SPECULATIONS ON THE BEGINNINGS OF LIFE
- From: jim7june@xxxxxxxxxxx (James Kendall)
- Date: Tue, 26 Apr 2005 01:00:30 -0400 (EDT)
SPECULATIONS ON THE BEGINNINGS OF LIFE
James D. Kendall
(Copyright March 2005)
1.SUMMARY AND CONCLUSIONS
I suggest: first, life originated deep in the Earth's crust, in water
filled crevices. The water, circulated by geothermal heat, carried
monomers that had been formed in the Earth's atmosphere or by other
natural processes. These crevices were in effect, complex chemical
reactors.
Second, the reactors became dominated by one or more species of DNA or
DNA/RNA systems since DNA chains, in the double helix form, are
chemically the most stable components in these systems.
Third, in time, some species of DNA/RNA systems developed or evolved
genes or analogous mechanisms that catalysed the production of other
molecules. Some of these may have entered into significant reactions.
In particular, a species of DNA/RNA evolved an enzyme or other means
of breaking down foreign species of DNA or RNA into components that
could be reconstituted into the attacking species.
Fourth, by changing the selection criterion this attack mechanism made
the system an evolutionary system, as defined below, and lead to the
evolution of a defence mechanism by other species: a protective
external layer. The initial, simple protective exterior coating
evolved further into a more complex coat to form prokaryotic cells.
Eventually, as new attack mechanisms evolved, a second protective coat
evolved to form eukaryotic cells.
Fifth, the only practicable systems of self-reproducing molecules are
binary or higher order systems. That is, in a binary system, one
molecule produces a second which then reproduces the first. For
instance, RNA and either one of the two chains of a split DNA double
helix, can act as a binary system. In combination, DNA and RNA can act
as either a third or a fourth order system or even as a higher order
system.
Sixth, these special crevice reactors and similar reactors, could have
produced raw materials that escaped and accumulated in characteristic
geological structures to form natural petroleum oils and gases.
This scenario for the origins of life implies that all life forms may
exhibit an immune system, either of a simple antibiotic form or a more
complex adaptive form. The production of penicillin by a mould should
be an example of the rule rather than an exception.
Further, this scenario implies the early separation of life into those
forms that live on raw materials in their environment and those that
live by breaking down and consuming the products of other life.
This primitive attack mechanism may be related to the adaptive immune
system of animals, the nonadaptive immune system of plants as well as
the processes that fungi use to break down other cells for
consumption. Or it may be related to at least some of the many
processes in modern cells that slice DNA and RNA.
Finally, the consistent left handed amino acid molecules associated
with Earth's life forms may be due to their greater stability or due
to a particular, associated mineral catalyst.
2.ASSUMPTIONS
To differentiate between a chemical system and an evolutionary system,
I will assume the following axiomatic definition that elucidates an
evolutionary system's essential characteristics. An evolutionary
system is one such that:
- a population of succeeding generations of propagating individuals
consisting of one or more species, each species with its own defining
traits;
- an individual's constituent elements and monomers are such that the
given environment's chemistry can produce a wide variety of associated
polymer chains;
- a stochastic process, or processes, for the passage of traits, i.e.
genetic material, from one individual to other individuals, in
particular, those within its own species;
- traits of successive generations are modified by a stochastic
process, or processes, of mutations in the individuals' genetic
material;
- a stochastic selection process, or processes, for individuals in the
population with specific traits, either by modifying the probability
of their reproduction or their mortality;
- the selection processes change continually, in respect to the
individuals that are selected, over relatively long periods of time
and the resulting changes in the evolving population feedback to
further changes in the selection processes.
These ongoing changes of the selection criteria is the critical
feature that distinguishes an evolutionary system from a chemical
system. With a fixed selection process, the evolution of increasingly
complex structures is limited. Instead, the structures will become
better and better adapted to the given selection criteria.
