Population Dynamics of Autocatalytic Sets in a Compartmentalized Spatial World

Abstract

Autocatalytic sets are self-sustaining and collectively catalytic chemical reaction networks which are believed to have played an important role in the origin of life. Simulation studies have shown that autocatalytic sets are, in principle, evolvable if multiple autocatalytic subsets can exist in different combinations within compartments, i.e., so-called protocells. However, these previous studies have so far not explicitly modeled the emergence and dynamics of autocatalytic sets in populations of compartments in a spatial environment. Here, we use a recently developed software tool to simulate exactly this scenario, as an important first step towards more realistic simulations and experiments on autocatalytic sets in protocells.

The Influence of Modularity, Seeding, and Product Inhibition on Peptide Autocatalytic Network Dynamics

“…Network modularity has been shown to be crucial for the potential evolvability of autocatalytic sets ,,. Such modularity clearly exists within the theoretically calculated peptide network, both in terms of the network analysis (in the form of closed RAFs) and in the dynamical simulations (in the form of different possible relative abundances of the various peptides).…”

Thresholds in Origin of Life Scenarios

“…In Figure 3 D, systems A and B both in α merge into a new system C located in β in a constant environment. Such transition is hypothesized when compartments meet autocatalytic chemistries ( Hordijk et al., 2018 ; Joyce and Szostak, 2018 ). Both may pre-exist separately, but evolution by natural selection requires autocatalytic chemistries to be compartmentalized in order to provide a collective level of selection ( Vasas et al., 2012 ).…”

Autocatalytic Networks at the Basis of Life’s Origin and Organization

“…For example, the RAF set in Figure 3, consisting of five reactions (labeled r1 to r5) contains the smaller subRAFs {r1,r2} (indicated in red) and {r3,r4,r5} (indicated in blue). This property provides one of the necessary conditions for autocatalytic sets to be potentially evolvable [39,40,41,42]. The concept of autocatalytic sets has also been studied in related models and contexts, all giving rise to similar results in terms of the probability of their existence and potential evolvability [17,18,19,43,44,45,46,47,48,49,50,51].…”

“…This requirement for initial spontaneous reactions, however, provides one of the basic requirements for autocatalytic sets to be (potentially) evolvable [39,40,41,42]. Since such spontaneous reactions are rare stochastic events, different repetitions of the same experiment or simulation can give rise to different combinations of subRAFs coming into existence dynamically, potentially giving rise to different types of “protocells” that can then compete with each other (e.g., for food resources) and undergo a rudimentary form of evolution [42]. In this form of evolution, inheritance is compositional (in terms of which subRAF are currently present, dynamically), and mutations are the (spontaneous) gain or loss of a (closed) subRAF.…”

“…Since the formal RAF framework has already been successfully applied to the existing experimental systems, providing useful additional insights [52,53,54], such theoretical and computational studies could hopefully also serve as a guide in constructing experimental autocatalytic sets with both RNA and peptides. Furthermore, simulation studies of “partitioned” autocatalytic sets within protocells, following recent initial dynamical studies of autocatalytic sets in compartments [42], could provide additional insights into the possible early evolution of such two-polymer type systems.…”