



































Unraveling the Tree of Life


DNA Decipher Journal | January 2012 | Vol. 2 | Issue 1 | pp. 01-35 
King, C., Biocosmology: Part I 

ISSN: 2159-046X DNA Decipher Journal 
Published by QuantumDream, Inc. 

www.dnadecipher.com 

 

1 

Article 

Biocosmology: Part I 
 

Chris King
*
 

 

 ABSTRACT 

Twenty years ago (King 1978) I proposed the biocosmological thesis that the form of life's origin and 

evolution is a cosmological interactive process defined in the cosmic symmetry-breaking at the origin of 

the universe. With the passage of time, the pendulum has shifted from the improbability of life as a 

random molecular accident to an awareness that central biomolecules may be cosmologically abundant 

products of the clouds forming young stars leading to an RNA-era in which both catalysis and 

replication emerged from one cosmologically dervied molecule RNA. . This paper unveils the non-linear 

quantum foundations of biocosmology as the founding science of life. Part I of this paper covers the 

following topics: 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; and 11. The Precocious Origins of Life 

on Earth. 

Key Words: cosmology symmetry-breaking, molecular evolution, chaos, complex system, 

neurodynamics, quantum non-locality, transaction, consciousness. 

 

1. Paradise on the Cosmic Equator 

Could biological structures such as tissues, and organisms be cosmological interactive structures as 

fundamental as stars and galaxies to the cosmic design? The conventional objections are obvious. Life is 

a fragile insignificance among the immense energies of black holes, galaxy formation and the big-bang. 

Its tiny entropy-reducing photosynthetic energy budget and fragile chemical bonds are insignificant on 

the cosmic scale. Biological structures are genetically coded in a vast variety of ways by specific nucleic 

acid sequences. Biological evolution is a stochastic process combining random mutation and selective 

advantage, many of whose manifestations are opportunistic. Nevertheless many features of life as we 

know it on Earth may be the product of cosmic factors determining the laws of nature which make life 

possible. 

Although traditional chemistry, despite its quantum foundations, treats molecules as arbitrary building 

blocks which can be arranged in almost any combination using suitable reagents and conditions, there is 

clear evidence for optimality of many prebiotic and biological molecules, giving life as we know it a 

cosmological basis as a culminating interactive structure. 

                                                           

*
 Correspondence: Chris King  http://www.dhushara.com E-Mail: chris@sexualparadox.org    

http://www.dhushara.com/
mailto:chris@sexualparadox.org


DNA Decipher Journal | January 2012 | Vol. 2 | Issue 1 | pp. 01-35 
King, C., Biocosmology: Part I 

ISSN: 2159-046X DNA Decipher Journal 
Published by QuantumDream, Inc. 

www.dnadecipher.com 

 

2 

 
 

Fig 1: Paradise on the Cosmic Equator: Darwin, the serpent and the hoopoe in Eden: Biological 

systems form a central cosmological manifestation of interactive complexity in the universe. 

When space-time is considered as a 4-manifold, biology's 'equatorial' position is as fundamental 

in cosmological terms, even though biological energetics are too weak to withstand either the 

polar big-bang at the origin nor the possible final fates, whether they are heat death by attrition 

in an ever-expanding universe, a big crunch, or fractal inflation, as shown at the left. 

This paper explains how and why the origins of chemical life, major aspects of biological evolution and 

the elaborate emergent structures of tissues, from biomolecules up to cellular organelles and even to the 

doors of perception of the conscious brain, are a fractal interactive consequence of the non-linear laws of 

nature established at the cosmic origin. This reverses the Copernican revolution, putting life and with it 

ourselves back to centre stage in the cosmic arena. 

Biology is a product of the twisted laws of nature dervied from cosmic symmetry-breaking. The rich 

diversity of structure in molecular systems is made possible by the profound asymmetries developing at 

the cosmic origin, between the nuclear forces, gravity and electromagnetism. The diversity of the 

elements and their asymmetric charge structure, with clusters of negatively charged electrons orbiting a 

massive nucleus containing all the positive charges in a concentrated nuclear 'droplet', is made possible 

only through the divergence of symmetry of the four fundamental forces. Without these asymmetries 

there would be only one or two simple atoms and none of the richness of the almost unlimited variety of 

molecular structures which can be generated by the over one hundred complex atoms occurring in nature 

as we know it. Chemical bonding is a consequence of the non-linear inverse square law of 

electromagnetic charge interaction in space-time. This non-linearity also gives rise to a succession of 

weak bonding interactions, generating the complex non-periodic secondary and tertiary structures of 

proteins and nucleic acids. 



DNA Decipher Journal | January 2012 | Vol. 2 | Issue 1 | pp. 01-35 
King, C., Biocosmology: Part I 

ISSN: 2159-046X DNA Decipher Journal 
Published by QuantumDream, Inc. 

www.dnadecipher.com 

 

3 

 
 

Fig 2: Galaxies and galaxy clusters illustrate the fractal self-similar nature of large scale 

fluctuations in the universe. According to some versions of inflation theory these may be 

inflated quantum fluctuations. Left: Galaxy MC 100. Right: a distant gravitationally-lensed red 

galaxy beyond a closer cluster, including blue galaxy lover right. Top right inset large scale 

structure of the universe including the 'great wall'. 

 

2. Generating a Complex Twisted Universe 

The four fundamental forces of nature - the strong and weak forces mediating nuclear binding and 

neutron decay respectively, along with electromagnetism and gravity are believed to have emerged from 

a single superforce, perhaps a form of higher-dimensional string, or membrane theory, in twelve, or so 

dimensions, immediately after the big bang, fig 3(a). The higher-dimensional space, containing a single 

generalized superforce compactified most of its dimensions to sub-particulate scales, leaving the four 

dimensions of space-time and broke symmetry to form the different forces we see today, in much the 

way a ferromagnet is polarized at minimum energy, breaking symmetry in space, so that at the lowest 

energy, all domains point in one direction. The forces nevertheless do appear to converge at extremely 

high energies - the unification temperature. 

The strong force is a secondary effect of the colour force between the three red, green and blue quarks 

comprising a proton or neurtron in much the same way that molecular bonding is a secondary 

consequence of the formation of atoms. The colour force has three colours and three anti-colours instead 

of two charges. It also comes in two ground flavours so that the proton and neutron are a composite of 

up and down flavours uud and udd as well as three different colours. The quarks' charges of u = +2/3 

and d = -1/3 thus generate precisely the integral charges of the proton and neutron. The weak force has 

become very short range because it is mediated by massive particles, which are believed to gain the 

required extra degree of freedom by assimilating another concealed particle, the mysterious Higg's 

boson (Georgi 1981, t'Hooft 1980, Veltman 1986). 



DNA Decipher Journal | January 2012 | Vol. 2 | Issue 1 | pp. 01-35 
King, C., Biocosmology: Part I 

ISSN: 2159-046X DNA Decipher Journal 
Published by QuantumDream, Inc. 

www.dnadecipher.com 

 

4 

Complementing this picture at the quantum field theory level is a description on the cosmic scale in 

which a central theme is inflation. Although recently questioned by difficulties finding enough dark 

matter to halt the universe's slide towards hyperbolic expansion (Krauss 1999, Bucher and Spergel 

1999), inflation concepts remain central to understanding how symmetry-breaking of the forces may 

have generated the expanding universe we know. In summary, a seed universe in the symmetrical state, 

below the unification temperature is in an unstable high-energy false vacuum, like a super-cooled liquid 

which could freeze to form a polarized magnet. The false vacuum in the Higg's field causes a 

gravitational repulsion representing the negative energy difference between temperature and that 

required to maintain the Higgs field. Under this 'antigravity', the empty universe, expands exponentially, 

smoothing quantum irregularities to structures on the scale of galaxies (Guth & Steinhardt 1984). The 

breakdown of the false vacuum (in 10
-39

 sec) halts this inflationary phase, releasing a shower of high-

energy particles as latent heat, forming the hot expanding universe under attractive gravitation we are 

familiar with. The gravitational potential energy gained almost exactly equals the kinetic energy of the 

particles, making the generation of the universe possible from a quantum fluctuation. Indications are that 

the universe will continue to expand suggesting a hyperbolic inflation or fractal cosmic inflation (Linde 

1992), in which the active tips of the universe are permanently inflating, to leave behind non-inflating 

bubble universes such as ours. 

 
 

Fig 3 (a) Divergence of the four forces from a single superforce. (b) The three non-gravity 

forces converge in strength at the unification temperature. 

What interests us here are the interactive consequences of this symmetry-breaking differentiation, 

because it leads to all the complex structures we see around us today. Cosmology is traditionally pre-

occupied with alpha and omega - initial and final causes - the origin and fate of the universe. But there is 

another perspective in which life and its complexity is as central to cosmology, fomring the central non-

linear interactive processes that make the universe the complex one we know and exist within, during 

the vast epochs of its mature evolution. 

Although life may be created and annihilated during the evolution of the universe from alpha to omega, 

just as the creation and anihilation of virtual particles are essential to quantum field theory, the 

biological forms and processes can have a cosmic origin as generic structures and a cosmic significance 

as culminating interactive complexity (fig 1). Although fragile, on the cosmic scale of energies, the 

complexity of life is the supreme culmination in complexity of the interactive quantum process initiated 

in the quantum symmetry-breaking. 



DNA Decipher Journal | January 2012 | Vol. 2 | Issue 1 | pp. 01-35 
King, C., Biocosmology: Part I 

ISSN: 2159-046X DNA Decipher Journal 
Published by QuantumDream, Inc. 

www.dnadecipher.com 

 

5 

 
 

Fig 4: The standard model of particle physics involves half-integer spin fermions which obey 

the Pauli exclusion principle and form matter and integer spin bosons which mediate force and 

radiation. Right: the composite structure of symmetry-broken fermionic mattter is molecular. 

