|This is a hypertext file from Rae West's archives. It is not his work and is reproduced here, unedited, so readers may judge for themselves the views expressed in this file when it was freely available on Internet.|
Christian Schwabe, Ph.D.
Department of Biochemistry and Molecular Biology
Medical University of South Carolina
171 Ashley Avenue
Charleston, SC 29425
Darwin wrote the theory about men, beasts, plants, and microbes, the latest revision of which is referred to as the new synthesis or neo-Darwinism and includes a new discipline called molecular evolution. Contrary to what it appears to do, the Darwinian model tells us nothing about causes but rather about possible avenues of evolution, overtly excluding all metaphysical arguments except chance. Is it possible to devellop models that can bring us closer to causality, i.e., that better fit the one and only set of data in our possession and at the same time push metaphysical claims naturally back to the beginn of the universe?
Conventionally evolution is supposed to walk us up a gentle slope from chemistry through simple life to complexity. This is the way man (with few exceptions) likes hypotheses about himself -- natura non facit saltum. Bacteria would agree for they have looked like they do today at the moment of their first appearance. How unchanging must these organisms be to remain recognizable on 3.5 billion year old "pictures." This most astounding observation is made so often in the history of life that one may presume it to be the rule and not the exception, nature does not move in jumps!? But there are other forms of life and stability is documented in their records as well. Jelly fish, horseshoe crabs, and coelacanths are only a few examples from the Paleozoic and there are more in the Mesozoic and the Cenozoic. How did we get to them, that is the supreme problem. The Cenozoic produced giraffide, one short-necked (okapi) and one long-necked (giraffe) and both still exist. But none of the "half-way" giraffes can be seen among extinct or extant animals. These are the seeds for new ideas; as concerns evolution, it seems that nature does everything in one jump!
One does not see the developmental stages upon which Darwin built his hypothesis. He spoke of "unimaginable numbers of intermediates" and continued "- but assuredly if this theory be true such have lived upon the earth". A clear and strong prediction that has inspired many a field trip and many experiments but about 150 years of intense search have not brought to light continuity, have not confirmed Darwins postulate. This has not gone totally unnoticed and consequently a group of biologists ( ) proposed a compromise called punctuated equilibrium which replaced the continuous slope of evolution with a staircase model. Even so the model retains all the Darwinian essentials this little concession to reality attracted a lot of hostillity from the mainstream who refered to it maliciously as evolution by jerks.
A drastically new idea called the genomic potential hypothesis has been built which could have just as well be (3) called the chemical potential hypothesis. The model combines the discontinuity of the fossil record and the stability of life forms with the pattern of incessant extinction. Nature, it contents allows only one jump, from the quasi ovum to the finished taxon, be it bacteria, arthropods, fishes or mammals , one jump for each genus* followed by only minor embellishments never to allow one genus to change into another. That is all available evidence tells us and in light of such clear singnals darwinism becomes one of the most remarkable and mysteriously enduring errors in science. The 21st century is lighting our horizon, bringing with it an irrational element of hope that such a symbolic change may bode well for the innovators and challengers and there effort to make space for new concepts in the minds of man.
Conceptual Limitations of Biogenesis.
Biogenesis has been a major battleground for science and religion and it may remain just that for the science of the 19th/20th century and of the centuries to come unless one can divert the debate from polemics back to the scientific fundamentalism that is embodied in epistemology. What can be known, what constitutes evidence, and what are truly dependend variables? These are the questions from which our conceptual limitations derive.
The fulminating growth of the old paradigm has burried the fundamental guidlines of science under political correctness and technological expedience. Upon re-examination of the phenomena of biochemical evolution in the light of scientific fundamentalism the Genomic Potitial Hypthesis ( ) hypothesis was developed beginning about 20 years ago.