For example, during an extended quiescent period, for a given species,
those traits that are selected for, will become common to all members
of that species, establishing an associated level of complexity.
However, traits that are weakly selected for, or not selected at all,
may evolve among subgroups within the species, broadening its gene
pool.
When the selection process changes significantly, new layers of
complexity may start to evolve, overlaid on the base of the existing
level of complexity. In addition, those traits weakly selected for, or
not selected at all, during the period of quiescence, may come to play
a significant role in defining which individuals are selected under
the modified selection criteria.
3.INTRODUCTION
People have long speculated about the origins of life. Since the early
twentieth century, the accepted view in the scientific community was
that life originated in Earth's oceans.
Experiments over the past seventy years indicate that, given the
assumed primordial atmosphere, natural effects such as lightning would
have produced the complex organic monomers of DNA and RNA as well as
some monomers of various cell structures. Also, experiments have shown
that each of these monomers will polymerize spontaneously to form
molecules of DNA, RNA and certain constituents of cell structures.
More recently, some people have suggested that life originated in
outer space. Experiments in radiation fields simulating outer space as
well as in actual fields of outer space, have produced a variety of
complex organics. In addition, other planets or planetary systems have
been suggested as sites for the origin of life. Possible signs of life
have been located in rocks from another planet. However, there is no
direct evidence that a life form arrived on, and was sustained on
Earth. An application of Occam's razor suggests that life originated
on Earth.
4.HOW
If modern chemists were given the tasks of making complex organic
molecules that would reproduce and of seeing to their continued
evolution, they might ask for the following.
- Their first requirement would be a chemical reactor with an aqueous
feed of a solution or entrainment of appropriate organic monomers.
- The reactor should have high pressures and temperatures to ensure
high chemical reaction rates, but not so high as to readily break down
desired reaction products.
- Catalysts for the reactor might be one or more of a wide variety of
sharply fractured crystals. The many crystalline minerals and
naturally occurring free metals could be candidates. The number of
possible catalysts becomes almost limitless if one is selected from
all those naturally occurring crystals with small quantities of one or
more naturally occurring impurities.
- The reactor's interior surfaces should be suitable for retaining
reaction products. Any of the naturally occurring crystals referred to
above are possible candidates to form retentive surfaces.
- Local flow-through rates should be slow enough that while some fresh
feedwater enters the immediate environs, reaction products are
retained and able to enter secondary reactions. Feed rates
considerably less than the diffusion rate may be required. Adhesion to
reactive surfaces may play a part in the retention of reaction
products.
- Oxygen and ultraviolet light would be restricted. Without the strict
controls inherent in modern cells for example, complex organic
compounds would soon oxidize or otherwise degrade.
- Significant but not excessive levels of ionizing radiation would be
advantageous to promote an ongoing cycle of breakup and recombination
of compounds to ensure a mutation rate of the reaction products and
their daughters.
- Sufficient time must be available to promote multiple generations of
polymerization and then the breakup and re-polymerization or
recombination of the organic compounds. Given enough time, these
compounds would move toward a state of equilibrium consisting of the
most chemically stable of all possible compounds.
5.WHERE
Sites for reactors which meet all of the above criteria are
subterranean crevices or passages in the Earth that are fed an aqueous
solution containing the required monomers and polymers and circulated
by differential geothermal heating. The monomers and polymers would
have been formed in the Earth's atmosphere and possibly in the oceans.
These reactors existed, and possibly still exist, at the intersections
of tectonic plates.
A reactor suitable for the formation of self-reproducing systems would
have been one with the optimum combination of a virtually limitless
number of temperatures, pressures, feed flow rates and velocities,
quite side chambers, mineralized walls and of different successive
arrangements of these and perhaps, other conditions. We can be certain
that the optimum conditions did exist for a significant period of time
and in one or more locations, at some time during the Earth's cooling
phase.
Therefore, I suggest an Earth bound origin for its life: of the Earth
and for the Earth's conditions.
