Biocosmology: Cosmic Symmetry-Breaking and Molecular Evolution
We now explore the structural relationship between cosmological
symmetry-breaking and the form of molecular evolution leading
to biological systems on Earth. It thus forms an alternative
to historical hypotheses in which the form of biogenesis is believed
to be the product of a linked sequence of specific conditions,
bridged by stochastic selection processes.
1 : A MOLECULAR BIOLOGICAL VIEW OF COSMIC SYMMETRY-BREAKING.
The rich diversity of structure in molecular systems is made
possible by the profound asymmetries between the nuclear forces
and electromagnetism. Although molecular dynamics is founded
on electromagnetic orbitals, the diversity of the elements and
their asymmetric charge structure, with electrons captured by
a spectrum of positively charged nuclei, is made possible through
the divergence of symmetry of the four fundamental forces. The
non-linear electromagnetic charge interactions of these asymmetric
structures is responsible for both chemical bonding and the hierarchy
of weak bonding interactions which result in the non-periodic
secondary and tertiary structures of proteins and nucleic acids.
It also provides the basis for a bifurcation theory which could
give biogenesis the same generality that nucleogenesis has.
Differentiation and Inflation: The Microscopic and Cosmic Scales
Force Differentiation: The strong (nuclear binding) and weak
(neutron decay) forces, electromagnetism and gravity are believed
to have emerged from a single superforce shortly after the big
bang, fig1(a). The strong force is believed to be a secondary
effect of the colour force in much the same way that molecular
bonding is a secondary consequence of the formation of atoms.
The weak force has become short range because it is mediated
by massive particles, which are believed to gain an extra degree
of freedom by assimilating a Higg's boson (Georgi 1981, t'Hooft
1980, Veltman 1986). The symmetry between the Z and W particles
of the weak force and the massless photon of elecromagnetism
is thus broken by the lower energy of the polarized configuration,
fig 1(b). Even heavier particles are believed to separate the
strong force from these two. Force reconvergence occurs at the
unification temperature fig 1(c). The strong force mesons gain
mass from a different mechanism, being the energies of the bound
states of the colour force, whose gluons are massless, but confined.
The separation of gravity from the other forces is more fundamental
because it involves the structure of space-time and may be described
by a higher-dimensional superstring force in which particles
become excited loops or strings in a higher dimensional space-time
which is compactified into our 4-dimensional form (Green 1985,
1986, Goldman et.al. 1988, Freedman & van Nieuwenhuizen 1985).
Cosmic Inflation: A universe in a symmetrical state, but below
its unification temperature is in an unstable high-energy false
vacuum. The energy of the Higg's field causes inflation, in which
the universe has net gravitational repulsion and expands exponentially,
smoothing irregularities to fractal structures on the scale of
galaxies (Guth & Steinhardt 1984). The breakdown of the false
vacuum then releases a stream of high-energy particles as latent
heat, to form the hot expanding universe under attractive gravitation.
The gravitational potential energy thus gained equals that of
the energetic particles, making the generation of the universe
possible from a quantum fluctuation. However variations in the
cosmic background radiation are consistent with a big-bang smoothed
by inflation (Smoot 1992).
The interaction between the resulting wave-particles also results
in distinct effects on the microscopic and cosmic scales, namely
galaxy and star formation and genesis of nuclei, chemical elements,
and finally molecules, in which the non-linear nature of chemical
bonding becomes fully expressed in complex tertiary structures.
These interactions are modified indirectly by the nuclear forces
which contribute asymmetries, spin-effects, weak decay and the
nuclear energy of stars.
Particle Interaction-1: Nucleosynthesis as a Cosmological Dynamical
System. The nucleosynthesis pathway generates over 100 atomic
nuclei from the already composite proton and neutron. Parity
between protons and neutrons is slightly broken via weak decay,
fig 1(e) to balance between the lowest nuclear quantum states
being filled and increasing electromagnetic repulsion. The process
is exothermic and moderated by the catalytic action of several
of the isotopes of lighter elements such as carbon and oxygen.
The cosmic abundance of the elements fig1(d) reflects the binding
energies of the nuclei and stable a-particle-like shells (Moeller
et. al. 1984). The nucleosynthesis pathway has a cosmologically-general
form despite having some variation in individual star systems.
Particle Interaction-2: Moleculosynthesis. The Culminating Dynamic
Although, by comparison with the energies of cosmic creation
or even astronomical bodies, the structures of biomolecules seem
much too fragile to be a cosmological feature, symmetry-breaking
of the forces leads inevitably to molecular structures as a hierarchical
culmination of the interactive phase. Quarks are bound by gluons
into composite particles such as the proton p+ and neutron n.
These interact by the strong force via the nucleosynthesis pathway
to form the elementary nuclei. Subsequently the weaker electromagnetic
force interacts, also in two phases, firstly by the formation
of atoms around nuclei and then by secondary interaction to form
molecules. The latter phase occurs in a sequence of stages through
successive strong and weak bonding interactions, producing the
complex tertiary structures of biomolecules, fig 1(f,g).
The Cosmic Interaction Sequence: The Pathway to the Planetary
Biosphere Galaxy formation is followed by the generation of the
chemical nuclei in the supernova explosion of a short-lived hot
star. In the second phase these elements are drawn into a lower
energy long-lived sun-like star, the lighter [bio]elements, occurring
in high cosmic abundance as a result of nucelosynthesis dynamics,
fig1(d), becoming concentrated on mid-range planets. The final
re-entry of the forces is thus represented by stellar photon
irradiation of molecular systems, under gravitational stabilization
on a planetary surface.
THE NON-LINEAR DYNAMICS OF QUANTUM CHEMISTRY
A Brief Survey of Non-linear Orbital Theory
The fact that the laws of chemistry were discovered sooner and
were relatively easier to explore than the conditions underlying
the unification of electromagnetism with the nuclear forces has
resulted in an anomalous historical perspective which has helped
to obscure some of the most interesting and complex manifestations
of chemistry as a final interactive consequence of cosmological
quantum symmetry-breaking. The increasing nuclear charge permits
an unparalleled richness and complexity of quantum bonding structures
in which electron-electron repulsions, spin-obit coupling, and
other effects perturb the periodicity of orbital properties and
lead to the development of higher-order molecular structures.
Although quanta obey linear wave amplitude superposition, chemistry
inherits non-linearity in the form of the attractive and repulsive
charge interactions between orbital systems. Such non-linear
interaction, combined with Pauli exclusion, is responsible for
the diversity of chemical interaction from the covalent bond
to the secondary and tertiary effects manifest in the complex
structures of proteins and nucleic acids.
