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Madame Curie Bioscience Database [Internet]. Austin (TX): Landes Bioscience; 2000-2013.

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The Condensation of Life

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The course of biogenesis was carved into molecular structures by the events of the primeval initiation of our universe. The speed at which pure energy segregated into baryonic matter leads one to think that there was no other possibility. (Physicists quipped that God may not have had a choice in the matter). The Genomic Potential Hypothesis extends this inevitability concept into the biogenic events and, the speed at which life assembled itself from molecules immediately (by geological standards) after the earth had become stable enough for chemical processes, certainly invites the conclusion that luck had no part in this matter either.

Darwinians view the origin of life as a lucky strike.1,2 Chance events, however, are irreducible and irreproducible so that comparison between the old and the new model becomes possible only from the moment when life had been established. Of course, every one invokes chemistry when it comes to the origin of life but for chemistry the ‘single’ is out of character. Nonetheless, the consequences of any origin of life scenario should be expressed in the fossil record and this is the part where comparison of models becomes possible. In as much as the Darwinists deal with the topic of this chapter with one word (chance), the Genomic Potential Hypothesis is alone in its effort to build a conceptual basis for biogenesis.

In the new hypothesis biogenesis is a series of processes that must be justified by the basic rules of the relevant scientific discipline, chemistry, and must lead to verifiable predictions. The genomist predicts that innumerable origins evolved at many places on earth and that chemistry was the rectifier that caused uniformity at basic levels of biochemistry up to and including the genomic code. Thus, it is the burden of the genomist to replace the chance events of the old model with a series of principally known reactions of predictable consequences.

Every component for cell assembly has to be there in large numbers at many places and functional when the individual units slide into the state of life. These ‘multi-origin’ ideas have been around3–6 but did not fall on fertile ground, and what remained of these mavericks' polyphyletic thoughts was wiped out by the discovery of the universality of the genetic code and the erroneous conclusions drawn from that observation.

We know with certainty that life condensed around nucleic acids because only nucleic acid remembers and transmits. Proteins are unstable and while they carry a lot of information, they do not reproduce. Only when the nucleic acid persisted from which proteins were made continuously could they become a factor in the equation of biogenesis. The nucleic acid buildup happened of necessity without a guide other than molecular properties and without a target.

The composition of nucleotide polymers at any locale depended upon the relative concentration of the nucleosides G, C, A or T, in the medium and may have varied as a function of time, ionic environment and other factors. The first chains that polymerized without a template produced variety whereas subsequently chains were duplicated more or less accurately by complementarity, and that process gave rise to families of nucleic acid polymers that formed the basis for similarity (clones) and diversity among organisms (Chapter 4).

Concepts of the ascent to life must follow a plausible path that will lead to a point where experimental verification becomes a prospect. Experience from the laboratory tells us that some of the key preparatory steps that involve nucleic acid and proteins do not require enclosure into cells in order to function. In fact, it was imperative for the biogenic process that the most important constituents of life could be produced by equilibrium chemistry, nudged on by reducing conditions and diffuse energy up to the moment when enclosure could be successful. Template-directed in vitro protein synthesis is quite well known to us and it seems reasonable that without an equivalent process in geo the primordial scene would not have worked. Cells must function in the moment they form and not a minute later. Heterogeneous reaction centers, the primordial aggregates composed of nucleic acids and the first few proteins produced by them, did not live but could persist, jump-skipping through their small puddle, until they met a complementary unit, one that had useful energy as an end product. These units were numerous in small volumes of liquid where they had been produced by mass-action from the same concentrated mixture of molecules. One must picture this process as one that provides a stage for many thousand years of progress and retreat, interspersed off and on by a success, i.e., a living unit produced in a few seconds. A few million years past the end of such a biogenic period an abundance of imprints of different fossilized cells should be visible in the Archean rocks and that appears to be true.7

Polymerization of nucleotides is an imperative for the story to come off. Clearly, catalysis by proteinaceous enzymes is a higher level complexity that had to await completion of the nucleic acid polymers. The recent discovery of nucleic acid catalysis has built a bridge between the nucleic acid and the protein world8 and simultaneously cracked open the door to the multiple origin world. Nucleic acid catalysts were not as versatile and efficient as proteineaceous ones, but catalysts nonetheless.

