1. Principle of gradualism

One of the cornerstones of the theory of evolution is the principle of gradualism, which implies that evolutionary changes tend to accumulate gradually through a series of small steps, rather than by sudden leaps. In this paper I show that the principle of gradualism yields non-trivial insights into the mechanisms and timing of the origin of life. One of its consequences is that complex living systems cannot emerge by pure chance. The origin of life was not a lucky event but a gradual increase in sustainable functional complexity of evolving primordial systems.

Gradualism has been criticized based on evidence from genetics and paleontology. For example, mutations of some genes (e.g., antennopedia in Drosophila fly) produce instant major alterations of the phenotype, which may lead to rapid evolutionary change. Paleontological records also show rapid changes of phenotypes in numerous lineages during very short transitional times between stable epochs; and these findings have prompted the concept of punctuated equilibrium (Gould & Eldredge 1977).

However, if we accept the arguments and evidence against gradualism, then we must assume that any rate of change is possible, and this assumption conflicts with reality in evolutionary reconstructions. For example, how is it possible that such complex organisms as bacteria with hundreds of genes appeared on Earth as early as 3.5 billion years ago (Furnes et al. 2004). Based on the punctuated equilibrium hypothesis, Koonin and Galperin have assumed that primordial evolution was much faster than normal simply because of the absence of competition (Koonin & Galperin 2003). Yet, if there was no competition, and if life began on Earth, what forces acted to rapidly accelerate genomic evolution such that a single replicon became a genetically complex prokaryote in just a few hundred millions years? Conversely, if we accept the classic definition of gradualism, we are faced with the same questions.

To defend the principle of gradualism, Dawkins argued that the discreteness of paleontological records resulted mostly from migration and propagation of already existing species, rather than from suddenly accelerated evolutionary process (Dawkins 1986). But the existence of macromutations and increased variability after environmental change are difficult to reconcile with classic conceptions of gradualism.

Gradualism is classically associated with morphology and herein lies the weakness of the theory. The principle of gradualism should be formulated in terms of complexity rather than morphology: complex systems can originate only from systems of comparable or higher functional complexity. Morphology is the tip of the evolutionary iceberg as the greatest changes mostly occur at the molecular level. Species have developed molecular mechanisms that can support rapid morphological changes in response to environmenal stress. These modifications do not change the total complexity of the system, they simply convert molecular and physiological complexity into new morphology. According to this new understanding of gradualism, complexity can increase gradually, whereas certain morphological and physiological characteristics of organisms may change much faster.

2. Life Did Not Start from Heteropolymers

The "RNA world" hypothesis assumes that first living systems had self-replicating nucleic acids (Gilbert 1986) or other kinds of similar heteropolymers (TNA, PNA) (Nelson et al. 2000; Orgel 2000). Although some RNA molecules can catalyze the polymerization of other RNA (Johnston et al. 2001), this reaction sustains only in the environment with abundant free nucleotides.

Individual nucleotides can be synthesized abiogenically (Powner et al. 2009), but it is unlikely that they can become concentrated in quantities sufficient to support RNA polymerization in a population of proto-organisms. Even if several molecules appear in close proximity due to a once-in-a-universe lucky coincidence and are then used to synthesize a complimentary RNA strain in a hypothetical protoorganism, there would be no nucleotides left for the reproduction of the next generation of replicons.

Although nucleotides can be synthesized from bases and sugars by RNA-mediated catalysis (Unrau & Bartel 1998), this synthesis is highly unlikely to have contributed to the origin of life because both bases and sugars are rare molecules which cannot be supplied in sufficient quantities.

Polymers like nucleic acids and peptides can appear in evolution only on condition of an unlimited supply of monomers, and this requires a heritable mechanism for their synthesis from simple and abundant organic and non-organic resources (Copley et al. 2007; Sharov 2009). Thus, the emergence of polymers was the second chapter in the history of life, whereas the first chapter belonged to nonpolymeric molecules that supported both metabolic and hereditary functions (Jablonka & Szathmáry 1995; Sharov 2009).