The source of this non-linear interaction is the foundation of
all chemical bonding, the electric potential. Although the state
vector of a quantum-mechanical system comprises a linear combination
of eigenfunctions, the electrostatic charge of the electron causes
orbital interaction to have non-linear energetics.
Quantum matrix methods are generally simplified to take account
of only one aspect of molecular interaction and involve extensive
approximations such as the independent particle approximation
and Hükel theory (Brown 1972). The non-linear interactions
of electron repulsions and spin-orbit coupling in the global
context of molecular tertiary structure require complex computer
techniques for example to predict the 3-D structure of protein
molecules. These are only beginning to simulate the folding of
complex molecules, again requiring approximation techniques.
The capacity of orbitals, including unoccupied orbitals, to cause
successive perturbations of bonding energetics results in an
interaction succession from strong covalent and ionic bond types
[200-800 kj/mole] through to their residual effects in the variety
of weaker H-bonding, polar, hydrophobic, and van der Waals interactions
[4-40 kj/mole] merging into the average kinetic energies at biological
temperatures [2.6 kj/mole at 25oC], (Watson et. al. 1988). These
are responsible for secondary structures such as the a-helix
of proteins and base-pairing and stacking of nucleic acids, and
result in the tertiary effects central to enzyme action, whose
energetics are determined by global interactions in complex molecules.
The cooperative reactivity of the active site of hexokinase
demonstrates how, even after resolving the covalent and successive
weaker bonding effects, and the local interactions of individual
sides chains, and the larger fractal structures arising from
weak bonds forming secondayry and tertiary protein structure,
the entire enzyme is still capable of marked global conformation
changes of a highly energetic nature. Chemical forces are thus
fractal, leading right up to the globally fractal tissue structures
we see in organismic biology, from the lungs to the brain. This
is confirmed in the fractal dynamics of key cell structures (Watson
Beloushov-Zhabotinskii type reaction giving rise to three-dimensional
scroll waves (CK).
2.2 Fractal and Chaotic Dynamics and Structure in Molecular
Most minerals adopt periodic crystal geometries. Although some
anomalies are disordered, many such as those superconducting
perovskites have higher-order geometrical regularity. By contrast,
the irregularties in polymers such as polypeptides and RNA is
critical are establishing the richness of their tertiary structures,
and their bio-activity. Variable sequence polymers with significant
tertiary structure are non-periodic because the unlimited variety
of monomeric primary sequences induce irregular secondary and
tertiary structures. These irregularities are central to biochemistry
because they result in powerful catalysts which can alter the
reaction dynamics because of the generation of local activating
sites globally potentiated through intermolecular weak-bonding
associations. They also permit allosteric regulation. Despite
being genetically coded, such molecules form fractal structures
both in stereochemical terms and in terms of their relaxation
Prigogine's theory of non-equilibrium thermodynamics, in which
maximum entropy is replaced by a more general critical point
of entropy production, which in an open system may not be a maximum.
The associated oscillating chemical systems such as the Beloushov-Zhabotinskii
reaction have demonstrated the capacity of chemical systems to
enter into non-linear concentration dynamics, including limit
cycle bifurcations. Period-doubling bifurcations and chaotic
concentration dynamics have also been observed . Similar dynamics
occur in electrochemical membrane excitation. The living cell
is a non-equilibrium open thermodynamic system whose boundary,
the memerane, exchanges material with the outside world. This
makes it possible for life to be a negentropic system within
a universe where entropy is increasing. The photosynthetic conversion
of light to chemical energy and structural growth in our great
forests is a prime example.
By contrast, viruses do not form a thermodynamic system as such,
but rather a system of pure information. The first emergence
of polynucleotides may similarly have been associated with the
acrual of such information by a more direct negentropic route,
Fig 2: (a) Symmetry-breaking model of selection of bioelements,
as an interference interaction between H and CNO, followed by
secondary ionic, covalent and catalytic interactions. (b) Boiling
points of hydrides illustrate the optimality of H2O as polar
H-bonding and structural medium for biological structure (CK).
3-D periodic table Sci Am. Sep 98
Biogenesis as a Central Synthetic Pathway
One of the central ideas of the cosmological biogenesis model
is that the molecular interactions forming the pathways to the
origins of life as we know it are not just an accidental set
of chemical reactions out of a great variety of ad-hoc initial
conditions, but that they represent a fundamental biforcation
arising ultimately from cosmological symmetry-breaking of the
four forces. The non-linear properties of electron orbitals cause
the periodic table to have a critical sequence of bifurcations
relating to the fundamental interactions.
Traditionally chemists have become so wedded to the idea of atoms
and molecules as simply the "building blocks of the universe",
as Isaac Asimov once put it that they cannot comprehend how they
might interact as a quantum dynamical system. The fact that chemical
bonding is possible between a large variety of atoms in some
form or other leads to the loss of an understanding for how the
non-linear electronic interactions gave rise to chemical bonding
in the first place. It also leads to a mechanistic view of biogenesis,
in which there is no underlying dynamical theory, but simply
a search for the underlying special or initial conditions which
caused the first self-replicating reaction to get going. The
aim is thus either to set up a laboratory reaction by placing
extreme order on the system, to elucidate this reaction pathway,
or an attempt to use random processes and probabilistc arguments
to model the likelihood that some collection of replicating molecules
might accidentally come together. This has marred prebiotic research
and profoundly slowed its advances.
Two illustrations hightlight this conceptual barrier. There is
a 40 year time span between Miller and Urey's first spark experiments
elucidating pathways from simple precursors to the purine nucleic
acid bases, and the modification of this synthesis which led
to good yields of the pyrimidines. Likewise there has been two
decades of research in attempting to polymerize ribonucleotides,
littered with failures due to oversimiplification of RNA interactions
and mechanistic variants such as peptide-nucleic acids, before
the ribonucleotide evolution techniques of Szostak and finally
simple relationship between polymerizing ribonucleotides and
montmorrilonite clays became obvious.
The cosmological biogenesis theory asserts the following three
1. All molecular interaction is highly non-linear, and forms
an unresolved fractal interactive milieu which permits not only
the cascade of weaking bonding and global interactions characterizing
protein enzymes and nucleic acids but also on a larger scale
the tissue structures of whole organisms. This means that, while
nature can be crystalline, it can also display emergent properties
on larger scales which are very difficult to predict from an
examination of the components "the whole is more than the
sum of the parts". The non-linear perspective realizes emergence
within an in-principle reductionist viewpoint because the underlying
principles are quantum chemistry, but the consequences are emergent
fractal interaction. This situation is clearly illustrated in
the great difficulty of fully accurate modelling of the electronic
dynamics of even simple atoms because they are many-body problems,
and by the complexity of the protein-folding problem (Sci Am.