The most important postulate of the Genomic Potential Hypothesis is that life was an inevitable consequence of the structure-energy manifest in atoms and molecules. Thus we have to address the question as to how one would build up something similar in different places when the nature of the product becomes apparent only many steps later? Obviously, words like goals or adaptation have no meaning in this setting. It would have happened only if there were limited possibilities, if energy and kinetics favored a set of reactions. Since the potential memory everywhere reads [(A)x (T)x (C)y (G)y], the nucleic acids in widely separated origins cannot look much different. But this “memory bank ”, why was it so important for the progression of biogenesis? Because complex structures, other than the memory itself, that have not been read from the surface of a nucleic acid, cannot evolve. A chance assembly of amino acids, for example, will soon be lost when thermal motion has shaken it apart.

The message for assembling life in three dimensions is two-dimensional, meaning that the information it contains is sequence-dependent, and since the nucleic acid polymers in all primordial reactors would have different sequences the new model would lead to an infinite number of different life-forms. Within each pool, however, there would be important equalizing factors that would cause main themes and variants to arise from each biogenic center (which may have been as small as a liter). Once primary strands had self-assembled, complementary strands would be produced faster than new primary ones, so that themes (primary strand copies) and variations (more or less accurately copied secondary and subsequent strands) could, for example, account for the variations that caused us to group species as families and super-families. That would put local order into potential chaos and would cause a viable mass of like organisms to occur and give each future species a reasonable base (number of members) for survival.

Global order is produced by the fact that life per se has a set of requirements such as energy, reproduction, and gas exchange that must be met regardless of the phenotype that a genome might produce, such as a worm, an insect, a mammal or a bird. From all the possible genomic forms only those succeeded that fulfilled these requirements and so it happens that a great deal of similarity is observed among the catalysts of similar reactions in each life-form. The bacterial protein synthesizing machinery, for example, will work in mammalian systems, and hormones from tunicates and salmon perform specific functions in humans.

The crucial event for a multiple origin paradigm is the development of the genetic code. The only acceptable path to a genetic code for any model of evolution is via a structure/function relation between the main actors of the scene, i. e., nucleic acids and amino acids. RNA chains of varying lengths might have interacted with the free amino acids that were produced by primordial conditions and a cavity of sequence-dependent geometry could have been formed by the coiled-up RNA into which an amino acid side chain of L-configuration would fit.9–12 These attempts to find evidence were not totally successful, possibly perhaps because the code-producing nucleic acid/amino acid match might involve more layers of interaction. The problem is delineated in Fig. 1, which shows a conceptual view of selection and activation conditions.

Figure 1. This is a structure-based proposal as to how the genetic code might have developed.

Figure 1

This is a structure-based proposal as to how the genetic code might have developed. It is hypothesized that the future coding region is in contact with the amino acids during the binding phase and folds away to interact specifically with the future tRNA. (more...)

The recognition region, folded away from the amino acid in the drawing, is shown in juxtaposition to the anticodon region of the tRNA. The major interaction may be between the loops of the RNA and the amino acids which, on account of their specific side-chains, may prevent or allow binding of another RNA and thus provide a selection mechanism. Only a properly binding RNA would bring the terminal alcohol group into proximity to form an ester catalyzed by an activating group (a di-imide for example). The selecting feature could be the region that we now call codon and that would, depending upon the amino acid bound in the RNA loop, allow or prevent binding to the hypothetical transfer RNA. Presently, the cavity-forming RNA is replaced by aminoacyl-tRNA-synthetases which seem to occur in large numbers in the genomes of all organisms.13

Nothing described so far could persuade one to exempt the code-developing process from the common mass-action ways of chemistry. Consider, for example, that the code, which is collectively referred to as unique, actually consists of 20-some genetic codes, one or more for each amino acid. Twenty times at least did this series of complex reactions occur and all were alike in concept but specific in detail such as to distinguish between differences as small as between the side-chains of alanine and valine and as large as the difference between glycine and methionine or tryptophan. Fitting complex amino acid side-chains (methionine and tryoptophan) would be more demanding so that one should expect less ambiguity in their codons. The original RNA binding loop postulated in Fig. 1 may have been specific only for L-configuration of the N-Ca-Ccarbonyl group, which is uniform in all protein amino acids (except glycine), whereas the RNA tail controlled the side-chain fit and thus the codon-specific interactions.

