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Pre-Biotic Evolution
Pre-Biotic Evolution:
I. From Stellar to Molecular Evolution
Joseph H. Guth*
Published by the
Introduction
The overall phenomenon known as life begins with and is inextricably connected to the
nucleosynthesis of the major elements of the Periodic Table. The production of those
elements occurred in various stellar and astrophysical processes. Past supernovae
provide just one of many sources of our elemental atomic building blocks. As Cosmos
astronomer Carl Sagan observed, "We are made of star stuff". Without the availability of
so many resultant and differing types of atoms with their various symmetries and
geometries, bonding potentials, and electronic energy states, life as we know it could not
even have begun. By extension, the subsequent molecules that inextricably formed and
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evolved from them, constituting the matter making up living systems on earth today, also
could not exist.
The lens through which the earliest stages of the origin of life may be illuminated begins
with the basic tenets of physical chemistry, combinatorial reaction chemistry,
biochemistry, bioenergetics, membrane biophysics, chaos theory, complexity theory and
evolutionary theory. The challenges that are ultimately addressed are as follows:
It is usually the complexities and unknown or uncertain workings of living systems that
baffles the scientific reductionist trying to probe or analyze the beginnings of life. But
that classical scientific mindset is exactly what needs to be overcome in order to embrace
a process that had innumerable components, steps, stages, variations and possible
outcomes. It is the complexity and non-linearity of the living process that imbues "life"
to inanimate matter. Life does not greatly depend upon random, stochastic processes. In
fact, it is commonly described in opposite terms as being thermodynamically of a
negative entropic nature. Though molecular biology is useful in observing and
describing the structure of the living cell, it is a misnomer in that it does not actually
address the complex "living" state. It only looks at snippets of the bigger, overall picture
and that is where we must be able to have a clear view and understanding. When looking
for the origin of life, a firm definition and operational design of life is quite
indispensable. But in this series of essays, the underlying, non-stochastic patterns of
molecular behavior and dynamic linkages create the necessary chaotic complexity that is
required to more accurately describe the living state. The complexity of the living
cellular system must not be dissected back into its parts to understand it. It is the way
those parts interact and work together that provides the whole being greater than the sum
of its parts. Can one understand how the space shuttle could fly and carry out its
missions from just its parts list?
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Our scientifically-based genesis story begins with inanimate atoms and logically carries
through to the biophysical formation of the first proto-cells. In this series of essays, we
find some new and interesting pieces of the puzzle fit together naturally. These stages of
molecular and early cellular evolution might rationally end at a waymark in this narrative
after prokaryotic and the earliest eukaryotic cells made their appearances for the first
time. The level of presentation is less rigorous and specific in order to facilitate
understanding by a wider, enlightened scientific audience. As such, brief introductory
comments about specialized theories will hopefully benefit the majority of readers while
not trying the patience of those more specialized in this subject.
After bringing the universal collection of various kinds of atoms into existence, we also
must find common ground to agree on certain basic assumptions. Such assumptions as
all atoms of a given element, no matter where they occur in the universe, are
indistinguishable in their makeup, chemical and physical behavior and characteristics.
Another assumption is a corollary to that which implies that all atomic reactions between
atoms of identical or differing elements behave the same anywhere in the universe when
under the same environmental conditions. That leads to the next corollary that all
specific molecules formed from such reactions will have the same identical properties no
matter where they occur if under the same environmental conditions. And the last
corollary is that all molecules with the same structure will behave indistinguishably from
one another if under the same conditions anywhere in the universe. These fundamental
assumptions allow us to accept spectroscopically-derived astronomical data and
interpreting it as being mechanistically identical with comparable laboratory or locally-
generated data. Such assumptions are commonly accepted in astrophysics,
astrochemistry and astrobiology.
We follow a similar trail to that which others described in which the pattern for protein-
based metabolism could have preceded the appearance and functioning of a nucleic acid-
connected, information-containing, accurately-transmitted, highly specific (genetic)
molecular replication scheme.1 We begin with describing a picture of nonmembrane-
bounded molecular evolution preceding that first membrane-packaged "cell" formation
(i.e., the proto-cell).