These ideas are not inconsistent with Thomas Gold's suggestion that
hydrocarbons survived the conditions that pertained during the
formation of Earth and that they were entrapped deep in the Earth.
These, he suggests, have come up to form petroleum deposits and to
initiate life. However, I have assumed that the raw materials were
probably soluble in the feedwater. Soluble monomers may or may not
have been available in the primordial hydrocarbons proposed by Gold.
Whether petroleum was a feed material to, or a product from, these
reactors, or both, is a moot point.
6.PROCESS
We can assume that at least one reactor with optimum conditions
existed some time in the past and we can sketch the processes leading
to proto-life forms that it promoted.
The first stage was a process characterized by the formation of DNA
and RNA chains from the monomers contained in the feedflow. They could
have been formed spontaneously, with the aid of natural catalysts in
the reactor, or both.
Any significant self-reproducing system formed by these chains would
have been of second or higher order. That is, first order systems,
i.e. self-reproducing molecules, if such a thing is even possible,
would be a limited set and could not have played a significant role in
the evolution of life. A self-reproducing molecule must have an even
number of valences and be anti-symmetric about the centre. That is,
each positive valance on one side would have a corresponding negative
valence on the other side.
The formation of DNA and RNA chains probably would have taken place in
quiet side volumes, out of the main flow channels. In addition, the
reactive monomers and the resulting chains may have adhered to the
sides of the chamber. Thus, successive generations of reactions would
have taken place.
Since RNA can catalyse both DNA and RNA and since DNA can catalyse
both DNA and RNA, these reactions could have taken any one of many
possible paths. In fact, some of the reactions that are seen within
cells now, or similar reactions, may have developed.
Over time, with the breakdown and recombination of DNA and RNA chains,
the local composition would have moved toward an equilibrium state
consisting of the most stable chains. A chemically quiescent state, it
would have been determined by the composition and volume of the feed
flow and the parameters of the chamber and its state.
Since the most stable form of the DNA/RNA system is the DNA double
helix, these chains would have been a dominate component of any long
lived system. As the more stable DNA chains were selected and
re-selected, they would have separated into one or more distinct
subsystems that one could characterize as species of DNA/RNA.
Monomers other than the DNA and RNA bases, may have entered into these
reactions. In particular, other monomers may have formed an open
structure that brought the DNA and RNA chains into a coordinated
system. This could have enhanced the stability and the ease of
formation of a particular combination of DNA and RNA chains.
However, nothing described above would have changed the system from a
fundamentally chemical system in which chemical stability was the
controlling selection process. A change in the selection process must
occur for the system to become an evolutionary system as defined
above.
The second stage was characterized by the development of DNA/RNA
species with genes or perhaps some kind of proto-genes or other
specialized DNA or RNA base sequences. The result would have been a
population of still more complex individuals, consisting of a number
of species of either DNA chains or systems of DNA and RNA chains,
possibly incorporating other monomer components as well. Mutations
would have occurred due to ionizing radiation or other phenomena. The
breaking up and recombination of existing individual DNA/RNA chains
would have provided a mechanism for the interchange of DNA/RNA.
However, because stability is synonymous with simplicity, the
evolution of complex DNA/RNA systems would have been limited.
This was not an evolutionary system. The chemical stability of the
resulting DNA chains, the DNA/RNA system or the more complex
structures would have provided the only, unchanging criterion for the
selection process.
During the third stage, a new selection criterion or set of selection
criteria launched the system into new levels of complexity and made it
a truly evolutionary system. I suggest this new selection process was
an attack mechanism that broke up the chains of other DNA/RNA species
while recognising and not attacking its originating species. These
broken chains were used to enhance the productivity of the attacking
species. Thus, one species interacted with another to the advantage of
the one and to the disadvantage of the other.
First, since the DNA/RNA systems were supported by a limited feed
flow, the success of the attacking species of DNA/RNA would have been
enhanced dramatically. Second, the utilization of ready made, complex
organic compounds derived from other DNA/RNA systems made feasible the
evolution of much more complex systems since the added complexity
required a minimum expenditure of energy.
