Other Theories of the Origin of Life

A review of theories for the origin of life. The intelligent design theory. Panspermia and extraterrestrial origin. The warm pond theory of Darwin and Oparin. The origin of life through replicators and the various mechanisms suggested for their emergence – the RNA world, chemical evolution on silicate surfaces, metabolism first theories. Theory of emergence at volcanic vents. The roles of emulsions, coacervates and vesicles.

 Review of Other Theories of Prebiosis

Theories of the Origin of Life

7.1     Making Comparisons
7.2     Other Theories of Prebiosis
7.3     Sequence of Biochemical Emergence
Copyright Statement

7.1     Making Comparisons

This chapter will review and compare other theories of prebiosis. One of the most accessible reviews of ideas in this field was given by Casti (1989, chapter 2), which, even today in 2006, still seems fairly complete - Wachtershauser's work being the major subsequent development. The theory of prebiotic oscillations thus seems a novelty in a field that produces new ideas quite slowly. One suspects that this apparent stability arises from the nature of the field and the difficulties inherent in choosing between the different theories and eliminating unsuccessful concepts.

7.1.1    Criteria to use in Judging Theories of Prebiosis

Scientists normally try to judge the merit of a theory by comparing its predictions with the outcome of observation. Unfortunately, in prebiosis, there is very little observational evidence upon which to base a decision. All these theories, the theory of prebiotic oscillations included, lack clear evidential support and, as a result, comparison with observation offers little opportunity to judge their correctness or falsity. This lack of empirical evidence seems unavoidable and will, perhaps, be a permanent condition. In other words, one may never be able to test theories of prebiosis through observation. Accordingly, one must seek other grounds to gauge their merits and it will be worthwhile to a formally state some reasonable alternative criteria for making such judgments. Three examples are :-

Parsimony or Occam's razor
The best theories are those that depend upon the fewest premises or which can be supported using well-established knowledge from other fields.

Analytical foundation
The best theories can be derived from, or at least shown to be compatible with, some deeper, underlying theory that has proved itself applicable in areas that are amenable to observational test.

The Coherence Criterion
The best theories form a single, united corpus of knowledge when associated with well-established results from neighbouring fields.
       An important particular case of the coherence criterion might be called the "evolutionary criterion," and stated as, "evolutionary theories should not propose the unselected emergence of complex entities," where a complex entity is any entity that is too complex to arise by chance in a single step. In the case of theories of prebiosis, this criterion would prohibit the proposal of any unselected entity that cannot arise from an uncontrolled chemical reaction in a prebiotic mixture. This rule arises because all modern biological theory is evolutionary and, therefore, all theories of prebiosis should be evolutionary if they are to cohere with the biological sciences. Given the unavailability of direct evidence, any scientific theory of prebiosis should either cohere with evolutionary theory or identify the points where it fails to cohere and explicate the arguments pertinent to that point.

In these respects, the theory of prebiotic oscillations seems to hold up well. It passes the first test because it makes very parsimonious assumptions that largely depend on well-established chemistry and information technology. In the second test, the theory of prebiotic oscillations is drawn from bioepistemic evolution, itself based on the concept of data which has a base in statistical mechanics. Bioepistemic evolution has proved uniquely applicable in understanding such aspects of human nature as sexuality, humour and social structure. In the third test, the theory of prebiotic oscillations coheres with genetics, biochemistry, molecular biology, chemistry, astronomy and information technology.

Thus the present work offers a theory of prebiosis that seems reasonable. It has aimed to interpret prebiotic evolution in a specifically bioepistemic way and to propose mechanisms that are consistent with and constrained by the requirements of, bioepistemic evolution. There are three aspects of bioepistemic evolution that have had the greatest impact on its development. These have been

1. The treatment of "evolving systems" as systems in the IT sense, with data and power inputs that operate separately and are identified separately, even if they are not physically separate.
2. The recognition that self-bounding is a prerequisite for competitive selection of evolving systems.
3. The distinction between controlled and uncontrolled chemistry and physics and the recognition that (adaptive) design is a necessary precursor to any form of controlled process in either chemistry or physics.

Insofar as it shows how adaptive design can lead to controlled processes, the theory of prebiotic oscillations also removes some of the motive for proposing ideas for the origin of life that are supernatural or are tantamount to the supernatural. It gives some transparency to what Behe called "Darwin's black box." This section will review some other theories for prebiosis, noting some points at which supposedly "scientific" theories of prebiosis come very close to being theories of supernatural intervention.

7.2   Other Theories of Prebiosis

Ideas about the origin of life have a very long history. The great majority of tribal societies seem to have had an "origin myth" or a theory of their own origin that was passed down their verbal generations and recorded as soon as the group adopted any written script. Purely as a matter of counting, it is clear that almost all, or absolutely all, of the origin myths were, in a scientific sense, wrong. Put simply, they cannot all have been right.

