Hypothesis
Driven by reaction to the Big Bang in a fully
deterministic process directed at opposing expansion of space/time, gravity
generates a logically sequential set of energy/matter transitions leading to
and incorporating intelligent life.
Background
At present origin-of-life science
is largely a hit or miss affair lacking any overall theory or guiding
principle, with the result that almost any suggestion concerning some possible
precursor physics or chemistry can be considered potentially relevant. This
proposal, in contrast, offers a coherent and rigidly deterministic framework
governing the mechanisms of cosmological evolution which extends to all classes
of energy transduction reactions from astrophysical to biochemical. If proven
correct, therefore, the effect would be to focus and organize investigation
into strictly circumscribed relevant subjects, thereby shortening the research
effort by at least several decades.
This hypothesis addresses relationships between cosmological expansion, evolution,
life and origins. The basic principle demands that in order to understand life
it is essential first to view it in its context, that of an expanding universe.
What is the connection between life and expansion? To answer this question we
need to consider gravitational attraction as a reaction to, and therefore
generated by, universal expansion. The forcible curving or distortion of
space/time by Big Bang expansion generates an equal and opposite
counter-force, gravity, which as a result acts as if to return energy/matter to
its primordial state in a singularity. Since the universe appears to be
expanding at an increasing rate, clearly gravitational forces are frustrated
in that they are not powerful enough to counter the energy released by the Big
Bang and re-condense it in its entirety in a single locality. Gravity is
therefore obliged to follow more circuitous routes to accretion. If, having
established these principles, we then consider the situation of intelligent
organisms 1011
years or so from now, when energy/matter density will have attenuated to an
extreme degree, we see that being critically dependent on a sufficient
concentration of energy/matter, organisms will be obliged to act as agents of
the gravitational force and develop mechanisms, such as manipulation of black
hole dynamics, to attract energy/matter and maintain it in their vicinity. This
fact suggests the intriguing possibility that live organisms may actually be,
in a physical sense, creations or extensions of universal gravitation –
robots compelled, with no particular outcome assured, to control the expansion
of space/time through a directed ability to analyze and manipulate the cosmos,
at least locally. Does gravitational accretion actually have the potential to
spawn such a high degree of complexity? In order to appreciate the organizing,
creative capacity of gravitation one need only consider its ability to acquire
an amorphous cloud of hydrogen atoms and to manipulate it by accretion alone in
order to generate the structural and functional complexity of the myriad
astrophysical objects now seen to populate our universe. Further examination of
this intellectually and emotionally challenging hypothesis does indeed reveal a
logically coherent sequence of obligate structures and processes, a continuous
series of phase transitions historically generated by graduated increases in
condensation of matter accompanied by their cognate energy transduction mechanisms
leading to the generation of biological functionality. One of the crucial
evolutionary transitions is the repeated frustration of energy/matter accretion
into black holes by interceding supernova events with a resulting
redistribution of elements, including radioactive isotopes. These radioisotopes
eventually settle in inner planetary bodies and following fractionation, gather
in placer deposits under pressures of 1-3 GPa. In such a highly energetic
environment, driven by a powerful flux of a-, b- and g-particles, the biogenic elements, CHNOPS, will
be rapidly generated by de novo
nucleosynthesis through activation of triple alpha reactions and the CNO cycle
normally associated with stellar cores. Held in close confinement under
supercritical conditions, these elements will then be obliged to assemble in
stable energy storing and transduction structures – cyclic peptides, polyamines
and chromophores including porphyrins, FMN, NTP, cAMP and highly conserved very
small catalytic micro RNAs consisting of two or three nucleotides, e.g. cyclic
diguanylic acid. Such reactions are clearly non-trivial as we now know that low
molecular weight signalling modulators and nucleic acids regulate a diverse
array of biological metabolic functions, catalyzing various types of
polymerization reactions as well as bond formation including C-C bonds. The
primary characteristic of these micro RNAs is that they are catalytic, meaning
that they possess the ability to acquire energy and use it to manipulate their
environment in specifically directed ways, an essential step on the road to
life.
Report and Conclusions
Could life be the result of random chemical
“accidents” or is it more likely to be rooted deterministically in the
fundamental physics of cosmological evolution? Our current knowledge of the
intricacy and complexity of biological function, together with hints of its
aetiology, clearly render the isolated chemical accident or serendipitous
hypothesis impossible to sustain. Furthermore attempts over many decades to determine
a point of origin for life, the standard approach, have met with little success
because they ignore the increasing evidence for continuity and tight
entaglement which characterizes global evolutionary processes. In other words,
there can not be a specific point of origin for life apart from the Big Bang
itself. So the question is – What are the physical processes which would
generate biological function as well as the qualifier we label intelligence? In order to understand
life it is essential first to view it in its context, that of an expanding
universe and, as described in the Summary, this context leads us to
consider the situation of intelligent organisms 1011 years or so
from now, when energy/matter density r(z) will have attenuated to an extreme degree. At that point our
critical dependence on a sufficient concentration of energy/matter will oblige
organisms to develop mechanisms which attract energy/matter and maintain it in
their vicinity, leading to a surprising interpretation of the nature of
organisms as extensions of the gravitational force. To be more precise,
according to this intellectually and emotionally challenging view, we are
robots literally generated by gravity and programmed to undertake the tasks it
is unable to accomplish in its primordial physical state. Our mission, whether
or not we wish to accept it, is to comprehend the mechanisms of time dilation
and cosmological expansion so as to manipulate and perhaps eventually control
them. Can this interpretation of life survive rigorous examination?
The first step in answering this
question involves understanding gravitational attraction as a reaction to, and
therefore generated by, universal expansion. The forcible curving or distortion
of space/time by Big Bang expansion generates an equal and opposite counter
force, gravity, which as a result acts as if to return energy/matter to its
original state in a singularity. If we can accept this notion, the rest follows
logically. This procedure involves tracing, step by step, the progress and
consequences of the gravitational force as it is exerted through time on
energy/matter in the universe.
Since the universe appears to be expanding
at an increasing rate, clearly gravitational forces are frustrated
in that they are not powerful enough to counter the energy released by the Big
Bang and re-condense it in its entirety into a single locality. As a
consequence gravity is obliged to take a more circuitous route to accretion.