The mayor difference between the new Idea and the old one is in the beginning. The outcome of a synthesis of the origin of life scenario is extremely sensitive to whatever initial assumptions are adopted. About 500 million years after the earth had cooled to moderate temperatures bacteria, in particular the blue green algae, looked already like they do today ( Fig 1 ). This observation is incompatible with the old idea where everything is in continual mutational flux. Evidence has reset the limits of speculation!
Chance which is, by its very nature, all-inclusive (luck, miracles, God and so on) is a most awkward ingredient of the old synthesis were it takes the form of directional mutational activity. Experimenters who measure the extent to which certain conditions favor a deviation from apparently random behavior are actually observing the effects of structure and not luck. Reactivity then becomes a function of the structure, the bonding angles, bond strengths and other thermodynamic properties of the molecules. Under conditions C the products will end up somewhere on the surface of chaotic attractor C(x) and no where else.This concept was demonstrated when Miller and Urey did their now famous experiment with primordial gases, which upon activation yielded a high percentage of biologically important compounds (2). One must imagine distributions of compounds on early earth to react to the constantly changing conditions until the last sets of normal distributions of molecules with certain qualities (Fig. 2) will have reached the point where very large numbers of living systems will arise within a few million years which then live by the same necessary maintenance functions (protein code, central nucleic acid memory ect.) but are shaped by different nuclear organizations.
Biology is a special case of non-equilibrium chemistry. Entropy may be imagined as a tightrope upon which life has to ballance. Furthermore every scenario of the origins has to consider getting onto the "entropy wire", i.e., the assembly of a living system as an all-or-none problem that must be solved in a split second. A great deal of effort has been applied to this problem but most of it has been boxed in by intuition and common sense, the human"s pride and joy which has suffered so badly in the world of physics. A revival of Henry Huxly"s primordial panprotoplasmatic medium in a modern form as part of the genomic potential hypothesis best fulfills all these requirements. In this model all the processes that are now uniform in living systems would have developed under the rules of inanimate equilibrium chemistry. Intuition in contrast will not allow uniformity in global chemical systems but nucleic acids do! To reiterate, the genetic code is uniform not because of a unique origin but rather because all the chemical reactions in many biogenic bodies of water were very similar; they were guided by nucleic acids in one form or another. There are other systems that will reproduce identically in widely separated places such as mineral crystals and, although slightly different crystal forms are produced under different conditions, none of them can compare in variety with what is produced by nucleic acids.
Functional nucleic acids came into existance by means of its limited catalytic capacity of oligo nucleotides. Strings of nucleotides would inevitably lead to catalytic units and these in turn would, through complementarity, bias the organic pool composition toward catalytic structures. By direct interaction amino acids would become part of the process until both, nucleic acid chemistry and protein assembly and lipid synthesis would run side by side. Cells were produced by acellular processes from aggregates, which were assembled somewhat like the liberty ships during the last war. If units were missing essential functions their osmotically active membrane would have ruptured again and the components would have become available to other incomplete units. This scenario predicts a very large number of variable origins.
Because of energy requirements, the final steps in cell formation had to have happend within the time frame of minutes or seconds. Is intuition fooling us again or s there any evidence?
There are hints and the argument goes as follows: Many if not all of the activities in a living cell today are associated with subcellular particles or sructures that can be isolated and recovered by differential centrifugation. Nuclei, mitochondria, microsomes, lysosomes, and ribosomes to name a few. The cell is not a bag of enzymes and also not a passive sphere. Lipids that make the membrane bulk also shape the intracellular particles which retain biological activity for a long time after isolation. Suspensions of mitochrondia will respire in vitro and nuclear material will produce proteins in isolation under the proper conditions. Some of the structures remained independent (mitochondria) others which were anchored in some nucleic acid sequence already at the precellular time gave up independence and fused with other particles to create an instant central memory repository. A diagrammatic display of these steps is shown in Figure 3. The structure of a modern cell and the principles of chemistry and biology leave us with general instructions for cell formation, though not with a blueprint.