There will be a very prominent role for the development of permanently oscillating, self-
propagating, oxidation-reduction chemistry that provides the first form of life energy
storage and conversion that future living systems will be built upon. Such systems can
involve purely inorganic reactions assisted by catalytic species or can be found in organic
chemically-based systems which can range from relatively simple to highly complex. In
modern biochemistry, such oscillatory behavior is found in both cell-free and intact
subcellular biochemical pathway dynamics. It is also reflected by oscillatory behavior in
various transmembrane fluxes of different biochemicals and bioenergetically-important
compounds and membrane-based ion transport mechanisms as well. Such oxidation-
reduction coupled oscillations will ultimately become packaged as one of many forms of
protocells which then survive as dynamic, chemically-reactive entities. Those protocells
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then would have been able to merge with other different, chemically-dynamic, oscillating
protocells containing differing supermolecular complexes that were carrying out different
sets of chemical reaction sequences. This aspect will be focused on in more detail in the
coming installments.
Think of this as a time when there were different subpopulations of protocells, each of
which contained all of the main enzymatic protein complexes for different future
metabolic pathways such as glycolysis, electron transport, tricarboxylic acid cycle,
pentose shunt, etc. Each subpopulation may have arose in a single body of water with a
combinatorial collection of all kinds of supermolecular complexes incompletely mixed
together or in different adjacent or nearby bodies of water. Each pond or lake contained a
variety of molecular mixtures and with hot rocky surfaces nearby. In this chemically-
evolving, catalytically active world, complexity drives this natural tendency for
molecular structure and reactivity to always spontaneously increase. As the different
mixtures' complexities grow, even low probability outcomes become more likely. Such
is the power of combinatorial chemical catalysis. As newer molecules form, some of
them will possess other catalytic capabilities that lead to even more subpopulations of
molecular species. That increasing complexity provides the driving force for the
development of highly complex, integrated systems. That ever-increasing complexity
can increase the likelihood of protocell and living systems eventually appearing. Once
such more complex assemblages of molecules and structure appear, if the selection
conditions are present, those more complex units become the dominant subpopulation if
they have developed any survival or propagational benefit from their environment at that
time.
PC1
PC1+2
PC2
PC FUSION
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One example of that self-amplification is the modern day Polynucleotide Chain Reaction
(PCR) used to replicate small amounts of DNA in vitro for analysis. Another is the
replication mode of PrPSC prion proteins which is thought to be devoid of any DNA-
directed involvement. It is even possible to place the first virus-like precursors within
such a milieu if enough of their needed molecular replication machinery and molecular
building blocks were co-constituents within our pre-biotic combinatorial ponds. Those
"proto-viruses" would become the first self-replication genes and genomes existing
before the first complete genomes, chromosomes or independent living cells were
formed. But in our early earth case, those products were initially amino acid-based
polymers possessing the same types of catalytic activity that initially produced them.
And what allowed this to happen with a high probability? It was that they were most
likely organized as multiple step, integrated reaction sequences that operated in a
controlled feedback loop-like fashion.2, 3, 4, 5
A Stellar Beginning
Let us start at the beginning. Our story of the origins of life began with simple chemistry
and its universal occurrences. Hydrogen, carbon, nitrogen, oxygen, sulfur, sodium,
potassium, calcium, magnesium and phosphorus are found throughout the universe.
Astronomically large clouds of these elements are found throughout the galaxy having
been transmuted through a sequential nucleosynthetic process occurring from the life and
death of stars and other high temperature, high energy sources. Depending on the
temperatures present, differing nuclear reactions and states of matter can exist within
them. At higher temperatures, those elements are found primarily as atomically
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Once these smaller molecules collect and concentrate on cooler planetary and sub-
planetary bodies, various chemical reactions and physical processes can continue to lead
to larger molecular structures under more molecularly stable conditions. The production
of life's complex mixture of starting chemical compounds could have formed in large
quantities on post-Hadean period earth as well as many other places in the universe.
Such is the inevitable driving tendency of synthetic dynamic combinatorial chemistry.