Fortunately it is still able to attract and condense, at least locally, limited
quantities of matter which can evolve into galaxies and eventually into solar
systems. At this point we can already begin to appreciate the creative,
organizing potential of gravitation – the ability to acquire an amorphous cloud
of hydrogen atoms and manipulate it by accretion alone to create structurally
and functionally complex astrophysical objects. This process of structuring by gravitational accretion and
condensation continues gradually in stellar cores of intermediate mass,
creating step by step all the stable elements up to iron, making use of the
fundamental particles and interactions to bind them into increasingly dense,
massive and complex but relatively stable units. In larger stars where
gravitational forces are powerful enough, this condensation continues unopposed
until a black hole singularity is reached – gravitation has finally achieved
its “goal”, as far as it can under the circumstances. But in smaller stars,
those which end their nucleosynthetic phase with a mass between 1.4 and 3 solar
masses, gravitational forces are not strong enough and the result is a Type II
core collapse Supernova – gravitation is
again frustrated, having been prevented from reaching its ultimate goal.
This is good news since the events that follow are what makes our universe
interesting because gravitation still continues to exert its influence, only
now through more devious and complex mechanisms. The universe would be an
exceedingly dull place if all stars ended their active lives with more than three
solar masses.
Following a Supernova explosion,
gravitation gradually starts to shed its purely compressive character and
begins a long metamorphosis through an endless series of phase transitions
which, to be more precise, we would refer to as energy transformations or
transductions. The first transition, in
a great compressive thrust, consists in transducing the gravitational potential
of the collapsing star, as it bounces off its iron and neutron core, into a
compact shock front. As this wave travels through the star’s outer layers
it delivers a compressive force highly magnified by its compactness, forcing
together numbers of free nuclei of various masses, along with free protons and
neutrons. The wave travels on leaving behind an expanding gas cloud composed
not only of all the elements up to iron but also a range of newly synthesized
heavier elements and their isotopes, many of which contain a large excess of
neutrons. Some of these nuclei are as a result unstable since they contain more
protons and neutrons than their binding energies can control, and they
immediately start to decay by ejecting excess particles in a process,
radioactivity, that must continue until they finally reach a low energy, stably
bound structural configuration. The
generation of radioactivity is the second major transduction of gravitational
energy. The supernova explosion then causes these radioactive isotopes to act
as vectors storing and transporting excess
gravitational energy throughout
the ISM.
During solar system formation, as molecular
clouds condense under the effect of gravitational contraction, heavier elements
fall in toward the center of gravity with the result that neutron-rich
radioactive nuclei are strongly represented in the inner planets as they form,
which is why they have become an important element of the Earth’s crust. There
is clear evidence that short-lived nuclides were originally present on Earth,
with initial abundances in general many times their present values. Similarly
longer lived isotopes, for example 235U, are believed to have been 100 times more abundant than at
present. Another long lived isotope, Thorium, 232Th, is about four times more abundant than uranium in the Earth’s
crust and is in addition present in uranium ores. Following the decline of
radioactive isotopes since the formation of the Earth, concentrations of
radiogenic nuclides, the products of decay, have increased at rates depending
on the different half-lives of their precursors, considerably complicating the
radioactive landscape. Subsequently, geochemical, hydrothermal and other
gravitationally driven geological fractionation processes tended to concentrate
radioactive nuclides in deep crustal placer deposits. Along with the fact that
radionuclides were considerably more abundant in the Archaean Earth, these
processes created compact centers of powerful radiogenic decay pressure.
Radionuclides can undergo many possible
modes of decay depending on the particular characteristics of the species in
question, however the three principal types concerning us here are alpha, beta
and gamma emission. A most important characteristic of a-particles, Helium nuclei 4He2+, is that a given nuclide will emit them at certain
discrete energy levels exclusively. For example 238U emits alphas of 5.2 MeV only, while 235U emits alphas of 4.39 MeV and 4.56 MeV in fixed proportions. b-decay is considerably more complex, but the most significant result
is emission of electrons over a wide spectrum of energies with, however, a
characteristic maximum energy for each nuclide. Typical b-electron emission energies range from several keV to a few MeV. g-ray photons are also emitted at certain defined energy levels
characteristic of each nuclide, commonly in the multi-MeV range.
The kinetic energy levels of these
emissions constitute a significant feature as surprisingly they lie within the
energy range of the universe approximately one second after the Big Bang,
during the era of nucleosynthesis. They also correspond to temperatures between
109K and 1010K obtaining in the
core of a large star in which iron is being synthesized. Given the conditions
of energy, pressure and confinement described above, it is reasonable to
conclude that processes such as the triple alpha reaction and the CNO cycle
operating at temperatures between 107K and 108K, which we normally
associate with stellar core nucleosynthesis, could easily have occurred on
Earth although clearly not at rates occurring in stellar cores. These processes would have generated, in a
highly confined locale, all the biogenic elements, C, H, N, O, P, S along with
others including some transition metals, by de
novo nucleosynthesis, constituting
the third major transduction of gravitational energy.
There are many indicators supporting this
thesis and hinting at a probable link between radioactivity and biosynthesis.
For example there is the fact that all known uranium deposits are enveloped in
thick layers of carbonaceous bitumens containing kerite crystals composed of C,
H, N, O and S. Kerite’s fibrous structure and properties are very similar to
those of simple organisms and its chemical composition is nearly identical to
that of proteins. Significantly, it also contains 13 of the 20 amino acids of
living cells. There is in addition the interesting connection between fossil
stromatolites, colonies of primitive cyanobacteria, and uranium deposits,
frequently found in close association with each other.
The next phase of prebiotic evolution is
more problematic as it involves the structuring and cooperative action of
complex molecules. In support of this phase we invoke many experimental
investigations performed in recent decades, demonstrating that, given biogenic
elements as a substrate, irradiation from various sources does result in
synthesis of an array of complex compounds with molecular weights up to
approximately 80 kDa. Most significantly not only have several amino acids been
thus produced but also all five DNA/RNA based nucleotides. Also included were
formic acid, oxalic acid and formaldehyde, all potential precursors for
synthesis of more complex organic compounds such as carbohydrates.
Polymerization and cyclization reactions were commonplace. These data lend
compelling support to the idea that radiation can indeed act as a particle and
energy source driving such bonding reactions.
As a result we can qualify the process of molecular bonding to be the fourth major
transduction of gravitational energy.
