Self-organization and Emergence in Life Sciences: 331 (Synthese Library)

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Varela - - Phenomenology and the Cognitive Sciences 1 2 Added to PP index Total views 48 , of 2,, Recent downloads 6 months 2 , of 2,, How can I increase my downloads? Over long timescales, these peptides would survive longer than those with weak affinities for targets or no stable secondary structure.

Thus, peptides with strong affinity ligand interactions would be favored at the expense of those that don't form stable complexes. This proposed modification of the chemical evolution model provides an abiotic selection mechanism for specific sets of peptides that bind to other compounds such as sugars, amino acids, metabolites, nucleic acids, etc.

Again, this portion of the model is based on first principles and the process of selection. Catalytic functionalization of peptides: The emergence of catalysis is a premise of the metabolism-first model [47]. Once peptides evolved to recognize molecules, some could possess weak catalytic activities that break or form covalent bonds, thus becoming primitive catalysis Figure 1, part III.

In fact, many short peptides are known to possess catalytic activities [see reviews [48—50]]. Even shorter peptides, such as Pro-Pro, have aldol condensation activity [52] and many other chemistries are catalyzed by short peptides []. Reaction products would be chemically distinct from the substrates, thus would likely have a less optimal interaction with the peptide catalyst. Since these catalysts were peptides and lack the intricate binding pocket of many enzymes, they many have acted on classes of compounds, rather than on specific molecules [53,54]. These primitive catalysts may represent an early predecessor step of more complex and efficient enzymes [55].

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There is also evidence supporting the hypothesis that short RNAs may also have emerged as weak catalysts [56]. Boundless propagating abiotic diversification of catalysts and molecules: As part of chemical evolution, I propose catalyst evolution through chemical synthesis. Catalytic peptides could have drastically altered the chemical composition of the primordial soup, concentrating certain chemicals, depleting others, and increasing the overall molecular complexity.

The evolution of primitive catalysts could provide a mechanism for generating new molecules including new types of amino acids, peptides, and possibly nucleic acids. The genesis of new peptides could give rise to new types of catalysts, akin to a concept called autocatalytic sets [7]. A feed-forward cyclic process could ensue wherein peptides catalyze the formation of newer catalysts that spawn new molecules and new peptide catalysts, gradually increasing the molecular and catalytic complexity of the primordial soup Figure 1, part IV. This scenario could set up an entropy-driven propagating abiotic diversification and expansion of more complex catalysts and more types of molecules, eventually leading to primitive metabolic pathways.

Many of the molecules in the glycolytic pathway may have arisen abiotically [57]. This expansion may be boundless, initially abiotic and still ongoing in living organisms, with new expansions of enzymes into the new catalytic spaces. At this point in the proposed model, the primordial soup would contain sets of peptides with strong affinity for small molecules and other sets of catalytic peptides. Two peptides, one with a binding activity and another with a catalytic activity, could fuse by peptide condensation reactions. This process could further drive the catalysts' generation cycle, ultimately producing primitive protein folds and enzymes that possessed both binding and catalytic activities Figure 1, part III.

Lupas et al.

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At some point in the above chemical and catalyst evolution, possibly at the earliest stages, peptides, perhaps working cooperatively catalyzed the synthesis of nucleic acids and other polymers such RNA. Peptides cooperating in catalysis have been observed and would provide a much broader depth of catalytic capability [55]. Like peptides, RNA served both a dual binding and catalytic function. However, I favor the emergence of RNA at later stages, given the apparent lack or breadth of catalytic diversity in extant RNAs where extant RNA catalysis is focused primarily on nucleic acids substrates and that abiotic synthesis of nucleic acids is difficult.

Peptides and proteins have a much broader repertoire of catalytic reaction types.

Metabolic evolution and the self-organization of ecosystems

This expanded view of chemical evolution need not be compartmentalized; however, for concentration of compounds and activities, encapsulation into self-organizing protocells is feasible. I suggest that some or many of the aforementioned steps could also have occurred within a bounded protocell type system as well, which is addressed later. A central concept applied so far in origin of life research is based on the premise that if synthesis of a compound under prebiotic conditions occurred, then it is feasible to have played a role in prebiotic evolution.