This attack mechanism could have been similar to one or more of the
many molecular processes in modern organisms. For example, modern
cells have attack mechanisms that break down other organisms and
molecules for food or, as immune mechanisms, destroy other organisms.
Further, it could have been similar to the enzymes in modern cells
that cut DNA and RNA into segments at specific locations.
In a different sense, this attack mechanism was a water shed. It
divided life into those organisms that derive sustenance from the raw
materials of their environment, i.e. plants, and those that break down
other organisms for sustenance, i.e. animals and fungi.
During the fourth stage, other species countered the attack mechanism
by evolving a coating that enclosed and protected the systems' DNA/RNA
and other components. Initially, the coating could not have enclosed
the structure completely. That would have both cut off the DNA/RNA
system from its source of raw materials and obstructed the rejection
of waste materials. Further steps were required to evolve features
such as receptor systems and eventually, a prokaryotic cell. Once
enclosed as a cell or a proto-cell, one or more DNA/RNA species could
have escaped the protected environment of its crevice and survived in
the oceans.
Evidence of the evolutionary paths followed by these systems must be
preserved in the genetics and the biochemistry of modern cells. For
example, if plants and animals separated at this early stage, their
characteristic cell walls should be fundamentally different. Cell
walls characteristic of animals and fungi may be more closely related
because they share the trait of deriving sustenance from other cells.
Also, genetic evidence indicates fungi are more closely related to
animals than to plants.
During the fifth stage, eukaryotic cells evolved. This could have
occurred in either the protected crevices, in the open ocean or even
in another environment.
Attacks by some newly evolved organisms may have been prompted by
structures consisting of DNA/RNA and other monomers, which had evolved
in vulnerable places on the exterior of prokaryotic cells. A second
coating evolved to provide a defence for these structures. However,
the second layer may have evolved simply as a defence against these
new attack mechanisms.
In any case, this second protective layer fostered the evolution of
more complex interior structures as well as more complex internal
processes. That is, the second cell wall was profitable as a defensive
mechanism and as an enclosure for a more complex cell that made
possible the complexities of modern life.
Thus, the system consisting of DNA/RNA species, passed from a chemical
system to an evolutionary system and then to cellular ecosystems:
first to a system of DNA/RNA species with attack and defence
mechanisms, to systems of prokaryotic cells and then eventually to
eukaryotic cells.
7.SUPPORTING EVIDENCE
Of course, we are not going to find a smoking gun proving these
hypothesises. However, some facts are very suggestive.
- Bacteria have been found at depths of several kilometres, at high
temperatures and in a variety of rock formations.
- Unexplained quantities of free gas and vapours have been found in
apparently solid rock at extreme depths.
- Bacteria and fungi exist that live in anaerobic conditions and
others that can live in either an aerobic condition or an anaerobic
condition.
- Bacteria, whose life cycle is based on sulphur, are emitted from
high temperature, high pressure "smokers" at the bottom of the ocean
near the boundaries of certain tectonic plates, in Juan de Fuca Strait
for example.
- Bacteria have been identified which excrete an acid that dissolves
some rocks.
- Petroleum and natural gas are found at the intersections of tectonic
plates. The oil and gas have seeped up from great depths over
geological time and accumulated in domed rock formations. They could
be the fossilized or otherwise modified remains, in whole or in part,
of a variety of products from these subterranean reactors, from
proto-life forms and, probably, higher life forms that have evolved at
great depths as well as just similar complex organic compounds. After
all, any process sufficiently complex and extensive to have created
the basis of life, must have left some fossilized remains. Even now,
these subterranean reactors may be functioning.
- Bacteria exist that appear to thrive by consuming petroleum. This
may indicate a common evolutionary link between the two. Some bacteria
found at great depths may be the most efficient species for such
tasks.
.
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