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The latest version of this research: Biocosmology

PDF versions:

  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)

Critical research developments

  1. Chemist Shows How RNA Can Be the Starting Point for Life May 14, 2009
    A pivotal article showing how nucleotides can be synthesized from simple molecules.
  2. First Cells, Proton-Pumping and Undersea Rock Pores (research article pdf password "model") Oct 19, 2009
    A breakthrough in understanding how the first living cells could have been created at an undersea rock-pore interface.


Fig 1 (a) Divergence of the four forces from a single superforce. (b) Non-zero vacuum polarization at minimum energy is the cause of electro-weak symmetry-breaking. (c) Cosmic abundances of the bioelements. (d) Global t-RNA structure and (e) protein lysozyme with substrate (purple). Primary, secondary, tertiary and global structures and conformation changes in biomolecules are the result of a fractal hierarchy of strong covalent and ionic and weaker chemical interactions - H-bonding, hydrophilic, polar and ven der Waal's interactions, arising from the unresolved non-linear nature of chemical bonding (figures from King, except (e) Watson et. al.).

Biocosmology: Cosmic Symmetry-Breaking and Molecular Evolution

We now explore the structural relationship between cosmological symmetry-breaking and the form of molecular evolution leading to biological systems on Earth. It thus forms an alternative to historical hypotheses in which the form of biogenesis is believed to be the product of a linked sequence of specific conditions, bridged by stochastic selection processes.

1 : A MOLECULAR BIOLOGICAL VIEW OF COSMIC SYMMETRY-BREAKING.

The rich diversity of structure in molecular systems is made possible by the profound asymmetries between the nuclear forces and electromagnetism. Although molecular dynamics is founded on electromagnetic orbitals, the diversity of the elements and their asymmetric charge structure, with electrons captured by a spectrum of positively charged nuclei, is made possible through the divergence of symmetry of the four fundamental forces. The non-linear electromagnetic charge interactions of these asymmetric structures is responsible for both chemical bonding and the hierarchy of weak bonding interactions which result in the non-periodic secondary and tertiary structures of proteins and nucleic acids. It also provides the basis for a bifurcation theory which could give biogenesis the same generality that nucleogenesis has.

Differentiation and Inflation: The Microscopic and Cosmic Scales

Force Differentiation: The strong (nuclear binding) and weak (neutron decay) forces, electromagnetism and gravity are believed to have emerged from a single superforce shortly after the big bang, fig1(a). The strong force is believed to be a secondary effect of the colour force in much the same way that molecular bonding is a secondary consequence of the formation of atoms. The weak force has become short range because it is mediated by massive particles, which are believed to gain an extra degree of freedom by assimilating a Higg's boson (Georgi 1981, t'Hooft 1980, Veltman 1986). The symmetry between the Z and W particles of the weak force and the massless photon of elecromagnetism is thus broken by the lower energy of the polarized configuration, fig 1(b). Even heavier particles are believed to separate the strong force from these two. Force reconvergence occurs at the unification temperature fig 1(c). The strong force mesons gain mass from a different mechanism, being the energies of the bound states of the colour force, whose gluons are massless, but confined. The separation of gravity from the other forces is more fundamental because it involves the structure of space-time and may be described by a higher-dimensional superstring force in which particles become excited loops or strings in a higher dimensional space-time which is compactified into our 4-dimensional form (Green 1985, 1986, Goldman et.al. 1988, Freedman & van Nieuwenhuizen 1985).

Cosmic Inflation: A universe in a symmetrical state, but below its unification temperature is in an unstable high-energy false vacuum. The energy of the Higg's field causes inflation, in which the universe has net gravitational repulsion and expands exponentially, smoothing irregularities to fractal structures on the scale of galaxies (Guth & Steinhardt 1984). The breakdown of the false vacuum then releases a stream of high-energy particles as latent heat, to form the hot expanding universe under attractive gravitation. The gravitational potential energy thus gained equals that of the energetic particles, making the generation of the universe possible from a quantum fluctuation. However variations in the cosmic background radiation are consistent with a big-bang smoothed by inflation (Smoot 1992).

