Genesis of Eden

Genesis Home

BIOCOSMOLOGY

Chris King
Department of Mathematics
University of Auckland, New Zealand
The 2007 version of this paper is in PDF form linked below
  1. Prebiotic Epoch: Cosmic Symmetry-breaking and Molecular Evolution (pdf)
  2. Evolutionary Epoch: Complexity, Chaos and Complementarity (pdf)
  3. Consummating Cosmology: Quantum Cosmology and the Hard Problem of the Conscious Brain (pdf)

CONTENTS 2009 edition

  1. Paradise on the Cosmic Equator
  2. Generating a Complex Twisted Universe
  3. The Abudantly Fecund Universe
  4. Quantum Chemistry as Non-Linear Complexity
  5. The Non-recurrent Table and the Elementary Bifurcation Tree
  6. Structural Dynamics of Core Polymerization Pathways
  7. RNA and Cosmology
  8. Diverse Horizons of the RNA Epoch
  9. Universal Stability Structures in Molecular Biology
  10. The Last Universal Common Ancestor
  11. The Precocious Origins of Life on Earth
  12. Quantum Evolution at the Edge of Chaos
  13. The Five Kingdoms as Ecosystemic Bifurcations
  14. Stochastic Accident versus the Relentless Limits of Selection
  15. Homeotic Universality
  16. Virus-Cell Complementarity
  17. Sexuality as Complementarity-based Symmetry-breaking
  18. The Mammalian Brain as a Universal Algorithm
  19. The Central Enigma of Consciousness
  20. The Cosmology of Life's Diversity
  21. References


Fig 24: Dion Wright The Mandala of Evolution detail (Arguelles). Is evolution just a series of fixations of accidental mutational opportunities or is it a situation where genetic algorithms and natural selection are exploring and optimizing potentialities derived from underlying bifurcations in the cosmological milieu?

The Tree of Life: Tangled Roots and Sexy Shoots: Tracing the genetic pathway from the first eucaryotes to Homo sapiens Chris King Jan 2009


EVOLUTION AS A QUANTUM PROCESS AT THE EDGE OF CHAOS

(a) Mutation, Bifurcation and the Quantm Limit
Evolution by mutation and selective advantage is traditionally regarded as an opportunistic drunkard's walk by random mutation into a variety of advantageous configurations, which then become fixed by selective advantage as stunningly effective incremental historical accidents. However if biochemical structures, from simple molecules through to nucleotides and major biochemical pathways may be stability structures arising through bifurcation of the fundanmental forces, only later captured by genetic takeover, how much of bioloigcal evolution is a reflection of funademntal bifurcations as well?

Evolution is partly a stochastic opportunistic process and partly an optimizing selective response to bifurcations in the eco-landscape, as T.H. Waddington emphasized in "The Strategy of the Gene" (1957) in his concept of the 'chreode'. The balance between the adventitious and the selectively optimized is a reflection of the deeper underlying process of quantum complementarity. In an interference experiment, the trajectories of individual photons are unpredictable by quantum uncertainty of position. The pattern of wave interference only becomes established statistically through the passage of many photons, which through their statistics of particle absorption by individual atoms demonstrate the wave amplitude variation of the interference pattern. This convergence to the probability interpretation is even more marginal in the complex macroscopic biological world than it is in the quantum world of small numbers of events, and for the same reason. Although their effects are large in macroscopic organisms, mutations themselves are unique kinetic events in the quantum world of molecules and molecular orbitals. Such highly specific mutational transformations are vastly rarer than the photons in a conventional interference experiment and tend to the uncertainty of a single unrepeated event. This makes it possibel for some adventitious aspects of evolution to be in effect historical manifestations of the underlying nature of quantum uncertainty and entanglement.

Complementing this, selective advantage has unrestricted gain, which will over time, given enough mutations, explores any bifurcations or optimalities in the physical environment. Thus many of the marvels of evolution such as the camera eye, far from being an impossibility are inevitable because of the immense optimality of accessing the fundamental quantum mode of directional photon absorption. This point is well-illustrated by Richard Dawkins in the evolution of the camera eye as illustrated in fig 25.


Evolutionary root of the tree of life and its diversification into archaea, bacteria and eucaryotes appears to have gone through an early period of cool temperature consistent with an RNA era, followed by a hot period (Anathaswamy R12, Boussau B, Blanquart S, Necsulea A, Lartillot N, Gouy M 2008 Parallel adaptations to high temperatures in the Archaean eon Nature 456 942-6).

(b) The Five Kingdoms and the auto-heterotrophic bifurcation
The five kingdoms of plants, animals and fungi, protista and procaryotes themselves reflect major bifurcations of the thermodynamic environment. There is a fundamental bifurcation of energy metabolism between photosynthetic fixation of incident solar energy, the principal incident energy source at the planetary surface and all other forms of heterotrophic energy-pillaging budget, including animals as frank predators, fungi as saprophytic and symbiotic composers, the highly catalytic biochemical pathways of procaryotes subtended by the diverse partially differentiated protista. The biochemical basis of both photosynthesis and respiration is through a common electron transport pathway which utilizes common primal molecules such as porphyrins and nucleotide coenzymes as receptors. The major divisions of life are thus clearly cosmological in nature.