The code selection, a series of events that is cited as an irrefutable reason for a single origin for all species, happened at least 20 times! In the mind of a genomist, twenty repeats of a series of complex reactions, leading to the activation of 20 L-amino acids, means that there have been very strong determinants. Code development happened before cell formation was complete because cells need proteins. Could one imagine that one aggregate of RNA/DNA would develop a code for 20 amino acids while the neighboring clones produced none? Of course not, but plausibility is of limited help in a decision-making process in science. Beyond likelihood we must recognize that, save the reaction of oxygen and hydrogen, chemistry is not that sharply limited, certainly not in primordial bio-reactors. For distributions of products to be limited to one bio-reactor, the energy (entropy) of the system would have to have been prohibitive as compared to the surrounding; it would be at the level of supernatural!

But would all codes have to be alike in all developing units of life to produce a fauna and flora as observed today? Of course not, as long as a protein is made of L-amino acids the feeding process would be undisturbed. Life as a global phenomenon would have functioned perfectly well if every species had its own code for producing proteins.

The actual code development must be viewed as a process, quite apart from, and independent of the accumulation of genomic material. The crucial event in code development is the direct or indirect interaction (Fig. 1) that ends with the covalent linkage of an amino acid with a very limited set of transfer molecules, all of which carry amino acid-specific triplets of ribonucleotides, called the anti-codons, at the tip of a hairpin turn. This is the beginning and the end of the codon selection process; it is all there is to it. The term anti-codon is not strictly correct because DNA (or the corresponding RNA transcripts) contains no codons. It is merely a string of deoxyribonucleotide phosphates whereas the genetic structure one refers to routinely is brought to life by the tRNA, which divides the string into three's, and by the ribosome, which stabilizes only one incoming tRNA at a time. Signals for start and stop of proteins are merely inconspicuous parts of a monotonous polymer until they are converted by recognition factors (feed-back proteins) to vital signals in a humming center of growth, control and maintenance, of an organism. The sequence of the DNA determines the organism; tRNA and ribosomes validate and translate the information. Thus, a string of nucleotides such as AUUACACCGAACAAA reads nothing but when the codon adds punctuation, three at a time, i.e., AUU ACA CCG AAC AAA then the sequence reads Ile-Thr-Pro-Asn-Lys, which is a defined string of amino acids. A human genome read by the ribosomes, tRNA et cetera from Bovidae would produce a human whereas a bovine genome read by the human translation machinery would produce a cow. That is what is meant when one refers to universality of basic constructs in life. It also vividly illustrates the high degree of independence of the coding process from the information carrier, the genome.

To explain the L-amino acid preponderance, which enters into the code production, processes such as parity violation at the level of electro-weak forces14 have been considered. That proposal is likely not correct because the signal is too weak and because selectivity based upon atomic properties seems to be important, rather than quantities. Carbon was not the most prominent element on earth by far when life assembled itself from carbon rather then silicon.

The role of the initial binding RNA in Fig. 1 is now fulfilled by aminoacyl-synthetases which were selected from a number of proteins of suitable activity. An inordinately large number of this type of structural motif is found in different genes which supports the basic concept of function selection as opposed to the development of function by targeted mutations.

The genomic DNA is of necessity without design. All of the information contained within the strand in form of sequence variability comes to light through the code. One could state that the nearly limitless potential information hidden in the tons of nucleic acid of the DNA or RNA type, regardless of which code would be adapted, would inevitably lead to all the life forms on earth. The total variety of life forms on a particular planet under proper biogenesis conditions becomes a function of the total amount and variability of nucleic acids available. That gives us a bio-potential theorem worthy of the new millennium.

Whatever the outcome, we can rest assured that a physical contact type selection (chemistry) has led to the genomic code because it is, with insignificant variations, the only code possible. Life anywhere in this universe will be C, H, N, O-based, and the genetic code will be found to be the same as well. If research would show that there is no structure-based connection between the genetic code and the structure of the amino acids and nucleic acids involved, then the multiple origin idea is, in my opinion, untenable and evolution would not be subject to scientific pursuit.