3. Life Did Not Start From Large Autocatalytic Sets

Autocatalytic synthesis is considered a rare property among organic molecules. Thus, Kauffman suggested that it can arise more easily in multi-component mixtures of molecules (Kauffman 1986). In particular, he suggested that a mixture of peptides can form a closed autocatalytic set, where the synthesis of each component is catalyzed by some members of the same set. He showed that in the case of random catalytic properties, such autocatalytic networks arise with high probability. The first problem with this model is addressed in the previous section: there is an insufficient supply of monomers (i.e., amino acids); and this rarity is even more profound on Earth. In fact, the model does not work even if applied to simple organics monomers due to the following problem: most abundant organic molecules (e.g., saturated hydrocarbons) are inert. Catalytically active organic molecules are rare and often unstable, thus it is unlikely that they would become concentrated together in a tiny space. High concentrations would be needed so that the rates of mutual catalysis would compensate for the loss of molecules due to their degradation and diffusion.

4. Minimal Heredity: Autocatalysis Which is Linked with Local Environment

The evolution of primordial living systems requires heredity (or some type of memory unit) to transfer their functions to the offspring systems. As discussed above, neither nucleic acids nor other complex polymers were present in sufficient quantities; a condition that becomes even more untenable if life's origins is confined to Earth. Thus, hereditary functions must have been carried out by simpler substitutes.

There is a consensus that autocatalytic reactions played an important role in the origin of life (Kauffman 1986). Autocatalytic synthesis is not that uncommon and can be maintained with a single type of molecules. For example, the formose reaction that produces formaldehyde is autocatalytic (Huskey & Epstein 1989).

These reactions can increase their rate and propagate in space, which is similar to the growth and expansion of populations of living organisms (Gray and Scott 1990; Tilman and Kareiva 1997). Strict autocatalytic reactions which cannot start without a seed, have two alternative steady states: either "on" or "off" (the "on" state is stabilized via a limited supply of resources). Thus, they represent the most simple hereditary system or memory unit (Jablonka & Szathmáry 1995; Lisman & Fallon 1999). For example, a reverse citric acid cycle, which captures carbon dioxide and converts it into sugars, may become self-sustainable, at least theoretically (Morowitz et al. 2000). Replication of DNA is not usually considered autocatalytic because it requires DNA polymerase. But if DNA polymerase is abundant in some artificial environment (e.g., in a tube), then DNA replication is a strict autocatalytic reaction, because it cannot start without a seed DNA (Jablonka & Szathmáry 1995). Autocatalysis is necessary for the origin of life, but it is not sufficient. The specific feature of autocatalysis in living systems is that it is linked functionally with the local environment (e.g., cell), and this linkage can be viewed as a coding relation (Sharov 2009). Specifically, the autocatalytic system modifies (encodes) its local environment, and this modification increases the rate of autocatalysis. This functional linkage is a necessary condition for cooperation between multiple autocatalytic components if they happen to share their local environment.

In contrast, unlinked autocatalytic systems can only compete but not cooperate. The role of cooperation is generally underestimated in evolutionary biology because of the common emphasis on competition and natural selection. But the growth of functional complexity of organisms is based mostly on cooperation between its subsystems (e.g., genes and cells), whereas the role of competition between organisms is limited to tuning up this cooperation via natural selection.

Thus, evolutionary potential of primordial systems depends on the functional linkage with the local environment, which promotes cooperation.

The local environment can be represented by either enclosure or attachment to a surface. Although all known living organisms have enclosures (cell membranes), life may have started from surface metabolism (Wächtershäuser 1988).

Lipids (diglycerides, triglycerides, or phospholipids) that are necessary for making the membrane were not available in sufficient quantities before the origin of life; and if we limit life's origins to Earth the problem becomes insurmountable. It is even less likely that the first organisms had protein enclosures similar to virus capsids, as proposed by (Deacon & Sherman 2008), because amino acids were not available in sufficient quantity and variety (see section 2), and autocatalytic sets of peptides cannot emerge by chance (see section 3). There is a possibility that autocatalytic systems could have occupied already existing solid enclosures, e.g., pores in hydrothermal vents (Copley, et al. 2007). However, solid enclosures have serious disadvantages: if they are tightly closed, then they prevent the influx of resources and propagation of the autocatalytic system; but if the enclosure is permeable, then the system would dissipate.

Liquid enclosure (e.g., hydrophobic molecules dissolved in oil microsperes) is another possibility (Segre et al. 2001). But all kinds of enclosures have a problem with chemical kinetics: autocatalysis has a much higher rate on a two-dimensional surface than in three-dimensional space (Wächtershäuser 1988). Thus, hypotheses of the origin of life in enclosures are less plausible than scenarios of surface metabolism, which explains both an easy access to resources and high efficiency of autocatalysis.