Significant as these processes may be,
however, they do not come close to solving the fundamental problems of
organization, coordination and self-primed action displayed by living
organisms. How and why do prebiotic reactions, no matter how complex, move on
from the physico-chemical to the bio-functional realm? What is the precise sequence of steps and
motive force directing molecular reactions along the path to metabolic
autonomy?
The first point to retain from the brief
history of energy/matter we have reviewed above is that, whether it concerns
fundamental particles or complex molecules, matter does not exist in isolation.
It is a social unit, functioning in groups. Furthermore every unit of matter
has an identity, a history and a memory of that history. In a paper entitled Computational Capacity of the Universe published in October 2001, Seth
Lloyd, then at MIT, says:
“Merely by existing all physical systems
register information, and by evolving dynamically in time they transform and
process that information. The laws of physics determine the amount of
information that a physical system can register and the number of elementary
logic operations that a system can perform… It is known that fundamental
interactions between … particles allow the performance of logic operations… and
every time those particles interact they perform one or more elementary
operations…”
In other words, by its very existence
matter contains information, and that information is its history – the state
it’s in now as well as all the influences it ever absorbed in order to reach
that state. That history or memory is held in and by the structure of matter,
in its electronic configuration, which is continuously being broadcast in the
form of electromagnetic waves forming an exquisitely fine and detailed image
not only of the matter in question but also of the environmental pressures
being exerted on it. This fact is what allows us to investigate the nature of
our cosmos, from elementary particles to proteins to galaxies. In precisely the
same way as they communicate with us through our specially designed sensors, particles
communicate with each other, that is to say that they radiate their message to
whichever other particle is able to sense, absorb and register it. We shall qualify this energy and
information radiation as the fifth major transduction of gravitational energy.
Matter is therefore constantly
interacting with other parts of its environment in a relationship one could
characterize as a flow of stresses, with each particle seeking to establish a
state of equilibrium or even dominance within its own zone of influence.
Stress, and stress response, are complex multi-level phenomena with internal as
well as external components but for our purposes we can say that any
configurational shift or change imposed on matter is the result of a stress,
and that change or adjustment is its response. Stress response adjustment
usually occurs in a hierarchical sequence or cascade, unless the stress is very
mild and fleeting. Response cascades unfold in a time sequence, the initial
protective nonspecific response being a rapid one of flight or when possible,
erection of an impervious shield. This is then followed by a more leisurely
specific sensing and analysis of the stress, allowing its effects to be
absorbed and a corresponding configurational adjustment to be made. The stress
is thereby integrated into the particle’s structural memory. At that point, if
the stress is disturbing enough and if the stressed particle can muster a
requisite amount of energy, it can broadcast a message back in a directed
reaction utilizing the data about the stressor it has just absorbed. This can
alter the stressor so as to either render it less disturbing or neutralize it
by forcing it to partake in a state of equilibrium. Further levels of response
could see the stressor absorbed in its entirety to become part not only of the
stressed particle’s structural memory but also of its energy/matter resources,
a metabolic response. So much for theory – now how does this relate to the
radiogenic micro-environments of the Early Archaean Earth?
As there is little we can find in the
literature relevant to evolutionary high pressure radiochemistry or
radiophysics, we shall be obliged to proceed largely by analogy. Clearly
therefore we are entering the realm of speculation, and it is particularly from
this point on that experimental investigation is required.
The principal feature of confined
radiogenic deposits is obviously the extremely high energy environment which
totally dominates and drives all reactions. Under these circumstances, although
molecular bonding may be strongly encouraged, bonds will tend to be disrupted
almost as soon as they are formed, the perfect paradigm for a stressful
environment leading, as in the biological realm, to rapid evolutionary species
divergence. This competition-driven evolutionary process has been convincingly
demonstrated recently (Mulkidjanian et al. 2003) by Monte Carlo simulation of a
sugar phosphate polymerization reaction in the presence of nitrogenous bases
under intense UV radiation. The conclusion reached by this investigation was
that accumulation of the first polynucleotides could be explained by darwinian
selection of biopolymers most effectively resistant to (UV) radiation. We could
extend these results to the case of radioactive bombardment in which survivors
in the short term would be molecules which can rapidly attain stability for
reasonable periods while effectively absorbing beta and gamma radiation. There
are in fact two possible adaptive responses dealing with such an attack: one
would be to assume a configuration able to store excess energy, in other words
to tolerate considerable instability, without disintegrating. Another method
would be to adopt a structure which rapidly ejects surplus energy in a
controlled and directed action, without suffering damage or alteration in the
process. The ideal structure would combine both responses, as in a catalytic
reaction. An interesting, perhaps essential, characteristic of such existing
structures is that they preserve their integrity by constantly metabolising energetic
particles, maintaining what one could term a state of controlled instability, a
more appropriate term might be dynamic stability, which is arguably the
defining state characterizing biological systems. Molecules of this type have
been synthesized for industrial purposes and are therefore convenient in order
to draw comparisons with natural analogs.
Industrial application of such structures
in recent years has focused on design and production of organic electro-optic
(EO) materials and devices based on chromophores with a large dipole moment.
Organic EO chromophores are dipolar charge-transfer
(transduction) molecules consisting of an electron donor, an electron
acceptor, and a pi-electron bridge providing communication between the two
moieties but more significantly also providing a variable energy storage
structure. These molecules are of interest to science because they act as
antennae, absorbing photons of specific wavelengths which can be precisely
selected by effecting appropriate structural adjustments. This means that
precise amounts of energy can be introduced simply by irradiation and stored,
transported or channelled for delivery in the required form to a designated
location. Examples of such uses are numerous and surprisingly diverse, including
memory storage, switching and logic devices, optical fiber communications,
electro-optic circuitry, photoactive polymer films and dyes, bio-sensors and
many others.
One of the most remarkable features of
this effort to develop efficient synthetic chromophores is the consistent
emergence of the same small number of almost identical structures in the
various labs around the world and their striking resemblance to forms found in
nature. Among the chromophores with the greatest polarizability and absorption
cross section, the most efficient were found to be asymmetrical units with a
heterocyclic purine nucleoside acceptor and a pentose ring for electron
storage. All that is missing is a phosphate donor to make up ATP or a DNA/RNA
nucleotide. Other commonly derived structures closely resemble a straight chain
tetrapyrrole or a short length of DNA/RNA backbone with sulfur atoms in place
of phosphates. Furthermore it was found that two-photon excitation of certain
dyes provides a means of activating chemical or physical processes with
extremely high spatial resolution. The large driving force available for
electron transfer reactions, even to relatively weak acceptors, allow this type
of molecule to function as a highly efficient and precise polymerization initiator.