Nonetheless, the prevalence of such ideas is a kind of warning to those scientists who presume to intrude upon such questions. It seems that human beings must have some kind of congenital need to construct ideas about their own origins, a need that drives them toward belief systems that are, objectively, unsustainable. One must wonder about the motives behind those actions, especially since, today, scientists are human beings intent upon constructing a belief system about their own origins. How, one wonders, will scientists escape from those same motives?

7.2.1    Intelligent Design

The theory of intelligent design (ID) is the theory that life, or some of the essential components of life, was assembled by an intelligent agency. This theory does not deny that evolution will exist as a process in the biosphere but it does deny that it alone is sufficient to have led to life as we now know it. Instead, proponents of ID argue, life has depended upon interventions by intelligent, external agencies that have, so to speak, helped life to climb over some of the more difficult hurdles. The theory does not identify the intelligent designers or present direct evidence for their existence and it does not describe the motives that lead to their interventions. Many scientific observers dismiss the theory of intelligent design as being a non-theory, a theory that does not solve the real problem of the origin of life and intelligence, but transfers that problem to some higher, spiritual realm.

However, intelligent design is more than a current topic of debate, it not only merges with the mythological ideas mentioned earlier but it also represents a type of theory that has a long history, even in purely scientific debate. For example, following Newton's analysis of the gravitational theory of planetary motion, it was soon realized that interactions between the planets would perturb their orbits away from the elliptical and lead, so it was then thought, to a breakdown of the gravitational solar system. Newton's response was to propose that such perturbations in the planetary orbits might be corrected by angelic hands, meaning by divine intervention, that moved the planets back onto their proper paths. Later, during the debate about natural selection, Darwin and Wallace were puzzled by the human brain which, they both agreed, could not have arisen by natural selection alone. Wallace suggested that divine intervention, implying ID, might be the answer but Darwin would not accept that argument, suggesting instead that sexual selection drove the evolution of the human brain.

Darwin noted an implication of this kind of "divine intervention" thinking which, he suggested, might be used to disprove natural selection and support what is now called intelligent design. Some structures, such as steam engines and the various other machines humans build, are quite complex and have only a single function, which function they achieve by the separate actions of several components. No one of these component is of any use on its own. For example, in themselves, the various components of a steam engine are useless, only when acting together can they perform their required function. Although the complete machine works very well, none of its component parts could perform any function in isolation. Machines with this kind of complexity, Darwin argued, are intrinsically unevolvable because evolution cannot anticipate a function that might arise sometime in the future. Hence, there is no selective pressure that can produce the separate components and such a device could not arise from evolution, it would require a designer.

Darwin suggested that, to disprove evolution, one could look through the biological world for structures that are complex in this way, which are assembled from mutually dependent components that could not have evolved separately. Finding such things would disprove natural selection. Behe, a prominent advocate of ID, adopted the term "irreducibly complex" to describe such structures and set about finding examples of biological structures falling into this category. Darwin considered the mammalian eye as a possible example, "What good is a lens," he might ask, "if the retina hasn't yet evolved, and what good is a retina if the lens has not yet evolved?" Surely, neither could evolve separately, by mere chance events, because they would need to evolve and improve simultaneously. Darwin reviewed the apparent evolution of the eye in various species and argued that it did seem to have evolved. However, Behe looked for other examples of possible irreducible complexity and suggested the immune system, the bacterial flagellum and the bombardier beetle as possible examples. The bacterial flagellum is particularly notable in that it exhibits a rotary motion, which is very unusual in biology. Rotary motions are very efficient and human designers like wheels but they are structurally complex and require a bearing, a support structure, an impeller (a wheel or propeller etc.) and a power source. Each of these would be useless independently and the whole system cannot evolve easily.

The debate about the eye and the bacterial flagellum continues and, as tends to be the way with these things, neither side gives ground. In principle, irreducible complexity could provide a criterion to distinguish evolution from design but, although Darwin devised this test, he identified no clear way to determine whether any particular structure is, or is not, irreducibly complex. As a result, one cannot say, beyond all possible doubt whether any one structure is, or is not, evidence of intelligent design and these debates tend to be moot.

Biologists dislike the ID theory and robustly reject it but, since there is no observational data through which it can be completely dismissed, scientists take recourse in more philosophical arguments. They note that ID is vacuous - untestable through being compatible with any possible observation - and they use the kind of arguments listed earlier - parsimony, analytical base and coherence. The intelligent design theory suffers when judged by such criteria. ID is not at all parsimonious (the designer would be a very complex and possibly supernatural entity), the intelligent design theory lacks any analytical base and it is incoherent when set into the framework of the rest of evolutionary theory and the rest of science.

So, the theory of intelligent design can and should be rejected but we should learn something from the episode. This whole discussion brings into focus the special form of the coherence criterion applicable to theories of prebiosis, namely that, "evolutionary theories for the origin of life should not propose the unselected emergence of complex entities."