Dependency of autocatalytic systems on their local environment is needed to prevent dissociation. Dependency develops if a system modifies its local environment and these modifications increase the rate of autocatalysis (Sharov 2009). In economic terms, the system invests in the modification of its environment, and therefore cannot leave its investment. This can also be viewed as a "property" relation at the molecular level. The autocatalytic system is the owner of its local environment, which plays the role of "home" or "body". Because the system is attached to its home, it is forced to cooperate with other autocatalytic systems that may appear in the same local environment.

5. Coenzyme World: Autocatalytic Coenzymes Modify Surface Properties

Very few hypotheses of life's origin follow the principle of gradualism and consider simple models based on non-polymeric hereditary molecules and abundant organic resources (Jablonka & Szathmáry 1995; Wächtershäuser 1988). Sharov (2009) has proposed a "coenzyme world" scenario where hereditary functions are carried out by autocatalytic non-polymeric molecules, named "coenzyme-like molecules" (CLMs) since they are catalytically active and may resemble existing coenzymes. Because many coenzymes (e.g., ATP, NADH, and CoA) are similar to nucleotides, CLMs can be viewed as predecessors of nucleotides.

The most likely environments for CLMs were oil (hydrocarbon) microspheres in water because (1) hydrocarbons are the most abundant organic molecules in the universe and are expected to exist on early terrestrial planets (Marcano et al. 2003), (2) oil microspheres self-assemble in water and (3) it is logical to project their evolutionary transformation into a lipid membrane (Sharov 2009).

CLMs can colonize the surface of oil microspheres in water as follows. Assume that rare water-soluble CLMs cannot anchor to the hydrophobic oil surface. However, some microspheres may include a few fatty acids with hydrophilic ends which may allow the attachment of CLMs. Once attached, a CLM can catalyze the oxidation of outer ends of hydrocarbons in the oil microsphere, thus providing the substrate for binding of additional CLMs. Accumulation of fatty acids increases the chance of a microsphere to split into smaller ones, and small microspheres can infect other oil microspheres, i.e., capture new oil resource. This process of autocatalytic adhesion creates a two-level hierarchical system, where CLMs play the role of coding elements. They encode surface properties of their local environment and benefit from this change.

Figure 1. Coenzyme world: coenzyme like molecules (CLMs) on the oil microsphere. (A) CLM can anchor to the oil microsphere via rare fatty acid molecules. (B) The function of a CLM is to oxidize hydrocarbons to fatty acids, which provides additional anchoring sites for new CLMs. (C) Accumulation of fatty acids increases the chance of a microsphere to split into smaller ones, and (D) small microspheres can infect other oil microspheres (i.e., capture new oil resource).

Alternatively, CLMs can be synthesized from precursors (e.g., from two simpler molecules A and B) on the surface of microspheres. As a potential mechanism, we consider that molecule A attaches to the fatty acid on the surface of a microsphere and changes its conformation after attachment. This new conformation helps it to interact with another water-soluble molecule B. As a result, the synthesis of A + B => AB is catalyzed by the oil microsphere. If the product AB is capable of oxidizing hydrocarbons into fatty acids, then the process becomes autocatalytic.

The model of metabolism on the pyrite surface, proposed by Wachterschausen (Wächtershäuser 1988), also fits the requirements of the coenzyme world. Pyrite is positively charged, hence it can absorb negatively charged organic molecules and promote their interaction. The products of these reactions may accumulate on the surface and change its local properties. However, Wachterschausen's assumption that fatty acids were synthesized from carbon fixation is questionable because this process requires a complex catalytic pathway similar to the reverse citric acid cycle ((Morowitz et al. 2000), which is unlikely to emerge by chance. It is possible that multiple autocatalytic systems existed both on pyrite and on oil microspheres, and some molecules were exchanged between these systems thereby contributing to life. However, oil microspheres are more likely to become predecessors of cellular life because they can be easily transformed into cell membranes (Sharov 2009).