When there are a few different kinds of atomic building blocks and sufficient energy
available to break chemical bonds along with conditions that allow new bond
reformations, small simple molecules becoming increasingly larger and more complex in
structure. And as new kinds of chemical structures come into existence in our mixtures,
new catalytic potential is introduced with them. New catalytic potential spurs even faster
development of ever-expanding libraries (i. e., collections) of newer compounds which
hadn't previously existed. Complexity in our early chemical incubators will ultimately
lead to collections of linked chemical catalysis. Linked reactions form the basic pattern
and framework for modern cell-based metabolism. And in our case it comes together on
a cooling earth a little less than 4.5 billion years ago. The physical incubator for
abiogenesis became available on the still hot, asteroid-bombarded surface of earth.
The chemical compounds which collected there initially must have originated from a
combination of meteorite/asteroid plus cometary deposition and higher-temperature
chemical reactions. These latter are known to occur between very simple molecules
composing the early earth surface deposits and atmosphere. Similar high energy-
associated chemistry could have already been occurring extra-terrestrially within the Oort
cloud surrounding the infant solar system. The solar wind and the ionizing
electromagnetic radiation it emitted bathed such frozen water- and methane-rich icy
bodies with high energy particles and chemical bond-ionizing photons. Low- to
extremely high-energy protons, electrons, neutrons, and other elementary particles (which
are commonly known as cosmic rays) catalyzed new element nucleosynthesis and
chemical bond formations after they traveled in on the solar wind, as well as from deeper
interstellar and intergalactic sources. Physical shock waves due to impacts and sound
vibrations and deep earth zones under very high compressive forces and temperatures can
induce unusual chemical reactions to occur (such as crystallization of elemental carbon to
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This early earth setting frames the period and some of the necessary steps, stages and
events leading up to and into the formation of the first cells on pre-biotic earth. It must
be a brief overview since there are publication limitations in time, space and reader
attention span. Such limitations were not present during the original story. That original
reality had the advantage of having all the time in the world to play out. It evolved over
the time span from approximately 4.2 to 3.6 billion years ago. This pre-life reaction
chemistry began almost immediately after the earth cooled sufficiently and limited
amounts of liquid water became available.
During the pre-biotic period, simple molecules were produced through a variety of
chemical and physical processes. Some were generated on early earth in manners already
described.6, 7, 8, 9, 10, 11, 12 Hydrogen, the most abundant (reducing) element in the cosmos,
will usually be part of the early gases that collected as atmospheres on cooling planetary
bodies. The hydrogen-rich reducing atmosphere, composed of gases found throughout
space as nebulae and molecular clouds in the galaxy, were generated from within
supernovae. And as modern exo-planetary research has repeatedly shown, they could
have been expected to be abundant around our youthful Sun.13, 14, 15 The simple atoms
and molecules of the periodic table found throughout the cosmos could have not only
been plentiful, they could have been gravitationally attracted to any sizable body in an
infant solar system. They collected on our newborn planet as it slowly swept through
them.
This reducing atmosphere was originally low in molecular oxygen content and oxidizing
potential. That was first postulated by Oparin and Haldane in the 1920s. It could have
coalesced and formed over the solid surface of primitive earth soon after it finished
cooling and solidifying out of a previous supernova cloud full of lighter and heavier
elements. Through high temperature processes such as volcanism, geothermal steam,
simple pyrolysis, high energy impacts, electrical arc heating (lightning) and ionizing
radiation, it is likely that brownish-black, tarry, keragen-rich ooze would have developed
and continuously accumulated over large land-based areas. Such organic molecule
building generally is not found in oxidizing conditions.1 Growing molecular sizes for the
organic compounds being generated abiotically would have built up over a great amount
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of time on or within various heated rock, sand and clay surfaces scattered around the
globe. This was an early period of not just fairly arid conditions, it could have also been
predominantly water-poor, dehydrating conditions for early reactive carbon chemistry to
become relatively facile.
As an example, the transition from the arid to aqueous world during earth's early history
would have involved water-requiring chemical reactions. Water would be both a
supporting solvent and a reactant. Variations in the yields of various products might have
depended upon the availability of super-heated steam above certain reaction
temperatures. When such water-based chemistry occurs along side of anhydrous heated
surfaces, many interesting compounds could result.20 Such closely juxtaposed reaction
sites, as are found in present day geothermal environments like Yellowstone National
Park in the United States, could have also more quickly modified the plethora of
molecular species that could combinatorially form. Reaction products from dehydration-
driven conditions would easily transport into more aqueous conditions where water-
requiring oxidation-reduction electrochemical reactions would have been incubating.