We can thus anticipate that forms of life based on the central bifurcation pathway will utilize lipid membranes porphyrins and nucleotides to elicit photosynthesis and respiration by a broadly similar mechanism We can also anticipate the emergence of multicellular plants, of animals themselves divided into herbivorous and carnivorous habits and of a division of the decomposing anabolic pathways between the 'fungal' and 'bacterial' strategies. One can also look for a variety of universals within the more complex scheme of life which, despite the varieties of mutational opportunity are still capitalizing on underlying bifurcations within the planetary and biochemical environment.


Fig 25: Two aspects of evolution, adventitious mutation and cumulative selection are contrasted. Left: Cantharanthus rosea makes the unusual indole vincristine, unusual in structure and almost unique to the biological world. While this has occurred through natural selection, it is an unusual avenue which appears to be the result of an initial fortuitous mutation. Right: By contrast, the development of the camera eye (Dawkins 1996), despite being touted by creationists as impossible for evolution, is virtually inevitable by natural selection, because its formation results from a simple topological bifurcation of a photoreceptive hollow and the fact that directional photon reception is a core quantum interaction as fundamental as photosynthesis itself, evidenced by the same carotenoids in both vision and as accessory pigments in photosynthesis. These two examples contrast the aspects of evolution which do and do not converge to the statistical limit as quantum phenomena.

In an interference experiment, the trajectories of individual photons are unpredictable by quantum uncertainty of position. The pattern of wave interference only becomes established statistically through the passage of many photons, which through their statistics of particle absorption by individual atoms demonstrate the wave amplitude variation of the interference pattern. This convergence to the probability interpretation is even more marginal in the complex macroscopic biological world than it is in the quantum world of small numbers of events, and for the same reason.

Although their effects are large in macroscopic organisms, mutations themselves are unique kinetic events in the quantum world of molecules and molecular orbitals, vastly rarer than the photons in a conventional interference experiment and tending at all times to the unique uncertainty of the single unrepeated event. And as Richard Dawkins (1976) has pointed out so ruthlessly and effectively, it is gene selection which drives the organism rather than vice versa. This is exactly what causes evolution theorists to emphasize the non-universal, idiosyncratic nature of mutational evolution, but it also confirms that evolution is potentially subject to the covert laws of quantum non-locality and rife with the consequences of quantum uncertainty.

Evolution is always a counterpoint between the adventitious and the inevitable beneficiaries of selective advantage, and selective advantage is itself an almost infinite gain mechanism which will exploit any bifurcations or optimalities in the physical environment. Thus many of the marvels of evolution such as the camera eye, far from being an impossibility are inevitable because of the immense optimality of accessing the fundamental quantum mode of directional photon absorption. This point is well-illustrated by Richard Dawkins in the evolution of the camera eye as illustrated in fig 25.


Fig 26: Homeotic genes. Left: Sequence of homeotic genes is compared in the insect and vertebrate, showing their common role in segmental organization (De Robertis et. al.McGinnis et. al.), Top right: Knotted maize mutants have a mutation in a homeobox gene regulating differentiation. Similar homeobox genes have been found in tomatoes and rice (Homeobox Harvest Scientific American June 91). Lower right: 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).

Homeotic Universality
Further signs of a universality in the evolutionary realm are the ubiquitous use of the homeotic genes for morphogenic organization of the organism, particularly the segmental organization from the head to the tail, which are common not only to all metazoa but to plants and fungi as well, fig 26. The underlying mechanism of homeotic gene morphogenesis may represent a type of universal solution to developing body plans. The development of this system seems to be the key step enabling the emergence of multicelled organisms and their divergence into plants, animals and fungi. Other signs are the predominance of bilaterally symmetrical organisms with an asymmetric ventro-dorsal and head-tail axis. The major division between arthropods and vertebrates also hints at a universality, which in addition to complementations, such as exoskeleton versus endoskeleton and anal versus buccal gastrulation, adopt broadly complementary roles in ecosystemic terms.

Although the homeobox sequence and their key proteins are more complex than can be accounted for by the cosmological argument, the principles by which they evolved may nevertheless be a type of universal solution. This is consistent with the long time from the first emergence of eucaryotes to metaphyta in the Ediacarian and Cambrian radiations about 600 million years ago. This long delay, fig 35(b), is indicative of there being only one, or a few effective solutions to this problem giving it potential universality beyond our own metaphyta.

