A formal model of autocatalytic sets emerging in an RNA replicator system

Background: The idea that autocatalytic sets played an important role in the origin of life is not new. However, the likelihood of autocatalytic sets emerging spontaneously has long been debated. Recently, progress has been made along two different lines. Experimental results have shown that autocatalytic sets can indeed emerge in real chemical systems, and theoretical work has shown that the existence of such self-sustaining sets is highly likely in formal models of chemical systems. Here, we take a first step towards merging these two lines of work by constructing and investigating a formal model of a real chemical system of RNA replicators exhibiting autocatalytic sets. Results: We show that the formal model accurately reproduces recent experimental results on an RNA replicator system, in particular how the system goes through a sequence of larger and larger autocatalytic sets, and how a cooperative (autocatalytic) system can outcompete an equivalent selfish system. Moreover, the model provides additional insights that could not be obtained from experiments alone, and it suggests several experimentally testable hypotheses. Conclusions: Given these additional insights and predictions, the modeling framework provides a better and more detailed understanding of the nature of chemical systems in general and the emergence of autocatalytic sets in particular. This provides an important first step in combining experimental and theoretical work on autocatalytic sets in the context of the orgin of life. 1 ar X iv :1 21 1. 34 73 v1 [ qbi o. M N ] 1 5 N ov 2 01 2 Background Recently, significant new experimental results on spontaneous network formation among cooperative RNA replicators were reported [1]. These results continue and strengthen a line of ongoing work on creating autocatalytic sets in real chemical systems [2–5]. Moreover, they show the plausibility and viability of the idea of autocatalytic sets, especially in the context of the origin of life, as already developed in various forms several decades ago [6–12]. However, such chemical experiments, important as they are, are difficult, costly, and time-consuming to perform. In contrast, in our own work we have developed a theoretical framework of autocatalytic sets, which we consider a necessary condition for the origin of life, that can be studied computationally and mathematically [13–20]. This framework has provided many important insights into the emergence and structure of autocatalytic sets in its own right, and is considered to provide theoretical support for experimental observations [1, 21]. The formal framework has, so far, mostly been applied to an abstract model of a chemical reaction system known as the binary polymer model. Even though this model already has a fair amount of chemical realism (for example, some recent experiments are an almost literal chemical implementation of the binary polymer model [5]), a direct application to a real chemical system was still lacking. Here, we construct and analyze a formal model version of the recent experimental RNA replicator system [1], and show how this results in: • an accurate reproduction of experimental results, • the correction of a misinterpretation of some of the original results, • additional results and insights that could not be obtained from the experiments alone, and • testable predictions about the behavior of the chemical system. With this, we claim that the formal framework can be applied directly and meaningfully to real chemical systems, generating additional insights and predictions that are hard to obtain from experiments alone, thus providing a better understanding of real (bio)chemical systems. This represents an important first step towards merging experimental and theoretical work on autocatalytic sets. Chemical reaction systems and autocatalytic sets We begin by briefly reviewing the relevant definitions and main results of the formal framework. A chemical reaction system (CRS) is defined as a tuple Q = {X,R, C} consisting of a set of molecule types