism, and to the learning psychologist it is the conditioned or unconditioned stimulus." Konner, Melvin. The Evolution of Childhood: Relationships, Emotion, Mind. 2010. Harvard University Press. Pp. 28-9.
 

"Indeed, it is likely that both the phylogeney and ontogeny of intersubjectivity begin with the ability to interpret the actions of others through our own incipient action or preparedness for action, a less purely cognitive but more realistic view of intersubjectivity." Konner, Melvin. The Evolution of Childhood: Relationships, Emotion, Mind. 2010. Harvard University Press. P. 152.
 

"At the leading edge of adaptation, experience during individual lives can establish a foothold for a new local dynamic of natural selection. Experience changes individuals, who enter new ecological niches, so that underlying genetic variation produces genocopies through genetic assimilation and/or the Baldwin effect; new features or capabilities of behavior, brain, and other aspects of functional morphology thus become innate. Experience, far from being wasted because of the independence of the genome from the rest of the organism, pioneers what may become fundamental genetic changes. Adaptability, a feature of phenotypes, leads to adaptation, a feature of genomes, populations, and species." Konner, Melvin. The Evolution of Childhood: Relationships, Emotion, Mind. 2010. Harvard University Press. P. 343.
 

"Enzymes can be both extraordinarily specific, catalyzing biochemical reactions accurately and with speed or catalytically promiscuous, exhibiting broad substrate specificities. The interplay between specificity and plasticity of function appears fundamental for metabolic evolution. Specificity enhances the adaptive value of the enzymatic system and allows high turnover rates, and high levels of optimization and robustness. In turn, plasticity enables new substrates to be recognized and new enzymatic activities to be discovered." Caetano-Anolles, Gustavo, L. Yafremava, H. Gee, D. Caetano-Anolles, H. Kim & J. Mittenthal. "The origin and evolution of modern metabolism." 2009. The International Journal of Biochemistry & Cell Biology. 41: 285-297. P. 286.
 

"Several processes that would explain metabolic evolution have been proposed, including de novo enzymatic discovery, specialization through canalization of multifunctional enzymes, pathway duplication and divergence, pathway retro-evolution, and enzyme recruitment models, ..." Caetano-Anolles, Gustavo, L. Yafremava, H. Gee, D. Caetano-Anolles, H. Kim & J. Mittenthal. "The origin and evolution of modern metabolism." 2009. The International Journal of Biochemistry & Cell Biology. 41: 285-297. P. 289.
 

"The shell hypothesis of Morowitz postulates that the reductive citric acid cycle, being the simplest autotrophic synthetic system (i.e. one that requires the minimum accessory molecular hardware), was the earliest pre-biotic self-replicating chemistry, and that it originally functioned in the absence of enzymes. This cycle led to a catalytic ‘energy amphiphile’ core which enabled the discovery of new carbon-based chemistries. This is turn facilitated the sequential discovery of crucial metabolites and reactions that added layers of chemical complexity (shells) to the existing reaction network. The hypothesis assumes that pre-biotic chemistries remain imprinted in modern metabolism as relics of the pre-biotic world, that primitive organisms were autotrophs, that at some point in early pre-biotic evolution there was phase separation through absorption on a surface or trapping in a coacervate, and that biogenesis manifests in a hierarchy of nested reaction networks of increasing complexity." Caetano-Anolles, Gustavo, L. Yafremava, H. Gee, D. Caetano-Anolles, H. Kim & J. Mittenthal. "The origin and evolution of modern metabolism." 2009. The International Journal of Biochemistry & Cell Biology. 41: 285-297. P. 289. Reference is to Morowitz, H. "A theory of biochemical organization, metabolic pathways, and evolution." Complexity 1999; 20:337-41.
 

"Recruitment represents a common phenomenon in biology that occurs when a molecule, ensemble, repertoire, or a more complex system adapts an existing feature for a new purpose and within a different context. In metabolism, enzymes that are performing a particular function in one biological context are clearly brought to perform a related or different function in a different one." Caetano-Anolles, Gustavo, L. Yafremava, H. Gee, D. Caetano-Anolles, H. Kim & J. Mittenthal. "The origin and evolution of modern metabolism." 2009. The International Journal of Biochemistry & Cell Biology. 41: 285-297. P. 291.
 