And as changes in the latter pools led to newer compounds, those could have been
recycled back to the hotter dehydration conditions building up larger molecular species
that were more resistant to hydrolysis and yet possessing of newer and unique molecular
reactivities and properties. The complexity of the resultant molecular mixtures becomes
the most important determinant as to whether the right combination of molecular species
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Comets carrying large amounts of water, rock, frozen gases, and dust also started
becoming more plentiful during this early period in earth's history. They subsequently
added sufficient free liquid water as the earth further cooled to begin forming pools,
ponds, lakes, seas and eventually-frozen polar caps. After that hydration phase passed
some critical threshold, membrane-bound life forms would have had an environment they
could call home.
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The originally dehydration-based pre-biotic chemistry now began to dissolve and suspend
a growing variety of small, medium and larger molecular weight precursory pre-biotic
molecules. It is this limited collection of compounds we shall refer to as the "starter set".
Niches and pockets of dehydration-based chemistry continued to generate the earlier
reaction products while the water-based chemistry began to form a newer collection of
pre-cursor, pre-biotic molecules. This latter group in part contained water-derived
oxygen atoms within their structure. That increased their inherent polarities, water
solubilities and reaction chemistry potentialities. Such wide climatic fluctuations simply
emulates what we can still find anywhere on earth. Even arid deserts can experience
infrequent flooding rainfall and rain forests can die off from drought-provoking climate
changes. Chemical complexity now becomes the new paradigm. Virtually every
chemical reaction pathway found in current synthetic organic chemistry could be co-
existing at some location under these early earth conditions.
Pockets of minerals containing more reactive elements and atomic species (such as
inorganic carbon, iron, manganese, cobalt, phosphorus, silicon, selenium, arsenic, iodine,
sulfur, or copper) would provide even greater richness of molecular diversity in their own
niche-like locations. A long-standing question has been "Why are so many inorganic
elements found in key metabolic sites within living cells? How did they evolve to be
there?"
Such an early history of exotic chemical reactions might have led to conservation and
parallel evolutionary paths for various metallo-organics (such as metallo-porphyrins),
metallo-enzymes, thiol/disulfide-containing proteins and unusual biochemical pathways.
Examples of the latter group are the selenium-based superoxide dismutase enzymes, the
iron-sulfur containing P450-FeS and cytochrome complexes in mitochondria and inner
cytoplasmic membrane systems, the hydrogen peroxide-hydroquinone defense
mechanism of the bombardier beetle, and the hydrogen, methanogenic and
carbon/nitrogen/sulfur-fixing pathways of the Archaea. The high G-C DNA base
composition and thermal stability of proteins in thermophiles in this latter group of
ancient microorganisms also provide present day examples of such likely long term
conserved lineages.
After dry-cooking for millions of years, new classes of carbon-based chemistry began to
become common in water-rich pockets. It is the aqueous environments that are typically
referred to as the "primordial or primeval soup" by many authors. Most theories
involving the origin of life speculate that first "life" began in such a liquid environment.
But without the earlier abiotic conditions and chemistry previously occurring in the
dehydration zones, the genesis of a complex mixture of higher molecular weight
polymers might have been much slower and present a statistically less-likely outcome. In
proteins, nucleic acids, and polysaccharides, the bonds forming the primary monomer
linkages are virtually all formed through the net removal of a water molecule and
subsequently are usually easily hydrolyzed through simple addition reaction with a water
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The higher temperature conditions the molecules are subjected to typically favor the
forward reaction for the reversible hydration-dehydration type reaction. The larger
molecular skeleton aids in favoring the formation of somewhat more stable bonds. Loss
of water is a common biochemical reaction found in biochemically important molecules.
And the formation of those is favored and preferentially induced under higher
temperature-driven, anhydrous reaction conditions. Increased temperatures will increase
the stretching and vibration modes in covalent bonds. As the mean bond lengths increase
even slightly, the bond dissociation energy is reduced and the bonds can more easily
come apart. When two heated molecules contain a more labile H atom and OH group
and are close together, they can thus form even stronger inter-molecular covalent bonds
while expelling a water molecule. And at elevated temperatures, the volatile H2O
molecule is quickly driven off leaving a less volatile larger or polymeric molecule as the
remaining reaction product. Besides condensation polymer formation, cyclic anhydrides
of varying compositions could also be a common class of reaction products occurring
from dehydrating conditions.