6. Combinatorial Heredity

Several kinds of autocatalytic coding elements can coexist in the same local environment (e.g., microsphere), creating a system with "combinatorial heredity" (Sharov 2009). Each kind of coding element performs a specific function and ensures the persistence of this function via autocatalysis. However, coding elements are not connected, and hence, are transferred to offspring systems in different combinations. Despite random transfer, the combinatorial heredity can be stable because (1) coding elements are present in multiple copies and therefore each offspring has a high probability to get the full set, and (2) natural selection preserves preferentially organisms with a full set of coding elements. The efficiency of the later mechanism was shown in a "stochastic corrector model" (Szathmáry 1999). Systems with combinatorial heredity have an increased evolutionary potential because different combinations of coding elements may easily generate novel effects.

New types of coding elements can be added by (1) acquisition of entirely new CLMs from the environment, (2) modification of existing CLMs and (3) polymerization of CLMs. New CLMs have to encode novel functions to persist within primordial systems (Sharov 2009). For example, they may enhance the ability to capture energy or facilitate the attachment to some substrate with beneficial consequences. The transformation of already existing CLMs can be achieved by adding functional groups. For example, accidental methylation of the parental CLM at a certain position can make a new catalyst capable of methylation. Then, this modified molecule can become a new coding element if it is capable of autocatalysis (via methylation of the parental CLM), and encodes the methylation of other molecules in the local environment.

Combinatorial heredity can eventually lead to the emergence of synthetic polymers (Sharov 2009). For example, if a new CLM, C, can catalyze the polymerization of another CLM, A, then together they encode long polymers AAAAA..., which can cover the surface of the microsphere and substantially modify its physical properties. If C can catalyze the polymerization of multiple monomers (e.g., A and B) then repetitive (ABABABAB) or random (ABBAABABAAABB) sequences can be produced. These polymers may show more advanced properties including 3- dimensional folding and secondary structures. Some polymers may catalyze polymerization and therefore become independent from C.

7. The Origin of Universal Coding

Initial steps of primordial evolution were probably slow and inefficient because there was no universal rule for producing new coding elements. Some improvement was likely achieved by transformation of old coding elements into novel ones via modification of functional groups or polymerization. However, there would still have been no streamlined procedure for making new coding elements.

Template-based (or digital) replication is a special case of autocatalysis, where each coding element is a linear sequence made of a few kinds of monomers, and copying is done sequentially via predefined actions applied to each monomer (Szathmáry 1999). Digital replication makes the coding system universal because the algorithm works for any sequence; hence, there is no need to invent recipes for copying modified coding molecules. The starting point for the origin of template-based replication is the existence of polymers with either random or repetitive sequence (Sharov 2009). Polymers may initially stick to each other to perform some other functions, e.g., to increase stability and facilitate polymerization. The shorter strand of the paired sequence can then be elongated by adding monomers that weakly match to the overhanging longer strand. Then natural selection would have supported the increase of specificity of this process and helped to produce better copies of existing polymers. Invention of digital replication, therefore, may have been the turning point in the origin of life which supported unlimited hereditary potential (Jablonka & Szathmáry 1995; Sharov 2009; Szathmáry 2006) and caused a rapid increase in the abundance and complexity of coding elements.

8. Evolution of Genome Complexity Indicates Life Did Not Originate on Earth

Functional complexity of organisms can be approximately measured by the length of the nonredundant functional portion of the genome (Adami et al. 2000). The data on the size of nonredundant functional genome of major phylogenetic lineages was plotted against the time of their origin (Sharov 2006) (Fig. 2). Mammals have a genome of ca. 3.2 × 10⁹ bp, however only 5% of it is conserved between species (Waterson et al. 2002). Besides conserved regions, there may be additional functional regulatory regions in the genome that are species-specific. These regions, which can be identified based on the absence of transposons, account for 12-20% genome size (Simons et al. 2006). If we take 15% as a rough estimate, then the size of functional and non-redundant genome in mammals is 4.8 × 10⁸ bp. Fish originated 0.5 billion years ago (Miller et al. 2003), and its genome size is 4 × 10⁸ bp with 1/ 3 of it occupied by gene loci (Aparicio et al. 2002). Worms existed for at least for 1 billion years (Seilacher et al. 1998). The genome size of the Caenorhabditis elegans is 9.7 × 10⁷ bp and 75% of its length is functional (C.elegans Sequencing Consortium 1998). Eukaryote cells appeared between 2.3 and 1.8 billion years ago (Hedges et al. 2004), and prokaryotes existed on earth as early as 3.5 billion years ago (Furnes et al. 2004). The smallest eukaryote genome (2.9 × 10⁶ bp) was found in Encephalitozoon cunicul (Katinka et al. 2001), and the smallest prokaryote genome size (5 × 10⁵ bp) was found in Nanoarchaeum equitans (Waters et al. 2003) and Mycoplasma genitalium (Fraser et al. 1995). Prokaryotes and eukaryotes with the smallest genome are parasitic and may have a reduced genome size due to parasitism. However they were selected them to get the most conservative estimate for the time elapsed since the origin of life.