Biogenesis happened within these restrictions and this is as close as we will ever come to understanding the origins of life. There are many details to be settled such as the abiotic polymerization of nucleotides, the catalytic roles of RNA, the mechanism of the change-over to DNA; it is altogether a wide field for experimentation. Only if one assumes redundancy reiteration and complementarity to have produced the genome; will such experiments make sense. Variety is the result of primordial chemistry and is a non-renewable resource which diminishes constantly during biological processes. The genomic potential hypothesis of evolution makes clear-cut predictions which are confirmed daily. Variety disappears at a fast rate and all that speciation ever amounts to is a different pigment, a shorter appendix or fewer toes -- but nothing like the revival of a gene pool that has lost its variety. When speciations in prehistoric times are mentioned as they often are, one is realy refering to the appearance of subforms without knowing where they came from; we only know that there is no evidence for what is religiously granted,i.e., the slow conversion from one form to another.
In the new model all the variety that comes on stage during the past 500 million years is an expression of latend properties of quasi ova as they come to fruition at different times after 3 billion years of devellopment. If the genomic potential idea is correct -- redundancy but not continuity will be seen in the fossil record and in protein structures.
Reading Across the Milky Way.
How much information it takes to make humans, all of them and all of life? That is an important question to answer for a counter proposal to the old model which produces variety as it evolves species. For the new hypothesis to be viable one needs consider concepts that that have rarely been acknowledged. Here they are.
The genomic potential hypothesis maintains that all the information ever available to living systems was produced in the primordial pool. The problem of abiotic nucleotide polymerization aside (it is part of every evolutionary hypothesis) the question would be whether or not it would be reasonable to postulate nearly infinite masses of information to be available at the origins? In that case subsequent evolution would amount to no more than a reorganization of genomic material (potential) and the development of genomic control mechanisms.
One mole of nucleotides contains 6 x 1023 molecules, weighs approximately 250 to 300 gram, and is enough to code for about 1014 human germlines. In fact 104 moles (1.5 tons) in many biogenic puddles all over the earth would be a minuscule number indeed as compared to about 500 million tons of nitrogen falling to the surface of the earth every year. Yet 104 moles would carry the string of DNA made from it clear across the Milky Way (Fig 5). Every species extinct and extant over and over again could be produced from that information if only 0.1% of it would be translatable into the protein language.
The enormous redundancy and near identity to be expected from a polymer that is assembled by the complementarity concept defies chance; complementarity is loading the dice. Any mixture of nucleotides would most likely produce the same type of life on any other planet situated near a star as the earth is to the sun. This is the reason for our expectation to find life like ours on other planets.
In the genomic potential hypothesis the origins of life and the origins of species are simultaneous events. They are causally connected and contiguous as required. In the Hadean rocks we see only microorganisms, albeit at least 300 different species, but fossils do not show the genomic potential of each of these organisms. Whatever modification chemistry subsequently affected on these genomes was dictated by their original configuration involving well-understood processes such as hairpin, lariat, and even tertiary structure formation, shifting of genomic materials from one site to another, (as opposed to changing it, i.e., evolving) and so on. The environment for all of these origins was by and large the same but not the genome, and the sensitive dependence upon the initial configuration dictated different future developments and not the environments.Origins therefore have world lines that are continous each with an extant life form (Fig 6).