Thus our increasingly complex pool of abiotically generated molecules all began from
some very common, simple, low molecular weight and universally available starter
molecules. All types of natural energy sources supplied the necessary energy to break
simpler compounds into reactive fragments and allow those fragments to rearrange and
reform into more complex and larger molecules. The process occurred over and over.
Different elements became caught up in various locations within these molecular card
shuffles. Hetero-atomic molecules brought a greater diversity of characteristics and
capabilities to the growing morass. With the increasing complexities of the resultant
mixtures, low probability events became more likely to occur. Certain combinations of
molecules found themselves more closely associated with one another than the vast
majority of the mixture components. Some of those closer associations had catalytic
capabilities that when the associated chemical reactions occurred, the products of those
coordinated reaction sequences generated more molecules of the same types. When those
complexes continued to generate more of their own types, a Darwin-like molecular
competition occurred in which one very well-established survival pattern was born.
Those complexes continued evolving at the expense of the less capable molecular species
surrounding them. Non-self propagating molecular species began to break down in
thermal and non-thermal bond dissociation events leading to their atoms becoming
recycled into the growing populations of self-propagators. It was the molecular analogy
of a predator-prey pattern and helped to clear the early environment of non-useful
molecular species that did not provide any useful paths to a greater level of overall
collaborative organization. What is meant by that is that in ecological terms, we have
food chains that have been established over time through evolutionary refinements. The
biosphere is considered as a complete, self-sustaining system. Such was not the case at
the molecular level just after the appearance of self-propagating molecular complexes
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and their associated chemistry. The less useful molecular species were cleared out while
the survivors perfected their higher level coordination of structure.
Next: Pre-Biotic Evolution. Part II. Pre-Biotic Chemical Oscillations and Linked
Reaction Sequences
*
Scientific and Forensic Services, Inc., Delray Beach, FL. and Norfolk, VA
scientificandforensicservices@gmail.com
References
1. Dyson, F. "Origins of Life". 2nd Ed. Cambridge University Press, Cambridge UK.
(1999)
3. Boss, G. R., and R. W. Erbe. (1982) Decreased Purine Synthesis During Amino
Acid Starvation Of Human Lymphoblasts. J. Biol. Chem. 257:4242–4247.
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7. Miller, S. L., And H. C. Urey. (1959) Organic compound synthesis on the primitive
earth. Science 130: 245–251
10. Oro, J., and A. P. Kimball. (1960) Synthesis of Adenine from Ammonium Cyanide,
Biochim. Biophys. Res. Commun. 2: 407−412.
11. Oro, J., and A. P. Kimball. (1961) Synthesis of Purines Under Possible Primitive
Earth Conditions. I. Adenine from Hydrogen Cyanide. Arch. Biochem. Biophys. 94:
217−227.
12. Oro, J., and A. P. Kimball. (1962) Synthesis of Purines Under Possible Primitive
Earth Conditions. II. Purine Intermediates from Hydrogen Cyanide, Arch. Biochem.
Biophys. 96: 293−313.
14. Kerridge, J. F. (1995) Origins of amino acids in the early solar system. Adv. Space
Res. 15(3): 107-11.
15. Kerridge, J. F. (1999) Formation And Processing Of Organics In The Early Solar
System. Space Sci. Rev. 90(1-2): 275-88.
16. Lazcano, A., and J. L. Bada. (2003) The 1953 Stanley L. Miller Experiment: Fifty
Years Of Prebiotic Organic Chemistry. Origins of Life and Evolution of the Biosphere
33: 235-242
18. Maude, S., L. Tai, R. Davies, B. Liu, S. Harris, P. Kocienski, and A. Aggeli.
Peptide Synthesis and Self-Assembly. In Top. Curr. Chem. "Peptide-Based Materials".
Ed. by T. Deming. pp. 27-70. Springer-Verlag, Berlin. (2012)
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23. Corbett, P., J. Leclaire, L. Vial, K. West, J. Wietor, J. Sanders, and S. Otto, (Sep
2006) Dynamic combinatorial chemistry. Chem. Rev. 106 (9): 3652–3711.
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