Figure 2. Regression of log genome complexity versus time of origin, modified from (Sharov 2006).

Using the regression of logarithm of functional complexity versus time (Fig. 2), it was shown that complexity increased exponentially with time, growing slowly ca. 7.8 fold per one billion years (Sharov 2006). This pattern of increase in complexity is consistent with the principle of gradualism. The exponential increase can be explained by several positive feedback mechanisms, which include gene cooperation, gene duplication, and creation of new functional niches for emerging genes (Sharov 2006).

The exponential model of increasing genome complexity can be used to predict the time of the origin of life. Based on the principle of gradualism, heredity started from single coding elements, and therefore, life originated at the time point where log genome complexity was zero. Based on the regression of log genome complexity versus time, the origin of life is projected around 10 billions years ago (Fig. 2), which implies the existence of panspermia or space transfer of primitive organisms, e.g., bacterial spores (Sharov 2006). Because two earliest points on the graph are most uncertain, Sharov (2006) did a sensitivity analysis by varying these points within the limits of uncertainty (± 300 Mya, and ± 0.3 log bp). With these variations the date of life origin may vary from 7 to 13 billion years which is still greater than the age of earth.

According to the exponential model, the early evolution of life was extremely slow. In particular, the "coenzyme world" stage of life may require >1 billion years of evolution because the emergence of a successful new coding elements without a universal coding mechanism was a rare event. If this model of biological evolution is correct (Sharov 2006), then the transition from the "coenzyme world" to "RNA world" occurred before the first living organisms appeared on earth.

The hypothesis of panspermia becomes more plausible if the solar system originated from the remnants of the exploded parental star (Joseph 2009). The increasingly powerful solar winds emitted by an expanding red giant, prior to supernova, can efficiently eject large numbers of microbes into space from a planet along with protective dust and debris. As the parent star loses mass which is blown into space by the solar winds, its gravitational hold on all orbiting planets would be lessened, and in consequence, entire planets would have been ejected from the dying solar system perhaps hundreds of millions of years prior to supernova (Joseph 2009). Under these latter conditions, billions of microbes and extremeophiles could continue to flourish deep beneath the surface of the ejected planets with no need to form spores. In fact, the Earth may have formed from the remnants of planets of the parent star, and the fragments of these primordial planets may have harbored large quantities of surviving microbes in the deep layers beneath the surface (Joseph 2009). Thus there is no need to limit panspermia to long inter-stellar travel of microbial spores. Therefore, these mechanisms may have brought life to Earth, and these same processes could be applied backwards in time, from solar system to solar system, to a point 10 billion years ago when the first living systems were formed.

The possibility of repeated and independent abiotic origins of life on other planets can be ruled out, if life indeed originated 10 billion years ago. For example, not only is the independent abiotic development of life unlikely, given the limiting conditions already detailed, but it would be unnecessary, as life could be transported from solar system to solar system and then from planet to planet, via panspermia (Arrhenius 2009; Burchell 2010; Joseph 2009). Only the discovery of extraterrestrial life with a completely different chemical organization and a genome radically different from that of life forms of Earth would call this theory into question, but certainly would not rule it out given the ability of prokaryotes to adapt to and colonize even the most extreme environments.

Future explorations of planets and satellites of the solar system can bring evidence supporting these hypothetical mechanisms of life's origin and transfer through space. In particular the following predictions can be tested. First, life should be present at least on some planets or satellites, because all of them are likely to be contaminated with microbial life during the formation of the solar system. Second, extraterrestrial life should have strong similarities to terrestrial life, including a phospholipid membrane, replication of nucleic acids, protein synthesis, and molecular chirality. The similarity may be even so deep that some extraterrestrial bacteria may fit well into the existing classification of Prokaryotes.Indeed, they may even possess the same genetic code, which would indicate the shared cosmic ancestry of all life in the Solar system.