"If an autonomously functioning cellular component acquires mutations that make it dependent for function on another, pre-existing component or process, and if there are multiple ways in which such dependence may arise, then dependence inevitably will arise and reversal to independence is unlikely. Thus, constructive neutral evolution (CNE) is a unidirectional evolutionary ratchet leading to complexity." Lukes, J., J. Archibald, P. Keeling, W.F. Doolittle & M. Gray. "How a Neutral Evolutionary ratchet Can Build Cellular Complexity." July 2011. IUBMB Life. 63(7); 528-537.
 

"Green showed that complex systems are isomorphic to networks." Paperin, G., D. Green & S. Sadedin. "Dual-phase evolution in complex adaptive systems." Journal of the Royal Society Interface. 2011. 8, 609-629. P. 610. Reference is to Green, D.G. "Emergent behaviour in biological systems." In Complex systems: from biology to computation. Green, D. & T. Bossomaier, Eds. Pp. 24-33. IOS Press. 1993.
 

"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, G., D. Green & S. Sadedin. "Dual-phase evolution in complex adaptive systems." Journal of the Royal Society Interface. 2011. 8, 609-629. P. 610.
 

"Dual-phase evolution (DPE) occurs when networks that dominate the dynamics of an evolving system repeatedly switch between well-connected and poorly connected phases." Paperin, G., D. Green & S. Sadedin. "Dual-phase evolution in complex adaptive systems." Journal of the Royal Society Interface. 2011. 8, 609-629. P. 611.
 

"We suggest that perturbations can cause systems to flip from high-connectivity phases dominated by stabilizing selection to low-connectivity phases of evolutionary exploration leading to ever new and diverse adaptations." Paperin, G., D. Green & S. Sadedin. "Dual-phase evolution in complex adaptive systems." Journal of the Royal Society Interface. 2011. 8, 609-629. P. 621.
 

"If there is a difference of opinion it relates to whether the single process of biological evolution is sufficient to account for cultural variation or whether a second process of cultural transmission is also necessary. Several gene-culture co-evolutionary analyses have provided evidence that single process models do not explain data as well as the gene-culture models do, that equivalent single process models either have (or would have) reached erroneous conclusions, and that the interaction between genes and culture can change the evolutionary process, for instance, by generating a new form of group selection or by modifying evolutionary rates. These theoretical arguments are now receiving strong empirical support in the aforementioned data from the human genome. These are compelling reasons to treat transmitted culture as a potent process in the shaping of human evolution." Laland, Kevin & G. Brown. Sense and Nonsense: Evolutionary Perspectives on Human Behaviour. 2011. Oxford University Press. P. 189.
 

"Mammals, along with the biologically remarkably similar birds, are the vertebrates that are most completely adapted to the physiological rigours of the terrestrial environment." Kemp, T.S. 2005. The Origin and Evolution of Mammals. Oxford University Press. P. 14.
 

"The ancestral pattern of growth of amniotes is described as indeterminate, because it is continuous throughout life and there is no absolute adult size. It is associated with polyphyodont tooth replacement, in which there are several to many successive replacements of each tooth. This process provides the necessary increasing size of teeth and length of tooth row as growth proceeds. In mammals, the growth is determinate, with a rapid phase of juvenile growth ending in adult size, after which no further growth takes place. This is associated with diphyodont tooth replacement, in which there is a single juvenile, deciduous, milk dentition, followed by a permanent adult dentition. The mammalian growth pattern is only possible with an extremely high rate of parental provision of nutrition to the young, in their case by lactation, although by comparison with the similar growth pattern found in birds, direct provision of foraged food can achieve the same end." Kemp, T.S. 2005. The Origin and Evolution of Mammals. Oxford University Press. P. 120.
 

"The second function of endothermy is the very high rate of sustainable aerobic activity that is possible. For reasons not readily explained, there is a roughly constant ratio between the basal or resting metabolic rate and the maximum sustainable aerobic metabolic rate of all vertebrates. The latter is typically 10-15 times the former, although there are exceptions. If the BMR of a typical ectotherm such as a lizard is taken as one unit of energy per unit time, then its maximum sustainable aerobic metabolic rate is about 13 units. For a typical mammal of the same body weight, the figures are a BMR of about 7 units and an expected maximum sustainable aerobic rate of 91 units, a huge increase in the latter property over the ectotherm. The mechanism behind the increase primarily involves a far larger number of mitochondria in the skeletal muscle, coupled with a greatly enhanced oxygen delivery system to them. The enhanced aerobic capacity does not affect the total maximum power output, or the top running speed attainable, because ectotherms can achieve similar values by anaerobic metabolism. However, ectotherms can maintain this level of exercise for no more than a very few minutes, after which time activity has to cease as the oxygen debt is repaid and lactic acid removed, a process that can take some hours to complete. In contrast, the maximum power output, and therefore maximum speed that can be sustained indefinitely, or at least until the body’s food reserves are exhausted, is far greater in mammals than reptiles. The biological functions of this enhanced endurance are fairly obvious: food capture, predator avoidance, size of territory, vagility, and energy available for courtship all spring immediately to mind." Kemp, T.S. 2005. The Origin and Evolution of Mammals. Oxford University Press. P. 123.
 