The interaction between the wave-particles emerging from the cosmic origin results in distinct effects on 

microscopic and cosmic scales. On the cosmic scale we find fractal structures - galaxy clusters, star and 

planetary formation, mediated by gravity, through contraction, heating and the ignition of the strong 

nuclear force, producing the energy of stars and the secondary photosynthetic energy of visible light. On 

the quantum scale we find integration of quarks to protons and neutrons then atomic nuclei in stars, then 

supernovas in the formation of chemical elements, and finally molecules, in the lower energetics of 

second generation sun-like stars. Quantum interaction of fermions reaches its full interactive complexity 

only in the molecular assemblies of biochemistry and finally, in tissues, organs and organisms, the brain 

being the most complex global expression of chemical non-linearities so far known, forming "the three-

pound universe" (Hooper ad Teresi). 

The hierarchical process leading to molecular complexity involves all the forces in sequence. Quarks are 

bound by colour force gluons into composite particles, such as the proton p+ and neutron n. These then 

interact by the strong force, via the nucleosynthesis pathway, to form the elementary nuclei. The 

nucleosynthesis pathway generates over a hundred atomic nuclei from the already composite proton and 

neutron. Parity between protons and neutrons is mediated by weak decay and is slightly broken at lowest 

energies to balance filling nuclear quantum levels with increasing electromagnetic repulsion of the 

positive protons, fig 6(b). Nucleosynthesis is a complex process catalytically moderated by several of 

the isotopes of lighter elements such as carbon and oxygen. Subsequently the weaker electromagnetic 

force interacts, firstly by formation of atoms through aggregation of electrons around nuclei and then by 

secondary interaction of complete atoms to form molecules. Molecular bonding is a non-linear quantum 

interaction, which is never fully resolved and thus perpetuates in a sequence of stages through 

successive strong and weak bonding interactions, making possible the complex tertiary structures of 

biomolecules. 



DNA Decipher Journal | January 2012 | Vol. 2 | Issue 1 | pp. 01-35 
King, C., Biocosmology: Part I 

ISSN: 2159-046X DNA Decipher Journal 
Published by QuantumDream, Inc. 

www.dnadecipher.com 

 

6 

 
 

Fig 5: The extreme variety of conditions on our own planets and between the moons of Jupiter 

and Saturn are only a foretaste of the bizarre variety of planets detected around other 

neighbouring stars. This extreme variety is consistent with the non-linear nature of gravity 

under inverse square law attraction in four-dimensional space-time and the resulting capacity of 

the universe to explore its own space of possibilities through chaotic dynamical interaction. 

 Super-Earth discovered in a habitable zone 2011 

 Impacts 'more likely' to have spread life from Earth 2011 

 Comets may be creating oceans on alien planet 2011 

 Fifty new exoplanets discovered 2011 

 Exoplanet near Gliese 581 star 'could host life' May 2011 

 Exoplanet hunt turns up 54 potentially habitable worlds Feb 11 

 'Trillions' of Earths orbit red stars in older galaxies Dec 10 

 New exoplanet like 'one of ours' Mar 10 First life-friendly exoplanet may not exist Oct 10 

 Not too hot, not too cold: New Earth-like planet could sustain life Sept 10 

 Billions of Earths in our Galaxy and 32 Discovered in 2009 

 Cool find in hunt for exoplanets Dec09 

 'Super-Earths' orbit nearby stars Dec09 

 Keeping the young Earth cozy 09 

Generation of the chemical nuclei requires a cosmic cycle through the supernova explosion of a short-

lived hot star, generation of heavier elements like gold possibly involving the collapse of twin neutron 

stars after supernova formation (Rosswog). In the second phase, these elements are drawn into a lower 

energy long-lived sun-like star, the lighter elements associated with terrestrial biology occur in relatively 

high abundance as a result of nucelosynthesis dynamics, fig6(a), and can become concentrated on mid-

range planets. The final re-entry of the forces occurs through irradiation of molecular systems from 

photons emitted by stellar thermal radiation, representing the final re-interaction of the residual lower 

energy electromagnetic bosons with their fermionic counterparts in the electromagnetic orbitals of 

molecules. The typical coupling of the 5000
o
C surface temperature of sun-like stars provides photonic 

energy suitable for energizing weak-bonded molecular structures, without destroying them. A pivotal 

environment in which this final negentropic low-energy re-entry occurs in abundance are the surfaces of 

rocky planets in the temperature belt where water is liquid. The variety of planetary systems so-far 

discovered demonstrates the capacity of the universe to explore through chatoic non-linearities in 

gravitational orbits, a diverse array of planetary surfaces, ensuring the phase space of potential molecular 

environments is well explored on a cosmic scale (fig 5). 

http://www.dhushara.com/Biocrisis/11/oct/superHabitable.pdf
http://www.dhushara.com/Biocrisis/11/oct/lifeSpread.pdf
http://www.dhushara.com/Biocrisis/11/oct/cometPlanet.pdf
http://www.dhushara.com/Biocrisis/11/oct/50exopl.pdf
http://www.dhushara.com/Biocrisis/11/jun/murky_planet.pdf
http://www.dhushara.com/Biocrisis/11/apr/rocky.pdf
http://www.dhushara.com/Biocrisis/10/dec/trilions_earths.pdf
http://www.dhushara.com/Biocrisis/10/apr/exoplanet.pdf
http://www.dhushara.com/Biocrisis/10/dec/no_planet.pdf
http://www.dhushara.com/Biocrisis/10/sept/goldilocksplanet.pdf
http://www.dhushara.com/book/quantcos/planets/billions_of_earths.pdf
http://www.dhushara.com/Biocrisis/10/feb/cool_find.pdf
http://www.dhushara.com/Biocrisis/10/feb/super-earths.pdf
http://www.dhushara.com/Biocrisis/10/feb/sexy_young_earth.pdf


DNA Decipher Journal | January 2012 | Vol. 2 | Issue 1 | pp. 01-35 
King, C., Biocosmology: Part I 

ISSN: 2159-046X DNA Decipher Journal 
Published by QuantumDream, Inc. 

www.dnadecipher.com 

 

7 

 
 

Fig 6: (a) Cosmic abundances of the bioelements. (b) The neutron excess of the stable nuclei 

reflects the interaction between the strong and electromagnetic forces via the weak force 

The Anthropic cosmological principle introduces the existence of observers as a boundary condition, 

effectively imposing the existence of life as a cosmological constraint. It asserts that fundamental 

properties of the universe may have been selected by the fact that only with such constraints on the laws 

of nature would there be a (complex biological) observer to witness the universe and examine its laws 

(Barrow and Tipler). Forms of many-universes or many-histories cosmology likewise allow for a 

spectrum of possible universes, only some of which would have laws of nature which would permit the 

complex interactive states we associate with living systems. Some cosmologies suggest selection 

principles may regenerate the universe as a whole, and predispose it to the complexity we find evident 

(Smolin). 

A key approach which seeks to define the laws of nature uniquely derives from super-symmetric string 

theories. In supersymmetry, each half-integer spin matter-forming fermion (e.g. electron, proton, 

neutrino, fig 4) is matched by a force/radiation-generating integer spin boson (e.g. Higgs, photon, Zo, 

gluon, graviton, fig 4). In string theories point particles become resonant loops, strings or membranes in 

higher dimensional space as distance shrinks, avoiding the infinite singularity of point particles. 

Consistent super-'brane' theories (Green 1985, 1986, Mukerjee 1996, Duff 1998) require a large number 

of dimensions, between 10 and 26 in which all but four dimensions (space-time) curl up on microscopic 

scales. Despite millions of possible compactifications, none has so far been defined which matches our 

particles and forces. Regardless of the fine details of the ultimate theory resolving the origins of the 

universe in unification, the formof the forces as we know them is consistently described as a 

conseuqence of symmetry-breaking. 



DNA Decipher Journal | January 2012 | Vol. 2 | Issue 1 | pp. 01-35 
King, C., Biocosmology: Part I 

ISSN: 2159-046X DNA Decipher Journal 
Published by QuantumDream, Inc. 

www.dnadecipher.com 

 

8 

 
 

Fig 7: The Orion nebula contains newly forming stellar systems possibly including the propylid 

(tiny black dot centre) with a dark 'planetary' disc (top and centre right) (Buhl). Some of these 

newly forming stars are also surrounded by clouds of HCN and HCHO (inset bottom-left) 

(Hubble telescope image). 

 Stars concoct complex molecules 2011 

3. The Abudantly Fecund Universe 

As time passes, more and more evidence is accumulating that, the universe and its galactic gas clouds 

are abundant in organic chemicals, from the simplest molecules to sugars, amino acids and nucleic acid 

bases. Since Fred Hoyle coined the term "wooden universe" based on infra-red spectral data indicative 

of carbohydrate emission, there has been an awareness of the potential of galactic gas clouds to be 

cosmically abundant sources of prebiotic molecules. 

Radio-telescope data as early as 1974 (Buhl) demonstrated clouds of multiple-bonded HCN and H2C=O 

spanning the region in the Orion nebula where several new stars are forming, fig 7. These are key 

precursors of complex polymerization pathways discussed below. Glycine has also been found in 

interstellar gas and adenine is an abundant product in simulations of collapsing interstellar gas clouds 

containing a dozen elements including hydrogen, carbon, oxygen and nitrogen (Chakrabadi 2000). 

Along with amino-acids, all of A, U, G, and C have been detected in carbonaceous chondrites (Hua et. 

al. 1986), such as the Murchison meteorite. These also contain amphophilic membrane forming products 

(Deamer and Pashley 1989). Cometary impacts are believed to have coated the Earth in a rich 

endowment of organics from the earliest stages of solar system evolution when impact rates were high. 

http://www.dhushara.com/Biocrisis/11/oct/complexMols.pdf


DNA Decipher Journal | January 2012 | Vol. 2 | Issue 1 | pp. 01-35 
King, C., Biocosmology: Part I 

ISSN: 2159-046X DNA Decipher Journal 
Published by QuantumDream, Inc. 

www.dnadecipher.com 

 

9 

 
 

Fig 8: Left: The cloud from which glycoaldehyde has been detected Right Droplets made by 

harsh radiation under interstellar conditions (Dworkin et. al.) 

