Defining Autocatalysis in Chemical Reaction Networks

Andersen, Jakob L.; Flamm, Christoph; Merkle, Daniel; Stadler, Peter F.

doi:10.48550/arxiv.2107.03086

Cited by 5 publications

(7 citation statements)

References 43 publications

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“…For anyone who knows Louis Pasteur’s gooseneck flask experiment and accepts that a bacterium is an autocatalyst, the idea of seeding should be straightforward – an autocatalytic system can, once seeded, propagate itself in the presence of food but cannot spontaneously emerge from food alone. Multiple researchers have stressed this feature of autocatalytic systems, although with different terminology and framing, for example “obligate autocatalyst” [ 59 ], “exclusive autocatalysis” [ 60 ], and “reactions that are part of autocatalytic cycles” but are not accessible by “direct synthesis reactions” [ 25 ].…”

Section: Discussionmentioning

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: Discussionmentioning

confidence: 99%

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

2022

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“…This is particularly relevant, as a number of papers (e.g. [31][32][33][34]) have pointed to the restrictive nature of RAFs in requiring that all reactions in the RAF must be catalysed. For example, the authors of [31] stated: 'Here, the assumption that all reactions are catalysed appears very unrealistic.…”

Section: The Interpretation Of Catalysis and Autocatalysis In Rafsmentioning

confidence: 99%

Self-generating autocatalytic networks: structural results, algorithms and their relevance to early biochemistry

Huson,

Xavier,

Steel

2024

J. R. Soc. Interface.

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The concept of an autocatalytic network of reactions that can form and persist, starting from just an available food source, has been formalized by the notion of a reflexively autocatalytic and food-generated (RAF) set. The theory and algorithmic results concerning RAFs have been applied to a range of settings, from metabolic questions arising at the origin of life, to ecological networks, and cognitive models in cultural evolution. In this article, we present new structural and algorithmic results concerning RAF sets, by studying more complex modes of catalysis that allow certain reactions to require multiple catalysts (or to not require catalysis at all), and discuss the differing ways catalysis has been viewed in the literature. We also focus on the structure and analysis of minimal RAFs and derive structural results and polynomial-time algorithms. We then apply these new methods to a large metabolic network to gain insights into possible biochemical scenarios near the origin of life.

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“…A potential general framework for describing adaptive change during origins of life lies in ecosystem ecology [32][33][34]. As discussed in the remainder of this paper, there is reason to suspect that by merging an ecological perspective with recent advances in understanding the properties and dynamics of chemical reaction networks [35][36][37][38][39][40][41] it may be possible to build a general, chemically agnostic theory for the origin of life. Such a theory would explain adaptive change independent of the existence of genetic polymers or cell-like encapsulation and could be used, therefore, to explore the possibility that genes and cells are products of gradual evolution.…”

Section: On the Origin Of Evolution: The State Of Playmentioning

confidence: 99%

The ecology–evolution continuum and the origin of life

Baum,

Peng,

Dolson

et al. 2023

J. R. Soc. Interface.

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Prior research on evolutionary mechanisms during the origin of life has mainly assumed the existence of populations of discrete entities with information encoded in genetic polymers. Recent theoretical advances in autocatalytic chemical ecology establish a broader evolutionary framework that allows for adaptive complexification prior to the emergence of bounded individuals or genetic encoding. This framework establishes the formal equivalence of cells, ecosystems and certain localized chemical reaction systems as autocatalytic chemical ecosystems (ACEs): food-driven (open) systems that can grow due to the action of autocatalytic cycles (ACs). When ACEs are organized in meta-ecosystems, whether they be populations of cells or sets of chemically similar environmental patches, evolution, defined as change in AC frequency over time, can occur. In cases where ACs are enriched because they enhance ACE persistence or dispersal ability, evolution is adaptive and can build complexity. In particular, adaptive evolution can explain the emergence of self-bounded units (e.g. protocells) and genetic inheritance mechanisms. Recognizing the continuity between ecological and evolutionary change through the lens of autocatalytic chemical ecology suggests that the origin of life should be seen as a general and predictable outcome of driven chemical ecosystems rather than a phenomenon requiring specific, rare conditions.

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Defining Autocatalysis in Chemical Reaction Networks

Cited by 5 publications

References 43 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

Self-generating autocatalytic networks: structural results, algorithms and their relevance to early biochemistry

The ecology–evolution continuum and the origin of life

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