"A relationship between endothermy and reproduction in mammals (and birds) has long been suggested. This can be in terms of either the need in an endothermic species for the parent to care and provide for its juvenile offspring because it has too small a body size to behave as an endotherm itself, or in terms of the enhanced growth rate of the juvenile that is possible via lactation." Kemp, T.S. 2005. The Origin and Evolution of Mammals. Oxford University Press. P. 126.
 

"... endothermy in living mammals serves two principal functions simultaneously, thermoregulation and elevation of maximum aerobic activity." Kemp, T.S. 2005. The Origin and Evolution of Mammals. Oxford University Press. Pp. 128-9.
 

"Mammals may be seen as the organisms that have evolved the highest capacity for regulation of their internal environment, which is to say, that have the highest degree of homeostatic ability." Kemp, T.S. 2005. The Origin and Evolution of Mammals. Oxford University Press. Pp. 131-2.
 

"But regulation is metabolically expensive. Maintaining chemical gradients requires the energetic process of active transport of molecules at the cellular level. Maintaining the temperature gradient requires a high level of aerobic respiratory activity by the mitochondria. Together these dictate the need for the 6-10 times greater BMR of endotherms over ectotherms. In order to achieve this, the rate of gas exchange and the rate of food assimilation need to increase proportionately. Efficiency of food detection, collection, ingestion, and assimilation must rise, with implications for the design of the sense organs, the locomotor system, and the central nervous control. Increase in gas exchange requires more effective ventilation such as is provided by a diaphragm and freeing of the ribcage from a simultaneous locomotor function. These add to the requirements of the actual regulatory systems, such as elaborate internal nervous and endocrinal monitoring systems and high blood pressure to increase the kidney filtration rate. For thermoregulation, variable insulation, cutaneous blood flow rates, and evaporation mechanisms are just some of the necessary components of the system.

"Organisms maintaining high chemical and temperature gradients with the environment cannot be very small because of the surface area to volume consideration. Therefore, a juvenile of an already small mammal cannot exist independently, relying on its own regulatory mechanisms, which in any case take a significant time to develop fully. Therefore, parental maintenance of what amounts to a regulated external environment become necessary. In the first mammals this was presumably in the form of a nest, or conceivably a maternal pouch in which the egg and neonate existed in a controlled temperature and humidity, with the molecular requirements provided by lactation.

"Seen in this light, there is no identifiable, single key adaptation or innovation of mammals because each and every one of the processes and structures is an essential part of the whole organism’s organisation." Kemp, T.S. 2005. The Origin and Evolution of Mammals. Oxford University Press. Pp. 132-3.
 

"However, the retinas of almost all anthropoids have a small central area, the fovea, in which all the receptors are cones. Each cone in the fovea has its own separate neuronal ‘wire’ running back to the brain. Images that fall on the fovea are therefore seen in color and in great detail.

"No other mammals have a fovea of this type. It gives large anthropoids sharper vision than almost any other animals on the planet. The only organisms known to excel humans and apes in keenness of sight are eagles." Cartmill, Matt & Fred Smith. 2009. The Human Lineage. Wiley-Blackwell. P. 91.
 

"The supposed lag between the initial adoption of a new way of life and the subsequent evolution of adaptations to it is often referred to as phylogenetic inertia. How much of the anatomy of an organism reflects its own way of life, and how much reflects the adaptations of its ancestors? This issue comes up over and over in the scientific literature on primate and human evolution. For example, early human relatives in the genus Australopithecus walked on their hind legs, but retained many apelike features of their limb bones. From those apelike features, some experts infer that these creatures must still have been spending a lot of time in the trees. But others say that Austalopithecus was fully terrestrial, and that its apelike features are functionally meaningless leftovers from a simian ancestry, preserved through phylogenetic inertia.

"Nobody doubts that phylogenetic inertia is a real phenomenon. Adaptation is never perfect, and the morphological novelties that an evolving population comes up with are always limited by the materials that the process of evolution has to work with. But it is not clear how much the speed of evolution is restricted by phylogenetic inertia." Cartmill, Matt & Fred Smith. 2009. The Human Lineage. Wiley-Blackwell. Pp. 113-4.
 