This effect will drive the synthetis of more complex morphologies including
long chain polymers allowing virtually infinite data storage capacity.
In the situation of radiogenic pockets on
the Archaean Earth, small heterocyclic molecules as described above, probably
combined with conjugated chains, would tend to be synthesized as a result of
constant bombardment by beta and gamma particles, and be competitively selected
in the first instance according to their efficiency in metabolizing and directing
highly energetic photons and electrons. This phase would most probably be
followed by evolution of macrocycles, a step particularly applicable to the
tetrapyrrole-like structures which will cyclize to form porphyrins, one of the
most ubiquitous and highly conserved molecules in the biological realm,
precisely because they are so efficient at processing photons and electrons.
Also generated because of their energy transduction efficiency would be low
molecular weight nucleic acids and other highly conserved very small catalytic
micro RNAs composed of two or three nucleotides, e.g. cyclic diguanylic acid
with two nucleotides joined in a macrocycle by phosphodiester bonds. Such
small-molecule modulators and nucleic acids are now known to regulate a diverse
array of metabolic functions and, without mediation of enzymes, directly to
catalyze various types of bond formation including C-C bonds. We shall characterize the synthesis of
directed charge storage and transfer molecules as the sixth transduction of gravitational
energy.
Assuming that, in this high energy bath,
a selection of such polymeric, cyclic and macrocyclic catalytic molecules
manage to establish a state of dynamic stability, the common adaptive response
directed toward stress neutralization by mutual equilibration of the molecules
would result in a process of symbiotic
mutualism. In such a phase, all unsuitable or non-complementary species
would be eliminated, leaving a series of complementary cooperative molecules,
each and every one partaking in maintaining mutual stability in what will have
become a functioning system. This
system is driven by the need to precisely control and process the constant
pressure emanating from its radiogenic environment, in a high energy photosynthetic analog. We shall characterize the process of
symbiotic equilibration by mutual charge neutralization to be the seventh major
transduction of gravitational energy.
The question now is – What species of
molecule would tend to form mutually stabilizing associations under these
conditions and why? Tackling the last part of the question first, obviously
species associate because each one provides some element which the other(s)
need in order to maintain equilibrium over time. Summarizing the various points
raised above, maintaining a state of temporal dynamic equilibrium, the primary
requirement for continued existence of any system, demands that species fulfill
the following specification:
1. Species must acquire, store and transduce energy in order to
maintain a state of dynamic equilibrium both internally and externally.
2. Based on No.1 above, species will sense, acquire and store
environmental data in their structure.
3. Based on Nos. 1 and 2 above, species must organize this energy and
data so as to permit manipulation and reconfiguration of their environment,
both internal and external, necessary for an effective stress analysis and
response leading toward equilibrium.
4. Due to continuously developing environmental conditions, species
must organize and maintain encoded in their structure a readily accessible
permanently updated and expanding database along with updated
environment-manipulation mechanisms.
Based on the above four points we can
hazard a definition of the term “fittest” as it applies to entities involved in
competitive darwinian adaptation, as follows:
The fittest entity is that which has
rapid access to the most complete and accurate data base concerning its
environment, internal and external, both proximate and remote. It must in
addition be able to treat these data combinatorially to create the largest
repertoire of coherent and relevant responses to stimuli in the shortest
possible time as well as to devise an appropriate, broadly anticipatory, longer
term response strategy the result of which must enable the entity to make use
of or to manipulate its environment so as to secure its own short and long term
existence.
Given this demanding specification it is
logical to suppose that molecules which evolve an aptitude for performing one
of these tasks will tend to associate with molecules better suited to one or
more of the others. Under conditions of high energy flux, as mentioned above
molecules with an aptitude for energy capture and transduction would form in
the first instance and be rapidly selected. Some of these molecules would be
chromophores strongly resembling RNA nucleosides and might well polymerize and
cyclize to resemble di- or tri-guanylic acid, structures exhibiting
considerable catalytic and regulatory activity. The shortcoming of such
molecules, however, is an extremely poor memory capacity, limited by the
repeated use of just four different base configurations linked by an invariant
backbone. Unable to satisfy condition 4, none of the other higher tasks could
be accomplished. The tendency therefore would be to associate with a more
varied or variable molecule or polymer having the potential to be organized as
a readily accessible database while also exhibiting complementary recognition
and binding sites. Which molecule satisfies these requirements?
Organic molecules displaying the greatest
morphological variation include sugars, lipids and amino acids, all of which
were represented in the results of irradiation experiments mentioned above and,
incidentally, form associations with nucleic acids in modern living cells.
These molecules possess conspicuously different structural characteristics
suited to their individual functions. Lipids consist mainly of long conjugated
unvarying hydrophobic linear chains with variable heads able to bond covalently.
Such molecules can hold some information, particularly in the head moiety, but
the uniformity of the tail section is too limiting for this purpose. The
structure of sugars, on the other hand, is so varied, forming no readily
discernible pattern, that using them as a database would pose virtually
insuperable packing, access and reading problems. The structure of amino acids
is ideal for encoding data because of its simple invariant polar head, the
peptide group, combined with the highly variable side chains displaying
differing electrostatic properties while maintaining compact, regular
configurations. The ready adoption of specifically determined secondary,
tertiary and quarternary configurations, although also true of nucleic acids
and sugars to a limited extent, adds significantly to the encryption potential
of amino acids.
It now seems reasonable to suggest that
the primordial function of radiogenetically synthesized molecules was to sense
and record environmental data. This task could initially have been accomplished
by cyclic peptides which would have formed as a chromophore-like analog
under steady bombardment by energetic gamma photons. These could have acted as
both sensors of the environment and catalytic activators of their own
transcription or polymerization, as is seen in NodD and related proteins
secreted by modern symbiotic rhizobia. Many such small cyclic peptides exist
today in vivo, e.g. nodularin or
microcystin, and in vitro, e.g. RAFT
molecules or beta-turn mimics containing as few as two residues. Particularly
interesting is the design of beta-turn mimics as bioactive cyclic peptides
where they function either as scaffolds or as molecular recognition sites. The
role of beta-turns in peptide-enzyme recognition and receptor reactions is clearly
not trivial and would seem to be related to their postulated origins.