Interactive Dynamics:
The interaction between the resulting wave-particles also results in distinct effects on the microscopic and cosmic scales, namely galaxy and star formation and genesis of nuclei, chemical elements, and finally molecules, in which the non-linear nature of chemical bonding becomes fully expressed in complex tertiary structures. These interactions are modified indirectly by the nuclear forces which contribute asymmetries, spin-effects, weak decay and the nuclear energy of stars.

Particle Interaction-1: Nucleosynthesis as a Cosmological Dynamical System. The nucleosynthesis pathway generates over 100 atomic nuclei from the already composite proton and neutron. Parity between protons and neutrons is slightly broken via weak decay, fig 1(e) to balance between the lowest nuclear quantum states being filled and increasing electromagnetic repulsion. The process is exothermic and moderated by the catalytic action of several of the isotopes of lighter elements such as carbon and oxygen. The cosmic abundance of the elements fig1(d) reflects the binding energies of the nuclei and stable a-particle-like shells (Moeller et. al. 1984). The nucleosynthesis pathway has a cosmologically-general form despite having some variation in individual star systems.

Particle Interaction-2: Moleculosynthesis. The Culminating Dynamic Although, by comparison with the energies of cosmic creation or even astronomical bodies, the structures of biomolecules seem much too fragile to be a cosmological feature, symmetry-breaking of the forces leads inevitably to molecular structures as a hierarchical culmination of the interactive phase. Quarks are bound by gluons into composite particles such as the proton p+ and neutron n. These interact by the strong force via the nucleosynthesis pathway to form the elementary nuclei. Subsequently the weaker electromagnetic force interacts, also in two phases, firstly by the formation of atoms around nuclei and then by secondary interaction to form molecules. The latter phase occurs in a sequence of stages through successive strong and weak bonding interactions, producing the complex tertiary structures of biomolecules, fig 1(f,g).

The Cosmic Interaction Sequence: The Pathway to the Planetary Biosphere Galaxy formation is followed by the generation of the chemical nuclei in the supernova explosion of a short-lived hot star. In the second phase these elements are drawn into a lower energy long-lived sun-like star, the lighter [bio]elements, occurring in high cosmic abundance as a result of nucelosynthesis dynamics, fig1(d), becoming concentrated on mid-range planets. The final re-entry of the forces is thus represented by stellar photon irradiation of molecular systems, under gravitational stabilization on a planetary surface.

THE NON-LINEAR DYNAMICS OF QUANTUM CHEMISTRY

A Brief Survey of Non-linear Orbital Theory

The fact that the laws of chemistry were discovered sooner and were relatively easier to explore than the conditions underlying the unification of electromagnetism with the nuclear forces has resulted in an anomalous historical perspective which has helped to obscure some of the most interesting and complex manifestations of chemistry as a final interactive consequence of cosmological quantum symmetry-breaking. The increasing nuclear charge permits an unparalleled richness and complexity of quantum bonding structures in which electron-electron repulsions, spin-obit coupling, and other effects perturb the periodicity of orbital properties and lead to the development of higher-order molecular structures.

Although quanta obey linear wave amplitude superposition, chemistry inherits non-linearity in the form of the attractive and repulsive charge interactions between orbital systems. Such non-linear interaction, combined with Pauli exclusion, is responsible for the diversity of chemical interaction from the covalent bond to the secondary and tertiary effects manifest in the complex structures of proteins and nucleic acids.

The source of this non-linear interaction is the foundation of all chemical bonding, the electric potential. Although the state vector of a quantum-mechanical system comprises a linear combination of eigenfunctions, the electrostatic charge of the electron causes orbital interaction to have non-linear energetics.

The atomic and molecular structure of molecular orbitals illustrate the geometrical complexity that arises from the asymmetrical charge distributions of atomic orbitals. If the nuclear force did not provide up to 100 stable nuclei and the electromagnetic force were not also asymmetrically distributed between the nucleus and the electrons this complexity would be impossible. Top left: the radial densitywaves of 1s 2s 3s orbitals. Top Right: the 1+3+5 pattern of s, p, and d orbitals showing their geometry. This explains the periodic properties of the table of elements. Bottom left: s and p orbitals can form hybrids by super-position in elements such as carbon, nitrogen, and oxygen. Botton centre: two types of molecular orbitals are illustrated in which s and p orbitals are combined to create a chemical bond. Bottom right: the linear, planar, and tetrahedral arrangement of the hybrid orbitals. Pi-orbitals are also capable of forming delocalized molecular orbitals which span a whole molecule. These and the tenrahedral sp3-hybrids form the backbone of biomolecular bonding.