Jan 91 see also Shape is All NS 24 Oct 98 42).
2. The entire molecular environment is non-linear in a way which
is capable of exploring its phase space in the manner of a chaotic
dynamical system. This means that planetary, terrestrial and
molecular systems display sufficient chaos to generate all the
varieties of structural interaction possible. These non-linearities
make the natural environment a quantum equivalent of a Mandelbrot
set in which a potentially infinite variety of dynamics are possible.
The overwhelming majority of chemical experiments into the origins
of life (with the notable exception of the original spark experiments)
attempt to defeat this process by introducing simple overweaning
conditions of order to force simple clear-cut products out of
3. Underlying this rich chaotic interaction is a universal bifurcation
pathway which is a direct consequence of the form of cosmological
symmetry-breaking of the four quantum forces. While there may
be more than one way that molecular replication could occur in
chemistry, the RNA-based form of life is nevertheless a central
bifurcation product of the interaction between the fundamental
forces and by no means a mere accident of unlikely circumstances.
Principal Symmetry-splitting : The Covalent Interaction of
H with C, N, O.
Quantum interference interaction between the two-electron 1s
orbital and the eight-electron 2sp3 hybrid. The resulting three
dimensional covalent bonds give C, N and O optimal capacity to
form diverse polymeric structures in association with H. Symmetry
is split, because the 1s has only one binding electron state,
while the 2sp3 has a series from with differing energies and
varied occupancy, as the nuclear charge increases. The 1s orbital
is unique in the generation of the hydrogen bond through the
capacity of the bare proton to interact with a lone pair orbital.
The CNO group all possess the same tetrahedral sp3 bonding geometry
and form a graded sequence in electronegativity, with one and
two lone pairs appearing successively in N and O.
Polymeric condensation of unstable high-energy multiple-bonded
forms. Some of the strongest covalent bonds are the multiple-bonds
such as - CC -, - CN, and > C = O. These can be generated
by applying any one of several high-energy sources such as u.v.
light, high temperatures (900oC), or spark discharge. Because
of the higher energy of the resulting pi-orbitals, these bonds
possess a specific type of structural instability in which one
or two pi-bonds can open to form polymeric structures, particularly
when bound to H and alkyl groups, as under reducing conditions.
Most of the prebiotic molecular complexity generated by such
energy sources can be derived from mutual polymerizations of
HCCH, HCN, and H2C = O, including purines, pyrimidines, key sugar
types, amino acids, porphyrins etc. They form a core pathway
from high energy stability to structurally unstable polymerization,
which we will examine in the next section.
Radio-telescope data demonstrates clouds of HCN and H2CO spanning
the region in the Orion nebula where several new stars are forming.
All of A, U, G, and C have been detected in carbonaceous chondrite
meteorites, which also contain membrane-forming products. HCN
and HCHO polymerizations also lead to membranous microcellular
structures. Although the presence of CO2 as a principal atmospheric
gas on the early earth could have reduced the quantities of such
reduced molecules, HCN could have been produced as a transient
in the early atmosphere leading to heterocyclic products. A variety
of microenvironments would still have had access to reducing
The formation of conjugated double and single bonds in these
reactions results is the appearance of delocalized pi-orbitals.
Such orbitals in heterocyclic (N, C) rings with conjugated resonance
configurations also enable lone pair n > p* and also p >
p* transitions, resulting in increased photon absorption. These
effects in combination play a key role in many biological processes
including photosynthesis, electron transport and bioluminescence.
Secondary Splitting between C, N, and O : Electronegativity
In addition to varying covalent valencies, lone pairs etc., the
8-electron 2sp3 hybrid generates a sequence of elements with
increasing electronegativity, arising from the increasing nuclear
charge. This results in a variety of secondary effects in addition
to the oxidation-reduction parameter, from the polarity bifurcation
into aqueous and hydrophobic phases to the complementation of
CO2 and NH3 as organic acid and base.
Optimality of H2O: Polarity, Phase and Acid-base bifurcations.
Ionic and Hydrogen bonding.
Outside metals such as mercury, water has one of the highest
specific heats. This is a reflection of the large number of conformational
degress of freedom it contains. It is also capable of a very
unusual number of interactions, ionic, polar, H-bonding, acid-base
and the polarity bifurcation into hydrophilic (water-loving)
and hydrophobic (oily) phases in biological molecules and structures
such as the lipid membrane, which is a sandwich of oily and watery
Dehydration is the common currency of polymerization, beginning
with the mineral pyrophosphate linkage of ATP. The central biopolymers,
polynucleotides, polypeptides and polysacharides are uniformly
linked by the removal of a molecule of water, dehydration in
the aqueous medium. Furthermore the three-dimensional structures
of the nucleic acid double-helix, globular enzymes, membranes
and ion channels are all made structurally and energetically
possible only through the interactions of these molecules with
water and the induced H2O structures that form around them in
solution. Both nucleic acids and proteins consist of a balance
of hydrophilic and hydrophobic interactions which in the former
give hydrophobic base-stacking within a polar back-bone and with
enzymes a non-polar micelle surrounded by hydrophilic groups.
Differential electronegativity results in several coincident
bifurcations associated with water structure. A symmetry-breaking
occurs between the relatively non-polar C-H bond and the increasingly
polar N-H and O-H. This results in phase bifurcation of the aqueous
medium into polar and non-polar phases in association with low-entropy
water bonding structures induced around non-polar molecules.
This is directly responsible for the development a variety of
structures from the membrane in the context of lipid molecules,
to the globular enzyme form and base-stacking of nucleic acids.
The optimal nature of water as a hydride is illustrated in boiling
points. By comparison with ammonia H3N, water H2O has balanced
doning and accepting H-bonds and a stronger polarity. Such polar
properties are also clearly optimal over H2S, alcohols etc.
The discovery by the ISO Infra-red Space Observatory, of widespread
incidence of water around stars, planets and throughout the universe
where stars are forming has led increasing weight tothe cosmological
status of water as a pre-cursor to life. - AP Apr 98
Water provides several other secondary bifurcations besides polarity.
The dissociation of H2O into H+ and OH- lays
the foundation for the acid-base bifurcation, while ionic solubility
generates anion-cation. H-bonding structures are also pivotal
in determining the form of polymers including the alpha helix,
base pairing and solubility of molecules such as sugars. Many
properties of proteins and nucleic acids, are derived from water
bonding structures in which a mix of H-bonding and phase bifurcation
effects occur. The large diversity of quantum modes in water
is exemplified by its high specific heat contrasting with that
of proteins (Cochran 1971). Polymerization of nucleotides, amino-acids
and sugars all involve dehydration elimination of H2O, giving
water a central role in polymer formation.