Cyclic nucleic acids (CNA) would also be synthesized as described above and initially
would compete with cyclic peptides (CP) and polyamines having a similar
structure. It is interesting to note that in small CNAs such as diguanylic acid
the backbone lies inside the circle with bases turned outward for obvious
reasons of steric hindrance, so that they bear a superficial morphological
resemblance to small CPs with consequently related functions. As is the case in
modern organisms, competing antigens frequently evolve into symbionts, and this
would occur with CNAs and CPs as their respective functionalities were
exploited. At this point CNAs would have been drafted into a symbiotic association
with CPs, acting as environmental sensors and catalytic activators, while still
retaining some memory function. Equally peptides would then be free to act
principally as databases, a role to which they are better suited particularly
as they eventually polymerize to become linear, while they still retain a
catalytic enzymatic function “learned” in their cyclic phase.
How would the interaction between these
species evolve over the long term? In the first place, if CPs lose their cyclic
morphology they can no longer act as energy transducing chromophores, at which
point CNAs and micro RNAs take over the sensor, polymerase and catalytic
functions required to enlarge the peptide database. Large cyclic peptides break
down to become linear, their polymerization regulated by CNAs and micro RNAs.
The essential state subsisting now between peptides and nucleic acids (NAs) is
that of symbiotic mutualism, each having specialized in a particular function
complementary to the other: NAs supply energy with its cognate environmental
data to the peptides, which in turn store this data first simply by
polymerizing and eventually by adopting secondary and tertiary conformations.
An interesting
by-product of NA polymerization of peptides is determination of amino acid (AA)
chirality. Why are almost all natural AAs L – enantiomers? Asymmetric
synthesis requires a means of distinguishing one enantiomer from the other but
this distinction can only be made by molecules which are themselves chiral.
Nucleotides possess several sources of asymmetry, in particular axial, backbone
and phosphorus chirality. Most important though could be the role of the
imidazole ring, acting as both ligand and catalyst, which has the remarkable
property of being electronically tunable by varying its substituent molecules
and surprisingly also by application of high atmospheric pressure which has
the effect of considerably enhancing enantioselectivity, to be discussed
below. Furthermore electronic tuning of ligands is known to have a dramatic
effect on selectivity, particularly in the case of metal-catalyzed reactions,
which may well be involved in prebiotic AA synthesis.
We shall now adress
the effects of high atmospheric pressure chemistry on prebiotic evolution. Many
of the reactions discussed above concerning asymmetric catalysis were first
characterized under conditions of supercriticality involving various solvents
including water, CO2, CHF3 and other classes of organic
solvents. Investigation of supercritical (SC) fluids over the last few decades
has provided a wealth of data relevant to the origins of biologically active
molecules, although in practice the pressures applied have seldom exceeded 100
MPa. As a result of liquid solvents’ very low compressibility, pressure has
little effect on the enantioselectivity of asymmetric catalysis in them except
at extremely high levels. However the high compressibilities of SCFs,
especially near their critical point, allow pressure effects to be more readily
achieved and precisely controlled. Under the right conditions of temperature
and pressure enantiomeric excess (ee) can reach close to 100%.
Supercritical fluids
can be defined as fluids or solvents above their critical temperatures and
atmospheric pressures, possessing properties between those of liquids and
gases, with densities similar to liquids while viscosities and diffusivities
are closer to those of gases. Apart from their effects on enantioselectivity
they have many important characteristics relevant to this discussion. Pressure
effects in particular are quite dramatic, fundamentally changing the electronic
character and physical properties of most solvents. Water, for instance, with a
critical pressure of 22 MPa at 647 K, can be pressure-tuned to behave like
almost any organic solvent of low dielectric constant, generating chemistry in
a single fluid phase that would otherwise require a multiphase system under
conventional conditions. SC water has the capability to dissolve organic
compounds, with the significant exception of enzymes, while simultaneously
retaining an active state of high hydrolysis performance, acting as solvent,
reactant and catalyst in organic chemical reactions. The character of water
under supercritical conditions changes from one that supports only ionic
species at ambient conditions to one that dissolves paraffins, aromatics, gases
and salts, partly as a result of the shift of dielectric constant from 78 to
approximately 6 at critical. The ion product, or dissociation constant, for SC
water as it approaches the critical point is about 3 orders of magnitude higher
than it is for ambient water. It therefore generates a higher H+ and
OH- ion concentration than liquid water. As such SC water is an
effective medium for both acid- and base-catalyzed reactions with organic
compounds. The dissociation of water near its critical point generates a
sufficiently high H+ concentration that some acid-catalyzed organic
reactions actually proceed without the presence of any acid, with resulting
hydronium ions being the primary catalytic agents. In fact approaching the
critical point, the density of any supercritical fluid becomes extremely
sensitive to even minor changes in temperature and especially pressure and this
affects several fundamental properties including dielectric constant, pH, polarity,
viscosity, diffusivity, solubility, mass transfer rates, activation volume and
rates, enantioselectivity, electrostriction and electron attachment rates. As a
result, it has been found that under certain conditions of supercriticality
chemical reaction rates can be accelerated by several orders of magnitude, a
fact with profound implications for prebiotic molecular evolution. Reaction
rates are classically controlled by catalysts. What is the connection between
catalysts and supercriticality?
The ideal catalyst
generates significantly accelerated reactions, often enhanced by a high degree
of selectivity. In the world of biochemistry, this role is generally filled by
enzymes, which may be proteins or nucleic acids or more likely both in tandem,
frequently with the participation of cofactors such as transition metal ions. In
the prebiotic world, the role of catalyst was probably occupied by
gravity-generated high “atmospheric” pressure exerted on molecules in solution
under conditions of supercriticality, which we shall characterize as the eighth
major transduction of gravitational energy. How do SC fluids and enzymes
produce their catalytic effects? Are their mechanisms fundamentally identical
or totally disparate? Can the first evolve into the second?