Glycolaldehyde has recently been detected by Jan Hollis (2000) in a cloud of gas and dust 2 light years 

across of a type from which new stars are formed. He notes "Interstellar clouds are spread throughout 

the galaxy and you often find the same molecule in many different clouds. Since these organic 

molecules are so widespread, it may mean that pre-biotic chemical evolution is an ongoing process." 

Glycoaldehyde can combine with other carbohydrate molecules to produce ribose. 

A team led by David Deamer, Jason Dworkin, Scott Sandford and Louis Allamandola has also formed 

complex organic molecules under the harsh condition sof outer space. The main ingredients of 

interstellar ices are simple chemicals frozen together. Mostly water, some ammonia, carbon monoxide, 

carbon dioxide and methanol. The team froze a mixture of these chemicals into a thin solid ice at 

temperatures close to absolute zero (-441Â°F/ -263Â°C) under extreme vacuum and exposed this to 

harsh ultraviolet radiation that mimics the radiation in space produced by neighboring stars. Instead of 

finding a handful of molecules only slightly more complicated than the starting compounds, hundreds of 

new compounds were produced in every mixed ice studied. The types of compounds produced are 

strikingly similar to many infalling meteorites and interplanetary dust particles. Thus much of the 

organic material found on the Earth in its earliest years probably had an interstellar heritage." (Dworkin 

et. al. 2001). 

The capacity of complex organic molecules generated in space to enter Earth's atmosphere intact has 

also been confirmed. Jeffrey Bada has found evidence that "mother lodes' of buckyballs, football-shaped 

molecules made up of carbon atoms, have fallen intact to Earth from outside the Solar System from 

Sudbtlry, Ontario, where a meteoroid the size of Mount Everest crashed 2 billion years ago. They were 

loaded with helium, an element rare on Earth, but abundant in inter-stellar space. The single impact site 

contained about 1 million tons of extra-terrestrial buckyballs. If complex buckyballs could fall on earth 

without burning up so could complex organic molecules (Cohen 1996). 

 



DNA Decipher Journal | January 2012 | Vol. 2 | Issue 1 | pp. 01-35 
King, C., Biocosmology: Part I 

ISSN: 2159-046X DNA Decipher Journal 
Published by QuantumDream, Inc. 

www.dnadecipher.com 

 

10 

4. Quantum Chemistry as Non-Linear Complexity 

The complex expressions of chemistry particularly in biology are manifest as a final non-linear 

interactive consequence of cosmological quantum symmetry-breaking. The stability of the nucleus with 

increasing nuclear mass number and charge permits an unparalleled richness and complexity of quantum 

bonding structures around the diverse chemical elements. Electron-electron repulsions, spin-obit 

coupling, delocalized orbitals 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 an inverse quadtaic non-linearity in the form of the attractive and 

repulsive charge interactions caused by re-distributing electrons 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 quadratic nature of charge interaction, leads to a situation in polymeric 

chemistry akin to the Mandelbrot set, (fig 22a) and which is central in making complex molecules (fig 

10) and the scale-dependent structures of tissues possible (fig 22b). 

 
 

Fig 9: Although all wave functions obey quantum superposition, the non-linear nature of 

electronic charge distribution and its resulting occupancy energetics, the Pauli exclusion 

principle and additional electromagnetic effects results in the non-linear energetics of chemical 

bonding. This non-linear interaction is never fully resolved by any single bonding step and 

gives rise through subsidiary weak-bonding interactions to the global interactivity of complex 

biomolecules and cellular organelles. 

The source of this non-linear interaction is the foundation of all chemical bonding, the electric inverse 

square law of charge interaction. Although the state vector of a quantum-mechanical system is a linear 

combination of base states, exemplified by the formation of linear combinations of s and p wave 

functions to form the four sp
3
 hybrid orbitals, the electrostatic charge of the electron causes orbital 

interaction to have fundamentally non-linear energetics. The total energy is represented by the resonance 

integral of the Hamiltonian composed with the wave function, divided by the normalizing overlap 

integral S. 

 



DNA Decipher Journal | January 2012 | Vol. 2 | Issue 1 | pp. 01-35 
King, C., Biocosmology: Part I 

ISSN: 2159-046X DNA Decipher Journal 
Published by QuantumDream, Inc. 

www.dnadecipher.com 

 

11 

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

solutions , as indicated: 

 

The capacity of orbitals, including unoccupied orbitals, to cause successive perturbations of bonding 

energetics results in an interaction bonding sequence, from strong covalent and ionic bond types, 

through to their residual effects in the variety of weaker H-bonding, polar, hydrophobic, and van der 

Waals interactions, merging into the average kinetic energies at biological temperatures (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 and quaternary sturctures determining the global 

form of large biomolecules and the globally-induced active-site effects central to enzyme action. 

 

By contrast with the periodic crystalline or random amorphous structures of most minerals, the non-

periodic scale-dependent primary, scondary and tertiary structures in proteins and RNA that are critical 

to establishing the richness of their forms and their bio-activity, fig 10. The almost unlimited variety of 

monomeric primary sequences induce higher-order secondary and tertiary structures through subsequent 

folding of the polymer. These are possible only because the non-linearity of charge interaction which 

causes chemical bonding also gives rise to further residual interactions at lower energies which are 

resolved by cooperative weak bonding. Proteins are powerful catalysts because the global coherence of 

action arising from cooperative weak bonding makes for very powerful and responsive active sites. 

Despite being genetically coded, such molecules form fractal structures both in their geometry and their 

dynamics, fig 31(e, f) (Ansari et. al. 1985, Liebovitch et. al. 1987, 1991). 

 
 

Fig 10: Global t-RNA and protein [enzyme] tertiary structures are the result of hierarchy of 

strong and weaker chemical bonding interactions operating on a non-periodic secondary 

structure. Both derive their structures in association with water. 



DNA Decipher Journal | January 2012 | Vol. 2 | Issue 1 | pp. 01-35 
King, C., Biocosmology: Part I 

ISSN: 2159-046X DNA Decipher Journal 
Published by QuantumDream, Inc. 

www.dnadecipher.com 

 

12 

Non-equilibrium thermodynamics (Glansdorff and Prigogine 1971) and the associated oscillating 

chemical systems such as the Beloushov-Zhabotinskii reaction (Epstein et. al. 1983) demonstrate the 

capacity of auto-catalytic chemical systems, and membrane electrochemistry (Chay & Rinzel 1985), to 

enter into non-linear dynamics and chaos (Epstein et. al. 1983, Agladze et. al. 1984). Quantum chaos 

and its suppression is also an emergent issue (Gutzwiller 1992). 

The prebiotic polymerizations leading to the chemical origins of life share an informational paradox in 

which a small number of simple reactant lead to a large array of complex interacting products with many 

potential catalytic interactions. The initial conditions are thus insufficient to causally determine the 

products, except for a few predominant products such as adenine, leading to a huge variety of possible 

end states with increasing complexity. This allows for a high degree of polymeric variability which can 

be influenced both by auto-catalytic feedback and stochastic effects. 

 

5. The Non-recurrent Table and the Elementary Bifurcation Tree 

Although the discrete quantum aspects of orbital occupancy are periodic, (fig 11 b, c) the properties of 

successive atoms in the same periods in the table are not exactly, or even approximately, periodic. 

Successive members of the same group differ significantly in nuclear charge, atomic radius and electron 

repulsion, resulting in trends which permit interactive bifurcations between their properties. For example 

the properties of sulphur are significantly different from oxygen, although they are a period apart. The 

same goes for sodium and potassium through to fluorine and chlorine. When this non-linear non-

periodicity complicating the underlying periodicity of the s, p, d and forbitals is further extended to 

molecular systems, the parameter space of possible interactions resembles a quantum Mandelbrot set 

(fig 22) forming an atlas of configurations in which the atomic interactions fig 11(a) and resulting 

molecular species supporting biogenesis (fig 14, 15) play a pivotal generic role. 

Such trends are illustrated in polar and H-bonding properties of hydrides for which H2O is optimal (fig 

11(b)), atomic and ionic radii in which the properties of elements like Na and K differ sufficiently to 

induce distinct H2O bonding structures, and electronegativity, fig 11(c) in which O is even more 

electronegative than Cl. Such partial, or quasi-periodicity is also illustrated by the intrusion of the 

transition element d-orbital series between the subsequent s and p series (Moeller et. al.). 

 
 



DNA Decipher Journal | January 2012 | Vol. 2 | Issue 1 | pp. 01-35 
King, C., Biocosmology: Part I 

ISSN: 2159-046X DNA Decipher Journal 
Published by QuantumDream, Inc. 

www.dnadecipher.com 

 

13 

Fig 11: (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 a polar H-bonding medium. (c) 

Electronegativities illustrate optimality of O and water as a hydride and emphasize the unique 

role of first row covalent elements C, N, O demonstrated in primitive polymerizations. Atomic 

and ionic radii also result in a two-way bifurcation of the properties of K, Na, Ca and Mg. 

Transition elements introduce unique catalytic activities partly through bringing the d-orbital 

into play. 

The stable aspects of quantum orbital interaction in biochemical evolution can be classified into a tree of 

fundamental bifurcations which distinguish the elements structurally and cause divisions between their 

properties in interaction. This forms a generative sequence in which the bioelements have key roles (fig 

11(a)). Each bifurcation gives rise to a reaction phase with added degrees of freedom and consequently 

greater interactive complexity. Describing the evolution of interactive chemical quantum structures in 

terms of funadamental force bifurcations sheds constructive light on the broad categories into which 

molecular free interaction differentiates and determines both the degrees of freedom and the constraints 

for development of interactive complexity in bio-molecules. Successive bifurcations are as follows: 

Principal Bifurcation : The Covalent Interaction of H with C, N, O. 

The central covalent quantum interaction in the table of the elements is between the two-electron 1s 

orbital and the eight-electron 2sp
3
 hybrid. This is the fundamental covalent 1-2 shell quantum interaction 

and the bifurcation through which biocosmology comes into existence. All the members of the CNO 

group have tetrahedral sp3 bonding geometry and form a graded sequence in electronegativity, from 

carbon in rough parity with hydrogen to electronegative oxygen, with one and two lone pair orbitals 

appearing successively in N and O. The resulting 3-D covalent bonds give C, N and O optimal capacity 

to form complex, diverse polymeric structures. Symmetry is split, because the 1s has only one binding 

electron state, while the 2sp
3
 has a series from 4 to 7 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. 