P and S as Low-energy Covalent Modifiers - the delicate role
The second-row covalent elements are sub-optimal in their mutual
covalent interactions and their interaction with H. Their size
is more compatible with interaction with O, forming e.g. SiO32-,
PO43- & SO42- ions including crystalline minerals. The silicones
are notable for their O content by comparison with hydrocarbons.
However in the context of the primary H-CNO interaction, two
new optimal properties are introduced.
PO43- is unique in its capacity to form a series of dehydration
polymers, both in the form of pyro- and poly-phosphates, and
in interaction with other molecules such as sugars. The energy
of phosphorylation falls neatly into the weak bond range (30-60
kj/mole) making it suitable for conformational changes. The universality
of dehydration as a polymerization mechanism in polynucleotides,
polypeptides, polysaccharides and lipids, the involvement of
phosphate in ATP energetics, RNA and membrane structure, and
the fact that the dehydration mechanism easily recycles, unlike
the organic condensing agents, give phosphate uniqueness and
optimality as a dehydrating salt.
The function of S in biosystems highlights a second optimality.
The lowered energy of oxidation transitions in S particularly
S-S ´ S-H , by comparison with first row elements, gives
S a unique role both in terms of tertiary bonding and low energy
respiration and photosynthesis pathways.
It has recently been discovered that oligoribonucleotides will
polymerize effectively on silicate clay surfaces, where the positive
ions of atoms such as Al make polar interactions with the phosphate
backbones of RNA, stabilizing the molecules and making further
polymerization possible in an ordered geometry. This consitiutes
a major breakthrough in the modelling of life's origins and demonstrates
the sensitivity of the biogenic pathway to the subtle differences
of electronegativity of the second-row covalent elements phosphorus
The cations bifurcate in two phases : monovalent-divalent, and
series (Na-K, Mg-Ca). Although ions such as K+ and Na+ are chemically
very similar, their radii of hydration differ significantly enough
to result in a bifurcation between their properties in relation
to water structures and the membrane. Smaller Na+ and H3O+ require
water structures to resolve their more intense electric fields.
Larger K+ is soluble with less hydration, making it smaller in
solution and more permeable to the membrane (King 1978) . Ca2+
and Mg2+ have a similar divergence, Ca2+ having stronger chelating
properties. This causes a crossed bifurcation between the two
series in which K+ and Mg2+ are intracellular, Mg2+ having a
pivotal role in RNA tranesterifications. Cl- remains the central
anion along with organic groups. These bifurcations are the basis
of membrane excitability and the maintenance of concentration
gradients in the intracellular medium which distinguish the living
medium from the environment at large.
Transition Element Catalysis
These add d-orbital effects, forming a catalytic group. Almost
all of the transition elements e.g. Mn, Fe, Co, Cu, Zn are essential
biological trace elements (Frieden 1972), promote prebiotic syntheses
(Kobayashi and Ponnamperuma 1985) and are optimal in their catalytic
ligand-forming capacity and valency transitions. Zn2+ for example,
by coupling to the PO43- backbone, catalyses RNA polymerization
in prebiotic syntheses and occurs both in polymerases and DNA
binding proteins. Both the Fe2+-Fe3+ transition, and spin-orbit
coupling conversion of electrons into the triplet-state in Fe-S
complexes occur in electron and oxygen transport (McGlynn et.
al. 1964). Other metal atoms such as Mo, Mn have similar optimal
functions, e.g. in N2 fixation.
Fig 3 : (a) The perturbing effect of the neutral weak force results
in violation of chiral symmetry in electron orbits. Without perturbation
(i) the orbits are non-chiral, but the action of Zo results in
a perturbing chiral rotation. (b) Autocatalytic symmetry-breaking
causes random chiral bifurcation (i). Weak perturbation results
in only one chiral form (iii) (King).
Although the electromagnetic force has chiral symmetry, the electron
also interacts via the neutral weak force when close to the nucleus.
This causes a perturbation to the electronic orbit causing it
to become selectively chiral, fig 3(a) (Bouchiat & Pottier
1984, Hegstrom & Kondputi 1990). In a polymeric system with
competing D and L variants, in which there is negative feedback
between the two chiral forms of polymerization, making the system
unstable, the chiral weak force provides a symmetry-breaking
perturbation. In a simulation, fig 3(bi) high [S][T] causes autocatalytic
bifurcation of system (ii), resulting in random symmetry-breaking
into products D or L. Chiral weak perturbation (iii) results
in one form only. The selection of D-nucleotides could have resulted
in L-amino acids by a stereochemical association (Lacey et. al.
Inner Circles New Scientist 8 Aug 98 11 reports on findings that
there is a 17% net circular polarization in light in gas clouds
in the Orion nebula where new stars are forming. Although this
was infra-red light James Hough says it should also apply to
the ultra-violet light. This would explain the excess of L-amino-acids
found in the Murchison meteorite, suggesting a cosmic rather
than accidental origin for the handedness of biological molecules
Polarized Life Sci Am Oct 98
Tertiary Interaction of Mineral Interface.
Both silicates such as clays and volcanic magmas have been the
subject of intensive interest as catalytic or information organizing
adjuncts to prebiotic evolution. Clays have been proposed as
a primitive genetic system and both include adsorbent and catalytic
sites. The mineral interface involves crucial processes of selective
adsorption, chromatographic migration, and fractional concentration,
which may be essential to explain how rich concentrations of
nucleotide monomers could have occurred over geologic time scales.
More recently a fundamental interaction between RNA and clays
has been elucidated wich appears to be central in enabling oligo-ribonucleotides
to polymerize in an ordered way while bound to the positively
charged metal groups in montmorrilonite clays, bridging the gap
between small random ribo-oligomers and RNA molecules of a length
capable of self-replication.
Key polymerizations such as those of HCN and HCHO are proposed
to generate a series of generic bifurcation structures through
combined autocatalytic and quantum bond effects, which include
major components of the metabloism including nucleotides, polypeptides
and key membrane components. These will be examined in the next
The astronomical perspective
The occurrence of the key precursors of biomeolecules are
not in any way confined to Earth of the specific conditions of
Earth. Much of the organic material on earth is believed to have
peppered down from comets and carbonaceous meteorites especially
earlier in the evolution of the solar systems when less of the
original material from the proto-solar gas and dust cloud had
been swept away by collision. Protosolar gas clouds in the Orion
nebula are known to contain precisely HCN and HCHO as shown above.
Certain parts of the universe give off an infra-red signal not
unlike that of carbohydrates. Interstellar dust grains are also
known to contain organic molecules. In fact the occurrence of
organic molecules is essentially ubiquiitous to all second generation
sun-like stars containing a mix of elements of nucleosynthesis
formed from the material of previous supernovas.
