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Detail from the Mandala of Evolution - Dion Wright (see below)

The Tree of Life: Evolution at the Edge of Chaos

2009 Lead Review: The Tree of Life: Tangled Roots and Sexy Shoots: Tracing the genetic pathway from the first eucaryotes to Homo sapiens. A fully referenced research review to overview progress in unraveling the details of the Tree of Life, from life's first occurrence in the hypothetical RNA-era, to humanity's own emergence and diversification, through migration and intermarriage, using research diagrams and brief discussion of the current state of the art, as of the beginning of 2009.

2007 Biocosmology Evolution Article Updates contents in this page as part of a research review

Large Pictures:

Tangled Roots and the Tree of Life

The base of the tree of life as we know it lies at the transition from the first forms of life in the RNA era to life as we can detect it from the fossil record. Three great groups stand out, the Archaea, including a variety of ancient types of bacteria living in extreme environments of temperature and high salt content, the ordinary Bacteria and Eucaryotes comprising protists, plants animals and fungi.

Giardia displays primitive eucaryote phenotype.

The genetic record shows eucaryotes are closer to archaea than archaea are to bacteria giving eucaryotes a potentially primal founding phenoype, consistent with their predominant RNA processing, splicing together split DNA genes with non-coding introns interspersed between the coding exonic gene sequences which translate to proteins, the presence of reverse transcriptases which convert RNA information to DNA and their unique capacity to engulf other life forms to form the mitochondria of respiration and the chloroplasts of photosynthesis. Eucaryote fossils date back as far as 2.1 billion years. The diplomonad Giardia probably diverged around this time as it has no mitochondria, and double haploid nuclei unlike most eucaryotes which fuse their haploid sexual gamete genomes during their life cycle to form a diploid one

Essential Evolution

Although the universe appears to be running down towards a heat death as a result of the increasing entropy or disorder of the second law of thermodynamics, on time scales of billions of years, similar to the age of the universe itself, life has been an immortal unfolding evolutionary process, which is negentropic, utilizing the incoming solar radiation to produce an ever-increasing abundance and complexity. This has happened even though evolution is an opportunistic drunkard's walk to progress, intermittently punctuated by catastrophic extinction episodes. Because evolution arises from the ostensibly random entropic nature of mutation itself, it is one of the fundamental processes creating order from disorder, utilizing the incoming free-energy of the Sun's radiation to form an open, far-from-equilibrium system at the edge of chaos.


Rapid evolution of guppies over observable time scales is a reflection of differing selection. In the absence of predators, males develop prominent tails (below) by sexual selection, but in the presence of significant predation, they naturally select for less conspicuous transparent tails (New Scientist). Chichlid fishes have dispersed even more widely over very short timescales in evolutionary terms, as little as 12,500 years. The apparent slowness of evolution of some species such as scallops may be a reflection of signficiant variations in the short term which average out over longer times to little significant change, because of strong conservation of the overall design/strategy.

Chance and Necessity

Some of the most elegant steps of evolution are at once the most obvious. Although creationists have deemed the evolution of the camera eye an impossibility, the profound selective advantage of camera vision and the existence of all the intermediate forms from pit eye to camera eye demonstrate the way in which evolution has followed a path of gradual and almost inevitable bifurcation.

Evolution as a process is a combination of opportunistic mutational change and selective advantage in an overwhelming sea of deleterious accidents, forming a creeping doorway. This raises the question as to what extent evolution is merely a directionless accumulation of random idiosyncratic changes as opposed to a process which explores through selective advantage the niches available in the world at large or even the cosmological environment determined by the laws of nature.


Cantharanthus rosea contains a unique anti-cancer agent vincristine, a result of a chance fortuitous mutation not found in other species (Ayensu 186).

Ever since Darwin first noted the key roles of natural selection and mutation, it has been clear that evolution displays both accidental qualities such as the occurrence of unique or unusual biochemicals confined to one or a few species on the one hand and on the other it displays major systemiatic developments which confirm evolution's capacity to explore the 'space of possibilities' and to open up the avenues made available by bifurcations of the natural and metabolic environment.