The march toward the world of proteins is another complex story of timing and contact. And again, well-behaved energy was needed, a gentle stream of useful quanta that would not destroy the molecules through which they were captured. The chemical bond, particularly in conjugated systems, can be activated by visible or UV light to provide excited electrons. The electrons need to be passed along to receivers that can convey them to reactants such as to push a nonproductive equilibrium into producing a steady supply of building blocks for biological structures. This passing along of electrons is usually done by proteins and supported by cofactors such as complex conjugated ring systems. The chain of electron transporters needed to be assembled under pre-life conditions such as to kick in at that critical moment of transformation to life. Our knowledge of biology pushes us on and on to more assumptions. Where is the bottom of this story?

The early amino acid condensations must have occurred without enzymes, or rather without proteinaceous enzymes, because the proteins are the products of that process. Proteins are not very stable molecules and need to be reproduced continuously to keep a certain catalytic process going. They are ‘virtual’ components of living systems that exist only as long as their coding sequence is active. The relative stability and accurate reproducibility of the nucleic acids that would eventually become the genome would guarantee the continuous production of proteins under biological as well as pre-biological conditions. Nucleic acids were the original template from which everything else derives. They are the reason for the variety of life forms, the uniformity of basic functions, and the stability of species.

It follows that the coding machinery must have come into existence in the pre-biotic world in order to produce the catalytic peptides to support minimal metabolic activity and communication at the moment of cell formation. Many of the pre-biotic associations of molecules might seem fortuitous when more likely the high redundancy of nucleic acids offered a great variety of proteins produced without a target. Eventually metabolic pathways will develop from the large offering of nucleic acid messages (proteins).

The Embden-Mayerhof pathway of glycolysis, also known as anaerobic metabolism, is perhaps an early function coupled directly to photosynthesis, which requires chloroplasts for the recovery of reduction potential from the photolysis of water.15 Chloroplasts were perhaps finished even earlier than any other structure but certainly 3.5 billion years ago lest blue-green algae could not have been blue-green!

As concerns communication functions, the first proteins had to be ready for their roles as osmotic and nutrient traffic regulators at the moment of cell closure. This again is most plausibly achieved by uniting smaller open catalytic units, referred to above, to form a closed functional body. Each of these units would contain genomic material to produce the proteins associated with it, and that would be the contribution to the start-up package for the new cell, the first potluck event on earth, as it were. The diffusion distances are very short in concentrated solutions so that a pre-biotic commune survived by sharing even before they united to form cells. Micro-organisms have a one-compartment structure, precisely what one would expect to get first when one would roll into a unit some of the catalytic foci that were floating in a concentrated suspension. The cell has all the making of an aggregate with interwoven lipid layers which, because of their chemical properties in water, tend to be double membranes as we see them in chloroplasts and mitochondria.

Once the early code reader had been produced from RNA, which is the active component even in modern ribosomes, the potential information stored in the nucleic acid chains became defined and accessible and the protein products could be recruited as expeditors of the expression of a limit-less reservoir of information. The reiteration of complementary strands of nucleic acids never stopped even when all possibilities of every possible protein plus all the failures were produced many times. All structural motifs were exhausted and all of them were potentially available to nascent cells; they just had to be there to be collected in a grab-bag fashion. How much nucleic acid material was there? Was it enough to buy all the tickets in the lottery?

The amounts of material of almost any description falling onto the earth crust per year is astounding. Between 500 million to one billion tons of nitrogen reach the earth per year. If the abiotic synthetic period produced only 10 tons of nucleotides that would be a modest estimate. One mole of nucleotides weighs (rounded off for simplicity) approximately 200 grams and the 10 tons would amount to 1000 moles or 1026 molecules which, made into a string (10 Å per nucleotide) would cross a substantial portion of our galaxy. Stepping along this string, codon by codon, would give one a fair idea about infinity, about the unlimited information available at the origins of life.

Images are almost as important as any arment when it comes to extreme stories. The best of presentations would not be understood if the audience cannot imagine the new concepts in worldly pictures. Can one see one's own genome on the tip of a needle with all that empty space around it? This picture introduces us kilo-sized organisms to the enormous space that exists in the submicroscopic world and this is the world where biogenesis occurred. It says that within the expanse of a needle tip plans for many creatures could exist so that mixing and matching among pre-genomic nucleic acids is well within the range of diffusion. The linear information would have to have been available in a small space in order to provide the benefit of limitless information to small units like the primordial cell Anlage in statu nascendi. The size of the human genome is about 3 × 109 base pairs and the length would be 3 × 109 times 10−10 meters, which amounts to 3 × 10−1 meters or 30 centimeters. Of the 3 × 109 base pairs, only 3 × 107 (30 million or 1%) are needed to spell out a human being! That would be about 3 millimeters of DNA. Mixing and accessibility during construction of a gene depends upon the bulk as well as the linear dimension. The thirty centimeters of the human genome is so narrow as to be invisible unless viewed through an electron microscope.