Sexuality as Complementarity-based Symmetry-breaking
Sexuality and its symmetry-breaking into male and female genders may be a biological manifestation of wave-particle duality itself. Sexuality's immediate cause appears to lie in an arms race between prarasites and their hosts in which sexual organisms survive epidemic disease and inherit recombinaltional diversity as a spin off. This is the key expalanation which can provide the 2:1 advantage in the first generation which can compensate for the 50% loss of our genes in sexuality by comparison with full parthenogenesis (Ridley). A symmetry-breaking can then occur as a result of cytoplasimic selfish gene-wars which causes cytoplasmic incompatibility between isogametes and precipitates gender by digesting the cytoplasm and organelles of one sex's isogamete to become the sperm. The lower reproductive investment of the sperrm and the male reproductive strategy of venture risk results inevitably (Ridley, Watson). The symmetry-breaking is a wave-particle complementarity between a huge enveloping ovum containing the wave-manifesting membrane and all the cytoplasm including cytoplasmic DNA, all cell organelles complementing millions of essentially particulate sperm - simply motile molecular DNA - which compete to fertilize it. Its basis is complementary aspects of molecular structure in forming the membrane on the one hand and particulate DNA on the other. Its effects are extreme in the human genders - a symmetry-breaking of reproductive investment in which men make a small multiple investment in many partners while women have to make an honest overt investment in massive pregnancy, lactation and early child-rearing. The complementarity between these competing genetic strategies has ensured the evolution of most species, including humans, is based on female reproductive choice in a situation of strategic gender paradox. Although gendered sexuality appers to arise late in the evolutionary tree, it may thus nevertheless be a response to complementarities of a fundamental physical nature which emerge as part of the interactive phase of cosmological re-entry.


Fig 26a: Engendered sexuality is a symmetry-breaking general to almost all higher organisms.

Virus-Cell Complementarity
(e) Immunity, Variation and Genetic Symbiosis
Common to plants and animals are a basic set of pathways to deal with microbial infection and tissue stress caused by injury and predation (Roots of Immunity New Sci 19 Feb 2000). The development of immunity and tissue complexity also comes with a major theme of gene and functional domain rearrangement, which has seen the interpenetration of transposable elements and structural gene sequences in a possible complementation between cellular and transposable element genes, particularly the almost ubiquitous retroviral and retrotransposon elements which still carry the reverse transcriptases capable of generating DNA from an RNA template. The advent of the LINE elements in humans extends far back to the origins of multi-celled organisms, as their transcriptase shares evolutionary homologies with telomerase and viral reverse transcriptases. Along with their more recent fellow-travellers, SINEs such as Alu they have been proposed to be in a form of genetic symbiosis permitting modular evolution of the genome and acting as regulators of cell stress (King 1992, Schmid 1998 , Int. Human genome Consort 2001). SINEs themsleves are derived from generic cellular RNAs such as tRNA and the signal recognition particle that admits nascent proteins into the membrane from the ribosome. They have recently been identified with transcribed functional genes, illustrating a form of convergent evolution based on genetic symbiosis evolving along several parallel routes within the mammalian radiation.


Fig 27: Evolution of the vertebrate brain shows reduction of the specialized sensory areas such as the optic lobe, which is replaced by outgrowth of primitive generalized cerebral tissue from the olfactory processing area to form a universal sense and conceptual organ embracing all sense (and thus quantum) modes.

Neurocosmology: The Mammalian Brain as an Emergent Universal Algorithm
An ultimate universality which is of great significance to homo sapiens as a species is the universality of quantum modes of perception and the nature of the edge of chaos, neurotransmitter-based electrochemical nervous system. Within the domain of nervous systems there is an evolution towards universality as significant as that of the homeotic genes. Firstly there is a great deal of commonality between wide varieties of organisms with seemingly very different nervous system organization, in terms of a universality of neurotransmitter types and the modes of communication between neurons. Although the nervous systems of arthropods and vertebrates are very different in net organization, they use a similar array of amine and other neurotransmitters which themselves may originate from primal interaction with the lipid membrane and its excitability as noted earlier. Also shared are the principles of parallel processing, edge of chaos dynamics and the use of 'silent' cells with continuous potentials as organizers.

Within the vertebrate phylum, there is a clear evolution from specific hard-wired dedicated structures for the senses, such as the primitive optic lobe towards generalized sense organs arising themselves from smell, the least differentiated of the senses, to form, not only a generalized sense organ, but also a universal cognition and experiential organ in the form of the cerebral cortex. This generalized organ by the time of the higher mammals has almost completely taken over the original sensory areas to the point where a new paradigm of sensory modelling which appears to use general rules to model all the senses from smell through hearing to vision using variations on the same general set of principles.

This development of cortical organization is also accompanied by a transformation of the genetic paradigm from the confines of the selfish gene and its direct generalizations in kin and reciprocal altruism to a much more general emotioanl connection which can transcend familial, racial and even species barriers to make possible a new paradigm of ecological evolution. Central to the evolution of the mammalian cortex is its foundation in the limbic system and with it fundamental questions of the relationship between flight and fight and personal transformation lurking in the regions linking the amygdala and the temporal cortex. This region, sometimes called the "god spot" illustrates how subtly evolution at the edge of chaos can reach towards an ecological manifestation which may permit a win-win solution through exploiting the firontiers of physical cosmology.

On to Consummating Cosmology: The Emergance of Sentient Consciousness