It is clear that bifurcation into plant and animal niches constitutes a basic division of metabolic strategy between photosynthesis and decomposition which is fundamental to all life. The fungal division follows similarly. The development of camera eyes the other senses, such as smell and hearing and of nervous systems and their neurotransmitters are likewise manifestations of selective advantage exploring the feasible phase space of sensory strategies through repeated mutational events. This means that evolution, like all quantum phenomena, lies in the grey area between single 'accidental' events and the inexorable adaption arising from many repeated events which explores the available domain of possibilities.

The inner indications of morphogenic algorithms can likewise be witnessed in the capacity of related, but distant species to use variations of morphogenic schemes to fluently mimic a variety of other species through minor mutational adaptions of a single morphogenic algorithm. These instances of adaptive mimicry thus illustrate an interplay between mutation and selection on the one hand and universal genetic algorithms common to all butterflies on the other. Mimicry thus attests not just to the adaptability of evolution but to fundamental algorithmic themes of morphogenesis common to wide groups of organism. It is these 'universal algorithms' we will now examine further.

Intermediate forms of the eye from Dawkins (1996) illustrate evolutionary stages in the formation of a camera eye from a pit or pinhole eye. Formation of vitreous matter both protects the pit and adds focussing potential.

Creationism and Evolution

Neither is evolution just an hypothesis and not an actuality as creationists pretend. Evolution is a central aspect of the creative process. It is apalling that religious ideas of divine creation by God are allowed to lead to a concept of a dead universe in which no new creative unfolding can occur. Evolution is the key to unfolding life and should be central to any visionary conception of the universe. Certainly every aspect of the scientific description of reality is hypothesis. It is true that scientific theories are only ever disproven by counter-example and the sceptical principle, (even if gracefully by Einsteinian relativity and quantum mechanics as Newton's grand design was), and are never proven true, as the affirmative self-fulfilling indoctrination of religious orthodoxy generally is. Violating the sceptical principle is the key pitfall of all religious doctrine - its very nemesis.

It is easy to see in human embryogenesis the imprint of evolution from the oceans still in the early phase of the development of each and every one of us in the fin-like form of the early limb appendages.Evolution is surely a foundation stone of the entire physical description of reality and one which religions can ignore or reject only at our living peril. The creationist positon is not merely anti-science, it is a pathetic fallacy about the nature of "God" - a fallacy which arises like the rest from the patriarchal imperative - divine order and transcendence over chaos, nature and the principle of ongoing creation of new life in the birth process and ultimately evolution itself.

Mutation is also a quantum mechanical process which may involve both quantum chaos and quantum non-locality in the rarer idiosyncratic events which do not fully converge to the law of averages of the correspondence principle. Each mutation and each transposition of a mobile genetic element is a unique quantum measurement, a single 'reductionof the wave packet' whose result is sometimes woven permanently into the evolving historial record.

It is also clear that the neutralist position, rather than natural selection, governs evolution of many highly-conserved structural genes, because the properties are already optimal and can tolerate only mutations which essentially preserve amino-acid sequence and function, and that sexual selection as opposed to natural selection - the red queen phenomenon - may also be pivotal to much of higher-organism evolution - something which gives added force to the chaotic perspective, because sexual selection is forever changing the adaptive landscape.

A mammalian regulatory gene, pax6 is able to elicit ectopic eyes on the leg of a fruit fly, showing the genes even have comparable action. (Dawkins 1996).

The Homeotic Paradigm

Although it is said in defence of natural selection that the eye has evolved up to 40 times independently, there is a deep genetic relationship between the apparently very different insect compound and vertebrate camera eyes. The homeotic genes which have been shown to elicit comparable differentiation between insects and vertebrates, especially in segmentation, also have strong sequence similarity for eye differentiation. The common nature of homeotic genes. between such widely spaced phylla suggests evolution had to find a common scheme of embyogenesis in the pre-Cambrian before the metazoa evolved. A similar identity pertains between decapentaplegic in the fly and Bmp-4 in the frog. Both are equally effective in either species, except their effect have inverted in a way which reflects the proterostome/deuterostome inversion (New Scientist 18 Oct 1997 30).


Analysing appropriate taxonomic relationships in evolution can lead to a significantly smaller number of branching diversifications than a simultaneous origin of all species in a single radiative adaption to all types. (Sci. Am. Nov 92)

There is continuing debate whether this could for example have precipitated the Cambrian radiation, which appears rapid from the fossil record, but somewhat slower by mutational clocks and may have extended further back into or even through the preceding Ediacarian epoch.