Most scientific observers may find this a reasonable requirement but, in fact, it is followed in the breach as much as in the observance, which reminds us also to be cautious about the motives of scientists themselves. Several theories, whose authors would vehemently deny any allegiance to the ID movement, nonetheless advocate theories of prebiosis that do involve the unselected emergence of entities that are not only complex but even seem irreducibly complex. Some major examples will be pointed out as this section unfolds.

7.2.2    Panspermia

Fred Hoyle and others supported the idea of panspermia, the idea that life arose on other planets and then became trapped on dust particles which were blown to earth on solar winds and under pressure from light waves (Hoyle, 1983). The essential idea behind this kind of thesis is to extend the period and the range of environments in which life might have evolved.

Panspermia seems like a solution in search of a problem. The only reason to reject the idea of earthly evolution is the difficulty of conceiving a mechanism for the origin of life. That problem is not solved by merely proposing that life arose in some other, unspecified place – that seems like a transfer of the problem rather than a solution to it. Moreover, the process does lack any substantial evidence. Panspermia seems unlikely to be true, given the intensity of cosmic rays in the solar system, but it does not seem completely impossible.

Less plausibly, one might even say rather absurdly, some scientists, such as Francis Crick, (Crick, 1982) had previously advocated an idea that fuses panspermia with intelligent design. He has suggested that life arose on other planets but was then transported to earth in spaceships. These spaceships presumably had intelligent designers who, for some reason, chose to seed the universe with primitive forms selected from the evolved ecosystem of which they were themselves a part. With due deference to Crick's considerable reputation, one can only reply that there seems to be no convincing reason to make that proposal.

7.2.3    Silicate Surfaces

The Scottish chemist Cairns-Smith (1971) suggested that prebiosis arose on defect structures on silicate (rocky) surfaces. As he originally described it, the silicate crustal was able to copy itself and was, effectively, the genome of the prebiotic organism. That idea has not been widely support but this line of thought has led to a large number of studies into the catalytic activities of some rocks, notably the clay montmorillonite. The feeling is that these surfaces might help to solve the problem of bounding by keeping reagents together, especially if lipids were also involved.

This idea has some links with the idea of an "RNA world" and that of primordial replicators. The various defect structures, so this version of the clay theory goes, would catalyze the formation of a variety of RNA molecules, one or more of which would turn out to be replicators that would trigger the evolution of life. On this basis, early life forms are conceived to be based on RNA rather than protein. This is the idea of an RNA world, or even a partially inorganic world, with primitive RNA "organisms" conceived as carrying particles of silicate catalyst around with them. Although often linked, these are separate ideas that will be criticized separately.

In terms of bioepistemic evolution, the theory of rocky surfaces seems unsustainable. The proposed data input, defect structures in a silicate surface, is neither a recurring signal nor is it high powered. The theory offers no a priori basis for defining the fitness of a defect structure. Rather, fitness is defined, a posteriori, as that structure that will catalyze the formation of a self-replicating RNA molecule. Other weaknesses of this theory are that it:-

Offers no indication of how high energy precursors for RNA synthesis might be produced and selected from the primordial soup or the nature of the energy source that produces these precursors.

Does not indicate why other molecules from the soup do not adsorb onto the bare catalytic surface of this defect structure and poison its catalytic activity.

Fails in one of its main claims of explaining how the reagents might be kept together, why the small molecular weight components in the prebiotic mixture do not simply diffuse apart. If surface binding were really so tight as to prevent this diffusion then, by the same token, it is likely that lateral diffusion would also slow down and slow the reaction.

Finally, since the products of RNA synthesis are postulated to be large molecules, they should be held to the surface by multiple bonds which, in their totality, would be stronger than those which hold small molecules onto the surface. Hence, it is hard to see how a large RNA molecule could ever emerge from the rocky surface, let alone become an independent replicator floating free in solution.

Perhaps in response to this problem, some workers have suggested that early organisms were partially inorganic and included small pieces of silicate as part of the bounded organism. There seems to be little merit in this suggestion. It is very hard to see how the silicate component of such an organism, with the correct defect structure, would have been replicated. Moreover, if small pieces of silicate were really part of some protocellular genetic apparatus, then those small pieces might be expected to have survived fossilization and be observable in the fossil record. There is no reported evidence for them. No archaic silico-organic organism has ever been found and many species are known that do not seem to need silicon at all, even as a trace element. (Though humans may require silicon in that role.) The silico-organic organism seems an unrealistic piece of theorizing.

Finally, one notes that many of the above arguments can be applied not just to RNA but to the formation of any large biopolymer at a silicate surface. Hence, this author finds it hard to justify the silicate surface theory. It is undeniable arguable that any reactions catalyzed at such surfaces would have been factors in producing the primordial soup but it seems unlikely that early cells were made there.