Cells would have persisted only because of extreme efficiency in self-maintenance. In cell compartments the catalyst concentration would be a hundred to a thousand times higher than on the outside where everything is large compared to the pico-liter size cell. A few protons, two to three in a lysosome (a digestive vacuole), would produce pH values of 1 (the equivalent of 0.1 molar hydrochloric acid), and two enzymes in that space would bring its concentration into the millimolar range. In a cell the affinity of the enzyme for its substrate determines the speed of the reaction as opposed to thermodynamic limitations of the chemical transformation per se.

It is very plausible that all of life should start with blue-green algae which were the only creatures around that were able to concentrate the diffused solar energy sufficiently to support growth and development. According to currently prevailing ideas, these organelles (pro-chloroblasts, pro-mitochondria) crossed the threshold to life as independent prokaryotic units and the residual nuclear material in them resembles the modern prokaryotic gene rather than the eukaryotic one. The mitochondria, the mediators of oxidative phosphorylation, are problematic for the Darwinians, not because they formed but because they formed when, according to their model, there was no “evolutionary pressure” (oxygen) to produce them. Oxidative centers of complex biology have developed when no oxygen was around which means that their assembly was not stimulated by adaptation to oxygen but was rather the consequence of a certain nucleic acid configuration, the product of un-erasable redundancy. Possessing these oxidative enzymes during the anoxic period was not a severe flaw, but became a tremendous advantage when oxygen levels began to rise. Not only could these organisms deal with oxygen toxicity and corrosiveness, they were able to oxidize hydrogen in a controlled fashion making off with 57 kilocalories of energy per mole parceled out in small and biologically acceptable units for the synthetic activities.

There is another line of threshold activity required, namely the fixation of nitrogen. Indeed, the blue-green algae that were just considered a single cellular organism may have shown a subtle beginning of cell specialization. Every eighth unit in a chain of blue-greens is a heterocyst that fixes nitrogen, neatly separated from the incompatible oxygen-producing capacity. This again is an activity that could not have been anticipated, it was the innocent product of aimless redundancy sorted out by compatibility.

Combination and endless reiteration of early messages is the concept that takes the mystery out of biogenesis. All basic functions are very similar as chemistry would dictate, but the subtlety of the same chemistry expressed in nucleic acids provides for different organization of the genome and thus causes different species to appear. No plan, everything that works together well will persist until the condition changes beyond the limits of flexibility of a unit at which time extinction becomes the only route; the fossil record agrees.

Further development comes from the organization of nuclear material into more efficiently functioning units. All appear as prokaryotes at first but after several hundred million years of rummaging through the genomic material some began to organize the genomic material around positively charged proteins that were encoded in some of the sequences uncovered by internal reorganization. Thereby much larger genomes became accessible for protein-read off and thus some cells were able to increase their sphere of living space by adding a balcony of protoplasm around the nuclear material. In the process genes that encode lamin and other nuclear envelope associated proteins were uncovered and activated by some eukaryotes and that seems to have been a key-step toward multicellularity.16 The age of eukaryotes, the animal and plant cell type had begun.17 In fact, reports are presently appearing that push back the range of recognition of eukaryotes to more than 2.5 billion years; their Anlage, however, dates back to the biogenic period about 3.5 billion years ago.

A mechanism of biogenesis must account for the fact that life is instantaneously demanding and there is no time to produce any vital component once the membrane has closed around a nascent cell. Each unit is sparked into being in seconds and if a burst of light were associated with that instant, a long-lived observer walking across the early earth would see for a few million years these flashes dotting the landscape. He would not be aware of the thousands of preparatory chemical steps that precede each finished cell. When scintillation stopped, the biogenic period was over for this planet. The bio-earth had created itself and every life form had started on its billion-year-trek to fulfill its potential as conditions changed.

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Bookshelf ID: NBK6546

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