Some of the strongest covalent bonds known to chemistry 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 (900
o
C), or spark discharge to the respective atoms. Because of the higher energy of 

the resulting p-orbitals, these bonds possess a specific type of structural instability, in which one or two 

p-bonds can open to form lower energy partially s-bonded heterocyclic and other oligomeric structures. 

Most of the prebiotic molecular complexity generated by such energy sources can be derived from 

mutual polymerizations of HCCH, HCN, and H2C=O, and realated hybrids in association with 'sister' 

molecules such as urea H2N-CO-NH2. These include purines such as nucleic acid bases adenine and 

guanine, their pyrimidine complements uracil and cytosine, key sugar types such as glucose and ribose, 

amino acids, polypeptides, porphyrins etc. They form a core pathway from high energy stability to 

structurally unstable polymerization, and to complexity, which we will elucidate. 

The formation of conjugated double and single bonds in these reactions results is delocalized p-orbitals 

(Pullman and Pullman 1962). Such orbitals in heterocyclic (N-C) rings with conjugated resonance 

configurations also enable lone pair n > &pi* and &pi > &pi* transitions (Rich and Rajbandry 1976), 



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resulting in photon absorption and electron transfer. These two effects in combination play a key role in 

many biological processes including photosynthesis, electron transport and bioluminescence. 

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, fig 11(c), arising from the increasing nuclear 

charge. This results in a variety of secondary effects in addition to the oxidation parameter, from the 

polarity bifurcation discussed below, to more subtle effects such as the complementation of -CO2H and -

NH2 as generalized organic acidic and basic moieties. 

Differential electronegativity results in several coincident bifurcations associated with water structure. A 

symmetry-breaking occurs between the relatively non-polar C-H bond and the increasingly polar N-H 

and O-H. This results in phase bifurcation dividing the medium into polar (aqueous) 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 fig 20, to the globular enzyme form and base-stacking of nucleic acids fig 10. 

Critical in this process are the optimal properties of water H2O among all molecules, making possible in 

turn polarity interactions, aqueous acid-base bifurcation, ionic solubility and hydrogen bonding. The 

optimal nature of water as a hydride is illustrated in boiling points Fig 11(b). Water provides several 

other secondary bifurcations besides polarity. The dissociation H2O &harr H
+ 

+ OH
-
 lays the foundation 

for the acid-base bifurcation, while ionic solubility generates anion-cation. Many key properties of 

proteins and nucleic acids, are derived from water bonding structures in which a counterpoint of H-

bonding and phase bifurcation effects occu, determining the form of the alpha helix and nucleotide base 

pairing. Hydrophilic-non-polar bifurcation is central to the tertiary structures of globular proteins as 

'micelles' and hairpins of RNAs, fig 10. The solubility or otherwise of a variety of molecules and ions is 

derived from the energies and entropies of their induced water-bonding structures. The large diversity of 

quantum modes in water is demonstrated by its very 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. It has also been suggested water is 

a two phase medium containing quantum-coherent domains, in association with boundaries such as 

macromoleculaes and membranes (Mae-wan Ho ISIS Report). 

http://www.i-sis.org.uk/Quantum_Coherent_Water_Life.php


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Fig 12: The diversity of snow crystals illustrates the complexity of water bonding structures 

and their diversity under very slight perturbation of initial conditions (Bentley and Humphries). 

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) . 

Ca
2+

 and Mg
2+

 have a similar divergence, Ca
2+

 having stronger chelating properties. This causes a 

crossed bifurcation between the two series in which K
+
and Mg

2+
 are intracellular, Mg

2+
 having a pivotal 

role in RNA transesterifications. 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. 

P and S as Low-energy Covalent Modifiers 

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. SiO3
2-

, PO4
3-

 and 

SO4
2-

 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 generic 

properties are introduced. 

PO43- is unique in its capacity to form a series of moderate energy 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 adenosine 



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triphosphate (ATP) energetics, ribonucleic acid (RNA) and membrane structure, and the fact that the 

dehydration mechanism easily recycles, unlike the organic condensing agents, give phosphate 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 as 

a mediating mild covalent linkage both in terms of tertiary bonding and low energy respiration and 

photosynthesis pathways. 

Transition Element Catalysis 

Transition elements add key 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 Fe
2+

-Fe
3+

 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. 

These five processes between them constitute the major quantum bifurcations in the free interaction of 

the elements. They are also the central processes operating in biogenesis. Put together this says the 

following: The central biogenesis pathways are themselves results of the central interactive quantum 

bifurcations of symmetry-breaking and its resulting non-linear interactions. While life may be possible 

from other combinations of elements and other temperatures and pressures, life as we know it has taken 

the sang raal or blood-royal route of quantum cosmology. 

 
 

Fig 13: (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 breaks stability to one chiral form (iii) 



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Kenso Soai (1998) and his team have demonstrated the autocatalytic bifurcation framework as well 

They took a mixture of compounds containing a small excess of one enantiomer of the amino acid 

leucine. In the presence of this imbalance, the components of the solution reacted to form a compound 

called a pyrimidyl alkanol, also with a small excess of one enantiomer. But this molecule then acted as a 

catalyst in its own formation, and soon almost all the pyrimidyl alkanol in the solution was of this sort. 

(see also New Sci 12 Dec 98 16) 

Did exploding stars shatter life's mirror? May 10 

Tertiary Interaction of Mineral Interface 

Both silicates such as kaolinite clays (Strigunkova et. al. 1986) and volcanic magmas (Lavrentiev et. al. 

1984) 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 (Cairns-Smith 1982, Weiss 1981). Clays also appear to play a key role in stabilizing 

ribonucleotide polymerization (Ferris 1996). 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. 

 

6. Structural Dynamics of Core Polymerization Pathways 

The initial polymerizations of energetic multiple-bonded monomers in the reaction in figs 14 and 15 

form a particularly interesting problem from a quantum-mechanical point of view, because they provide 

some of the richest examples of growth in quantum-mechanical complexity, in which a relatively small 

number of simpler entities give rise to increasingly complex structures whose properties cannot be fully 

predicted from the initial conditions. 

H2C=O in aqueous solution gives rise to 4 to 7 carbon sugars, including ribose, as well as 

branched polysaccharides. HCN gives rise to heterocyclic purine and pyrimidine nucleic acid 

bases, and in addition several amino acids, polypeptides, porphyrins, and many other types 

of biomolecule (Lowe et. al. 1963, Calvin 1969, Mizutani et. al. 1975). A similar array of 

products arises from hybrids such as cyanogen NC-CN (Schwartz et. al. 1975) and 

cyanoacetaldehyde NC-CH2-H2C=O. Although several of these products, such as the ring 

polymers adenine (HCN)5 and ribose (H2CO)5 are stable product structures, many of the 

more complex products, such as particular oligopeptides are metastable or stochastic products of the 

reaction. These conditions differ markedly from the current biochemical regime in which structurally-

stable metabolic pathways are maintained through genetically-coded enzyme catalysis except where 

recombinational stochasticity is specifically initated as in generation of antibody immuno-diversity. 

http://www.dhushara.com/Biocrisis/10/sept/life'smirror.pdf


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Fig 14: Known product structures and pathways in HCN polymerization. 

Since the initial conditions do not contain sufficient information to determine the final products, the 

system contains many potential outcomes. The lower energy configuration of key products, such as 

adenine's resonance stabilization, leads to some stable conformations based on free energy. Stochastic 

indeterminacies in the interaction of simpler molecules lead to multiple branching pathways. Products of 

increasing complexity such as polypeptides possess increasingly active catalytic potential, which may 

alter the structural-stability of polymerization to favour certain types of product. The dynamics may 

trigger a sequence of autocatalytic bifurcations, some of which may result in the formation of attracting 

molecular products. These reaction pathways are capable of producing a vast variety of complex 

molecules with generic relationships to key biomolecules, including amino acids, polypeptides, HCN 

polymers, purines, pyrimidines and porphyrins. 

Both HCN and HCHO polymerizations have prominent cyclic products which act as spontaneous end 

points of polymerization, because cyclization mutually neutralizes reactive moieties. The purines, 

pyrimidines, ribose and porphyrins all display structure consistent with being cyclic terminators. The 

capacity of polymers for non-periodic primary sequencing gives rise to complex tertiary structures, 

which are fractal as a result of structure on several overlapping scales from the atom, through local 

groups, to structures such as a-helices through to global conformation changes. This fractal nature is 

reflected both in the geometry and the quantum energetics of molecular transformations (Ansari et.al. 

1985, Liebovitch & Toth 1991). Substrate form is dependent firstly on local active sites, and in turn on 

the global tertiary structure of catalytic molecules. 



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Fig 15: (a) One of several synthesis pathways for pyrimidines. (b) Sample HCHO 

polymerization routes. Phosphorylation of the oligo-aldehydes causes the reaction to favour 

ribose. (Eschenmoser 1992). 

Although the first syntheses produced the purines adenine and guanine readily, cytosine and uracil, the 

complementary pyrimidine bases making up the other half of the pair A-U and G-C, however Stanley 

Miller, forty three years after his original pioneering experiment in spark synthesis, with Michael 

Robertson, discovered a way for the primordial pond to make them in high yield. Although urea is 

produced in Miller's original experimental setup, it never reaches a high enough concentration. When he 

added more urea, it reacted with cyanoacetaldehyde, another by-product of the spark synthesis, churning 

out vast amounts of the two bases. Urea would have been able to reach high enough concentrations as 

shallow pools of water on the Earth's surface evaporated. (Cohen 1996, Horgan 1996). 

