Diversity, stability, and evolvability in models of early evolution

Scheuring, István; Szilágyi, András

doi:10.1016/j.coisb.2018.12.007

Cited by 3 publications

(2 citation statements)

References 57 publications

(58 reference statements)

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“…Being autocatalytic is necessary but not sufficient for evolution. There has been much discussion about what additional ingredients are needed for evolvability [28][29][30][31], but several scientists have suspected that the accretion of complexity is possible when chemical reaction systems contain multiple interacting autocatalytic motifs that can be triggered sequentially by rare, stochastic events [26,[32][33][34]. However, we still lack a clear understanding of how stoichiometrically autocatalytic motifs are organized in real chemical reaction networks and whether that organization allows for gradual, adaptive complexification.…”

Section: Introductionmentioning

confidence: 99%

The hierarchical organization of autocatalytic reaction networks and its relevance to the origin of life

2022

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Prior work on abiogenesis, the emergence of life from non-life, suggests that it requires chemical reaction networks that contain self-amplifying motifs, namely, autocatalytic cores. However, little is known about how the presence of multiple autocatalytic cores might allow for the gradual accretion of complexity on the path to life. To explore this problem, we develop the concept of a seed-dependent autocatalytic system (SDAS), which is a subnetwork that can autocatalytically self-maintain given a flux of food, but cannot be initiated by food alone. Rather, initiation of SDASs requires the transient introduction of chemical “seeds”. We show that, depending on the topological relationship of SDASs in a chemical reaction network, a food-driven system can accrete complexity in a historically contingent manner, governed by rare seeding events. We develop new algorithms for detecting and analyzing SDASs in chemical reaction databases and describe parallels between multi-SDAS networks and biological ecosystems. Applying our algorithms to both an abiotic reaction network and a biochemical one, each driven by a set of simple food chemicals, we detect SDASs that are organized as trophic tiers, of which the higher tier can be seeded by relatively simple chemicals if the lower tier is already activated. This indicates that sequential activation of trophically organized SDASs by seed chemicals that are not much more complex than what already exist could be a mechanism of gradual complexification from relatively simple abiotic reactions to more complex life-like systems. Interestingly, in both reaction networks, higher-tier SDASs include chemicals that might alter emergent features of chemical systems and could serve as early targets of selection. Our analysis provides computational tools for analyzing very large chemical/biochemical reaction networks and suggests new approaches to studying abiogenesis in the lab.

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Section: Introductionmentioning

confidence: 99%

The hierarchical organization of autocatalytic reaction networks and its relevance to the origin of life

2022

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“…However, Maynard Smith [19] raised important objection that hypercycles are vulnerable to parasites in homogeneous solutions [22,25,[30][31][32][33]. It has been shown, that while such system is able to maintain its diversity, it is evolutionary and ecologically unstable and its evolvability is limited [34,35]. Boerlijst and Hogeweg were the first to show that the problem of negative impact of parasites can be reduced by considering spatially organized systems [22].…”

Section: Introductionmentioning

confidence: 99%

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

2020

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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.

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Hitting Times of Some Critical Events in RNA Origins of Life

Bastian

Rabitz

2021

Life

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Can a replicase be found in the vast sequence space by random drift? We partially answer this question through a proof-of-concept study of the times of occurrence (hitting times) of some critical events in the origins of life for low-dimensional RNA sequences using a mathematical model and stochastic simulation studies from Python software. We parameterize fitness and similarity landscapes for polymerases and study a replicating population of sequences (randomly) participating in template-directed polymerization. Under the ansatz of localization where sequence proximity correlates with spatial proximity of sequences, we find that, for a replicating population of sequences, the hitting and establishment of a high-fidelity replicator depends critically on the polymerase fitness and sequence (spatial) similarity landscapes and on sequence dimension. Probability of hitting is dominated by landscape curvature, whereas hitting time is dominated by sequence dimension. Surface chemistries, compartmentalization, and decay increase hitting times. Compartmentalization by vesicles reveals a trade-off between vesicle formation rate and replicative mass, suggesting that compartmentalization is necessary to ensure sufficient concentration of precursors. Metabolism is thought to be necessary to replication by supplying precursors of nucleobase synthesis. We suggest that the dynamics of the search for a high-fidelity replicase evolved mostly during the final period and, upon hitting, would have been followed by genomic adaptation of genes and to compartmentalization and metabolism, effecting degree-of-freedom gains of replication channel control over domain and state to ensure the fidelity and safe operations of the primordial genetic communication system of life.

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Diversity, stability, and evolvability in models of early evolution

Cited by 3 publications

References 57 publications

The hierarchical organization of autocatalytic reaction networks and its relevance to the origin of life

The hierarchical organization of autocatalytic reaction networks and its relevance to the origin of life

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

Hitting Times of Some Critical Events in RNA Origins of Life

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