In the Schrödinger equation for the hydrogen atom, where ,

the potential function results in charge attraction and a negative energy. The electric potential provides the principal non-linear basis for subsequent bonding phenomena because it results in an inverse square law force and non-linear attraction-repulsion dynamics in four-dimensional space-time. Further effects such as spin-orbit coupling add complicating terms to the Hamiltonian.

The the underlying linearity of wave superposition is illustrated in the formation of linear combinations of s & p wave functions to form the four sp3 hybrid orbitals. The treatment of more complex atoms is generally simplified by approximation by perturbation theory or the self-consistent field method, in which a hydrogen-like orbital is based on purely radial repulsion factors for the inner electrons. Variation theory succinctly illustrates the interactive non-linearity of bond formation. The total energy is represented by the resonance integral of the Hamiltonian composed with the wave function, divided by the normalizing overlap integral S.

In the case of the one-electron Hydrogen molecule ion, with Saa= Sbb normalized to 1, we have 2 solutions, as indicated:

Quantum matrix methods are generally simplified to take account of only one aspect of molecular interaction and involve extensive approximations such as the independent particle approximation and Hükel theory (Brown 1972). The non-linear interactions of electron repulsions and spin-orbit coupling in the global context of molecular tertiary structure require complex computer techniques for example to predict the 3-D structure of protein molecules. These are only beginning to simulate the folding of complex molecules, again requiring approximation techniques.

The capacity of orbitals, including unoccupied orbitals, to cause successive perturbations of bonding energetics results in an interaction succession from strong covalent and ionic bond types [200-800 kj/mole] through to their residual effects in the variety of weaker H-bonding, polar, hydrophobic, and van der Waals interactions [4-40 kj/mole] merging into the average kinetic energies at biological temperatures [2.6 kj/mole at 25oC], (Watson et. al. 1988). These are responsible for secondary structures such as the a-helix of proteins and base-pairing and stacking of nucleic acids, and result in the tertiary effects central to enzyme action, whose energetics are determined by global interactions in complex molecules.


The cooperative reactivity of the active site of hexokinase demonstrates how, even after resolving the covalent and successive weaker bonding effects, and the local interactions of individual sides chains, and the larger fractal structures arising from weak bonds forming secondayry and tertiary protein structure, the entire enzyme is still capable of marked global conformation changes of a highly energetic nature. Chemical forces are thus fractal, leading right up to the globally fractal tissue structures we see in organismic biology, from the lungs to the brain. This is confirmed in the fractal dynamics of key cell structures (Watson et. al.).


Beloushov-Zhabotinskii type reaction giving rise to three-dimensional scroll waves (CK).

2.2 Fractal and Chaotic Dynamics and Structure in Molecular Systems.

Most minerals adopt periodic crystal geometries. Although some anomalies are disordered, many such as those superconducting perovskites have higher-order geometrical regularity. By contrast, the irregularties in polymers such as polypeptides and RNA is critical are establishing the richness of their tertiary structures, and their bio-activity. Variable sequence polymers with significant tertiary structure are non-periodic because the unlimited variety of monomeric primary sequences induce irregular secondary and tertiary structures. These irregularities are central to biochemistry because they result in powerful catalysts which can alter the reaction dynamics because of the generation of local activating sites globally potentiated through intermolecular weak-bonding associations. They also permit allosteric regulation. Despite being genetically coded, such molecules form fractal structures both in stereochemical terms and in terms of their relaxation dynamics.