There is another astoundingly simple aspect to the story, namely that all the nucleic acid strands produced were senseless in the true meaning of the word. They contained a latent potential code but at the moment of polymerization it would not have developed directionally as regards survivability or any other Darwinian property simply because there was no measure of success at this stage. The sense that we detect in these messages in retrospect could only be deciphered after the reading device had developed by chemical physical necessity. Three residues are recognized in the nucleic acids because a simple stabilized structure suited to read the binary code of the nucleic acid chains assumed a hairpin configuration. Such a structure typically has three residues projected outwards from the hairpin which could easily interact with an external target. There are many plausible scenarios for the self-assembly of such "readers" in the literature, but the point to be made again is that the code-reader is without possible design goal, without a feedback possibility guided by some ever so minuscule purpose. This is a good example of a process that appears random when viewed from the vantage point of its ultimate function, yet at the level of reactivity the chemistry is restricted by the boundary of thermodynamics and kinetics. Furthermore, there is no obvious relation between the amino acid that is later found on the 3' end of the reader (tRNA) on one hand, and the triple codon on the other. It is reasonable to propose that if the codon for each amino acid would have been different, proteins would still have appeared as functional units. They would look a little different and arise from different regions of the genome, but considering the astronomical size of the primeval information reservoir man might have resulted all the same. Since the soluble RNA in the codon development scenario is also read off some templates it is possible that any shift would have been uniformly transmitted to every coding level so that the code we have is the inevitable consequence of nucleic acid structure. The reader will be struck by the similarity to a "Turing Machine", a hypothetical reading device that produces messages from endless strings of 0"s and 1"s. These thought would make one predict that any as yet undiscovered earth-like planet would harbor biological complexity proportional to the mass of genomic material present at life"s inception.
What would place certain amino acids at the end of certain tRNAs and not others? One plausible answer to that question is depicted in Figure 7. It has been shown that RNA can form cavities which will specifically bind mainly one amino acid of one absolute configuration such as L-alanine, L-leucine or L-isoleucine. The grove will recognize one specific side chain but the carboxyl group sticks out into the water ready to react with the 3' end of a putative tRNA. Any hairpin-like DNA can interact with the carrier only if two recognition sites match up. One at the major bend which makes codon assignments and one in the neck portion that orients the tRNA such that bond formation between the sugar alcohol group and the carboxyl group of the bound amino acid is possible. Clearly there is a structural basis for specific aminoacylation but it is recorded in a type of nucleotide language that we do not understand.
THE GREAT DIVIDE, MULTICELLULARITY
Fossils do suggest that the threshold to multicellularity was crossed not like a trickle from one source but like a tidal wave that extended from what became the Canadian northwest to the eastern reaches of China, and the Chinese fossils match those of the Burgess shale in quality, quantity, and most remarkably in kind. The argument that all 30some major forms of 120 genera came from one origin within the time between the Tomotian and the mid-Cambrian and still had time to spread across the world is hard to defend; yet such views are common.
It seems far more likely that the transition was not A (single) to B (multi) followed by divergence of the offspring of B but rather (A1,A2,A3,---An) single cells transformed to (B1,B2,B3---Bn) multicellular organisms (Fig. 6). Although the fossil record is unmistakable on this point the lack of intermediates is notably not seen as evidence for the multiple origins scenario but rather as proof for the incompleteness of the fossil record.
The genomic potential view shown in Figure 6 provides independend world lines for each origin. Now the sequence of appearance of taxa in the fossil record does not indicate branching points but the time of the metamorphic phase transition, the change of cells into organisms. The phase transition shown as a irregular cone is a non-linear function af time.
The single cell transition to multicellularity must have occurred because below one geological horizon there are no macroorganisms and in the layer above they are abundant. Sudden and multitudenous are the hallmarks of this transition. Was it one type of cells producing trilobites and variants (trilobitoforms) via a direct oviparous route while other cell groups produced anilids and so on or were there cell colonies fusing nuclear material to give rise to organisms which then, like larvae, were feeding, moving eggs of yet another form. Both types of propagation which are still in use by many successful species, notably insects, may have been a once in a lineage affair for all other taxa (homo included). Once the research community has accepted that intermediates at the macroscopic level are not there the search might begin for the ovi-forms of species. The metamorphic schemes of nature tell how it is that animals can appear sudden and complete without providing an obvious fossil record of the process.
If the abrupt appearance of taxa is troublesome for the darwinian model, the shear volume of forms surfacing at once is intolerable for the Darwinian picture. Beginning with one organism (as they do) the transition to multicellularity would follow a simple arithmetic series , i.e., 1, 2, 4, 8, 16, 32, 64, 128 and so on. If, as generally assumed, 10 million years will be required to produce a new species then only about 32 new species could be expected from the middle to the end of the Cambrian, provided that every transition was a success. The symbol for this type of growth is a tree, i.e., a slow start followed by major branches and bursting into near infinity as the crown fills out. The prediction made from such a model is that variety is most abundant at present and that variability tends toward infinity which is simply not true.