Eschenmoser (1992) has found that glyceraldehyde phosphate in the presence of HCHO will produce 5-

carbon sugars with up to 33% ribose. In the absence of HCHO the reaction tends to produce 6-carbon 

sugars. The phosphate-induced reaction is key here because RNA, ATP and glycolysis all involve 

phosphate dehydration energy. This indicates a specific link to phosphate energy primordial to the 

formation of oligonucleotides and even ribose. 

 
 

Fig 16: (a) MgATP-complex illustrates linkage between primal stability structures. Cyclic 

pentamers of HCN (adenine) and HCHO (ribose) are linked by phosphate dehydration, 

stabilized by cation and water structures. (b) Heterocyclic form of heme. Porphyrins have also 

been detected in primal syntheses. (c) Nucleophilic attack of adenine N9 on ribose. 

 



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7. RNA and Cosmology 

In 1981 Francis Crick commented that 'the origin of life appears to be almost a miracle, so many are the 

conditions which would have to be satisfied to get it going." (Horgan 1996) Now, several findings 

bolster the dominant theory of genesis - that life began in an era in which RNA was both the genetic and 

catalytic basis - the RNA era (Gilbert 1986, Benner et.al.) in which simple replication and 'enzymatic' 

process based purely on RNA catalysis established evolutionary biochemistry. 

The general outlines are clear. Ribose, unlike the deoxyribose in DNA, has plausible prebiotic syntheses. 

RNA's capacity to both form double-helices, like DNA and to also three-dimensional tertiary structures 

similar to proteins through base-backbone bonding to ribose fig 10(a), causes RNA to have both genetic 

and catalytic capacity. Simple biological RNAs have been demonstrated to have autocatalytic self-

assembling capacity. The catalytic activity of polynucleotides, hinges on various forms of proton 

transfer fig 17(a,b,c) (Pace and Marsh 1985), in particular transesterification. 

The essential core of the protein-assembling ribosome remains RNA as does the signal recognition 

particle which shepherds nascent proteins through the membrane. The ancient fossil nucleotide 

coenzymes including ATP, NAD, coenzyme-A and Vitamin B12 are all ribonucleotides. Eucaryote 

organisms continue to have a massive commitment to RNA processing within the nucleus, including the 

use of many small small nuclear ribonucleotides or snuRps involved in RNA splicing. This suggests 

eucaryotes have never fully transferred from an RNA-based metabolism. Reverse transcriptases also 

remain ubiquitous and essential for such basic functions as telomere extension, and have a common 

evolutionary tree, giving retrotransposons and retroviruses a potentially ancient origin in the 

commonality of the RNA era. 

There is still debate about whether RNA was actually the primordial genetic molecule and other hybrid 

molecules such as peptide-nucleic acids which use peptide rather than sugar linkages also have genetic 

potential and plausible prebiotic status (Nelson et. al.), however it is clear RNA itself has generic status 

as a cosmological molecular structure on several grounds. Adenine is a principal thermodynamic 

product of HCN polymerization in industrial yields. All of A, G, U and C now have prebiotice status as 

favoured products of such reactions. Ribose is an optimal sugar conformationally in terms of permitting 

complementary double helix formation, and has a synthesis route from glyceraldehyde phosphate. The 

complementations of A-U and G-C posses a type of structural optimality among the bases. The 

heterocyclic polymers are restricted in their variety by the positions of N atoms required by the 

polymerization process. The tautomeric states of A, U, G and C indicate AU and GC may be optimal for 

base-pairing among close prebiotic variants. 

The nucleotide unit, as exemplified in ATP consists of a direct concatenation of key products of HCN 

and HCHO polymerizations. Adenine and ribose are the cyclic pentamers of HCN and HCHO linked via 

dehydration to a dehydrating oligo-phosphate giving it the statues of a generic structure, fig 16(a) 

stabilized by water and Mg
2+

, Positive ions also play an important role in stabilizing mono- and oligo-

nucleotides. It was originaly synthesized under primitive conditions by Ponnamperuma et. al. (1963). 

Mg
2+

 ions are also bound to transfer RNA and play a critical role in transesterification, balancing the 

negative phosphates. The fact that the polymerizing phosphodiester bond results from the removal of 

H2O from phosphate suggests that phosphate was the active moiety linking of the base-sugar-phosphate 

complex, fig 16(c) and thus drove the entire formation of nucliec acids. 



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RNA proved difficult for a time to induce into complementary replication in enzyme-free systems, but 

its relative difficulty of synthesis may be essential to its function. It is necessary that RNA be 

thermodynamically unstable, or life could not exist dynamically but would 'crystalize' all the way to 

non-genetic polymers. A variety of partial model systems of complementary replication have been 

realized by Orgel and his coworkers, however instabilities in polymerization have hindered experimental 

enzyme-free complementary polymerization of RNAs (Orgel 1992). It is clear that a regime of 

polynucleotide chemistry would have to have occurred stably over evolutionary time scales for an RNA-

based form of life to evolve to the point where it had established translation and captured metabolic 

synthetic pathways. 

Ferris reported (1996) that he had found a means by which the first large chains could have been forged. 

When his team added montmorillonite, a positively charged clay believed to be plentiful on the young 

Earth, to a solution of negatively charged adenine nucleotides, it spawned RNA 10-15 nucleotides long. 

If these chains, which cling to the surface of the clay, were then repeatedly 'fed" more nucleotides by 

washing them with the solution, they grew up to 55 nucleotides long. Ferris notes the clay gets RNA off 

the hook of having to take on the tasks of information storage and catalysis in one fell swoop. It would 

catalyse RNA synthesis, stocking pools with a large range of RNA strands that, as Szostak and others 

have shown, would evolve a catalytic capacity of their own. (Horgan 1996). Thus complementary 

replication can come into existence after a phase of single-stranded polymerization has given rise to a 

fractal RNA environment with a diverse array of oligomeric and polymeric structures, which in turn 

feedback autocatalytically on replication and monomer synthesis. 

 



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In 2009 Sutherland discovered that pyrimidine nucleotides can be readily synthesized from simple 

prebiotic molecules bypassing the more difficult routes depending on synthesizing ribose, bases 

independently and trying to then attach them to phosphate. In fact phosphate was pivotal in producing 

new intermediates which would then in good yield polymerize to nucleotides. 

Chemist Shows How RNA Can Be the Starting Point for Life May 14, 2009 

Since then he and his colleagues have proposed one-pot pathways to both purine and pyrimidine 

nucleotides (Powner, Sutherland and Szostack 2010 Chemoselective Multicomponent One-Pot Assembly 

of Purine Precursors in Water J. Am. Chem. Soc. 2010, 132, 16677â€“16688). 

 
Hypothetical pathways to both purine and pyrimidine nucleotides fro the above paper 

Powner and Sutherland have also investigated interconversion of sugar bases between ribo and arabino 

nucleotide intermediates (Powner MW, Sutherland JD. 2010Phosphate-mediated interconversion of 

ribo- and arabino-configured prebiotic nucleotide intermediates. Angew Chem Int Ed Engl. 

49(27):4641-3). 

A central scenario out of many, including volcanic hot pools, and hydrothermal vents, is the three-phase 

boundary of a phosphate-rich, clay shore line under tidal or weather-related variations in a pool in which 

the margin is reversibly dehydrated e.g. by sun-drying. Both clays and volcanic basalts have been cited 

as possible mineral interfaces. Precipitated phosphate at 37
o
, leads to pyrophosphate formation and 

hence phosphate bond energy (Hermes-Lima 1990). Since the energy for nucleotide polymerization is 

driven by H2O removal, reversible dehydration of a medium containing phosphate, bases and sugars 

provides one of the most direct and simple routes to polynucleotide formation. 

http://www.dhushara.com/book/bchtm/suth/sutherland.htm
http://www.dhushara.com/book/bchtm/suth/sutherland.htm
http://www.dhushara.com/book/bchtm/suth2.jpg


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8. Diverse Horizons of the RNA Epoch 

A whole new field of RNA research has developed from the discovery of spontaneous splicing of RNAs 

in living systems by Tom Cech and the demonstrated capacity of such RNAs to function as catalysts in 

transesterifications and the work of Jack Szostack's teams in selective RNA catalysis (Cech 1986a). This 

immediately made the idea of the RNA world before proteins a natural hypothesis. This work has grown 

with artificial selective evolutionary studies, culminating with the development of a ribozyme which is 

capable of high fidelity complementary replication of short RNA oligomers of arbitrary sequence 

(Johnston et.al. 2001). This has become a turning point in the credibility and maturity of the RNA world 

as a precursor to DNA-based life which can develop as an autonomous molecular system. 

The model has been extended to others for RNA-based error-correction, synthetases and the ribosome 

(Bass and Cech 1984, Cech 1986b, Zany and Cech 1986, Garriga et. al. 1986, Weiner and Maizels 

1987). Modified ribozymes are capable of acting as polymerases which can replicate complements to 

subsections of themselves (Green et. al. 1990, Doudna et. al. 1991). 

The discovery that RNA appears to be the agent of peptide-bond synthesis in the modern ribosome 

(Guthrie 1992, Pace 1992, Noller et. al. 1992) and the capacity of modified ribozymes to act as amino-

acyl esterases (Picarilli et.al. 1992), the first step of ribosomal action in protein synthesis, establish RNA 

has the potential to act as synthetase as well as transfer, messenger and ribosomal functions. This gives 

RNA the capacity to act on its own to catalyse both its own replication and the ordered polymerization 

of proteins. Simpler model systems have also been advanced of the stereospecific capacity of D-

nucleotides to act as a catalyst of L-amino acid polymerization (Lacey et. al. 1990). These results enable 

RNA to be the key prebiotic molecule generating ordered polynucleotide and polypeptide structures. 