7.2.4    The RNA World

The idea of the "RNA world" is that all life on earth was, at some early stage, based on RNA and the protein and DNA came along later. (See Gilbert, 1986; Orgel, 2004) The chief argument for the prebiotic existence of this prebiotic RNA world is that, in some respects, RNA is a dual purpose molecule. Like DNA, RNA is a data carrying molecule (in fact, it is the genome of some viruses) but RNA can fold up into various shapes and exhibit catalytic activities; in the terminology of these things, RNA can be a ribozyme, a "ribonucleic acid enzyme." RNAs display a much narrower range of catalytic activity than do proteins but still, the argument goes, RNA would be a good starting point for life because, as a dual purpose molecule, it can deliver both biochemical activity and data storage. In bioepistemic terms, this argument is equivalent to saying that RNA interprets its own data content but one should note that proteins also do this. Advocates of the RNA world theory, point to the presence of RNA in ribosomes and to the role of tRNA in protein synthesis. They suggest that some precursor to the ribosome was responsible for replicating RNA and that tRNAs are enzyme like molecules. Proteins, they argue, came along later with the "protein takeover" and the theory is then elaborated to explain why this event took place.

However, this whole theory has some serious problems.

First, RNA is chemically labile and, unless protected by a protein coat, it breaks down much more easily than does either DNA or protein. It is hard to see how an RNA world would have survived the depredations of random chemical events and yet been stable enough for the process of evolution to be maintained. One would expect labile molecules to emerge last.

Second, at the heart of the RNA world theory, there is a special entity, an extraordinary RNA molecule or replicator ribozyme complex that is stable enough to survive in a hostile environment, able to catalyze its own replication and able to catalytically copy other RNA molecules. This special RNA molecule cannot have emerged by selective adaptation but still needs to have some remarkable properties. The whole theory hinges on the idea that this specially "fit" RNA will emerge by chance synthesis, possibly on a silicate template. It must be synthesized de novo and immediately possess all the catalytic activities needed to copy both itself and other RNA molecules. Subsequently, it must have lost this capacity because, even under laboratory conditions, no current RNA molecule is able to do these things.

Third, even if, or when, this remarkable RNA structure appeared in the prebiotic soup, it would have proved reproductively "unfit" unless the environment into which it emerged were already supplied with the substrates used up by its catalytic activity. The replicator ribozyme would have been as nought unless all the necessary, energetically activated precursors for RNA synthesis were already available in the necessary amounts. The theory says little about how or why these chemicals were created.

Fourth, the RNA world theory does not address, let alone solve, the bounding problem. Even if this remarkable RNA molecule and all the necessary activated precursors were to appear in the prebiotic soup, still it would prove reproductively "unfit" because they would not be maintained in the necessary concentrations. The bounding problem must be solved to stop all those precursor molecules diffusing away from one another and from the ribozyme itself, failing which all RNA synthesis would cease. The theory is silent on how this problem is solved but it is very hard to see how this special RNA molecule could marshal all these small molecular weight substrates and energy sources needed for its catalytic role. How could all these components be kept together for the synthesis to proceed? The RNA world theory seems to demand the prior existence of some controlled forms of chemistry, implying either some earlier history of evolution or intelligent design. Thus, this theory cannot describe the first steps in prebiotic evolution; it might be a theory of some later step, still distant from modern life, but that does not seem a good place to begin theorizing. A better to approach to theory building might be to identify plausible candidates for the very first steps in evolution, steps that require no prior evolutionary history, and then consider feasible second stages.

In sum, there seems at present to be no real reason to think the "RNA world" ever existed as a stage in evolutionary history or that RNA ever had a catalytic role greater than currently seen. Indeed, the RNA world theory seems improbable and over-elaborated with ad hoc hypotheses. In particular, the replicating ribozyme seems an irreducibly complex entity. Unless its advocates can realistically address such shortcomings, the RNA world theory should be seen to fail.

Finally, in this section, an honourable mention should go to the work of Lathe (2004) who suggested that early nucleic polymerization might arise at coastlines, due to the cycles of wetting and drying that occur in tidal pools. For the reasons outlined above and later, it seems unlikely that nucleic synthesis was the first step in the origin of life. Nonetheless, Lathe's recognition of the importance of periodic variation of conditions was an original insight that predates this author's work.

7.2.5    Replicators

The idea of a replicator is closely related to the RNA world and to the special ribozyme described in the previous section but the idea of a primordial replicator has roots in general evolutionary theorizing rather than in discussions of prebiosis. In fact, the idea of a replicator arises from a basic error in modern evolutionary theory and from the need to merge two different but closely related strands of biological science - Darwinism and genetics.

In Darwin's original conception, the theory of natural selection depends upon the ability of whole organisms to reproduce or replicate. The theory considers the degree of success, the fitness, of a whole organism in replicating or reproducing itself. Fitness is simply a measure of the ability to produce succeeding generations.