In the genomic potential hypothesis scenario it is the egg that evolves to the point where it gives rise in a very rapid succession to the final organismic form which suddenly then appears in the fossil record and usually does not change for as long as it can be recognized. This concept can be read from the fossil record directly. Failure to master the surrounding, it says, leads to extinction not adaptation; the absence of intermediates would therefore be a major postulate of the genomic potential hypothesis (Fig 6).
In the new transitions from micro to foci of macroorganisms occurred sequentially during different periods beginning in the Ediacaran and Cambrian periods and continuing as a trickle with a few spurts interspersed up to the Pleistocene all the while mimicking speciation. If a billion billion, i.e., 1018 cells would give rise to only 108 organisms, could anyone reasonably expect those organisms to arrive at the multicellular state in the same instance in the mid-Cambrian period? Assuming that the the ripening of such quasi ova would be spread over about 10% of the 3.5 billion years then the process of development of animals could have lasted from the Cambrian to the Tertiary period. Next one may relate the time of appearance to the degree of complexity of organisms and realize that the simple organisms came first and the most complex ones last. When the last ones appeared they did so because of structural (genomic) necessity not because of any experience gleaned from an underprivileged predecessor or because of selection and adaptation.
The complexity of the finished organism is paralleled by the complexity of its ova and the timing of evolution may be loosely related to quantum phenomena, i.e., may be an all or none concept. The number of factors that need to come together to form a human or an annelid are significantly different and the point may be illustrated by assuming that a certain set of genomic elements would have to occur in pairs in order to be potentially viable.. Thus the chain of AAA and B would not start an organism until a second set of the same group has been accumulated. For example, A2 five times and one B2 may make a frog and A2, B2, C2, D2, E2, F2 -- N2 makes a human being. Conversely, the same string of factors except with an unpaired one, i.e., an E instead of E2, would make nothing until the series is complete. A practical mind would perceive the need for an even number of factors as a symmetry requirement. It is clear that a long string of characteristics A2, B2,C2--N2 takes longer to fill up its "symmetry orbitals" than a shorter one and hence the inverse relationship of the length of the fossil and the relative complexity of the phenotype. Humans have the shortest fossil record because their quasi ova took longest to develop as it should be if indeed it was the egg that evolved and not the organism. It is equally possible that different types of complexity could develop if one lets the subscripts represent different symmetry parameters. Most vertebrates have only a twofold symmetry, i.e., left-right. This symmetry is partially broken as in the case of some internal organs but not others. A series of many letters A,B,C,...-N would determine complexity and the subscript symmetry. For example A2 or A2B2 would be simple bilateral forms and A2 . . . . . N2 complex ones. High subscript numbers (symmetry parameters) i.e., A3,4,5, n would give rise to a multisymmetric body (some sclerodermata) but to fill so many symmetry orbitals for a long string of complexity letters (A,B,C,D, - N), such as mammals, was not possible even in 3.5 billion years of genomic evolution and hence four legs is the limit for large animals and therefore no six-armed Shiva is seen among humans even though this would still be bilaterally symmetrical. Multiple appendices are essentially limited to insects and arthropods and multidimensionally symmetrical animals are less complex yet (sea star). These ideas are in principle testable. Science is not yet at that level of technical advance but in 10 years we might have a better chance. After all, theories are built for the future.
ON THE BALANCE --- .
On the balance it was the egg that evolved and evolution as generally percieved may not have occurred.