The difficulty in comparing phenotypic and genotypic evolution is notorious and both methods have pitfalls. Although mutational clocks are widely assumed to have constant rates, iot is well known that changing error-correcting paradigms, generation times, and environmental stresses all play havoc with the constancy hypothesis. Phenotype is equally capricious. Convergent or drifting evolutionary change can mask major genetic divergences over time.

The single species on the left successfully mimics three distinct obnoxious tasting species right. Although these can be distinguished by phenotype from their models, they illustrate the dilemma of convergent phenotypes within divergent genotype and emphasize that underlying developmental algorithms are strongly conserved in evolution and can generate far greater versatility than the genotype alone would suggest (Gould [ed.] 1993).

Fecal pellets have been discovered at Islay dating to 600 million years (New Scientist 13 Dec 97 20). In fact the commonality extends even deeper than the proterstome/deuterostome bifurcation where gut from mouth and gut from anus divided the arthropods and vertebrates for even the lowly coelenterates have been shown to have a good complement of homeotic genes and they have also been found in both fungi and plants.

This suggests that the development and elaboration of metazoan oraganization has depended on the establishment of one comprehensive scheme of morphogens which are capable of distinguishing periphery from axis, dorsal from ventral head from tail etc. It is possible that the Cambrian radiation resulted from a breakthrough in the application of homeotic genes to development of flexible modular and even transmutable organization of body plan.

Evolution and Sexuality

Sexuality is central to the development of metazoan complexity because sexual recombination is the most powerful modifier of genetic form in existence and virtually all the rearrangements are viable. The Red Queen hypothesis explains the origins of sexuality in gnetic competition between parasites including diseases and their hosts, leading to histocompatibility genes and ultimately the immune system.

It may even be that evolution is a complemenataion between fundamental bifurcations of type, such as that between the proterstomes and deuterostomes and the more accidental adventitious aspects of evolution which have resulted in the unusual alkaloids such as vincristine found in individual species. Limits on adaptability arising from such fundamental bifurcations and the constraints of developmental paradigms have even been called Darwin's third force.


The evolution of Homo sapiens presents particular problems because the species represents a meta-niche. Unlike the other great apes, which have continued to diversify into several existing species, the generalization of Homo sapiens has removed all its immediate cousins from the historical record. Note that chimps are more closely related to humans than gorillas, a point of chagrin to creationists.

Evolution and Cosmological Biogenesis

One can even ask whether some fundamental aspects of the nature of life such as RNA have cosmological status as a common catalyst information molecule, and even the nature of the genetic code come from fundamental non-linear bifurcations arising from the nature of cosmic symmetry-breaking. RNA is a triple unit composed of two polymers of HCHO and HCN in the presence of urea. Arguments for the universal nature of the genetic code have also been proposed.

The question for evolution is precisely the one originally posed by T.H. Waddington in "Strategy of the Gene" - to what extent has the bifurcations of cosmological symmetry-breaking laid out an interactive set of bifurcations which shape the reality of evolution in the way a chreode or canalizing selection landscape shapes adaption? This is an area where ultra-Darwinists fall down very badly. Their arguments assume natural selection without understanding this potential landscape the selection hypothesis implies.

There are many aspects of the central biochemical pathways from RNA-based replication, phosphorylation energy, dehydration reactions, through the elements of glycolysis, the tri-carboxyllic acid cycle, membrane transport and excitation all of which may actually be early adaptions of genetic replication to a wider biochemical bifurcation sequence. One can then validly ask "Would life on another planet be likely to be also carbon-based, RNA-dependent life, and if so would it also use the porphyrin ring for photosynthesis?"


Arthur Koestler's doppelgangers. Marsupial and placental carnivores display great developmental similarity.
This may require more than convergent evolution and hints at universal developmental algorithms (Koestler 1967 171).

One obvious constraint in our current evolutionary context is Darwin's third force., the development process itself, as pointed out by Brian Goodwin in his review. This is consistent with the perspective of homeotic genes we have seen above. It is unlikely the exact coding for the homeobox is universal, but the overall plan of arginine and hydroxl and amide groups may be. Futhermore the type of developmental algorithm used to develop the body plan may be universal , just as Turing's equations are in a sense general for solutions like the Leopard's coat.

