Multi-agent approach to sequence structure simulation in the RNA World hypothesis

Abstract

The origins of life on Earth have been the subject of inquiry since the early days of philosophical thought and are still intensively investigated by the researchers around the world. One of the theories explaining the life emergence, that gained the most attention recently is the RNA World hypothesis, which assumes that life on Earth was sparked by replicating RNA chains. Since wet lab analysis is time-consuming, many mathematical and computational approaches have been proposed that try to explain the origins of life. Recently proposed one, based on the work by Takeuchi and Hogeweg, addresses the problem of interplay between RNA replicases and RNA parasitic species, which is crucial for understanding the first steps of prebiotic evolution. In this paper, the aforementioned model has been extended and modified by introducing RNA sequence (structure) information and mutation rate close to real one. It allowed to observe the simple evolution mechanisms, which could have led to the more complicated systems and eventually, to the formation of the first cells. The main goal of this study was to determine the conditions that allowed the spontaneous emergence and evolution of the prebiotic replicases equipped with simple functional domains within a large population. Here we show that polymerase ribozymes could have appeared randomly and then quickly started to copy themselves in order for the system to reach equilibrium. It has been shown that evolutionary selection works even in the simplest systems.

RNA World Modeling: A Comparison of Two Complementary Approaches

“…The replicase-parasite model (RP model) was initially developed by Takeuchi and Hogeweg [38] and later extended in [41,42], where it was simulated and analyzed using multi-agent systems (MASs). In this model, the population of RNA molecules consists of replicases and parasites.…”

“…The above-mentioned replicase-parasite surface model was further extended and verified in [41,42], where, in order to increase the model precision, a multi-agent-based approach (MAS) with more realistic assumptions regarding the movement of entities (diffusion) was applied. As in typical MAS implementation, it consisted of agents and their environment.…”

“…In [41], each molecule was equipped with only two parameters, with l being the fraction of time spent in the folded state and a being the affinity towards replicases. Next, in [42], the RP model was modified by taking into account the RNA sequence (structure) information and a mutation rate close to the real one. The obtained results provided grounds for drawing the conclusion, which was that, in a prebiotic environment, RNA replicases could have appeared randomly, and that evolutionary selection can be observed even in a very simple network [42].…”

“…On the other hand, the MAS model represents a microscopic description, where a discrete population is composed of single particles (agents) interacting in a given dynamic environment. Here, in contrast to [41,42], a simplified model is considered, where each molecule is characterized by only one parameter connected with the affinity towards replicases.…”

Emergence of structures from parasitic species in a spatially distributed molecular system

“…Such approach is particularly relevant to test for the probability of emergence of a given phenomenon (Rabajante et al, 2015;Hickinbotham et al, 2021) or scenarios based on hypothesis of the conditions of the early Earth (Scharf et al, 2015). For instance, chemical systems that are hard to reproduce in-vitro, such as the RNA world hypothesis (Gilbert, 1986), can be thoroughly examined under a large range of parameters, showing that, given the right conditions, RNA replicator system may not be overrun by parasites (Synak et al, 2020).…”