Ready to brave space-time unity, time dilation, curved space, black holes, red giants and quantum uncertenties? Please do not forget to bring along evolutionary concepts in a form that can exist in a world that physics has unlocked for us. It is the major hypothesis of life and far more complex than hypotheses about inanimate nature because it is the branch that has assembled what is known about our universe. Einstein, Plank, Heissenberg, Weinberg and Hawkins all have been produced by biochemical phenomena, hammered out by a Turing machine that runs on the endless and eminently variable tape of four different bases and is ruled by the energy-selective, structure guided chemistry that is so well known to us. Perhaps this authors view has not been and will not be popular for a while but then, science is not democratic.
Conceptually evolution has become a little more dificult in the genomic potential hypothesis, just complex enough to be able to account for life"s complexity. The newer concepts of deterministic chaos in chemistry, leading to billions of ova which develop in step like ballet dancers jumping onto the stage in large numbers at certain intervals, all dressed differently, dancing as long as they last, to be replaced not by offspring but newly hatched creatures until the last pulse gives way to silence; these are uncomfortable ideas that will spread only when all else fails. But they are closer to the evidence, they may also be closer to reality. The larger question whether our brain can still develop enough to recognize objective reality in a world largely of it's own making may never be answered, but if it were somehow read from the face of nature science will have been holding the candle.
Figure 1. Cyanobacteria (blue green algae )
shown at three different stages of evolution.
Figure 2. This illustration is meant to depict the massive movement of chemical reactions toward the threshhold of life and to transmit the impression of the chemical pressure that would propel the last cycle of eqilibrium chemistry into the roam of non-eqilibrium systems of life. Each wave of normal distributions of chemicals gives rise to a new ,more complex one under the influence of directionally changing conditions (dc) as a function of time (dt). Chemistry may have been driven as in a zone melting process by the uniqe conditions on the early earth.
Figure 3. The reader is asked to imagine a cubic micron of a primordial pool during biogenesis . DNA/RNA particles gave rise to synthetic reactions while continuously releasing products and utilizing what fits the chemistry of this catalytical particle. Complexity increases by fusion and when cells ultimately appeared they all had different information cores but used the same basic reaction through which they communicated (chemically) during the formative period.This panorama may help the reader to free himself from the notion of a single origin.
Figure 4. A chaotic attractor is superimposed upon a powerful wave which displays all the features of a R"ssler band.The chaotic (unpredictable) but generally directional power symbolizes the biogenic process as it is perceived within the genomic potential hypothesis and should be viewed in contrast to the uncertainty of a chance process in the Darwinian model.
Figure 5.Reading across the Milky Way dramatizes the potential information contained in nucleic acids.When galaxies are measured in molecular dimensions the most astaunding realization is that about 1.5 tons (104 moles) of nucleotides, when strung end to end, will reach from one edge of our galaxy to the other, bridging about 100 000 light years. This illustration brings to mind how much "information" in form of nucleic acid sequences may have been synthesized abiotically during primordial times. The assumption of 1,5 tons of nucleic acid is fairly conservative considering that abaut 500 million tons of N2 arrive on the earth surface every year. With so much potential information available at the begin of life mutations and gene duplications in biological systems would pale to insignificance as biodiversifiers.The origin of diversity may instead be found in reiterative repetitiousness of nucleotide chemistry.
Figure 6. The cone of contiguity of life and taxa. The enlarged section that depicts the panprotoplasmatic pool at the origins of life reveals many biogenic puddels in which mayor forms of life are rooted. Eminating from the origins the worldlines of the various major forms of life reach the macroorganismic interface either early (trilobites), half way up (saurians), or near the end like mammals ; Homo sapiens taking the longest time to appear.
Figure 7. Hypothetical events for the fixation of the genetic code.Direct binding of L-amino acids in pockets formed by RNA coils and the juxtapositioning of tRNA are shown together with an abiotically produced coupling agent (a carbodiimide).
Figure 8. In this figure the age of the universe is shown in relation to the age of the earth ,life on earth, and the beginning of multicellularity. According to the Neo-Darwinian proposal the reader is asked to imagine that multicellularity should have started at a spot on this graph that is much narrower than the line pointing to the Cambrian period which is on this scale about 10 million years wide.
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