We can then begin to examine some wider principles. Would another planet also have plants, animals and fungi? These are fundamental divisions of the energy strategy, which seem in a sense universal responses to the photosynthetic fixation of free-energy. Would these use the same sodium-potassium ionic excitation, or even possibly amine-based neurotransmitters? What about the relationship between the insects and the vertebrates? Is this a fundamental bifurcation of strategy too, just as it has arisen from a bifurcatory inversion of the developmental axis? But couldn't this problem be solved in a wild variety of ways, just as the Cambrian spawned a wild variety of body plans?

Possibly, but there is a fundamentally deeper problem, to do with the famous myth of evolutionary progress, decried by neo-Darwinists and Stephen Jay Gould's ilk alike, perhaps their only point of agreement - the opposition to the idea that evolution means inevitable progress of types in some teleological or utopian sense.

This leaves these players in a serious abyss of paradox. Surely genetic replication, with some notable exceptions below, clings to a mutational rate no higher than about 0.5 per generation, and sure mutation is opportunistic and idiosyncratic and deletrious in the majority of cases, but while we are mutationally exporing our selection landscape we also appear to be relentlessly, over the epochs, increasing in complexity and diversity too. There is nothing in this that needs to spell a deterministic teleology, but it may involve convergence to a universal algorithmic solution which may itself be cosmological in a fundamental sense, just as is the equation E = mc^2.

It is ludicrous for Stephen Jay Gould to decry the progress of evolution when it is clear that more recent evolutionary steps clearly have built on changes induced by past evolutionary change. We are not simply wandering anywhere, we are wandering everywhere and once the land plants are finally established, land animals and eventually mammals and man have followed, not because of progress per se but because of that very rachet which natural selection itself provides. This sequence of chages is fraught with genetic drift and mass extinctions and other setbacks but it is broadly cumulative in complexity and diversity.

Evolution is an example of genetic algortihms in action - certainly nature and the universe's finest. Genetic algorithms have very dangerous characteristics, they operate in parallel at the molecular level and they are among the most efficient algorithms known for arriving at a univerally optimal solution. That IS progress!

Teihlard de Chardin in addition to a life-ban from the Catholic Church for his evolutionary viewpoint is almost universally decried for his almost 'Lamarckian' naivette in proposing a final convergence of the evolutionary process because it breaks with the supposedly free, random and blind purposelessness of mutational change - as Richard Dawkins makes a dismal fetish of, almost to the point of destroying our love for and beauty of nature herself. But is Teihlard actually wrong in his intuition of convergence? Whan then is the evolution of culture which now seems to be growing like a carcinoma upon nature and her evolutionary diversity? What is the evolutionary source of culture and the noosphere of human knowledge, this explosive force which is forever changing the evolutionary face of the planet? Who is it that has their heads in the sand here?

Teihlard de Chardin's culmination of the evolutionary process in the noosphere and its final omega point. Although somewhat gnostically described as the body of Christ, the idea of evolution reaching to a universal solution is a valid cosmological postulate (Morton, John Man Science and God).

The paradox we have with the evolution of Homo sapiens is that the species has become in effect a meta-species through a massive generalization of brain function. We no longer occupy a single evolutionary niche, but every niche to the detriment of biodiversity as a whole. This is the mystery that Teihlard, studying the evolution of Homo sapiens teried to come to terms with. It is a paradox which is emphasized by the successive drop in hominid species from the great apes through Australopithecus to sapiens sapiens.

This change has come about, not through Richard Dawkins' merciless rule of fang and claw, and the blind watchmaker groping endlessly for the wheels of complexity, but through a succession of long-lived individuals with a life-span not dissimilar to ourselves who have had much time to ponder their existence between the short rounds of foraging and gathering - generating through this beneficent, indeed paradisical epoch, a general algorithmic solution to the neurodynamical problem of perception and cognition.

We have generalized our perceptual and mental processes through neotonic evolution to the point where these converge to the quantum limit. Our senses are as generalized and adaptible as they can theoretically be. Our immediate senses are sensitive to the quantum level. Some analyses of our brain even suggest it is already optimal and cannot evolve to a larger capacity because of connectivity and timing problems. The processes themselves are driven not by fixed developmental schemes and rigid instincts, but by dynamic excitation and non-linear feedback in the developing organism. Central nervous circuitry retains major plasticity throughout adult life. We find ourselves steeped in the mystery of subjective consciousness reflecting on the ultimate fate of the universe and the nature of existence.