Surprising though it may seem today, Darwin's work has not always been popular, even among scientists, and by the end of the nineteenth century, his evolutionary ideas were in something of a decline. That decline was not too surprising; his ideas are certainly logical but there is a real circularity about them, so that, while Darwin's ideas certainly explain many observations, they are not very good at predicting anything. However, at the beginning of that twentieth century, evolutionary theory received a boost from Bateson and breeding studies of the type originally devised by Mendel. Those breeding studies led to the idea of genes and to a merger between evolutionary theory and genetics that is often called the neodarwinism or the new synthesis. It also led to the subsequent resurgence in Darwin's own reputation.

That great synthetic achievement was followed and supported by more reductionist analyses, notably from Sir Roland Fisher, a well-known statistician who worked on the analysis of breeding experiments. Fisher was very influenced by Boltzmann's work in statistical mechanics, the branch of physical science that tries to understand the macroscopic properties of materials from a statistical analysis of their atomic properties, and Fisher brought a similar approach to genetics. His studies had many successes. In particular, he was able to show, from a purely genetic analysis of populations, that natural selection would work, in the sense that it would lead to an increase the incidence of "fit" genes in a population. The methods he pioneered have since become known as population genetics and he has come to be regarded as the father of that science.

However, Fisher worked before the growth of modern molecular biology and he treated genes as independent atoms of evolution that replicated independently along with the rest of the organism. In that respect Fisher's assumptions are wrong. Genes are not independent of one another and they are not replicators at all, they are sections of DNA, usually with a base sequences that can lead to the synthesis of proteins with a certain biochemical activity, and they are joined with other genes on the molecular thread that is a chromosome. Genes do not self-replicate, they are copied, along with the rest of the cell or the organism as it replicates. Thus genes are not independent atoms of evolution and some of the assumptions that underlie population genetics are wrong. It follows that, in some circumstances, the science of population genetics will make incorrect predictions. This is not, in itself, a criticism of population genetics; it simply means that this science, like many other sciences, should be applied only across the experimental domains to which it is applicable. In the case of population genetics, this means the experimental domain in which the assumption that genes are independent atoms of evolution is approximately correct. Put simply, it means that the limitations of population genetics should be recognized.

The problem is that the limitations of population genetics are not generally recognized and it is often treated as the fundamental and correct approach to evolutionary theory in general. Many evolutionary theorists seem oblivious to its faults and apply population genetics without regard to its limitations. For example, Dawkins' well-known work, The Selfish Gene, explicitly sets out to reduce all evolutionary theorizing to its fundamental unit which is, supposedly, the gene. The error in this argument is that genes are not fundamental to evolution, only to biology, and this error becomes significant whenever the evolutionary process under study does not primarily involve genetic data. This is not the place to criticize Dawkins' work in any detail though, in the opinion of this author it contains serious errors and does need criticism. Prebiosis is one of the places where these errors become manifest, with the widely known claim that all evolution must involves replicators, which is incorrect, and that genes somehow emerged from primordial replicators, which they almost certainly did not.

In attempting to circumvent the problems in evolutionary theory, theorists have linked the idea of a gene with that of an organism and have asserted that not only are organisms replicators but so are genes. One can see why the idea is attractive, it has an apparent simplicity. If both genes and organisms were replicators then this, at a stroke, justifies the merger between genetics and Darwinian evolution. So, in this framework, all evolution is seen to be based on replicators – organisms as the replicators we see around us, genes as fundamental replicators that we cannot see but from which organisms are made. Of course, all workers know that genes in the modern world are not replicators but this inconvenient fact is brushed aside with the suggestion that genes derive from some kind of primordial replicators. Once, long ago in the prebiotic soup, these protogenes, these primordial replicators, could replicate themselves but now their ability to do so has withered and been lost as they prefer to invest all their energy in the collaborations with other genes that lead to organisms. Modern genes, in short, no longer need the ability to copy themselves independently that their forebears once possessed. See Dawkins (1989), for this proposal.

It cannot be overstressed that that this notion of the gene as derived from some primordial replicator is a theory of prebiosis and that it is, perhaps, the most influential theory of prebiosis in current circulation. However, it also cannot be overstressed that this notion is entirely devoid of observational foundation. The smallest known replicators in biology are cells - genes do not self-replicate and there is no genuine reason to think that they arose from primordial replicators. Thus, while replicators, as cells, are characteristic of biology, they are not prototypical of evolution in general and one should not simply assume that prebiotic evolution involves replicators.

It is disheartening to see so many theories of prebiosis and other ranks of evolution shaped by such a widely publicized and egregiously erroneous claim. There is no more evidence for the notion of genes as replicators than there is for the idea that God created the heavens and the earth.  For good measure one may add that even the concept of organisms as replicators is, technically, false. Organisms do replicate their data content, their pattern, but it is only their data that is replicated. An organism's material content must be recruited from the environment as it is copied and the pattern to be replicated impressed upon it. Achieving those things is always complex, leaving the prebiotic replicator theory with no theoretical foundation. Hence, it can never be a parsimonious theory or cohere with the rest of science.