Prigogine's theory of non-equilibrium thermodynamics, in which maximum entropy is replaced by a more general critical point of entropy production, which in an open system may not be a maximum. The associated oscillating chemical systems such as the Beloushov-Zhabotinskii reaction have demonstrated the capacity of chemical systems to enter into non-linear concentration dynamics, including limit cycle bifurcations. Period-doubling bifurcations and chaotic concentration dynamics have also been observed . Similar dynamics occur in electrochemical membrane excitation. The living cell is a non-equilibrium open thermodynamic system whose boundary, the memerane, exchanges material with the outside world. This makes it possible for life to be a negentropic system within a universe where entropy is increasing. The photosynthetic conversion of light to chemical energy and structural growth in our great forests is a prime example.

By contrast, viruses do not form a thermodynamic system as such, but rather a system of pure information. The first emergence of polynucleotides may similarly have been associated with the acrual of such information by a more direct negentropic route, phase transition.


Fig 2: (a) Symmetry-breaking model of selection of bioelements, as an interference interaction between H and CNO, followed by secondary ionic, covalent and catalytic interactions. (b) Boiling points of hydrides illustrate the optimality of H2O as polar H-bonding and structural medium for biological structure (CK). 3-D periodic table Sci Am. Sep 98

Biogenesis as a Central Synthetic Pathway

One of the central ideas of the cosmological biogenesis model is that the molecular interactions forming the pathways to the origins of life as we know it are not just an accidental set of chemical reactions out of a great variety of ad-hoc initial conditions, but that they represent a fundamental biforcation arising ultimately from cosmological symmetry-breaking of the four forces. The non-linear properties of electron orbitals cause the periodic table to have a critical sequence of bifurcations relating to the fundamental interactions.

Traditionally chemists have become so wedded to the idea of atoms and molecules as simply the "building blocks of the universe", as Isaac Asimov once put it that they cannot comprehend how they might interact as a quantum dynamical system. The fact that chemical bonding is possible between a large variety of atoms in some form or other leads to the loss of an understanding for how the non-linear electronic interactions gave rise to chemical bonding in the first place. It also leads to a mechanistic view of biogenesis, in which there is no underlying dynamical theory, but simply a search for the underlying special or initial conditions which caused the first self-replicating reaction to get going. The aim is thus either to set up a laboratory reaction by placing extreme order on the system, to elucidate this reaction pathway, or an attempt to use random processes and probabilistc arguments to model the likelihood that some collection of replicating molecules might accidentally come together. This has marred prebiotic research and profoundly slowed its advances.

Two illustrations hightlight this conceptual barrier. There is a 40 year time span between Miller and Urey's first spark experiments elucidating pathways from simple precursors to the purine nucleic acid bases, and the modification of this synthesis which led to good yields of the pyrimidines. Likewise there has been two decades of research in attempting to polymerize ribonucleotides, littered with failures due to oversimiplification of RNA interactions and mechanistic variants such as peptide-nucleic acids, before the ribonucleotide evolution techniques of Szostak and finally simple relationship between polymerizing ribonucleotides and montmorrilonite clays became obvious.


Atomic radii and electronegativity scales indicate the optimal bonding energetics of CNO and particularly the strong polarity of O. A clear differentiation can also be seen between the ionic potentials of Na and K.

The cosmological biogenesis theory asserts the following three points:

1. All molecular interaction is highly non-linear, and forms an unresolved fractal interactive milieu which permits not only the cascade of weaking bonding and global interactions characterizing protein enzymes and nucleic acids but also on a larger scale the tissue structures of whole organisms. This means that, while nature can be crystalline, it can also display emergent properties on larger scales which are very difficult to predict from an examination of the components "the whole is more than the sum of the parts". The non-linear perspective realizes emergence within an in-principle reductionist viewpoint because the underlying principles are quantum chemistry, but the consequences are emergent fractal interaction. This situation is clearly illustrated in the great difficulty of fully accurate modelling of the electronic dynamics of even simple atoms because they are many-body problems, and by the complexity of the protein-folding problem (Sci Am. Jan 91 see also Shape is All NS 24 Oct 98 42).