"A plot of body weight against brain volume shows that A. africanus had a larger brain than would be expected for a living ape of its estimated size. To put it another way: Australopithecus had a bigger brain than any animal of its size known from all the previous history of life on earth.

"Likewise, although the face of A. africanus is apelike in its general proportions, the teeth set in that face are very different from those of any living ape. The most conspicuous differences involve the permanent canines, which are small and incisor-shaped–much like ours and unlike the big stabbing fangs found in most apes." Cartmill, Matt & Fred Smith. 2009. The Human Lineage. Wiley-Blackwell. P. 133.
 

"With the possible exception of the foot, the pelvis is probably the most distinctive part of the human skeleton. Some small monkeys have vaguely human-looking skulls, with big braincases and short faces, but no other living mammal has a pelvis like ours." Cartmill, Matt & Fred Smith. 2009. The Human Lineage. Wiley-Blackwell. P. 138.
 

"Most mammals have hands that look quite a lot like their feet. The embryological development of the hands and feet is governed by a set of regulatory genes that affect the distal parts of the forelimb and hindlimb in similar ways. But when the hands and the feet need to take on divergent forms and functions, as they have in the course of human evolution, the developmental linkage between hand and foot anatomy can be overridden by natural selection acting on alleles further down in the hierarchy of the genome." Cartmill, Matt & Fred Smith. 2009. The Human Lineage. Wiley-Blackwell. Pp. 149-50.
 

"Despite all these ongoing disagreements over the boundaries, functional anatomy, and relationships of the various species of Australopithecus, the overall picture of early hominin evolution is clear enough. Bipedal apes evolved in Africa around the end of the Miocene. By 3.5 Mya, they were found throughout most of the continent, from Chad to South Africa. They underwent a modest evolutionary radiation into several species. The earliest forms had chimpanzee-like skulls, but with more downward-facing foramina magna, bigger cheek teeth, and smaller canines with apical wear and reduced C/P3 honing. Later species of Australopithecus tended to develop more humanlike hands and feet, bigger brains, flatter faces, and still smaller canines. However, these trends in the direction of humanity were correlated with parallel trends toward megadonty, an apomorphic specialization that is generally thought to exclude the later Australopithecus species from the human lineage. As far as is known, all the species of Australopithecus had limb proportions somewhere in between those of humans and apes, and the details of the upper limb skeleton suggest that ‘... the structure and function of the upper body ... was different from that of modern humans’. When they walked on the ground, they walked bipedally, but their bipedality was unlike ours in some respects." Cartmill, Matt & Fred Smith. 2009. The Human Lineage. Wiley-Blackwell. P. 201. Subquote is from Alemseged, Z., F. Spoor, W. Kimbel, R. Bobe, D. Geraads, D. Reed, & J. Wynn. 2006. "A juvenile early hominin skeleton from Dikika, Ethiopia." Nature 443:296-301.
 

"In short, the evidence indicates that A. robustus was an opportunistic mixed feeder, which ate many different types of food from many different sources without being specialized for any one of them." Cartmill, Matt & Fred Smith. 2009. The Human Lineage. Wiley-Blackwell. P. 203.
 

"Laden and Wrangham suggest that hominin divergence from the other African apes was driven by a switch in fallback foods, from the fibrous tissues of forest herbs and trees to bulbs, tubers, and other underground storage organs (USOs) of savanna plants. They propose that this shift drove the early-hominin evolutionary trends toward large jaws, premolar molarization, megadonty, and thick enamel." Cartmill, Matt & Fred Smith. 2009. The Human Lineage. Wiley-Blackwell. P. 203. Reference is to Laden, G. & R. Wrangham. 2005. "The rise of the hominids as an adaptive shift in fallback foods: Plant underground storage organs (USOs) and austalopith origins." JHE. 49:482-498.
 

"In mammals, intestines and brains are both particularly expensive tissues to maintain. Aiello and Wheeler contend that the size of the two is negatively correlated in anthropoid primates: for a given body size, leaf-eaters (which need to have big guts) generally have large guts and smaller brains than fruit-eaters." Cartmill, Matt & Fred Smith. 2009. The Human Lineage. Wiley-Blackwell. P. 204. Reference is to Aiello, L. & P. Wheeler. 1995. "The expensive-tissue hypothesis: The brain and digestive system in human and primate evolution." CA 36:199-221.
 