The textbook
description of biological catalysis states that enzymes reduce the energy
required to surmount the barrier between reactants and products, thereby
leading to accelerated reaction rates. The mechanism of this concept known as
transition state theory (TST) is little understood. Recently the theory itself
has been brought into question and fundamentally modified by the demonstration
that quantum tunneling is responsible for catalytic action in a growing number
of enzymes and may prove to be a general strategy used by all enzymes
catalysing highly energetic transformations with large activation barriers. In
fact the majority of enzymes catalyze by hydrogen transfer in some form,
including proton movements in acid/base catalysis, hydride transfer in redox
catalysis or radical transfer. How do these biological enzymatic
transformations relate to inorganic catalysis? It is certainly not coincidental
that H-transfer in inorganic non-biological systems also occurs by
vibrationally assisted quantum tunneling as a means of proton transfer in
metals or, for instance, along hydrogen bonds in benzoic acid dimer and similar
reactions. How are these transfers effected and more significantly, how are
they controlled, in biological as well as in non-biological systems?
Many hypotheses
analyzing the factors contributing to catalytic potential have been proposed
but definitive experimental investigation in support of these concepts has been
sadly lacking. The basic problem remains elucidation of the mechanisms of energy
transduction by charge transfer which relies on controlling two essential
components: relative distances and positioning of reactants. This principle
known as orbital steering has been shown to play a major quantitative role in
the catalytic power of enzymes accounting under the right conditions for rate
acceleration by many orders of magnitude. There are naturally many secondary
influences on reaction rates but these only come into play if the fundamentals
are also satified. One of the most significant secondary states concerns
application of external fields that may couple to the transfer particle’s
dipole moment. Experiments provide evidence that pressure-driven external
fields can direct optimal orientation of overlap in reacting orbitals thus directing
both angular positioning and distance. This would be particularly important in
tunneling effects which rely crucially on distance between donor and acceptor.
As H-tunneling occurs over relatively short distances (≈ 0.5 Å), high pressure in inorganic
systems would clearly be a major factor in achieving the necessary molecular
compression. In biological systems a key feature of the thermal vibration or
dynamic barrier model is the role of protein motion in transiently compressing
the width of potential energy barriers, thereby promoting tunneling reactions.
We can therefore see that, in providing a mechanism for controlled charge
transfer by orbital steering, high pressure under supercritical conditions
can be considered as a general physical analog of enzymatic or at least
catalytic function, greatly accelerating as well as directing molecular
reactions.
At this point we must be conscious of the fact that we have
wandered well away from direct gravity-driven effects into the realm of
biological function which is dominated by electrostatic forces. How can we
justify a hypothesis which demands that gravitational effects undergo a “phase
transition” to processes driven by electrostatics? How can electrostatics
suddenly come into the picture? What is the link, if any exists, between these
two apparently different forces? To answer this question we must return to the
Big Bang and Grand Unification (GU). Under GU, of course, the four fundamental
forces - strong, weak, electromagnetic and gravity – are all united, but only
at extremely high energies obtaining immediately after the BB. Furthermore
until recently gravity has managed to stay firmly out of any proposed
unification scheme – until recently, that is. Today (2004) it is probably safe
to say that this is no longer true.
In the course of the last five years or so enough confirmed
evidence has accumulated to justify the statements which now follow. Several
investigators have, over the years, proposed unification schemes but the one
which appears most coherent and convincing is authored by Dr. Myron W. Evans
and his colleagues at A.I.A.S. (www.aias.us). His approach expresses the
gravitational and electromagnetic field in terms of the geometry of spacetime,
thus unifying the description of these fields within General Relativity. The
metric therefore becomes the fundamental potential field for both
gravitation and electromagnetism. In a private communication Dr. Evans says
– “AIAS has proven that electromagnetism and gravitation are parts of the same
field, described by the tetrad form of differential geometry…The AIAS website
describes papers suggesting new experiments designed to detect the influence
of gravitation on electrostatics”. He goes on to demonstrate that the electric
field strength between charged particles (electrostatic field) originates
in their acceleration due to gravity and is therefore a purely
gravitational effect. In his 2002 paper entitled Electromagnetic Energy
from Curved Spacetime Dr. Evans says – “In this paper Einstein’s
perturbation method is applied to General Relativity to demonstrate the
existence of the B(3) field for a simple metric corresponding to
an expanding universe. The result is used to derive an expression for the
electromagnetic energy density due to B(3) and to show that in
principle energy density can be obtained from curved spacetime without
source charges being present”. Elsewhere he states that as gravitational and
electromagnetic fields are both generated by the curvature (expansion) of
spacetime, “This means that one field can be converted into another and that gravitation
can give rise to electromagnetism and vice-versa”. Dr. Evans has thus
completed the conceptual framework begun by Einstein concerning the unified
geometrization of the four fundamental forces, and demonstrated conclusively
that they all stem from the expansion with concomitant spin and curvature of
spacetime. Here we demonstrate that life, as a functional extension of
gravity, also is a direct consequence of spacetime expansion, spin and
curvature, thereby establishing the principle of the geometrization of life and
unifying it with the other fundamental forces of nature.
With this essential background information we can now return to
our investigation of the relationship between cyclic peptides (CP), a term in
which we shall include polyamines, and cyclic nucleic acids (CNA), which we
interrupted on page 8 in order to discuss supercriticality. Beyond the
supposition that evolutionary processes affecting CPs and CNAs would be vastly
accelerated under supercritical conditions it is difficult to be more precise,
exposing an important subject for experimental investigation. Nevertheless
clues to functional associations between these molecular types can be found by examining
highly conserved small RNA/protein complexes, the ribonucleoproteins (RNP), and
in particular the signal recognition particles (SRP), universally conserved
complexes found in all domains of life. Recent advances in X-ray
crystallography, NMR and related imaging technologies have permitted dramatic
insights into the structure and function of RNPs as well as many other
biological molecules. One of the major discoveries concerns the fact that
proteins invariably function in intimate association with nucleic acids
either in the form of RNA or as small molecules such as GTP or ATP, frequently both. The RNA world of recent
years has turned out to be largely an RNP world, the classic example naturally
being the ribosome comprising over 70 different proteins and several classes of
RNAs. What is the nature of the relationship and interaction between these two
molecules? Why do they need each other in order to function?
Examining proteins first, it has now been convincingly
demonstrated that these molecules exist as modular units, each type dedicated
to performing a certain limited and highly specific class of function. It would
appear that such modules probably originated as small molecules responding to
a specific stress such as temperature,
pressure, pH, etc. In time they speciated, becoming more selective and forming
diverse population types, now known as domains. More complex functions are
accomplished not by larger proteins but by assemblies of several complementary
domains, each of which is assigned its specific role in a precisely targeted
and coordinated mechanism. How is this synchronization achieved?