2. The entire molecular environment is non-linear in a way which is capable of exploring its phase space in the manner of a chaotic dynamical system. This means that planetary, terrestrial and molecular systems display sufficient chaos to generate all the varieties of structural interaction possible. These non-linearities make the natural environment a quantum equivalent of a Mandelbrot set in which a potentially infinite variety of dynamics are possible. The overwhelming majority of chemical experiments into the origins of life (with the notable exception of the original spark experiments) attempt to defeat this process by introducing simple overweaning conditions of order to force simple clear-cut products out of the system.

3. Underlying this rich chaotic interaction is a universal bifurcation pathway which is a direct consequence of the form of cosmological symmetry-breaking of the four quantum forces. While there may be more than one way that molecular replication could occur in chemistry, the RNA-based form of life is nevertheless a central bifurcation product of the interaction between the fundamental forces and by no means a mere accident of unlikely circumstances.


The unique and key nature of H-bonding in biogenesis is illustrated in the
structure of the alpha helix of proteins and the pairing of nucleotide bases (Watson et. al.).

Principal Symmetry-splitting : The Covalent Interaction of H with C, N, O.

Quantum interference interaction between the two-electron 1s orbital and the eight-electron 2sp3 hybrid. The resulting three dimensional covalent bonds give C, N and O optimal capacity to form diverse polymeric structures in association with H. Symmetry is split, because the 1s has only one binding electron state, while the 2sp3 has a series from with differing energies and varied occupancy, as the nuclear charge increases. The 1s orbital is unique in the generation of the hydrogen bond through the capacity of the bare proton to interact with a lone pair orbital. The CNO group all possess the same tetrahedral sp3 bonding geometry and form a graded sequence in electronegativity, with one and two lone pairs appearing successively in N and O.

Polymeric condensation of unstable high-energy multiple-bonded forms. Some of the strongest covalent bonds are the multiple-bonds such as ­ CC ­, ­ CN, and > C = O. These can be generated by applying any one of several high-energy sources such as u.v. light, high temperatures (900oC), or spark discharge. Because of the higher energy of the resulting pi-orbitals, these bonds possess a specific type of structural instability in which one or two pi-bonds can open to form polymeric structures, particularly when bound to H and alkyl groups, as under reducing conditions. Most of the prebiotic molecular complexity generated by such energy sources can be derived from mutual polymerizations of HCCH, HCN, and H2C = O, including purines, pyrimidines, key sugar types, amino acids, porphyrins etc. They form a core pathway from high energy stability to structurally unstable polymerization, which we will examine in the next section.

Radio-telescope data demonstrates clouds of HCN and H2CO spanning the region in the Orion nebula where several new stars are forming. All of A, U, G, and C have been detected in carbonaceous chondrite meteorites, which also contain membrane-forming products. HCN and HCHO polymerizations also lead to membranous microcellular structures. Although the presence of CO2 as a principal atmospheric gas on the early earth could have reduced the quantities of such reduced molecules, HCN could have been produced as a transient in the early atmosphere leading to heterocyclic products. A variety of microenvironments would still have had access to reducing conditions.

The formation of conjugated double and single bonds in these reactions results is the appearance of delocalized pi-orbitals. Such orbitals in heterocyclic (N, C) rings with conjugated resonance configurations also enable lone pair n > p* and also p > p* transitions, resulting in increased photon absorption. These effects in combination play a key role in many biological processes including photosynthesis, electron transport and bioluminescence.


The dynamical subtlety over simple crystalline form is demonstrated by the exterme variety of snowflake form which displays both fractal dendrite growth from the vapour solid interface, which varies with external conditions of temperature and humidity and a global coherence of geometry which develops partly from quantum interactions including H2O molecules'walking' across the crystal surface.

Secondary Splitting between C, N, and O : Electronegativity Bifurcation.

In addition to varying covalent valencies, lone pairs etc., the 8-electron 2sp3 hybrid generates a sequence of elements with increasing electronegativity, arising from the increasing nuclear charge. This results in a variety of secondary effects in addition to the oxidation-reduction parameter, from the polarity bifurcation into aqueous and hydrophobic phases to the complementation of CO2 and NH3 as organic acid and base.