Indeed their presence is so commonplace and the incidence of
life on Earth is so early that the possibility that arose previously
to the formation of Earth cannot entirely be ruled out. Cosmological
biogenesis is however ideally suited to the conditions actually
occurring on Earth with plentiful water, a temperature just above
the liquefaction of water, a good supply of organic molecules
and a steady mild solar input.
Just as one can consider the non-linearities of the electromagnetic
force in developing the fractal dynamics of molecules, one can
also appreciate the significance of non-linearities in gravitation
in forming the rich diversity of planets and satellites we see
in our own solar system. Other stars now seem to be quite richly
endowed with planets, but these again show very marked variation.
Such marked variationis characteristic of non-linear dynamics,
which serves to accentuate existing differences for example in
temperature and composition between the planets to cause unique
effects, such as the highly acidic, electrified runaway greenhouse
atmosphere of venus.
Far from considering these extreme variations as reducing the
likelihood of finding life on other planets, what it demonstrates
is that on an astronomical scale as well as the microscopic,
the universe behaves very much like a Mandelbrot set in establishing
dynamics of uniqueness and diversity which explores the dynamical
space of possibilities.
The first stage of this path of increasing molecular complexity
is the generation of organic molecules from simple precursors
such as the primitve gasses that may have constituted the primal
atmosphere. Although there has been some debate whether the primal
atmosphere was actually as reducing as the original Miller-Urey
experiments, there is likely to also have been a vast amount
of organic matter deposited directly on the earth from astronomical
impact during the earlier more active phase ofthe solar system.
Recently millions of tons of buckyballs have been found deposited
intact from space suggesting that such impacts could leave organic
molecules realtively unscathed (see below).
The fact that a variety of energy sources from heat through spark
chemical exudates from ocean vents, to solar radiation are all
capable of generating the key monomers of the biosynthetic polymerization
pathways lends weight further to the centrality of these pathways
to the sturctural interaction of the four forces.
Central polymerization pathways from HCN, HCCH and associated
molecules to purines, pyrimidines (the bases of RNA) to polypeptides
and amino acids and to porphyrins (King).
The first section has already discussed how a variety of energy
sources can give rise to organic molecules of a wide variety
of types. Central to these polymerizations is a process where
the high energy favours the formation of the multiple bonded
forms - CC-, - CN, and > C = O because they are the strongest
and hence most likely to survive high energies. These in turn
become capable of further polymerization, because at low energies
their multiple bonds are energetically liable to open to form
chain and ring interactions. The wide variety of products of
these types is illustrated above for HCN and HCCH and below fro
HCHO. The products include both the pyrimidine and purine bases
of nucleic acids, a variety of amino acids often joined as polypeptides,
porphyrins and a wide variety of other organic molecules including
many capable of performing further condensations.
These reactions are also capable of producing larger structures
such as microcells (see top of article) which sometimes display
the bilayer structure of lipid membranes in living cells. HCN
can also aggregate to a less diverse 'black polymer', although
the occurrence of this will depend on the reaction conditions.
Understanding the products of these polymerizations is complicated
by the quantum information paradox they present. The initial
conditions consist of only a few simple molecules and the final
conditions are a diverse array of increasingly complex polymers.
The simplified and highly ordered conditions of traditional chemical
laboratory reactions are not well-attuned to handling such complexity
and the great potentialities for feed back they present.
Stanly Miller in Nature June 95 also reported that they had synthesized
copious ammounts of cytosine and uracil the two pyrimidine bases
that had remained difficult under plausible prebiotic conditions
from cyanoacetaldehyde and urea under conditions which simulated
a warm tidal pool. This comes 40 years after Miller as a 23-year
old graduate student first synthesized peptides and large amounts
of the purine bases adenine and guanine by spark discharge of
ammonia, hydrogen, water vapour and methane.
Although people have since suggested that this mixture did not
occur on the primitive earth, which would rather have had a high
CO2 atmosphere, the discovery by Jeffery Bada of "mother
lodes of undestroyede buckyballs - soccer-ball shaped carbon
polymers containing galactic helium arrived unburned in an early
meterioid - confirms that large quantities of complex organic
molecules would have reached the earth's surface.
Structural Features of the - CC-, - CN, and > C = O polymerizations.
At least three distinct factors are capable of influencing the
products of the polymerizations of multiply-bonded forms:
Free Energies and Resonance: The lower energy configuration of
key stable products such as adenine leads to their formation
based on free energy considerations.
Stochastic Kinetics: Accidental kinetic association between initial
molecular species may form an organizing centre for subsequent
structural evolution. For example, the HCN dimer is a key bifurcation
point in the reaction. Stochastic kinetics ultimately derives
its indeterminacy from quantum uncertainty.
Autocatalytic Bifurcations: Products of increasing complexity
such as polypeptides and polynucleotides may generate autocatalytic
pathways which alter the structural-stability of the polymerization
to favour certain types of product. Polypeptides and polyribonucleotides
both provide a rich variety of possibilities for autocatalysis
through non-random association factors during polymerization.
Cyclic terminators: Both the HCN and HCHO polymerizations have
prominent cyclic products which act as spontaneous terminators
of polymerization, because the self-interaction of cyclization
terminates oligomerization by removing the principal reactive
moieties. The purines, pyrimidines, ribose and porphyrins all
display structure consistent with being cyclic terminators. Eschenmoser
(1992) has discovered that the phosphorylated oligo-aldehydes
have a selective propensity to form ribose. These conditions
coincide precisely with those we would expect to occur during
nucleotide formation and oligomerization as a result of phosphate
Sample HCHO polymerization routes (King). Phosphorylation
of the oligo-aldehydes causes the reaction to favour ribose,
explaining how ribose could have been selected by the presence
of phosphate energy. (Eschenmoser 1992).
Ribonucleotides as Universal Stability Structures
Adenine is one of the principal thermodynamic products of HCN
polymerization. Guanine is also formed from the same pathway.
The cross-reaction of HCCH with HCN leads to a direct synthesis
of the pyrimidines. The synthesis of pyrimidines has recently
been found by Miller to be strongly facilitated by the presence
of urea, another component of the polymerization pathway. These
stages are illustrated above.
Ribose is produced in HCHO polymerization in concentrations around
2%, but the polymerization of phospho-glyceraldehyde is selective
for ribose, supporting the conclusion that ribose is itself a
product of the same phosphate environment that facilitates nucleotide
polymerization. The particular conformation of ribose as opposed
to arabinose or the other sugars appears to be important in providing
the free rotation of the base and phosphate moieties and the
chirality of the resulting polymer.