So what is the answer to this? What I am suggesting is something wildly non-Copernican, undoing all the cultural revolutions back to the dark ages. I am suggesting that evolution explores a phase space of possiblities, many of them underlying bifurcations of interaction of a cosmological nature, using the genetic algorithm, and in so doing, converges to an ultimate optimal interactive consequence of cosmological symmerty-breaking, not through a deterministic teleology but through quantum chaos converging towards the realization of the subjective cosmological state. This state, while expressed implicitly in the excitable nervous systems of all animals, indeed the chaos of the winds and even in principle in the wave function of a single quantum, is converging towards - not a final solution, but certainly a universal one, expressed in that most elaborate and complete interactive catastrophe of the symmetry-breaking of the fundamental quantum forces of nature - the conscious sentient brain.

This is a cosmological responsibility we need to grow up and come to terms with, before, in our witless worship of the machine, we destroy our own evolutionary heritage and cast upon ourselves the genuine curse of the Fall and have to live for the next evolutionary epoch in biological poverty of our own doing.

Modular Transposition and Genetic Symbiosis

Another favourite dogma of 'classical' Darwinists is that all genetic systems try to avoid at all costs any adaption to evolutionary change itself. The reasoning goes that genetic systems try as hard as possible to maintain the current successful genetic scheme against predominantly deleterious mutational changes and that only clear cut selective factors provide the sort of advantage that can be significant for one individual over one generation.

The idea is thus that that even selfish genes try to conserve their identity and it is only when this rule of order is very occasionally overthrown by advantageousor at best neutral mutation that the evolutionary process occurs. It does seem at first sight disadvantageous for an organism which could conserve its identity to intentionally allow this process to become leaky and noisy, however evidence is beginning to become forthcoming that bacterial hotspots of mutation are associated with mutation-promoting factors which become immediately advantageous when a change on selective conditions makes the predominant successful type unviable or at a significant disadvantage.

The enormous variety of transposable elements, selfish genes, plasmids and viruses, which often also integrate into the germ-line of organisms and thus hitcha ride in parallel with evolution, the structure of introns and other modular architecture, the large amount of non-coding DNA in higher organisms suggests this simplistic selectionist dogma is a lame duck.

Transposable elements are known to play all maner of regulatory roles from flower and seed patterns through to sexual mating type. Selfish genes also make possible a variety of new types of selective change which have been proposed to be of evolutionary significance to the organisms possessing them, casting the simplicity of the selfish gene concept in a paradoxical light.

Transposable genetic elements such as the SINE Alu element ubiquitous in human genomes,as well as the ancient LINEs which support them have recently also been shown to play a regulatory role. RNA-directed viruses and Retroviruses similarly have a wide distribution and their own evolutionary tree which is consistent with a comprehensive and potentially symbiotic relationship with the organisms they inhabit, despite many being frank pathogens. The reactive immune system appears to have also been generated by a transposon.

There is a fundamental reason why the advent of transposable elements may completely alter the parameters of evolution in a manner which ensures both their own survival in the germ-line and the regulatory evolution of higher organisms. This is a simple matter of informational complexity. A transposable element contains a specific sequence of bases and genes which is very far from random. It thus represents an insertional mutation which has vanishing probablility of occurring by chance. Because of recombination with cellular genes or their functional exon components, such transpositional events have astronomically higher probabilities of inducing a favourable mutation than a sequence of random events would. Hypermutations have recently been found to be selectively advantageous in bacteria leanding respectability to the concept of evolutionary evolution. The strategic advantage of allowing hypermutation in certain classes of contingency gene, while keeping housekeeping genes stable provides a specific strategy of evolutionary evolution.

One can thus postulate that organisms have adapted to allow certain types of transpositional mutation with at least the same frequency as point mutations and possibly higher. It is even possible that they have defied the dogma of deterministic replication and adapted to specifically allow such transpositional processes to occur although this remains to be demonstrated. I suggested this possiblity in a paper in Genetica in 1992, citing an integral evolution model to explain the develepmental evolutionof long-generation time organisms like Homo whose yearly tolerable mutational rate is decimated by their long reproduction time.