 

Fig 17: The ribozyme world: (a) Phospho-imidazole. Proton transfers in (a) imidazole, (b) in 

base tautomerization, (c) in Tetrahymena intron. (d) The first effective ribozyme RNA 

polymerase (iii) - a 172 unit molecule bred by molecular selection from a ligase ribozyme (i) 

through selcctive evolution of a pool of other intermediates (ii). This ribo-RNApolymerase will 

faithfully perform complementary replication of oligo-ribonucleotides of arbitrary sequence up 

to 14 units long with accuracies of up to 98% per base pair. (e) The RNA polymerase ribozyme 

tC19Z, that was able to synthesize a spectrum of RNA sequences, including the accurate 

synthesis of an enzymatically active RNA 



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Szostak and Wilson (1996, Wilson and Szostak 1995) have evolved ribozymes capable of a broad class 

of catalytic reactions. The catalysis of previous ribozymes tended to involve only the molecules' sugar-

phosphate "backbone," but these could also promote the formation of peptide bonds (which link amino 

acids together to form proteins) and between carbon and nitrogen. (Horgan). David Bartel a former 

member of Szostak's team, has evolved RNAs that are as efficient as some modern protein enzymes. The 

problem with most ribozymes is that they are as likely to snip an RNA molecule apart as stitch one 

together which makes copying a molecule fifty nucleotides long (the minimum size necessary to 

catalyse a chemical reaction) difficult or impossible. Bartel's new ribozymes, on the other hand, can 

stitch small pieces of RNA together without breaking larger molecules apart. These ribozymes use high-

energy tri-phosphate bonds similar to ATP as their fuel, speeding the reaction up several million-fold. 

"We've got ribozymes doing the right kind of chemistry to copy long molecules" says Szostak "We 

haven't achieved self-replication from single nucleotides yet, but it is definitely within sight". (Cohen) 

Zhang and Cech have reported a step towards the goal of linking amino-acids. They isolated RNAs that 

could efficiently link specific amino acids together (Zhang and Cech 1997). These pseudo-ribosomes 

were selected from a random pool of 1015 synthetic RNAs. They then elicited a trans-acting by coupling 

one of the amino acids to a short RNA with complementary sequence to the ribozyme achieving a 

ribozyme which whould join a ribosynthetase-amino acid to form a peptide bond with another thus 

relicating even more closely ribosomal function. They also found that a small region of many of the 

RNAs they selected was 70 per cent identical to some regions of the ribosomal RNA. "We not only 

copied ribosome function, we seemed to have recapitulated its evolution," says Cech. The two 

researchers then removed or mutated these sequences in the synthetic RNAs (Zhang and Cech 1998) any 

change to this region cut the activity of the RNA by a factor of between 20 and 600. This suggests this 

region in both the modern ribosome and the synthetic RNA may have the same role in the fusion 

reaction, such as holding the amino acids in the correct position and that they may have converged on 

the same molecular solution. 

In 2011 a breakthrough has been made by recombining traits evolved separately in different ribozyme 

lineages in combination with in-vitro evolution and engineering producing an RNA polymerase 

ribozyme (tC19Z in fig 17), capable of synthesizing RNAs of up to 95 nucleotides in length, that was 

able to synthesize a spectrum of RNA sequences, including the accurate synthesis of an enzymatically 

active RNA, a hammerhead endonuclease ribozyme (Wochner A, Attwater J, Coulson A, Holliger P 

2011Ribozyme-Catalyzed Transcription of an Active Ribozyme Science 332 209-212). 

The alternative hypothesis is that life may have begun as a molecular hybrid, PNA or peptide nucleic 

acid. PNA has a similar structure to RNA except for having a peptide backbone based on prebiotically 

abundant glycine and can co-instruct complementary RNA sequences and vice versa (Bohler, Nielsen 

and Orgel). The bases of PNA are joined together with peptide links like those in proteins which may 

not present the instabilities which sugars may have faced on the early earth. Matthew Levy and his 

colleagues (Nelson, Levy and Miller) persuaded up to 78 per cent of plausible prebiotic chemicals to 

transform into PNA backbone subunits amino-ethyl glycine or AEG. The acetic acid derivatives of the 

bases A, G U and C can likewise be generated from prebitotic reagents including NH4CN with glycine 

and cyanoglyceraldehyde. AEG units link up readily at 100 deg C, which may have been common 

temperature four billion years ago when our planet was rich in volcanic activity. PNA is clearly an 

alternative route to establishing the RNA era which also has a good cosmological foundation. However 

researchers concede that there is no evidence such alternative molecules have existed in Earth's history 



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"You don't see a smoking gun," says Gerald Joyce, of the Scripps Research Institute. (Marshall M 

2011 First life: The search for the first replicator New Scientist 15 Aug). 

 

 

9. Universal Stability Structures in Molecular Biology 

The previous discussion of the RNA era can unravel a double-bind that is central to biogenesis - how did 

the core biochemical pathways become generated? The traditional viewpoint is that they were 

successively created starting from a simple chemical-feeding heterotroph, through mutational evolution, 

building one-by-one the protein components necessary to make a working whole. This however does not 

explain how integrated systems such as electron transport and the citric acid cycle could have functioned 

at all with only a vestigial complement of enzymes. 

This suggests that many of the major features of molecular biology are generic structures which can 

come into existence under suitable conditions, through bifurcation, independently of the emergence of 

genetic RNA, and that these were subsequently captured by genetic takeover as genetic complexity 

permitted. Such generic structures include the polymeric structure of proteins and nucleic acids, 

nucleotide coenzymes, bilayer membrane structure and the topological closure of the cell, ion transport 

and membrane excitability, membrane-bound electron transport, glycolysis and the citric acid cycle. 

Such a perspective has far-reaching consequences for molecular biology in cosmological terms, for 

while the details of mutational evolution will be unique to each environment, the major features 

underlying biology could be universal. 

(a) Nucleotides and the Nucleotide Coenzymes.  

The nucleotide co-enzymes are widely regarded as ancient molecular fossils retained from the RNA-era. 

In addition to the key role of ADP and ATP as energy currency in the bio-metabolism, GTP is used in 

protein synthesis, and the nucleotides UDP and CDP are carriers of glucose and choline and other 

membrane components. Model prebiotic reactions have successfully coupled UDP and CDP to glucose 



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and choline (Mar et. al. 1986). Both NAD, and FAD function as carriers of redox energy. Coenzyme A 

consists of adenosine coupled to pantothenic acid and functions as a carrier of acyl and other groups via 

the terminal SH bond (Reanney 1977). Vitamin B12 also illustrates how a di-nucleotide can bind a 

metallic porphyrin ring. Eschenmoser (1988) has also discovered a plausible prebiotic pathway 

generating the more complex B12 molecule which involves two nucleotides and a Co-

porphyrin.Prebiotically such a molecule could have also utilized a lowered Fe
2+

- Fe
3+

 activation energy 

as a carrier of electrons. 

(b) Translation.  

According to the genetic takeover hypothesis, evolution of RNA captured existing stability structures in 

the prebiotic medium. The most central of these is clearly the use of proteins as coded enzyme catalysts. 

Such a process could only have occurred in an environment in which RNAs coexisted with amino-acids 

and in which a very small additional genetic advantage could capitalize on simple coding of existing 

structures to good effect. 

A variety of amino acids and oligopeptides are common products of prebiotic syntheses. The 

polymerization of amino acids and the development of peptide backbones with cyanide side chains from 

the linear HCN oligomer fig 14, provide alternative routes to oligopeptide structure. A natural 

propensity for -NH2 and -CO2H moieties as basic and acidic groups arises directly from the 

electronegativity bifurcation. 

The discovery that ribosomal, synthetase, messenger and transfer functions of protein synthesis can all 

in principle be carried out by RNAs alone leads to a natural interpretation of the development of the 

genetic code from a protein-free translation system. The major partitions of the genetic code have 

structural features consistent with an origin in underlying chemical bifurcations. The fundamental 

bifurcation sequence, fig 18 is as follows: 

(1) Polarity bifurcation: There is a major bifurcation in polarity between amino acids with anticodons 

having centre bases U & A. Uracil is correspondingly more hydrophilic than adenine, as reflected in 

their dominant split in hydrophobicity A(3.86)>G(2.3)>C(1.5)>U(1.45) and water solubilities 

A=1/1086, U=1/280. This leads to the idea that the polarity bifurcation was a principal symmetry-

breaking factor in the origin of the nucleic acid code (King 1982). 

(2) Abundance and GC: The initial base G also codes the most abundant amino acids, consistent with a 

GXY code starting with GAY=polar (anticodon U), GUY=non-polar (anticodon A) providing binding 

strength of GC and frame shift suppression (Y=pyrimidine). 

(3) Four-fold code: Extending to include GGY, GCY, provides a fourfold specificity for polar 

(Asp/Glu), non-polar (Val and larger), along with Gly, and Ala as most abundant. 

(4) Eight- and Twelve- fold codes: This could have then doubled to and 8-word code by including 

CAY, CUY, CGY, and CCY coding for non-polar and basic groups, and then a similar series based on 

AAY, AUY, AGY, and ACY Wong (1975) originally noted a correspondence between the first codon 

base and biosynthetic pathways in primitive organisms such as sulphur bacteria with Pro, Arg, Gln Leu, 

His derived from Glu and having first codon base C and Ser, Thr, Ile, Asn, Met, Lys being derived from 



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Asp having first codon base A (Knight, Freeland and Landweber 1999). OH- and SH-containing amino 

acids also form a single additional block (UA)(GC)Y, suggesting a third bifurcation for H-bonding, with 

UAY reading stop. Notably these is significant stereospecific affinity between certain amino acids such 

as Ile and Arg and their codons (ibid). 

(5) Evolutionary takeover: From this point evolutionary selection begins to optimize the bifurcations 

caused by stereospecificity and the growth of these interactions into synthesis pathways, based on error 

minimization and the incorporation of the last of the amino acids. Later assignments such as Trp are 

consistent with evolutionary adaptions. 

Freeland and Hurst (1998), have shown that strong selective pressures must have acted on the code 

during its evolution. Hurst found that single-letter changes to a codon, inserting the wrong amino acid 

into a protein, tended to specify amino acids that were very similar chemically to the correct ones, 

minimising the impact on the protein. Freeland then reasoned that the code should minimise chemical 

differences most between the correct and incorrect amino acid at the third base in the codon since 

translation misreads this base 10 times as often as the second. In an analysis that gave extra 

mathematical weight to the vulnerable sites most likely to be mistranslated, Freeland showed that no 

more than one in a million random codes was better at reducing the impact of errors than the natural 

code. The possibility of evolutionarty change in the code is affirmed by both mitochondrial and nuclear 

variants (Knight, Freeland and Landweber 1999). 