Not only is it wrong to describe genes as replicators, it is even wrong to assume that biology is a prototype for all evolution. Evolutionary thought is applied to several fields besides biology, including neurobiology, social evolution, epistemology and evolutionary computing and none of those fields involve identifiable replicators analogous to organisms or genes.

Nonetheless, explicit statements of the replicator theory are made and there have been many attempts to identify some plausible, "primordial replicator" that can serve as the archetype of the gene (see Segré et al., 2000, for an example.) The RNA ribozyme theory described in the last section is such a theory but it fails and Shapiro (2000) has criticized replicator theories in general.

All primordial replicator theories will fail for much the reasons given for the ribozyme theory. Any replicator, primordial or otherwise, requires the simultaneous presence of multiple functions, demanding intrinsically implausible postulates in the theory. It is not genuinely  believable that any entity as complex as a replicator, with energy and precursor supplies already on tap, with membrane lipids ready to provide a boundary, could rise like some biochemical phoenix from the embers of our newly formed planet. Any replicator, possessed of those multiple functions would be an irreducibly complex object and its sudden, appearance from the primordial soup would be an intrinsically improbable event, raising issues of intelligent design. Such a replicator could not arise by chance alone but must arise from design. In other words, the theory of emergence from primordial replicators seems incompatible with modern evolutionary theory.

The primordial replicator concept seems a shallow and erroneous idea that should be dismissed. Theoreticians should search for more rational foundations from which to build their theories. All forms of evolution require replication or copying of data or pattern but that does not mean that a physical object must be able to replicate itself. We know of simple, physical processes, that inherently replicate data and pattern and which can and do arise by chance, notably rotations, oscillations and wave motions. It is to these simple, replicative processes that one should look for an understanding of the origin of life.

7.2.6    "Metabolism First" Theories

A core debate in theories of prebiosis is, "which arose first, biochemical metabolism or biological data on DNA or RNA sequence." Most current discussion seems to focus on the "data first" approach and leads to ideas like that of a ribozyme replicator discussed earlier.

The alternative to "data first" is "metabolism first," the idea that biochemical pathways emerged before the data that later came to describe them. Several metabolism first theories have been proposed, many of which centre around the idea of some kind of self-organizing, autocatalytic cycle that may or may not depend on a mineral surface acting as a catalyst; see Shapiro (2006) for a review. Perhaps the most popular, current, metabolism first theory was proposed by Wachtershauser (1990), who suggested a metabolic cycle catalyzed on a pyrites surface. There is test tube evidence for the kind of reactions he proposes but the idea falls short of being a mechanism for the origin of life and severe problems remain. Orgel (2000) gave a general critique of the idea of autocatalytic cycles. He notes the great improbability that such closed reacting cycles could arise by chance, describing the proposal as an "appeal to magic." His criticism was valid; even in the laboratory, it is very difficult to create examples of such autocatalytic cycles and the proposal that they might emerge by chance is no more plausible than proposing that replicators might do so. Put simply, metabolism first theories have suffered from very similar problems to data first theories, they depend upon the postulate that a complex, evolving system can arise by chance and emerge, preadapted for survival in the harsh prebiotic world.

The theory of prebiotic oscillations is a metabolism first theory but it is fundamentally different from other such theories and does not suffer from such defects. It takes a random chemical mixture as its starting point and is entirely evolutionary from the outset.  The theory of prebiotic oscillations suggests an evolutionary, selective mechanism for the emergence of biochemical pathways from a prebiotic soup. It even suggests a mechanism for the evolutionary selection and emergence of autocatalytic cycles. Hence, the theory of prebiotic oscillations seems to overcome Orgel's objections to metabolism first theories and the improbability of autocatalytic cycles emerging by chance.

7.2.7    Undersea Vents

Many scientists suggest that prebiosis occurred at undersea vents, similar to the volcanic "smokers" identified at the mid-ocean ridges. This idea is popular for a number of reasons.

First, since new, bare rock is being produced at these surfaces, they might offer a clean catalytic surface, (clean in the sense of free from previously adsorbed material) on which the kind of catalyzed reactions discussed above might occur.

Second, there is a good energy supply at these sites. They would be continuously emitting energy-rich chemicals, produced in the bowels of the earth. These volcanic emissions would generate temperature gradients and a wide variety of environments upon which life's evolution might be initiated. It is even possible that such smokers could modulate their energy supply to produce a data input, since many volcanic vents have an oscillatory character. (For example, consider the "old faithful" geyser in the Yellowstone national park, a volcanic event that recurs at intervals of about 90 minutes.)