Mammalian LINEs are coordinated to the period of meiosis just as crossing over is taking place and may both aneal any breaks and introduce new variation. There is also increasing evidence that Alu elements which a free riders on the LINE process are functioning as genetic symbionts. Several Alu inserts have now been shown to have functional regulatory status implicating Alu as a factor in primate regulatory evolution. They congregate strongly around functional genes indicating an essential function and there is evidence that they play a critical role in coordinating the cells reaction to stress by regulation of proteins activating the genes involved in repair processes such as heat shock genes (updated by jody). They are also respond differentially to methylated and non-methlyated DNA in a way which may imply a role for Alu in sexual imprinting of genes, the chromatin organization of sperm and signaling events in the early embryo.

Punctuating Equilibrium: Nature complementing Nurture

Although I am not an ultra-Darwinist and can very much appreciate the role of punctuated equilibrium in mass extinction events and the chaotic dynamics of population in the fate of ecosystems, I still find many socio-biological arguments compelling, particularly because society and culture ignores these aspects, and in failing to appreciate them, acts them out in stereotyped ways. Patriarchal cultural imperatives have also if anything tended to accentuate some socio-biological aspects while mercilessly repressing others which clearly have been influential, if not pivotal, in the evolution of human society and intelligence.

Another point upon which I have to concede acknowledgement to people like Richard Dawkins is that selection ultimatley happens upon genes, rather than whole organisms, and particularly species as a whole (group selection), although gene and organism are complementary nodes on the warp and weft of the genetic garment in space-time, neither of which can ever be fully independent of the other. However the myth of the "sefish gene" coined by Dawkins attributes emotional flaw to a necessary survival mechanism which contrdicts the actual role of emotions as revealed in sociobiological studies of original virtue. While self-sacrificing altruism is counter-evolutionary in most circumstances, emotions if anything provide a bridge of cooperative diplomacy to facilitate commitment to transaction which are likely to benefit all participants.

Given this position, the politics of evolutionary psychology still seems a little of a fence-saving compromise, avoiding the issue of individual genetic differences by claiming essentially a 'group selectionist' position that individual differences are not significant in evolutionary psychology, but only characteristics shared by society or the human species. On the other hand it is clear that sociobiology, genes, culture, individual effort and ethical choice all play a role in individual decision-making and the actions we take, so attempting to reduce freedom of choice to genetic determinism is clearly another kind of mechanistic fallacy.

If you think this "nature complements nurture" position is fence-sitting, it is so in the name of the diversity and complexity of human social reality.

This is only the bare beginning of this discussion. What it does emphasize is that evolution while not JUST a matter of opinion IS still very much a matter of opinion is specific detail.

Evolution and Diversity

Natural genetic variation arises in any reasonably sized gene pool and is continually enriched by sexual recombination. Most populations of organisms display such variation which is at all times capable of responding to changes in the natural and organismic environment of host, predators and parasites.

Whenever populations become temporarily isoloated into separate pools, a large number of varieties or even separate species can be generated, as these pictures of Darwin's finches and the fishes previously illustrate. Thousands of species of chichlid fish have appeared only thousands of years ago in African lakes as a result of such processes.

Sexual rcombination is continually generating new variety which becomes a source of diversity under any divergences in natural, sexual or other interactive forms of selection. Diversity in turn makes the species in any ecosystem robust and adaptible to changing circumstances both over time and in space. Ecosystems are made robust by the diversity of life they contain because it is from a diverse pool of genetic diversity that a strong adaptible ecosystem and an abundant productive biosphere arises. It is thus essential for us not just to preserve species but to preserve them in their natural diversity.

Evolution is modelled as a process of complexification at the edge of chaos. Populations fluctuate chaotically and may even go suddenly extinct as a result of the complex feedbacks between predators, parasites and prey, the changing circumstances in any ecosystem and the interactive selection ongoing between individuals and species in the round of survival and reproduction.

The Ediacarian Era and the Cambrian Radiation

The Cambrian Radiation 543-510 m yrs was responsible for a massive diversification into new body plans, many of which are unique to the epoch and others of which are the founders of our major orders.

There is continuing debate about the nature of the earlier Ediacarian fossils 570-543 m yrs and their link to the richly diversifying Cambrian.