In order to answer this question it is revealing to examine SRPs.
Their precise cellular functions are not relevant to this discussion, but what
is interesting is that they exhibit most of the significant characteristics of
the protein/RNA connection. In higher eukaryotes SRP holds six different
proteins retained by an RNA acting as a scaffold consisting of ~300
nucleotides. The secondary structure of the RNA moiety is shaped somewhat like
a backbone or a nerve cell with the roots (synapses), stem (axon) and branches
(dendrites) each attached to one of the various proteins. If the stem were cut
in the middle, the complex would form two separate domains, each of which
performs a clearly differentiated but complementary function. In fact if the
RNA were disassembled into its component parts each attached to its cognate
protein and then reassembled, we would probably have a simplified picture of
the evolutionary origin of such complexes. The RNA moiety clearly plays a
“nervous system” type of role in assembling, guiding and coordinating the
proteins in their eventual catalytic or enzymatic function.
Another revealing example of the protein/RNA connection consists
of the highly conserved Sm proteins which are always associated with
U-rich RNA sequences. The protein moiety functions in a heptameric
doughnut-shaped ring formation with part of the RNA moiety forming a smaller
ring inside the central 15Å cavity. Each of seven RNA uridines make stacking
contacts with aromatic residues projecting into the inner cavity, reading the
instructions contained within the Sm structure and processing that information
in order to carry out its cognate function. It is particularly interesting that
certain Sm-like proteins, specifically E. coli Hfq which plays
wide-ranging roles in RNA metabolism, reciprocate in this relationship by
acting as an RNA chaperone, inducing structural changes in mRNA, thereby
helping to maintain the RNA’s specific functionality.
In a series of recent papers (Lai et al., 2003) it has been
reported that certain RNA sequences can act as sensors of various environmental
factors, in particular temperature or the presence of specific small
metabolites and cofactors. This information could then be relayed to selected
proteins for storage and later reference, or as was actually determined in
these investigations, it is used by the RNA to directly regulate the
transcription or translation of associated mRNA, including itself. These RNAs,
known as riboswitches, thereby simultaneously perform both sensing and
regulatory functions without the mediation of any proteins, similarly to
miRNAs, clearly demonstrating that the principal function of protein is
information storage rather than molecular activation. This intimate
relationship between sensing and regulating on the one hand, and environmental
state-and-response data storage on the other, between RNA and protein, seems to
be at the core of biological function. It would appear furthermore that each
needs the other in order to achieve its active tertiary or higher order
structure, suggesting that their respective structures probably evolved
together as physically and functionally bound units.
During this stage of evolution electrostatic forces finally
establish their domination over biomolecular interactions, a highly complex
subject which unfortunately remains poorly understood in spite of being the
focus of considerable investigation. A simple definition of electrostatics
would state that it concerns the interaction of positive and negative charges
at rest or moving at low speeds such that their fields are not affected. The
problem is that, like gravity, as they unfold electrostatic forces take on many
different and subtle forms, occasionally producing quite counter-intuitive
effects. Added to that is the fact that intricately structured biomolecules
such as those we have been discussing generate highly complex and mobile
electronic fields. Nevertheless if we are to understand the coevolution of
peptides and nucleic acids, even at a very simple level, we must come to grips
with the subject.
The first point to consider is the fundamental force causing
positive and negative charges to interact, which is of course the tendency
toward equilibration, the search for stability. To understand this force we
again turn to GU and the geometry of curved spacetime. Curvature, the
tension-stress caused by expansion, as we saw above gives rise to reactions
manifested as gravity and electric charge. Response to tension will result in a
minimization of charge in accordance with the Evans Principle of Least
Curvature, an effect which causes positive and negative (opposite) charges to
relieve stress by neutralizing each other. This stress-relieving neutralizing
response is so basic that it is probably at the root of all forces and events,
but it becomes most apparent in molecular and biomolecular interactions. Any
charge by definition seeks to be equilibrated, to be counterbalanced or
neutralized, and will therefore naturally tend to combine with its opposite
charge and to avoid any like charge which would increase its imbalance pushing
it further away from neutrality. This may seem obvious but it bears repeating
because it is the basis for all biomolecular interactions and, with the added
element of selection, it forms the stress-responses-selection triad
(SRS), the mechanism leading to molecular and biological evolution.
Molecular biologists have come to give electrostatic interactions
different names such as van der Waals, induced dipole, hydrogen bond,
dispersion forces, etc. according to their particular range, energy,
circumstances and effects, as if they were separate and distinct forces in
their own right, thus adding confusion to an already complicated situation.
Adding further to the difficulty is the fact that biological reactions occur in
solvent which of course drastically alters the charge environment and has far
reaching solvation effects of its own. The most significant of these is the
so-called hydrophobic effect which is due largely to the charge-related
energetic structure of the bulk solvent, in most cases water.
We can now pick up the discussion on page 10 concerning
interactions of nucleic acids and peptides including polyamines which are
likely to have originated as amino acid precursors. One of the significant
energetic features of these two sets of molecules is that nucleic acids are
highly negatively charged, particularly at the backbone phosphates, while
polyamines are highly positively charged, this charge being concentrated on the
mobile amine and amide moieties. Many amino acids also carry significant mobile
positive charges, in particular at the guanidium moiety of arginine closely
resembling a polyamine, as well as at their amino ends, so that these two sets
of molecules, peptides and nucleic acids, will tend naturally to complement
each other, at least partially neutralizing each other’s charge. Also available
for attenuating charge are various elements such as salts, monovalent and
multivalent metal cations and of course water itself, whose hydration shells
are quite effective at screening charge while remaining mobile and loosely
bound, thereby permitting more stable reactions to take place by replacement of
water molecules.