Third, some observational evidence supports this argument, since these undersea volcanic environments support populations of archea, the oldest known, extant life forms on earth.

The third argument, about archeal populations, seems immaterial. While it is true that these species seem very ancient, their biochemistry is not remotely prebiotic - as Lazcano and Miller (1998) phrase it, "they may be simple but they are hardly primitive." The present location of these organisms is not a worthwhile indicator of the point of prebiotic emergence. The simple nature of these populations may arise because undersea vents are in locations that are well protected from environmental variation. Thus the archeal populations that reside there would have faced fewer of the selective pressures that led to evolutionary change elsewhere.

That said, these undersea vents and volcanism do seem a serious possibility for the origin of life on earth. Volcanism offers a credible alternative to the sun as an energy source and might even act as a data source. Choosing between the sun and volcanism is a matter of judgment. This author would argue for the sun, since it exerts its influence across a wider range of habitats, while being a more reliable and larger source of energy and data than volcanism. Still, the volcanic alternative would be the better source of chemicals and deserves serious thought, as does the possibility of combined effects, with volcanism acting in concert with the sun.

7.2.8    Lipids

Much thought about prebiosis has been concerned with phenomena such as lipid vesicles and the kind of amphipathic molecules that form them. This line of thought began with the Russian Alexander Oparin, who argued that life began with a group of colloids called coacervates. These are formed as water droplets surrounded by an organic materials. In this sense they are similar to cells surrounded by membranes and they can physically resemble living things. Of course, they lack the ability to reproduce and many of these containerised water droplets are quite leaky. In other words, the organic bundary is often porous so that coacervates, in general, would not be able to bound evolving systema.

Lipid, as found in cells, form vesicles that can be perceived as a form of coacervate. However, lipid vesicles are not leaky and the modern trend, which is to focus on them and this does seem the correct approach. (See for example, Segre et al. 2001, and Hanczyk and Szostak, 2004, for recent discussions and Deamer is a major figure in the field.) Some workers view this approach as the "container first" approach to the origin of life and such reflections do indicate concern for the general problem of bounding. As such, their approach is very consistent with bioepistemic evolution, based as it is on self-bounding data sets, and it is the need for self-bounding that drives the ideas about lipids and amphipaths presented in this study.

However, one might suggest that the field could pay more attention to the droplets and micelles that tend to form under uncontrolled conditions, as well as to the vesicles that can form under controlled chemistry. Spherical droplets do have bounded surfaces and seem the more natural starting point for understanding self-bounding in evolution. Lipid vesicles seem likely to have emerged only when adaptive design had progressed to the point where controlled chemistry could create protolipid vesicles.

7.3     Sequence of Biochemical Emergence

The theory of prebiotic oscillations discusses various general properties of chemicals but does not attempt to specify the oscillations that were most important in initiating the evolutionary process or try to detail its subsequent development. Even assuming the present theory to be correct, there is insufficient information to be specific about the chemistry involved and such questions might be better addressed experimentally. However, we know a great deal about the biochemistry of the life forms that subsequently emerged and it will be useful to consider the likely sequence of their emergence.

One can, rather coarsely, place biochemistry into five non-exclusive compartments – first, all biochemical pathways, second the lipids, third the proteins, including enzymes, fourth the carbohydrates and, lastly, the nucleic acids, RNA and DNA. The present study implies that life's emergence began with biochemical pathways, these beginning as oscillations, separately selected from the primordial soup. A great many such oscillations could have existed, some would have led to the minor biochemical pathways found in so many organisms. Some oscillations would have been especially successful and led to the four major groups of biochemicals and their polymers, the fats, carbohydrates, the amino acids which polymerized to produce proteins and the purines and pyrimidines that produced the nucleic acids. Some of the emergent biochemical pathways would have involved amphiphilic molecules which, through their self-bounding properties, would have lead to the lipid bilayers and bounded vesicles, the protocellular entities that would, one day, become single-celled organisms. At this point, selection would be moving on and would no longer be based on the properties of individual oscillations but on the phenotype of the protocells that grouped several oscillatory pathways into a single droplet or vesicle.

Amino acids would have been part of these pathways. Amino acids with hydrophobic sidechains are amphiphiles while mixtures of hydrophilic and hydrophobic amino acids will form amphiphilic peptides and proteins. The most selected peptides would have been the amphiphiles that associated with the surfaces of droplets or bilayers formed from protolipids. Modern phospholipids have a negatively charged phosphate group providing their hydrophilic region, so that positively charged proteins can become associated with droplets or vesicles. One thus surmises that early phospholipids would tend to associate with either hydrophobic amino acids or basic amino acids, which would have carried a positive charge. Thus, the earliest common amino acids would be hydrophobic and basic. (In modern lipids the phosphate is often partially neutralized by an outer positive but, still, the bilayer remains negative overall.)