The nucleotide unit, as exemplified in ATP, is a quantum stability
structure linking cyclic oligomers of HCN and HCHO, [adenine
and ribose are pentamers of each] linked via dehydration to the
dehydration-mediating phosphate group which appears to be responsible
for their linkage in the first place. This structure is further
stabilized by water and Mg2+. In combination with the cosmic
occurrence of HCN and HCHO, this gives RNA the potential status
of a generic structure in cosmology, taking the form of a non-periodic
The fact that polymerizations of nucleotides, amino acids and
sugars alike involve a common dehydration step similarly emphasizes
the direct relationship between polynucleotides, polypeptides,
polysaccharides and their monomers in the phase transition from
aqueous to dehydrated.
There has been a great deal of debate about whether life could
have started from RNA because it is relatively difficult to polymerize
under ordered laboratory conditions and has types of self-affinity
which can hinder replication. This has led to a variety of suggestions
from genetic takeover, the idea that some other replicative process,
for example replicating crystal defects in clays might have preceded
and aided RNA replication, resulting in an RNA takeover. Other
people have suggested that another type of polymer might have
preceded RNA. Alternatives such as Orgel's peptide nucleic acids
have been suggested as a potential basis of such thinking.
However many of these arguments stem from the very difficulties
experimentalists place in the way of their own understanding,
by reducing their model systems to simplified controlled conditions
which cannot then display the more convoluted feedback responses
displayed by the wider environment, which thmselves can be very
selective, as evidenced by natural separation processes such
as chromatography. The fact that it has taken so long to discover
the the role of the mutual interaction of clays in stabilizing
ribonucleotide polymerisation emphasizes this point.
The real lesson of the evolutionary behaviour of ribozymes devised
y Szostack and his co-workers, which we discuss next, despite
depending on clonal selection techniques is that RNAs are very
capable of strongly adaptive responses, when allowed wider behavioural
interaction than simple liear polymerizations.
Informational phase transition
The key idea about the development of replicative life is that
it is a fractal negentropic phase transition. We have seen that
the central biological polymerizations involve dehydration. The
energy currency for nucleotide polymerzation is the phosphate
energy of ATP. Usually prebiotic reserchers look for an energy
metabolism to support life, generally a catalytically complicated
and indirect heterotrophic chemical conversion.
However it is much more likely that the initial emergence of
genetic replication arose directly from an informational phase
transition, rather than indirectly from a metabolism. Even today,
a virus outside a cellular metabolism functions only as information.
Certainly viral replication requires energetic cellular enzymes
and substrates. Nevertheless the role played by the virus is
precisely to produce an informational phase transition in the
The essential dilemma of RNA polymerization is how information
should increase (and entropy decrease) by a dehydration polymerization
in an aqueous medium. RNA is energetically prone to hydrolysis,
because of the free energy of dissociation of its monomers. The
answer to this problem is that the aqueous medium has to be in
repeated phase transition from aqueous to dehydrated. If we combine
a medium in which the primal polymerizations are producing reasonable
quantities of the purine and pyrimidine bases and ribose (which
itself requires a high-phosphate milieu) we are led to a high
phosphate dehydrating environment typified by the margins of
evaporating ponds, the 'salinated' ocean edge etc. These could
lead directly to the formation of oligophosphates and hence high-energy
pyro-phosphate bonds typified by ADP and ATP.
It has recently been found that RNAs can be polymerized to large
enough oligomers to support the replicative process by forming
a binding association with silicate clays, because of the interaction
of the positively charged metal groups in the clay with the phosphate
groups in the oligonucleotides. This allows a geometrical stability
to the polymerization process as well.
A natural model for fratal phase transition thus consists of
the following four components:
1. A micro-environment which is rich in phosphate and receives
a relatively strong mix of oligomers of aldehyde and cyanide
polymerization providing the four bases and ribose.
2. Sufficient dehydrated phosphate energy to form a variety of
short ribonucleotide oligomers.
3. An intermittently dehydrated clay interface where these relatively
random short oligomers can be bound to clay in a more ordered
way and thus polymerize to polymers of up to 50 units in a selective
4. An RNA phase which permits catalytic and self-replicative
cross-interaction of RNAs and their catalytic effects on other
mlecules such as polypeptides.
The RNA Era
Like proteins, RNA is capable of forming tertiary structures
as illustrated for tRNA, partly through H-bonding to the free
OH group in ribose. Catalytic activity of polynucleotides, including
transesterification, hinges on proton transfer . A popular concept
concerning the development of genetic specificity is that the
combined roles of RNA as a genetic replicator and catalyst through
its tertiary structure solves a fundamental problem concerning
the order of appearance of nucleic acids and coded proteins.
In this model an RNA era preceded coded enzymes, in which simple
replicative and enzymatic process based purely on RNA catalysis
maintained a simple form of evolutionary biochemistry.
Fig 6 : Nulceotide coenzymes remain ubiquitous to modern energy
metabolisms and attest to the primary involvement of nucleotides
as active moieties: (a) Nucleophilic attack of adenine N9 on
ribose. (b) 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. (c) Heterocyclic form of heme. Porphyrins
have also been detected in primal syntheses. (d) Nicotine-adenine
dinucleotide illustrates a possible ancient molecular fossil
from the RNA era. (e) Cyancobalamin - vitamin B12. Eschenmoser
(1988) has discovered a plausible prebiotic stability structure
generating the complex B12 molecule which involves two nucleotides
and a Co-porphyrin (King).
RNAs which can partially replicate
A new perspective has developed from the discovery of spontaneous
splicing of RNAs in living systems and the capacity of such RNAs
to function as catalysts in RNA-RNA reactions. The experimental
demonstration using the G-rich template sequence of the Tetrahymena
rRNA intron core to act as a C polymerase, converting C5 is into
C4 and C6 has made the idea of the RNA world before proteins
a natural hypothesis. The model has been extended to others for
RNA-based error-correction, synthetases and the ribosome.
The ribosome showing the large and small subunits and the
step by step formation of a new
amino-acid subunit of a protein chain, using transfer tRNAs curled,
each with a specific
triplet code, and coded messenger mRNAs horizontal (Watson et.
The ribosome consists of three types of RNA subunit the mRNA
which codes the message the large and small rRNA subunits and
the short tRNAs which code each amino acid to a particular triplet
code of nucleotides. The ribosome, itself one of the most complex
pieces of molecular machinery in the cell, containing over 50
protein units in its two-component structure, has proved capable
of carrying out the essential act of translation even when virtually
all of the proteins are stripped off indicating that the RNA
components are not a mere scaffolding used by proteins, but the
catalytic core of the process. This is consistent with the idea
that the ribosome was originally a way that RNAs instructed and
made proteins directly and autonomously.