In the Hadean and early Archaean high-pressure radiogenic
environment, highly reactive radicals and ionic species will inevitably abound
exerting considerable stress on many molecules. In particular beta and gamma
bombardment lead to rapid radiolysis of water releasing free electrons and OH-
hydroxyl radicals. The .OH generated by these reactions can abstract a hydrogen
from the ribose sugar of RNA and DNA backbones leading to cleavage of the
phosphodiester bonds. The long term result, in accordance with the SRS
principle, will be darwinian selection favoring those nucleic acids whose
negatively charged backbones are best and most rapidly protected, either by
metal cations such as Mg2+ or by polyamines or of course by
peptides, thus tending to drive these molecules together in a symbiotic
relationship. In modern cells polyamines are present in millimolar
concentrations and, together with magnesium ions, account for the majority of
intracellular cationic charges. Clearly charge neutralization of intracellular
anions, in particular those of DNA and RNA, are among their most important
physiological roles, however polyamine binding also has profound effects on
nucleic acid structure, causing bending, folding and transitions to different
forms. The process of charge neutralization is undoubtedly also at the origin
of protein folding whereby susceptible scissile bonds exposed to solvent are
protected by complementary moieties within the same molecule. These
conformational changes directly affect binding and as a result influence
enzymatic function. Most interestingly, it has also been found that polyamines
promote and increase rates of RNA polymerization.
RNA backbone charge-stress and neutralization processes would
therefore appear to be at the origin of biomolecular functional evolution. As
nucleic acids and peptides, with the active participation of waters, metal
cations, salts, and polyamines, evolve new mechanisms and conformations
increasing their stability, both in isolation and as a complex, the
evolutionary history of these events is recorded in their physical and
electronic structure. The molecular structure best able to store complex
information is, as discussed previously, that of peptides which as a result
constitute an accessible data bank containing a complete memory of the stresses
and successful responses experienced by the molecules. This process involves
nucleic acids receiving stress signals which may be briefly stored or instantly
transmitted to their cognate peptides which in turn may make the structural
adjustments necessary to neutralize or compensate for the particular stress.
The most efficient and successful RNA-peptide complexes will survive the SRS
elimination process and thereby maintain a record of these events.
Stress-charge excitation transfer to peptide…relaxation…release.
The question we now need to examine is this – Can
the cyclic nucleic acids and peptides discussed earlier emerge from radiogenic
supercritical conditions to evolve into catalytic systems able to function in
ambient conditions? Why and how do they emerge from these high energy
conditions?
Proposal Objectives
The objectives of this proposal generally
include those of the NASA Astrobiology Roadmap but seek to go further, first in
demonstrating the existence of a process linking life directly to the Big Bang
and second in providing evidence indicating that biological function stems
deterministically from the fundamental physics of cosmological evolution. Use
of the term deterministic means that every step in this process is
logically and sequentially guided both in its mechanism and its direction, at
no point relying on the exercise of possibilities or probabilities. Synthesis
of the molecular precursors and generating mechanisms leading to biological
function are explored from an entirely new perspective, that of gravitationally driven condensation. It
is suggested that this putative metamechanism, generated by and in reaction to
the Big Bang and directed at opposing subsequent cosmological expansion,
accounts for all the structures and cognate processes displayed by the
universe, including galaxies, molecules and living organisms.
The immediate objective of this proposal would
be to test the initial claims of the cited hypothesis, particularly those
concerning de novo nucleosynthesis of the biogenic elements, CHNOPS,
followed by chromophore, cyclic peptide (polyamine) and nucleotide synthesis,
under high pressure supercritical and radiogenic conditions.
Technical Approach and Methodology
Suggestions are made below for the performance
of exclusively ground based theoretical and experimental investigations testing
the relevance of this hypothesis to those physical and chemical principles
which underly the origins and evolution of life. It
should be made clear from the outset that to elucidate all the stages of
evolution at the molecular level, starting from formation of solar systems and
proceeding up to the emergence of recognizable ab initio biological function, must be a process which will at best
occupy scientists for many decades and will necessarily be highly
interdisciplinary, employing specialists in several domains.
Although this proposal attempts to cover
the entire evolutionary process at a general theoretical level, at the experimental
investigation level only the initial critical steps will be mentioned. These
steps are concerned exclusively with high pressure radioactive chemistry and
may possibly involve design and construction of bespoke equipment. One of the
major problems facing this equipment is the need to flush solvents through a
flow reactor system continuously under high pressure without stopping or
interrupting the experimental procedure, while at all times maintaining a safe
radiation shield.
The initial experiments will be designed to
reproduce conditions in the Earth’s crust about 600 million years after its
formation, or about 4 Gyr ago. It will be particularly important to arrive at
an accurate definition of crustal radiological conditions at that time and of the
evolution of these conditions as radiogenic isotopes accumulate.
Plan of Initial Experimental Investigation
Experimental investigation of these putative phenomena
would be aimed at establishing the degree to which they actually do occur as
predicted and would require an initial research program designed to
focus mainly on the procedures listed below. The purpose of these procedures
would be to simulate gravitational pressure and radiological conditions in the
Archaean Earth’s crust as well as their subsequent evolutionary history.
1.
PHASE I –
Simulate high pressure radiochemical reactions under various conditions of
pressure and temperature in the presence of selected elements and compounds
including water and other solvents. The purpose of this step would be to
determine the elements and species of molecular structures synthesized and the
character of bonds formed in confined high energy and high pressure radiogenic
environments.
2.
PHASE II – Using
molecules generated in Phase I, impose accelerated reduction of radiogenic
energy and pressure to simulate changing conditions over geological time. The
purpose of this step would be to characterize the effect of an evolving
radiogenic environment on molecular structures and reactions.
3.
PHASE III - Using
molecules generated in Phases I and II again by varying environmental
conditions, characterize the reaction kinetics and mechanisms determining
structural responses to various types of radiogenic environmental stress.
4.
PHASE IV – Using
molecules generated in Phases I and II, determine mechanisms for encoding and
storing information relative to specific environmental stress factors in
molecular structures and for accessing these data in order to permit adaptation
by eliciting targeted stress responses through variations of structural
configuration.
5.
PHASE V –
Following the results of Phase IV, further reduce energy regime until
equilibrium is reached and molecules are observed to react by influencing and
eventually controlling previously dominant environmental stress factors.
Once the radiogenic energy regime has reached equilibrium
levels, further investigation will be needed to determine how heterogeneous
molecular systems encode, store and access large databases on environmental
conditions to elicit targeted stress responses. It will also be necessary to
characterize the mechanisms using these databases and directed at manipulating
the environment specifically to extract energy and matter required to
substitute for the reduced radiogenic input. These investigations will clearly
involve many more phases of highly interdisciplinary intensive research lasting
a considerable time which, needless to say, at this point it would be difficult
to estimate.