The tetrahedral H-bonding of H2O molecules in ice. In liquid water, 80% of the molecules are in such ordered relationships at any given time. The structures of DNA and proteins derive their energetics from their interaction with water. The stability of polynucleotides is a combination of hydrophobic base-stacking and polar interaction with the phosphate-sugar backbone. Soluable proteins (myoglobin is illustrated) derive their stability and energetics through their interactions with induced water structures. Generally these form micelle structures which have a hydrophobic interior surrounded by polar amino acids (see the illustration of lysozyme). All polymerization pathways of polysaccharides, polynucleotides and polypeptides share a common feature - dehydration is the basis of polymerization, making water the common factor in the negentropic assimilation of order (Watson et. al.).

Optimality of H2O: Polarity, Phase and Acid-base bifurcations. Ionic and Hydrogen bonding.

Outside metals such as mercury, water has one of the highest specific heats. This is a reflection of the large number of conformational degress of freedom it contains. It is also capable of a very unusual number of interactions, ionic, polar, H-bonding, acid-base and the polarity bifurcation into hydrophilic (water-loving) and hydrophobic (oily) phases in biological molecules and structures such as the lipid membrane, which is a sandwich of oily and watery moieties.


(a) Isolation of non-polar molecules into the hydrophobic phase is facilitated by water-bonding clathrate structures whose impressed order is reduced and entropy increased, by reducing these strictures to one common envelope. (b) polypeptides and (c) polynucleotides both form by elimination of H2O, accompanied by ATP energy in the latter as illustrated in the left of the two monomers.

Dehydration is the common currency of polymerization, beginning with the mineral pyrophosphate linkage of ATP. The central biopolymers, polynucleotides, polypeptides and polysacharides are uniformly linked by the removal of a molecule of water, dehydration in the aqueous medium. Furthermore the three-dimensional structures of the nucleic acid double-helix, globular enzymes, membranes and ion channels are all made structurally and energetically possible only through the interactions of these molecules with water and the induced H2O structures that form around them in solution. Both nucleic acids and proteins consist of a balance of hydrophilic and hydrophobic interactions which in the former give hydrophobic base-stacking within a polar back-bone and with enzymes a non-polar micelle surrounded by hydrophilic groups.

Differential electronegativity results in several coincident bifurcations associated with water structure. A symmetry-breaking occurs between the relatively non-polar C­H bond and the increasingly polar N­H and O­H. This results in phase bifurcation of the aqueous medium into polar and non-polar phases in association with low-entropy water bonding structures induced around non-polar molecules. This is directly responsible for the development a variety of structures from the membrane in the context of lipid molecules, to the globular enzyme form and base-stacking of nucleic acids.

The optimal nature of water as a hydride is illustrated in boiling points. By comparison with ammonia H3N, water H2O has balanced doning and accepting H-bonds and a stronger polarity. Such polar properties are also clearly optimal over H2S, alcohols etc.

The discovery by the ISO Infra-red Space Observatory, of widespread incidence of water around stars, planets and throughout the universe where stars are forming has led increasing weight tothe cosmological status of water as a pre-cursor to life. - AP Apr 98

Water provides several other secondary bifurcations besides polarity. The dissociation of H2O  into H+ and OH- lays the foundation for the acid-base bifurcation, while ionic solubility generates anion-cation. H-bonding structures are also pivotal in determining the form of polymers including the alpha helix, base pairing and solubility of molecules such as sugars. Many properties of proteins and nucleic acids, are derived from water bonding structures in which a mix of H-bonding and phase bifurcation effects occur. The large diversity of quantum modes in water is exemplified by its high specific heat contrasting with that of proteins (Cochran 1971). Polymerization of nucleotides, amino-acids and sugars all involve dehydration elimination of H2O, giving water a central role in polymer formation.

P and S as Low-energy Covalent Modifiers - the delicate role of Silicon.

The second-row covalent elements are sub-optimal in their mutual covalent interactions and their interaction with H. Their size is more compatible with interaction with O, forming e.g. SiO32-, PO43- & SO42- ions including crystalline minerals. The silicones are notable for their O content by comparison with hydrocarbons. However in the context of the primary H-CNO interaction, two new optimal properties are introduced.