One would, therefore, expect that the early proteins would have been made predominantly from basic and hydrophobic amino acids. The genetic code may offer some support for this inference in that the simplest codons UUU, GGG, AAA and CCC code for two hydrophobic amino acids, phenylalanine and glycine and two basic amino acids, lysine and proline. These four amino acids being selected to be the simplest codons for their ability to associate with the amphiphilic but negatively charged surfaces of droplets and vesicles. On that basis, some early genetic code would have been based on the catalytic synthesis of simple proteins from these few, early amino acids. The code would then have been elaborated into its modern form by adaptive design and by the addition of other amino acids. (However, others workers would dissent. For example, Copley, Smith and Morowitz (2005) have argued that the early code was based on a two base pair codon, basing their arguments on the pattern of amino acid biosynthesis. This whole discussion is a major topic that cannot be pursued within the bounds of this study.

Carbohydrates have the general formula Cm(H2O)n and many observers believe they may have arisen from polymerizations of methanal CH2O or some other low hydroxyaldehyde, which have long been known to undergo polymerizations capable of producing carbohydrates. Although carbohydrates are important sources of energy in modern organisms, they were probably not the first major energy source on the early earth; it is more likely that inorganic compounds, such as hydrogen sulphide, would initially have performed this role. However, it also seems likely that, as proto-organisms switched from one energy source to another, they would have retained the same general organization in their energy utilization. Thus, the fact that carbohydrates are hydrophilic, suggests that early fuel sources were also hydrophilic. In addition, when carbohydrates were first used as energy sources, it would have been anaerobic respiration that provided the energy, their being no oxygen on the prebiotic earth to enable aerobic respiration.

Moving on to the nucleic acids, RNA and DNA, both these polymers, and their small relative molecular mass precursors, are hydrophilic materials carrying a negative charge due to phosphate groups. Therefore, nucleic acids will not become associated with negatively charged lipid droplets or bilayers and neither would they diffuse across such bilayers. This means that nucleic acids cannot have appeared as information carrying molecules in protocells until after the evolutionary bounding problem had been solved by the emergence of lipid bilayers and after the emergence of proto-enzymic catalysis. Hence the nucleic acids would have been the last of the major groups to have acquired their biological role as data carrying macromolecules. In other words, both lipids and proteins emerged before the nucleic acids.

In itself, the theory of prebiotic oscillations gives no clue as to whether it was RNA or DNA that emerged first. Most observers believe that RNA would have been first, (see, for example, Darnell and Doolittle, 1985) with DNA following, the reason being that RNA is today, the proximal mediator between nucleic acid sequence and protein sequence. The author takes those points but leans toward DNA being the first of the nucleic acids. The arguments for DNA arising before RNA are, first, DNA is chemically more stable than RNA, which would give it survival value in the prebiotic soup, second, DNA makes use of only four bases whereas RNA adds several minor bases and, third, under unusual conditions, single stranded DNA can serve as a template for protein synthesis, giving it potential to both self-copy and to direct protein synthesis. In any event, self-copying is currently very unusual for RNA and, at some point in time, the nucleic acids did evolve their current ability to both self-copy and determine amino acid sequence. These are both data processing operations, which would have required energy inputs so that the energy metabolism of modern cells, especially the role of nucleotides such as ATP (adenosine triphosphate, an important energy carrying molecule) presumably predated the role of similar compounds used as data carrying molecules.

This leaves us with a time sequence of prebiotic emergence that looks broadly like this

1. High energy data input and primordial soup producing chemical oscillations
2. Selection of oscillations leading to specificity and metabolic pathways
3. Amphiphiles, enzymes and protocells
4. Energy metabolism and carbohydrates
5. Data carrying molecules, RNA and DNA.
   

The next stage in the development of this discussion would be to address the origin of the genetic code that converts the data of nucleic acid sequence to that of protein sequence. Such a study would be of value but this would be a large undertaking and it seems most natural to stop this discussion here.

Copyright Statement

© John A Hewitt MA PhD (Cantab.)
The work described here was performed as an independent investigation by John A Hewitt who asserts the right to be recognized as its author and as the originator of the novel ideas presented here. The topics to which this claim applies include, but are not limited to, the application of bioepistemic evolution to the prebiotic situation, the discussion of the sun as a data and power source for prebiotic evolving systems, the recognition of sun-induced chemical oscillations as information carriers subject to evolutionary selection and to the theories for the origin of biochemical pathways and self-oscillatory, allosteric and cyclic biochemistry that result.
This study is a greatly extended version of a poster originally presented at the Royal Society meeting on conditions for the emergence of life on the early earth, London, 13 & 14 February, 2006. This internet version was made available on 6 September, 2006. Comments and criticism are solicited - see the "contact & copyright" link for contact details.

 

Edited November 7, 2006. Revised phrasing of Cairns_Smith paragraph. Inserted mention of Lathe's work.