"This so-called expensive-tissue hypothesis makes sense in terms of the hominin fossil record. It explains why relative brain size and megadonty are positively correlated in Australopithecus: increasing specialization of the teeth and jaws might have allowed more effective use of new food resources (USOs?) and provided fuel for a larger brain. And it suggests an underlying reason for the co-occurrence of markedly bigger brains and stone tool use in early homo–namely, that the new tools afforded increased access to higher-quality dietary items (animal flesh?), allowing the gut to become smaller and freeing up part of its energy budget to be invested in a larger brain." Cartmill, Matt & Fred Smith. 2009. The Human Lineage. Wiley-Blackwell. P. 204.
 

"Yet though the savanna is a rich and productive habitat, few primates have managed to adapt to it. The main exceptions are swift-running terrestrial cercopithecids–baboons, vervets, patas monkeys–that rely on varying combinations of wariness, agility, threats, social organization, and speed to discourage or elude predators on the ground. And whatever the locomotor behavior of early hominids was like, they were surely not swift runners, because modern humans are not." Cartmill, Matt & Fred Smith. 2009. The Human Lineage. Wiley-Blackwell. P. 205.
 

"Lovejoy’s theory postulated that perfected terrestriality evolved in forests or woodland-savanna mosaics, not in open country. But as noted earlier, there is not much to eat on the ground in a closed-canopy tropical forest. Wide-ranging male foragers would have fared better by venturing into open areas in search of more diverse food sources, including ‘... fruits, berries, nuts, seeds, underground tubers, and roots ... a wider range of young animals than in the tropical forests ... and termite hills–the last a visible source of attraction from far away.’ Digging up USOs and carrying food back to the core area would have stimulated the invention of several sorts of artifacts. Sticks and stones might have been used as weapons in killing prey or driving competing scavengers away from carnivore kills, although this sort of foraging was probably infrequent and restricted to relatively small game until the advent of the genus Homo." Cartmill, Matt & Fred Smith. 2009. The Human Lineage. Wiley-Blackwell. P. 214. Subquote is from Tanner, N. & A. Zihlman. 1976. "Women in evolution. Part I: Innovation and selection in human origins." Signs: Journal of Women in Culture and Society. I:585-608. Reference is to Lovejoy, C. 1981. "The origin of man." Science 211:341-350.
 

"Rose reviews 19 different accounts of the causes of human bipedality that have been put forward in the scientific literature, grouped under four headings:

"1. Pre-emption of the forelimb for nonlocomotor jobs (throwing; carrying food, infants, and-or tools).

"2. Social behavior (threat displays, sexual displays, aggression, vigilance, evasion).

"3. Feeding behavior (bipedal gathering, scavenging, or predation, either on the ground or in the trees–or even in the water, in the so-called ‘aquatic ape’ theory.

"4. Other–including thermoregulation, biomechanical necessity (e.g., for a long-armed gibbon-like ancestor), locomotion on slippery substrates, iodine deficiency, and various combinations of other listed factors." Cartmill, Matt & Fred Smith. 2009. The Human Lineage. Wiley-Blackwell. P. 215. Reference is to Rose, M. 1991. "The process of bipedalization in hominids." From Coppens, Y. & Senut. Pp. 37-48.
 

"Using our approach we cannot allow separation of cognitive from metabolic activity as an excuse for removing human kind from general evolution as some biologists appear to wish to do since we are analysing by continuous chemical thermodynamics. Human beings present as great a change in evolution of chemotypes in 10,000 years as in the preceding four billion and in one sense they were predictable with hindsight. They seem to represent the last steps of the expansion of cooperation from energised chemistry inside organisms to that outside them...."

"... Our major point is that development is based on access to new chemicals and new energy sources together with new space and organisation and the necessary communication systems, that is in exactly the same way as all previous biological evolution, to aid survival while generating heat." Williams, R.J.P. & J.J.R. Frausto da Silva. The Chemistry of Evolution: The Development of our Ecosystem. 2006. Elsevier. P. 449.
 

"Thus, historically the ages of the history of mankind are labelled Stone (physical, not chemical, but note bricks and mortar), Bronze (Cu, Sn), Iron, and finally Industrial or should it be called The Age of all the Elements, when evolution has entered a final stage. (Mankind could be considered as a very rapid succession of chemotypes and note that the order of elements used is that of availability as in all other stages of evolution.) The availability of the appropriate elements has followed the rise in working temperatures from 300 K (primitive) via 1,000 K (Iron Age) (coal) to 3,000 K (Al) in element production." Williams, R.J.P. & J.J.R. Frausto da Silva. The Chemistry of Evolution: The Development of our Ecosystem. 2006. Elsevier. P. 450.

 

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