Modified ribozymes have proved capable of acting as polymerases
which can replicate complements to subsections of themselves.
Experiments from Szostak's group give the clearest indication
to date of how RNA-based replication might occur. Experimental
cloning and mutation of a variety of RNAs has successfully evolved
RNAs with extensive catalytic powers including partical self-assembly..
Replication in a Fractal Phase Transition
The sunY polymerase illustrates fractal RNA dynamics which could
both explain the difficulties facing non-enzymic syntheses and
illustrate how RNA replication developed prebiotically. The polymerization
is structurally a three-level fractal process:
(a) The catalytic RNA is itself composed of separate subunits
each of whose structures is simpler and shorter than the assembled
enzyme, both permitting higher error rates and providing less
competing secondary structure.
(b) On a second fractal level the subunits have as complements
a collection of small oligomers which are small enough for any
variant to exist in acceptable concentrations but long enough
to provide specific binding regardless of predominant base type.
(c) Finally the oligomers require synthesis from individual nucleotides.
For oligomers of length up to 4 or 5 this could be random single-stranded
polymerization without reducing concentrations by more than 3
orders of magnitude. For longer oligomers a catalysed reaction
using oligomer templates could maintain a non-random population
of suboligomers of a multi-unit catalytic RNA. The onset of replication
is then naturally modelled as a phase transition in the fractal
Catalytic nucleotide interactions: (a) Phosphoimidazole. Proton
transfers in (a) imidazole, (c) in base tautomerization, (c)
in Tetrahymena intron. (d) Tetrahymena intron core is an oligo-C
RNA polymerase, (e) trimer-mediated replication of modified hexameric
RNA of self-complementary sequence, structure of the modified
sunY modular RNA polymerase, (g) the ligation carried out on
oligomers on the fragment C template (King).
RNAs polymerize proteins:
The major discovery that RNA appears to be the agent of peptide-bond
synthesis in the modern ribosome and the capacity of modified
ribozymes to act as amino-acyl esterases (Picarilli et.al. 1992)
[the first step of ribosomal action] establish RNA can act as
synthetase as well as transfer, messenger and ribosome. 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.
These results pinpoint RNA as the key prebiotic molecule generating
ordered polynucleotide and polypeptide structures.
The development of RNA replication is modelled as a fractal phase
transition. A central bifurcation pathway is coutlined, which
could be capable of generating the major structural features
of molecular biological evolution, including protein and nucleic
acid structures, glycolysis, the tricarboxylic acid cycle, electron-transport,
ion-pumping and the excitable membrane. These aspects of molecular
evolution could thus be cosmologically general.
Following Thomas Cech's discovery of ribozymes, Jack Szostak
and Charles Wilson revealed in Nature April 95 that they had
made ribozymes capable of a broad class of catalytic reactions,
not simply confined to the sugar-phosphate backbone of RNA, but
including the peptide bonds of proteins and between carbon and
nitrogen. They took between 100 and 1000 million 200 unit nucleotides
and selected them for catalytic activity mutating and re-cloning
the most successful candidates. Although the transesterficiations
are as likely to snip RNA as join it David Bartel has developed
ribozymes which can stitch together RNA oligomers without breaking
the larger molecules.
Szostak and Eric Ekland and David Bartel argue in Science July
95 that although they have selected such ribozymes out of trillions
in lab selection experiments, the ease with which they were generated
suggests they are almost certainly part of a vastly larger class
of similar molecules which nature is capable of producing.
* Let There be Life New Scientist 6 July 96
* The World according to RNA Scientific American Jan 96
* Molecules of Ancient Life Born Again NS 17 Oct 98
It remains possible RNA has had a more primitive precursor.
Leslie Orgel has also in Nature announced the formation of peptide
nucleic acid PNA, which can serve as a template for its own replication
and for formation of RNA from its subcomponents. However Jim
Ferris reported in Nature May 95 that he had overcome basic problems
in the polymerization of short RNA oligomers by making adenine
oligomers 10-15 nucleotides long on positively charged motmorillonite
clays which grew to 55 units on repeated washing with nucleotides.
This bridges the gap by providing a potential source for large
quantities of the oligomers similar to those used in Szostak's
Carl Woese doubts that RNA copying was the central mechanism
because a study of RNA-copying genes from the diverse branches
of the evolutionary tree display different solutions to this
process. However the evidence of the RNA world is diverse.
Summary of evidence for the cosmoligical status of RNA
1. The ribonucletide inherits a structure linking the bases
and ribose which are themselves both direct cyclic oligomers
of cyanides and aldehydes observable in galactic gas clouds such
as the Orion nebula.
2. Dehydration and phosphorylation are common factors in key
bio-polymerizations, membrane lipid formation, glycolysis, ribose
and nucleotide formation and nucleotide polymerization.
3. Ribonucleotides can be polymerized through interactions with
common silicates forming a symmetry-splitting of polarity between
Si and P and can catalyse their own formation through auto-catalysis
4. Remaining fossils of RNA metabolism appear to exist in the
nucleotide cofactors which pervade the electron transport chain,
fatty acid synthesis and the tricarboxyllic acid cycle and in
the RNA-based action of the ribosome.
UNIVERSAL STABILITY STRUCTURES IN MOLECULAR BIOLOGY
The previous discussion of the RNA era highlights a problem that
is central to the form of molecular biology - how did the central
molecular biological structures become generated, starting from
a simple RNA-based genetic system? The traditional viewpoint
is that they were successively created during evolution through
mutations building one-by-one the protein components necessary
to make a working whole. This however does not explain how systems
as electron transport and the citric acid cycle could have functioned
with only a partial complement of enzymes. A further problem
is how such enzymes would be advantageous and evolve selectively
if the system they were supporting did not function in some form
without coded enzymes.
The alternative thesis is that many of the major features of
molecular biology have arisen in parallel as generic structures
through bifurcation, independently of the emergence of RNA, and
were subsequently captured by genetic takeover as genetic complexity
permitted. The candidates for this primal status as stability
structures include the following : The polymeric structure of
proteins and RNA, the form and function of nucleotide coenzymes,
bilayer membrane structure and the topological closure of the
cellular environment, ion transport, concentration gradients
in the cytoplasm and excitability, membrane-bound electron transport,
glycolysis and the citric acid cycle.
Such a parallel model requires mutational evolution as a takeover
process in fixing these stability structures into the biological
scheme, but also has far-reaching conclusions concerning the
generality of molecular biology in cosmological terms, for while
the details of mutational evolution would be unique to each environment,
the major features underlying biology would be universal.