Following on from this Freeland et. al. (2000) have analysed other work showing that more optimal 

global solutions do exist to propose that stereochemical and synthesis path constraints fixated the code 

ealy on into one which was later evolutionarily optimized on error minimization constraints, the modern 

code being optimal under these constraining conditions. This analysis gives strong weight to the idea 

that the form of the code is derived from chemical, historical and selective factors rather than being a 

frozen accident which happened to the predecessors of the last common ancestor of living cell lines. 

 
 

Fig 19: Left and centre: Microcellular formations generated by the author from HCN and 

HCHO. Right: Spores of a psilocybe species at the same magnification for size comparison 

(King 1991b). 

(c) The Membrane, Excitability and Ion Transport  



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All life as we know it is dependent on maintaining a distinct internal micro-environment as an open far-

from-equilibrium thermodynamic system (Glansdorff and Prigogine), through the topological closure of 

the cell. Viruses for example all depend on cellular life. The structure of the bilayer membrane is a direct 

consequence of the polarity bifurcation. The formation of amphophilic lipid-like molecules, joining a 

linear non-polar hydrocarbon section to an ionic or H-bonding polar terminal, leaves 2 degrees of 

freedom for layer formation. Backing of the non-polar moeties to one another, fig 20(b), completes the 

bilayer. Cell structure can then arise directly from budding of the bilayer, as illustrated in budding in 

several types of prebiotic reaction medium. Microcellular structures are abundant in many origin of life 

syntheses, fig 19. The use of CDP associated with choline, inisotol & lipids in membrane construction is 

consistent with membrane formation in the RNA era. The structure of typical biological lipids such as 

phosphatidyl choline display a modular structure similar to ATP, consisting of fatty acid, glycerol, and 

substituted amine again linked by dehydration and involving phosphate, fig 20(e). 

The existence of the membrane as a non-polar structure leads to segregation into ionic and non-polar 

reaction phases. Ion transport is essential in maintaining the concentration gradients that distinguish the 

cytoplasm from the external environment and thus must develop in the earliest cellular systems 

(MacElroy et. al. 1989). Ion transport is a source of significant electronic effects, because the membrane 

under polarization is piezo-electric and is capable of excitation in the presence of suitable ions. Model 

systems using the simple 19 unit oligopeptide Na-ionopore alamethicin and artificial membranes display 

action potentials (Mueller and Rudin 1968). Similar results have been reported for microcells produced 

by prebiotic techniques containing light irradiated chromophores (Przybylski and Fox 1986), 

demonstrating that such effects are fundamental to the quantum architecture of lipid membranes (King 

1990). Four groups of non-polypeptide neurotransmitters: acetyl-choline, catecholamines, serotonin and 

histamine are amines, the latter three being derived from amino acids tyrosine, tryptophan and histidine 

by decarboxylation. Two others are amino acids and thus also contain amine groups. Notably 

alamethicin also has glutamine amides located in the core of the pore (Fox & Richards 1982). The 

catecholamines are linked to indoles such as serotonin by a prebiotic pathway, fig 20(c). 

 
 

Fig 20: (a) NAD structure permits linkage of other energies to a redox bifurcation. (b) H+ and e- 

transport linked by H2 in membrane due to insolubility of e- and solubility of H+. (c) Prebiotic link 

between catecholamines and indole via quinone-type photoreduction. (d) Hypothetical form of primitive 

electron transport as a non-equilibrium limit cycle. (e) Acetyl-choline and phosphatidyl choline 

compared. Phosphatidyl choline lipid stacks tail to tail as shown in the clothes pegs (b). 



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(d) Electron Transport 

The fact that the proton is soluble in water to form the hydrogen ion, but the electron is not, unless 

attached to another group such as a protein, causes a physical linkage to exist between the polarity 

bifurcation and the charge bifurcations associated with electron and proton transfer, fig 20(b) mediated 

by H transport through quinone reduction, (c). Despite the complexity of modern electron transport in 

photosynthesis and respiration, there is considerable evidence that membrane electrochemistry could 

have arisen before translation could produce coded enzymes. Firstly there is a consistent basis for the 

existence of many of the components of electron transport during the RNA era, since the nucleotide 

coenzymes NAD, FAD, a nucleotide-bound Mg & Fe-porphyrin ring similar to B12, a cysteine-bound 

FeS group (Hall et. al. 1974), possibly based on glutathione (g-glutamyl-cysteinyl-glycine) and quinones 

provide all the key components of electron transport in an RNA dependent but protein-free form, fig 

20(d) (King 1990). Both porphyrins and quinones have obvious prebiotic syntheses and the primal role 

of nucleotide coenzymes has already been discussed. Secondly, membrane structure and the solubility 

differences between the electron and proton guarantee a link between electron and hydrogen ion 

transport fundamental to quantum symmetry-breaking. Electron transfer does not require the complex 

coded active sites required to catalyse specific molecular transformations. Model systems using Fe-

porphyrins and imidazole can couple oxidative electron transport to phosphorylation (Brinigar et. al. 

1966) and photo activated Mg-porphyrin to phosphate link (Goncharova and Goldfelt 1990, Lozovaya 

et. al. 1990). 

 
 

Fig 21: (a) Di-phosphorylation of sugars leads to glycolysis through interaction of charged 

phosphates. (b) Generic examples of group transfer in the tricarboxylic acid cycle. 

(e) Glycolysis 

Glycolysis forms a bridge between six and three carbon sugars, reversing the structural pathway from 

H2CO, glycoaldehyde and glycderaldehyde to cyclic sugars, fig 15(b). Glycolysis is made energetically 

possible by phosphorylation, and releases high energy phosphate capable of driving other 

phosphorylations (Hermes-Lima and Vieyra 1989), fig 21(a). It is notable that glycolytic di-

phosphorylation of fructose is homologous with the route for nucleotide formation of fig 16(c). The high 

phosphate environment leading to RNAs would then naturally lead to similar phosphorylation of other 

sugars, and release of the high-energy phosphate bond through cleavage of the sugar. Mineral catalysis 

associated with phosphate gives the glycolytic pathway a natural basis for lysis of sugars as a dissipative 



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structure. Biological UDP-glucose coupling is consistent with nucleotide-dependent glycolysis in the 

RNA era. 

(f) The Tricarboxylic Acid Cycle 

forms a pool of multiply carboxylated molecules which carry CO2 in various states of energy, and result 

in reducing energy via nucleotide coenzymes NAD and FAD, which coupled with the use coenzyme A 

provide a basis for the tricarboxylic acid cycle in the RNA era. This could have existed as a limit cycle 

of di- and tri-carboxylated molecules acting both as an acceptor of acetate (a carbohydrate-equivalent 

i.e. (H2CO)2) and as an emitter of molecular CO2 and reducing H, thus bifurcating carbohydrate level 

redox potential into reduced and oxidized components. 

The linkage to nucleotide coenzymes such as NAD would have served to create a bifurcation of redox 

potential in the molecular milieu contributing to the diversity of reacting species. The cycle may have 

been hypercyclic (Eigen et. al. 1981) or chaotic, consisting of a population of molecules undergoing 

various generic transformations with net inflow of carboxylic acids and net emission of CO2 and transfer 

of H, due to generic transformations as illustrated in fig 21(b). Isomerization would have been catalysed 

by Fe
2+

. Several steps may have been driven by sunlight photolysis (Waddell et. al. 1989). 

The probability that the the central structures of molecular biology existed in the RNA era is consistent 

with their being chemical stability structures utilized by catalytic RNAs. The small genomes during the 

RNA era and limited catalytic capacity of RNAs by comparison with protein makes it likely that the 

emerging RNA-based system had to capitalize on existing chemical stability structures becase it lacked 

enzyme-based biosynthetic pathways. Genetic takeover also places these stability structures in a 

category determined by the cosmological milieu, thus giving evolutionary biology a cosmological 

foundation. 

 
 

Fig 22: Modern stromatolites (left), structures built of cyanobacteria (blue-green algae) grace 

Shark Bay, Australia. J. William Schopf has found remnants of 3.6 billion-year-old 

stromatolites lying near fossils of 3.5 billion-year-old cells that resemble modern 

cyanobacteria,. resembling strings of microscopic cells (right). Life thus arose within the first 

billion years of earth's formation from the planetary disc (Scientific American Feb 1991). 

 



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10. The Last Universal Common Ancestor 

Recent research suggests that the last universal common ancestor (LUCA) of all life on the planet may 

have arisen from a phase interface between alkaline hydrogen-emitting undersea vents and the archaic 

acidified iron-rich ocean (Martin and Russel 2003), giving rise to an active iron-sulphur reaction phase 

still present in living cells and associated with electron transport and some of the most ancent proteins, 

such as ferredoxin, in which differential dynamics in membranous micropores in the vents managed to 

concentrate polypeptides and polynucleotides to biologically sustainable levels (Baaske et. 

al. 2007, Budin et. al. 2009), giving rise to the RNA era, while at the same time providing a free energy 

source based on proton transport across membranous microcellular interfaces resulting from fatty acids 

also being concentrated above their critical aggregate concentration. 

 

Fig 1a: Proposed scheme for the universal common ancestor (Martin and Russel 2003) 

http://www.dhushara.com/book/bchtm/biocos.htm#Anchor-Martin-47857
http://www.dhushara.com/book/bchtm/biocos.htm#Anchor-Baaske-11481
http://www.dhushara.com/book/bchtm/biocos.htm#Anchor-Baaske-11481
http://www.dhushara.com/book/bchtm/biocos.htm#Anchor-Budin-35882
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The universal common ancestor of the three domains of life may have thus been a proton-pumping 

membranous interface from which archaea and bacteria emerged as free-living adaptions. This is 

suggested by fundemantal differences in their cell walls and other details of evolutionary relationships 

among some of the oldest genes. 

1. Biocosmology An overview of how the origin of life may arise from cosmic symmetry-breaking. 

2. 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. 