PO43- is unique in its capacity to form a series of dehydration polymers, both in the form of pyro- and poly-phosphates, and in interaction with other molecules such as sugars. The energy of phosphorylation falls neatly into the weak bond range (30-60 kj/mole) making it suitable for conformational changes. The universality of dehydration as a polymerization mechanism in polynucleotides, polypeptides, polysaccharides and lipids, the involvement of phosphate in ATP energetics, RNA and membrane structure, and the fact that the dehydration mechanism easily recycles, unlike the organic condensing agents, give phosphate uniqueness and optimality as a dehydrating salt.

The function of S in biosystems highlights a second optimality. The lowered energy of oxidation transitions in S particularly S-S ´ S-H , by comparison with first row elements, gives S a unique role both in terms of tertiary bonding and low energy respiration and photosynthesis pathways.

It has recently been discovered that oligoribonucleotides will polymerize effectively on silicate clay surfaces, where the positive ions of atoms such as Al make polar interactions with the phosphate backbones of RNA, stabilizing the molecules and making further polymerization possible in an ordered geometry. This consitiutes a major breakthrough in the modelling of life's origins and demonstrates the sensitivity of the biogenic pathway to the subtle differences of electronegativity of the second-row covalent elements phosphorus and silicon.

Ionic Bifurcation.

The cations bifurcate in two phases : monovalent-divalent, and series (Na-K, Mg-Ca). Although ions such as K+ and Na+ are chemically very similar, their radii of hydration differ significantly enough to result in a bifurcation between their properties in relation to water structures and the membrane. Smaller Na+ and H3O+ require water structures to resolve their more intense electric fields. Larger K+ is soluble with less hydration, making it smaller in solution and more permeable to the membrane (King 1978) . Ca2+ and Mg2+ have a similar divergence, Ca2+ having stronger chelating properties. This causes a crossed bifurcation between the two series in which K+ and Mg2+ are intracellular, Mg2+ having a pivotal role in RNA tranesterifications. Cl- remains the central anion along with organic groups. These bifurcations are the basis of membrane excitability and the maintenance of concentration gradients in the intracellular medium which distinguish the living medium from the environment at large.

Transition Element Catalysis

These add d-orbital effects, forming a catalytic group. Almost all of the transition elements e.g. Mn, Fe, Co, Cu, Zn are essential biological trace elements (Frieden 1972), promote prebiotic syntheses (Kobayashi and Ponnamperuma 1985) and are optimal in their catalytic ligand-forming capacity and valency transitions. Zn2+ for example, by coupling to the PO43- backbone, catalyses RNA polymerization in prebiotic syntheses and occurs both in polymerases and DNA binding proteins. Both the Fe2+-Fe3+ transition, and spin-orbit coupling conversion of electrons into the triplet-state in Fe-S complexes occur in electron and oxygen transport (McGlynn et. al. 1964). Other metal atoms such as Mo, Mn have similar optimal functions, e.g. in N2 fixation.

Fig 3 : (a) The perturbing effect of the neutral weak force results in violation of chiral symmetry in electron orbits. Without perturbation (i) the orbits are non-chiral, but the action of Zo results in a perturbing chiral rotation. (b) Autocatalytic symmetry-breaking causes random chiral bifurcation (i). Weak perturbation results in only one chiral form (iii) (King).

Chirality bifurcation.

Although the electromagnetic force has chiral symmetry, the electron also interacts via the neutral weak force when close to the nucleus. This causes a perturbation to the electronic orbit causing it to become selectively chiral, fig 3(a) (Bouchiat & Pottier 1984, Hegstrom & Kondputi 1990). In a polymeric system with competing D and L variants, in which there is negative feedback between the two chiral forms of polymerization, making the system unstable, the chiral weak force provides a symmetry-breaking perturbation. In a simulation, fig 3(bi) high [S][T] causes autocatalytic bifurcation of system (ii), resulting in random symmetry-breaking into products D or L. Chiral weak perturbation (iii) results in one form only. The selection of D-nucleotides could have resulted in L-amino acids by a stereochemical association (Lacey et. al. 1988).