Nucleotides and the Nucleotide Coenzymes
In addition to the key role of ADP and ATP as energy currency
in the bio-metabolism, the other nucleotides have generic roles
which may predate the development of coded proteins. GTP for
example is used selectively in protein elongation, in the ribosome,
and the nucleotides UDP and CDP are generically selective as
carriers of glucose and choline and other membrane components
respectively, suggesting an RNA-based selectivity for each of
these classes of molecule during the RNA era. Model prebiotic
reactions have successfully coupled UDP and CDP to glucose and
choline (Mar et. al. 1986). Similarly other nucleotide coenzymes
have generic roles consistent with a primal function. Both NAD,
fig 11(a), and FAD function as carriers of redox energy through
ring bond transformations, coupling H on the nicotine and flavin
bases. 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). Although CoA is currently
used in different processes, its structure is consistent with
an initial role in pre-translatory protein synthesis. The pantothenic
acid moiety appears to be a molecular fossil of two such polymerized
amino acids. Vitamin B12 also illustrates how a dinucleotide
could bind an Fe-porphyrin ring, lowering its Fe2+- Fe3+ activation
energy and thus form a carrier of electrons. Such coenzymes would
extend the nature of phosphorylation energy by linking it to
H+ and e- transfer reactions, hydride ion, and peptide transfer,
consistent with a model for RNA-based electron transport involving
Fe-porphyrins, FeS groups, FAD & NAD.
Fig 9 The genetic code contains evidence for several primal
bifurcations. Centre position AU selects polar/non-polar as broad
groups. VLIP are Val-Leu-Ileu-Phe. First position G determines
primally abundant amino acids. Subsequent bifurcations include
H-bonding block and acid-base (King).
The Form of Translation
The discovery that ribosomal, synthetase, messenger and transfer
functions of protein synthesis can all in principle be carried
out by RNAs without proteins 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 9 which should be read
in conjunction with the bifurcation scheme for the amino acids
in 5.1 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), consistent
with the polarity bifurcation of the amino acids in 5.1.1.
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. The fourfold 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. The eightfold code: This could have then doubled to and 8-word
code by including CAY, CUY, CGY, and CCY coding for non-polar
and basic groups.
5. The H-bonding block: OH- and SH-containing amino acids also
appear to form a single additional block (UA)(GC)Y, suggesting
a third bifurcation for H-bonding, with UAY reading stop.
6. Evolutionary takeover: The development of translation becomes
an evolutionary process. Later assignments such as Arg and Trp
are random mutational fixations.
* Genetic Code is Top Translator New Scientist 18 April 1998
The Membrane, Excitability and Ion Transport
The structure of the bilayer membrane is a direct consequence
of the polarity bifurcation. The formation of amphophilic lipid-like
molecules, based on a linear hydrocarbon non-polar section combined
with an ionic or H-bonding polar terminal, leaves 2 degrees of
freedom for layer formation. Backing of the non-polar ends completes
the bilayer. Cell structure then arises directly from budding
of the bilayer, as illustrated in budding in several types of
prebiotic reaction medium. 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
phosphateThe existence of the membrane as a non-polar structure
leads to segregation into ionic and non-polar regimes. 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) consistent with a primal role for amine
neurotransmitters in moderating ion flow through the membrane.
The catecholamines are linked to indoles such as serotonin by
a prebiotic pathway.
The amine-based neuro transmitters, comprising the indoles
and the catecholamines have plausible primitive origins and are
linked by a photo-induced quinone bridge, making it possible
that membrane electrochemistry was also a very early development
of living cells. Choline is also a quaternary amine and the membrane
lipid hosphatidyl-choline has a similar aetiology specifically
utilizing phosphate as a link between the components (King).
Electron Transport H+, e- & H2O
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 quinone through reduction, causes a physical linkage
to exist between the polarity bifurcation and the charge bifurcations
associated with electron and proton transfer, fig 10(b). 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 10(e) (King 1990).
Both porphyrins and quinones have obvious prebiotic syntheses
and the primal role of nucleotide coenzymes has already been
mentioned. Secondly, membrane structure and the solubility differences
between the electron and proton guarantee a link between electron
and hydrogen ion transport. Electron transfer does not require
the coded active sites catalysing 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).
Glycolysis and the Involvement of Phosphate in Sugar Metabolism
Glycolysis forms a bridge between six and three carbon sugars,
reversing the structural pathway from H2CO to the cyclic sugars,
(see below). This is made energetically possible by phosphorylation,
and releases high energy phosphate capable of driving other phosphorylations
(Hermes-Lima and Vieyra 1989), fig 11(a). It is notable that
the di-phosphorylation of fructose in glycolysis is homologous
with the model route for nucleotide formation of fig 6(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
structure. UDP-glucose coupling is also consistent with the involvement
of glycolysis in the RNA era.
(a) Di-phosphorylation of sugars leads to glycolysis through
interaction of charged phosphates. (b) Generic examples of group
transfer in the tricarboxylic acid cycle (King).
The Tricarboxylic Acid Cycle
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 coenzyme basis for
the tricarboxylic acid cycle in the RNA era. This could have
thus 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. This gives at least one possible role for
Eigen's hypercycle concept however the process could have also
been more 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 11(b). Isomerization would
have been catalysed by Fe2+. Several steps may have been driven
by sunlight photolysis.
(a) A conventional heterotrophic origin based on glycolysis
or a more primitive mechanism. All major features are developed
randomly by mutational evolution. (b) Divergence of dissipative
structures including major biochemical features is followed by
capture via mutational evolution during the RNA era. A minimal
genome is required because the dissipative structures have a
spontaneous basis (King).
Genetic Takeover of the Generic Systems
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 an RNA-based
system had to capitalize on existing chemical stability structures
without requiring enzyme-based biosynthetic pathways. Genetic
takeover of the major features illustrated in fig 12(b) is consistent
with such a limited role for RNA catalysis. However it also places
these stability structures clearly in a category determined by
cosmological symmetry-breaking, thus giving evolutionary biology
a common pattern of inheritance on a cosmological footing. The
model thus gives a more plausible account of the RNA era and
makes specific predictions about the aspects of biology likely
to be common to the universe at large.
The Terrestrial Record
Evidence fo life has been found in the earlist rocks leaving
only a few hundred million years for life to form. The prebiotic
syntheses of uracil and cytosine have been established by Miller
himself, a prebiotically-plausible synthsis for RNA is emerging
from Ferris's work and the selection of RNAs with catalytic activity
has been amply demonstrated by Szostak and others. What was once
a major impenetrable mystery is rapidly becoming a straightforward
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).
Taz Home Page 2
First life on Earth survived battering by meteors New Scientist
9 Nov 96
In Nature (384 p 55) Gustaf Arrhenius studying tiny apatite grains
in the Isua 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. This suggests that
life evolved on earth as soon as environmental conditions allowed.
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