Autocatalytic Sets and the Origin of Life

Abstract

The origin of life is one of the most fundamental, but also one of the most difficult problems in science. Despite differences between various proposed scenarios, one common element seems to be the emergence of an autocatalytic set or cycle at some stage. However, there is still disagreement as to how likely it is that such self-sustaining sets could arise "spontaneously". This disagreement is largely caused by the lack of formal models. Here, we briefly review some of the criticism against and evidence in favor of autocatalytic sets, and then make a case for their plausibility based on a formal framework that was introduced and studied in our previous work.Keywords: origin of life; autocatalytic sets; RAF sets The Origin of LifeThe origin of life (OoL) remains an elusive problem, although much progress has been made in recent years. Having gone from a problem considered 'beyond science' to 'solvable in principle but maybe not in practice', many researchers now believe it will be solved in the next few decades. In fact, there are currently several OoL scenarios, but all still have some difficulties and lacunae. Although often quite different in their details, one common element which most of these scenarios have is the appearance of an autocatalytic set or cycle at some stage.Entropy 2010, 12 1734 1.1. An RNA world All life as we know it depends on a delicate interplay between DNA and proteins. However, this DNA-protein machinery seems too complex to have arisen all at once. So there appears to be a "chicken-and-egg" problem: which came first, the chicken (protein, phenotype), or the egg (DNA, genotype)?The most widely accepted resolution of this problem is that of an RNA world [1-3] preceding DNA and proteins, i.e., a collection of (self-)replicating RNA molecules, using template complementarity plus the ability to perform and catalyze their own (or each others) synthesis as a way of achieving reproduction and self-sustainability. The possibility of an RNA world has some experimental support, and is now generally considered to have been an important step in the origin of life [4,5]. However, an RNA world "spontaneously" generating proteins and DNA is not straightforward, and is certainly not (yet) proven beyond any doubt. Moreover, and perhaps more importantly, the initial appearance of an RNA world itself is still mostly an open question [2,3,6,7]. Prebiotic metabolismThe idea of a "primordial soup" [8] spontaneously generating the basic building blocks for life sounded attractive after some initial experiments along these lines [9,10], but has been much debated since then and criticized as not being capable of creating these building blocks in sufficiently large concentrations. So, there must have been something more sustainable to get anything like an RNA world started.A basic element underlying all metabolism (and therefore believed to be of very ancient origins) is the citric acid (or Krebs) cycle. This is a chemical reaction network involving a cyclic sequence of 11 substrates and reactions. It ...

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“…Autocatalysis is a basic property of life [9,14,15,63,64]. Furthermore, the catalytic functionalities and self-reproduction processes of life are supported in intrinsically chiral systems: this means that there is experimental evidence that life is based on enantioselective autocatalysis [65].…”

“…Autocatalysis is a necessary condition for life [2,14] and emerges during the evolutionary stage of the onset of replicator molecules and template mechanisms of self-reproduction. The emergence of primordial replicators is simulated in systems leading to steady state dynamics, such as those of the living cell, as was already quoted by Oparin [15] and later, subsequently formulated on a physical chemistry basis (see for example [16][17][18]).…”

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“…While initially that process of imperfect replication might involve the preferential formation of the more rapid replicating oligomeric sequences, as demonstrated in the classic RNA replication experiments of Mills et al [16], the emergence of replicating networks (also termed autocatalytic sets) [2,6,47,48] with their enhanced replicating capability in comparison with individual molecular replicators, would open up new kinetic options within replicator space. And those particular sequences that would be capable of catalyzing the formation of other chemical classes, e.g., peptides, that exhibit catalytic activity with respect to the replication reaction itself, would further add to the process of complexification and evolution toward more stable dynamic kinetic systems.…”

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“…Hordijk and Steel [34] and Hordijk et al [35] define their chemical reaction system by a tuple Q = {X, R, C}, (their symbols) in which X is a set of molecular types, R a set of reactions and C a set of catalytic relations specifying which molecular types catalyse each member of R. The system is also provided with a set of resource molecules F ⊆ X, freely available in the environment, to serve as raw materials for anabolism (noting that whilst we are defining an organisational closure, we may (and indeed must) permit the system to be materially and thermodynamically open). The autocatalytic set is that subset of reactions R ⊆ R, strictly involving the subset X ⊆ X, which is:…”