Inner Circles New Scientist 8 Aug 98 11 reports on findings that there is a 17% net circular polarization in light in gas clouds in the Orion nebula where new stars are forming. Although this was infra-red light James Hough says it should also apply to the ultra-violet light. This would explain the excess of L-amino-acids found in the Murchison meteorite, suggesting a cosmic rather than accidental origin for the handedness of biological molecules on earth.

Tertiary Interaction of Mineral Interface.

Both silicates such as clays and volcanic magmas have been the subject of intensive interest as catalytic or information organizing adjuncts to prebiotic evolution. Clays have been proposed as a primitive genetic system and both include adsorbent and catalytic sites. The mineral interface involves crucial processes of selective adsorption, chromatographic migration, and fractional concentration, which may be essential to explain how rich concentrations of nucleotide monomers could have occurred over geologic time scales.

More recently a fundamental interaction between RNA and clays has been elucidated wich appears to be central in enabling oligo-ribonucleotides to polymerize in an ordered way while bound to the positively charged metal groups in montmorrilonite clays, bridging the gap between small random ribo-oligomers and RNA molecules of a length capable of self-replication.

Key polymerizations

Key polymerizations such as those of HCN and HCHO are proposed to generate a series of generic bifurcation structures through combined autocatalytic and quantum bond effects, which include major components of the metabloism including nucleotides, polypeptides and key membrane components. These will be examined in the next section

The astronomical perspective


The presence of HCN and HCHO clouds in the Orion nebula (left) attests to the ubiquitous nature of the energetic monomeric precursors of biomolecules, in particular RNA. CO clouds (right) occupy a protosolar disc 20 times the size of the orbit of Pluto (King, Scientific American).

The occurrence of the key precursors of biomeolecules are not in any way confined to Earth of the specific conditions of Earth. Much of the organic material on earth is believed to have peppered down from comets and carbonaceous meteorites especially earlier in the evolution of the solar systems when less of the original material from the proto-solar gas and dust cloud had been swept away by collision. Protosolar gas clouds in the Orion nebula are known to contain precisely HCN and HCHO as shown above. Certain parts of the universe give off an infra-red signal not unlike that of carbohydrates. Interstellar dust grains are also known to contain organic molecules. In fact the occurrence of organic molecules is essentially ubiquiitous to all second generation sun-like stars containing a mix of elements of nucleosynthesis formed from the material of previous supernovas.

Indeed their presence is so commonplace and the incidence of life on Earth is so early that the possibility that arose previously to the formation of Earth cannot entirely be ruled out. Cosmological biogenesis is however ideally suited to the conditions actually occurring on Earth with plentiful water, a temperature just above the liquefaction of water, a good supply of organic molecules and a steady mild solar input.


Terrestrial planets Venus to Uranus: It is clear that the extreme variety of our own planetary system and the like variety of the many galilean satellites spells out a very important feature of astronomical law. In four-dimensional space-time gravitational forces are inverse square law. In addition to the natural graduation of temerature noted above in the proposolar disc, prviding for life as we know it on the outer edge of the inner region where water is liquid, the chaotic variation of conditions produced by such non-linear force fields generates a situation of extreme variety in the universe, much like the Mandelbrot set does. While this may seem to make the other planets of our system a little alien, it does guarantee the universe will explore its entire phase space of possibilities virtually guaranteeing it will leave no stone (planet) unturned in its exploration of the possibilities that life will emerge (Hubble public gallery).

Just as one can consider the non-linearities of the electromagnetic force in developing the fractal dynamics of molecules, one can also appreciate the significance of non-linearities in gravitation in forming the rich diversity of planets and satellites we see in our own solar system. Other stars now seem to be quite richly endowed with planets, but these again show very marked variation. Such marked variationis characteristic of non-linear dynamics, which serves to accentuate existing differences for example in temperature and composition between the planets to cause unique effects, such as the highly acidic, electrified runaway greenhouse atmosphere of venus.

Far from considering these extreme variations as reducing the likelihood of finding life on other planets, what it demonstrates is that on an astronomical scale as well as the microscopic, the universe behaves very much like a Mandelbrot set in establishing dynamics of uniqueness and diversity which explores the dynamical space of possibilities.

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On to Biocosmology Part 2: Central Polymerization Pathways?