Considering that the time scale of the above events may be more than a billion years, any system that propagates molecular and catalytic diversity, as I have proposed, could explain abiotic synthesis of many of the molecules of life. I offer that a catalytic propagation model would be favored. As noted by Orgel, the puzzle is how we get from a soup of prebiotic organic molecules to the RNA world [61]? Others have questioned this as well, suggesting that genetic systems simpler than RNA may have served as a predecessor [8,24,].

In contrast to the sophisticated high-fidelity nucleic acid-based inheritance observed in extant organisms and proposed in the RNA world, I hypothesize a lower fidelity predecessor where a simpler, less-exact stepwise process gave rise to the first hereditary information system.

In early protocells, or life forms it was important to pass on the catalytic information needed for metabolism. At the onset of life, it would seem beneficial to have catalytic and hereditary functions embodied in the same molecule such that specific molecular recognition and catalytic capability could be inherited together.


Since ribozymes are catalytic, RNA could have served a dual function - as both a catalyst for reactions and as the hereditary material [66]. This is an attractive feature of the RNA world model. I consider the inverse: How could a catalytic system based on RNA be almost completely supplanted by proteins? Is it not possible that peptides were the original catalysts and, like RNA, had a second hereditary function that was supplanted by RNA?

Many have suggested a predecessor of the RNA world, so herein, I focus on evidence consistent with the minimotif synthesis hypothesis. However, it is entirely possible that peptides as catalysts, and RNA as hereditary material, were born of abiotic chemical evolution and then converged into a translational system later in protocells and biopoesis of the first life forms. As long as a template could be used to self-replicate peptide catalysts, nothing more is required for the genesis of peptide-based inheritance of molecular recognition and catalysis.

Proteins clearly have a much wider breadth and efficiency as catalysts than RNAs.

There is evidence that peptides could have had such templates, in that many extant protein structures and protein-protein interactions show secondary structure interactions with degeneracy. Those peptides that formed peptide-peptide interactions may have served as the initial pre-genomic genetic material. This hypothesis is akin to the Graded Autocatalysis Replication Domain GARD model previously proposed for chemical inheritance, but has the advantage of a potential replication mechanism [67].

The amino acids aligned on the template through side chain interactions could be covalently joined forming peptide bonds with the aid of a catalyst, similar to the mechanism of semiconservative DNA replication Figure 2A. Alternatively, as previously hypothesized, peptides could have replicated through a autocatalytic cyclic network involving two our more peptides [72].

Furthermore, several small peptides, such as Ser-His and Gly-Gly, have been shown to catalyze peptide bond formation [58,59]. These peptides could have served as a primitive form of the non-ribosomal peptide synthesis prevalent in modern life [see Norine tabase [73]. Figure 2.

Minimotif synthesis model for peptide catalyst evolution from primordial soup. In Part I, stable interactions occur between compounds and amino acids, and among amino acids. The grayed figures are compounds and the colored compounds are amino acids. In Part II, peptide:compound and peptide:peptide complexes are more stable than uncomplexed peptides. Te most stable complexes, and molecules emerge out of the primordial soup. In Part III, some peptides or peptide complexes produce the first catalysts. These catalysts evolved, producing new molecules leading to new molecular interactions and new peptide interactions, and thus new catalysts in a cycle parts III and IV. Inger et al. However, one limitation noted was that such a system is incapable of evolution [75]. My model of minimotifosome replication provides an intuitive solution to this problem.

These minimotifosomes could have had dual functionality, serving both as primitive catalysts and as the hereditary material, thus providing a simpler, primitive means for inheritance of catalytic capabilities.

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The semi-conservative replication of minimotifosomes need not be perfect to provide a mechanism to pass on chemical catalysis information and to allow for mutation, selection, and thus, evolution. The lack of fidelity for non-contact amino acids could have been the first genetic source of mutation and genetic diversity, and acted upon by selection. Some random coil minimotifs might have offered the highest genetic fidelity. A subset of such random coils could have been primitive genetic information with mutation occurring by degenerate recognition.