3. First Cells, Proton-Pumping and Undersea Rock Pores (Lane 2009 with abstracts 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. 

It has also been proposed, on the basis of the highly-conserved commonality of transcription and 

translation proteins to all life, but the apparently independent emergence of distinct DNA replication 

enzymes in archaea/eucaryotes and eubacteria, that the last universal common ancestor had a mixed 

RNA-DNA metabolism based on reverse transcriptase, pinpointing it to the latter phases of the RNA era 

(Leipe et. al.1999). 

 

Fig 1b: Hypothetical branching and evolution of RNA and DNA replication machinery (Leipe 

et. al. 1999). 

 

11. The Precocious Origins of Life on Earth 

Far from being an improbable accident taking billions of years to find the right conditions, life appears 

to have become established on Earth as soon as the conditions permitted a liquid water ocean, 

suggesting either that Earth was richly bombarded with complex organic molecules which quickly found 

within the diversity of microclimates on Earth some which were directly conducive to the processes 

leading the to the genetic epoch, or that life's had already begun in the gas and dust cloud initially 

forming the solar system. Gustaf Arrhenius, (Mojzsis et. al.) studying tiny apatite grains in the Isua 

http://www.dhushara.com/book/bchtm/biocos.htm#Anchor-Three-47857
http://www.dhushara.com/book/bchtm/biocos.htm#anchor1540797
http://www.dhushara.com/book/bchtm/suth/sutherland.htm
http://www.dhushara.com/book/bchtm/origins_of_life_proton.pdf
http://www.dhushara.com/book/bchtm/biocos.htm#Anchor-Lane-23240
http://www.dhushara.com/book/bchtm/biocos.htm#Anchor-Leipe-14210
http://www.dhushara.com/book/bchtm/biocos.htm#Anchor-Leipe-14210
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formation of Greenland, has found carbon 12 to 13 ratios consistent with the grains originating from 

living matter. The Isua rocks date from 3.85 billion years ago. Although indications from zircon crystals 

indicate a solid crust 4.2 billion years ago, no intact rocks have been discovered older than 3.96 billion 

years. The moon and probably the Earth likewise was heavily bombarded with meteors up to 3.8 billion 

years ago, suggesting that life evolved on earth as soon as environmental conditions allowed. 

There is continuing debate about whether these chemical and 'fossil' traces, now further 

studied with Raman spectroscopy to give carbon isotope evidence, really represent early 

cyanobacterial life, prebiotic 'soup' or volcanic or meteorite material [Schopf et. al. 2002, 

Brazier et. al. 2002, Mojzsis 2002]. However some researchers contend on the basis of 

inorganic simulations that these microfossils are purely mineral [Hogan 2003]. Jacques 

Touret [2003] has found that methane as well as high salt water trapped in pillow lava from 

Isua suggesting the involvement of hydrothermal vents beside an undersea volcano. 

However these findings are questioned by David Vanko [Necht 2003]. John Parnell has also 

suggested radioactivity trapped in oily grains may have had a role [Lawton 2003]. In any 

case there is consensus agreement that life was under way by 3.5 billion years the age of the 

fossil stromatolite in fig 22, although the nature of these is also debated. These fossils could 

be the earliest evidence of life on Earth, yet these relics, with names like Chromoccoceae 

and Oscdlotorioceoe, are morphologically identical to modern cyanobacteria that cover the 

globe from Antarctica to the Sahara [Cohen 1996]. In July 2011 Brazier who had questioned the 

biological nature of the earliest fossils, himself claims to have discovered a genuine biological fossil of 

sulphur bacteria dating to 3.43 billion years. 

 
 

a,b,e, Clusters of cells, some showing cell wall rupturing (arrows in a,b), folding or invagination (arrow 

in e). c,d,h, Chains of cells with cellular divisions (arrows). f., Cells attached to detrital quartz grains, 

exhibiting cell wall. 

 Oldest fossils show early life was a beach August 2011 New Sceintist The oldest compelling 

fossil evidence for cellular life has been discovered on a 3.43-billion-yearold beach in western 

http://www.dhushara.com/book/bchtm/fossil_earliest.pdf


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Australia. Its grains of sand provided a home for cells that dined on sulphur in a largely oxygen-

free world. 

 The First Breath (pdf password="model") Ongoing debate about the first origins of life-driven 

oxidation 

The origins of the first fossil life forms including the stromatolites in fig 23, likewise lie at the limits of 

the geological record. At 3.5 billion years old, fossilised bacteria are the earliest evidence of life on 

Earth, and yet these relics, with names like Chromoccoceae and Oscdlotorioceoe, are identical to the 

sophisticated modern cyano-bacteria that cover the globe from Antarctica to the Sahara (Let There be 

Life New Scientist 6 July 96). 

The emergence of the eucaryotes that lead to the higher organisms is also almost as ancient as the 

geological record. Traces of oil extracted from Australian shale have pushed the date for the origin of 

complex cells back another half a billion years. Compounds in the oil suggest that eucaryotic cells, 

which make up all life on Earth except for bacteria, had evolved as early as 2.7 billion years ago. It is 

not until about 2.1 billion years ago that fossil imprints appear in the geological record that are so large 

that they can only be eucaryotes. A team of researchers in Australia has found steranes, molecules with 

26 to 30 carbon atoms arranged in four rings, in droplets of oil extracted from rock 700 metres below the 

surface in the Pilbara region of north-western Australia. These are produced by the decay of cholesterol 

and other steroids found in the membranes of eukaryotes, but not bacteria (Brocks et. al.). Genetic 

analysis of the base of the tree of life indicates the oldest branches of both archaea and (eu)bacteria are 

thermophilic suggesting a period in hot pools or significant meteoric impact leaving only the 

thermophiles as survivors. 

The Copernican principle asserts that the Earth is a typical rocky planet in a typical planetary system, 

located in an unexceptional region of a common barred-spiral galaxy, hence it is probable that the 

universe teems with complex life. This is supported to a reasonable extent by the discovery of an 

increasing number of planets including some putative "Goldilocks" zone planets where water would be 

liquid and life as we know it could potentially exist. Set against this, the Rare Earth hypothesis argues 

that the emergence of complex life requires a host of fortuitous circumstances including a galactic 

habitable zone, a central star and planetary system having the requisite character, the circumstellar 

habitable zone, the size of the planet, the advantage of a large satellite, conditions needed to assure the 

planet has a magnetosphere and plate tectonics, the chemistry of the lithosphere, atmosphere, and 

oceans, the role of "evolutionary pumps" such as massive glaciation and rare bolide impacts, and 

whatever led to the still mysterious Cambrian explosion of animal phyla. This might mean that planets 

able to support a bacterial level of life are not so uncommon, but those supporting complex multicellular 

life might be. 

Bringing this question to a pivotal crux in our context, the emergence of mitochondria as 

endosymbionts has been proposed to be a critical bottleneck which allowed complex life to evolve only 

once, because, only in this effectively fractal cellular architecture, can the membrane surface areas 

necessary to support the chemical reactions enabling the vastly larger number of genes in a complex 

organism's genome to maintain metabolic stability (Lane and Martin The energetics of genome 

complexity 2010 doi:10.1038doi:10.1038/nature09486). Whether such endo-symbiosis is rare. or a 

common extreme of parasitic relationships would then determine how likely or unlikely complex life 

might be. 

http://www.dhushara.com/book/bchtm/first_breath.pdf
http://en.wikipedia.org/wiki/Rare_Earth_hypothesis
http://www.newscientist.com/article/dn18734-why-complex-life-probably-evolved-only-once.html
http://www.newscientist.com/article/dn18734-why-complex-life-probably-evolved-only-once.html


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Offset against both the uniqueness of the mitochondrial endo-symbiosis and the closely linked, but 

independent question of the origin of the nucleus and nuclear envelope, has been 

the discovery of mimiviruses and mamaviruses infecting amoeba (Raoult et, al. The 1.2-Mb Genome 

Sequence of Mimivirus doi: 10.1126/science.1101485) and related very large aquatic viruses such 

as CroV infecting single celled plankton species, which despite their recent discovery, appear from 

ocean gene analyses to be potentially ubiquitous and widespread in the oceans and possibly playing a 

crucial role in regulating the atmospheric-oceanic pathways, such as carbon sequestration (Fisher, Allen, 

Wilson and Suttle 2010 Giant virus with a remarkable complement of genes infects marine 

zooplankton PNAS doi: 10.1073/pnas.1007615107). These form an intermediate genetic position 

between viruses and cells, having the largest genomes, with extensive cellular machinery and larger than 

the smallest completely autonomous bacterial and archaeal genomes. 

Mimiviruses also host parasitic virophages, affectionately named sputnik as viral satellites, which piggy 

back on the metabolism of the large viral factories set up by these giant viral genomes causing the 

mimiviruses to sicken, and these virophages also contains genes that are linked to viruses infecting each 

of the three domains of life Eukarya, Archaea and Bacteria (La Scola et. al. The virophage as a unique 

parasite of the giant mimivirus Nature doi:10.1038/nature07218). It has thus been suggested that they 

have a primary role in the establishment of cellular life and that they may have been instrumental in the 

emergence of the nuclear envelope. 

 
 

Fig 23: A quadratic iteration compared with the interactive effects of inverse quadratic charge 

interaction. The fractal structures of tissues have features similar to the Mandelbrot set on 

changes of scale. The fractal effects reach from the molecular (a) in which individual proteins 

are illustrated embedded in the lipid membrane, through cell organelles (b) to the intercellular 

structure of whole organs as illustrated by skin (c). Such scale-dependent coherence of structure 

is possible only because of the highly non-linear nature of the electromagnetic force in quantum 

charge interactions of fermionic matter (Campbell). 

http://www.k8science.org/news/news.cfm?art=1288
http://en.wikipedia.org/wiki/Mimivirus
http://en.wikipedia.org/wiki/Mamavirus
http://www.newscientist.com/article/dn19625-giant-virus-with-tiny-victims-carries-a-monster-genome.html
http://www.nature.com/news/2008/080806/full/454677a.html

