Compositional Inheritance: Comparison of Self-assembly and Catalysis

Wu, Meng; Higgs, Paul G.

doi:10.1007/s11084-008-9143-4

Cited by 15 publications

(5 citation statements)

References 42 publications

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“…The GARD has recently been pursued in several additional publications [20,39,68,70] and has been chosen as an archetypal metabolism-first realization [68]. This suggests that despite being a simulated toy model, the GARD has sufficient complexity to shed light on some important questions in the field of prebiotic origins.…”

Section: Resultsmentioning

confidence: 99%

“…This is repeated for GEN splits (Table 1). This protocol is based on the classical Moran process [36,68,70], and to some degree reflects an earlier attempt to simulate GARD populations [38]. The frequency of the target in each population is defined as the number of assemblies that are highly similar (H ≥ 0.9) to the target compotype taken from regular GARD for the same h network ( Figure 13 in Appendix A.4).…”

Section: Selection Dynamics In a Population Of Compositional Assembliesmentioning

confidence: 99%

“…Previously, GARD population dynamics has been studied by addressing various emergent properties, including a comparison of finite and infinite chemical environments [38]. Another study [70] showed that compositional inheritance also emerges in the GARD model variants involving assembly populations and spatial proximity interaction effects, and that it emerges in both a thermodynamic and a kinetic interaction regimen.…”

Section: Selection In a Gardmentioning

confidence: 99%

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Excess Mutual Catalysis Is Required for Effective Evolvability

Markovitch

Lancet

2012

Artificial Life

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It is widely accepted that autocatalysis constitutes a crucial facet of effective replication and evolution (e.g., in Eigen's hypercycle model). Other models for early evolution (e.g., by Dyson, Gánti, Varela, and Kauffman) invoke catalytic networks, where cross-catalysis is more apparent. A key question is how the balance between auto- (self-) and cross- (mutual) catalysis shapes the behavior of model evolving systems. This is investigated using the graded autocatalysis replication domain (GARD) model, previously shown to capture essential features of reproduction, mutation, and evolution in compositional molecular assemblies. We have performed numerical simulations of an ensemble of GARD networks, each with a different set of lognormally distributed catalytic values. We asked what is the influence of the catalytic content of such networks on beneficial evolution. Importantly, a clear trend was observed, wherein only networks with high mutual catalysis propensity (p(mc)) allowed for an augmented diversity of composomes, quasi-stationary compositions that exhibit high replication fidelity. We have reexamined a recent analysis that showed meager selection in a single GARD instance and for a few nonstationary target compositions. In contrast, when we focused here on compotypes (clusters of composomes) as targets for selection in populations of compositional assemblies, appreciable selection response was observed for a large portion of the networks simulated. Further, stronger selection response was seen for high p(mc) values. Our simulations thus demonstrate that GARD can help analyze important facets of evolving systems, and indicate that excess mutual catalysis over self-catalysis is likely to be important for the emergence of molecular systems capable of evolutionlike behavior.

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Section: Resultsmentioning

confidence: 99%

Section: Selection Dynamics In a Population Of Compositional Assembliesmentioning

confidence: 99%

Section: Selection In a Gardmentioning

confidence: 99%

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Excess Mutual Catalysis Is Required for Effective Evolvability

Markovitch

Lancet

2012

Artificial Life

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“…One other concept that will require convincing future corroboration is that composition is a valid form of cross-generational information transfer. A highly relevant study by Paul Higgs [60] has investigated this question in depth. The study highlights the complexity of the genetic apparatus controlling inheritance in modern cells and brings forth the question of whether "some other form of heredity is possible without polymers".…”

Section: The Future Of Lipid Worldmentioning

confidence: 99%

Twenty Years of “Lipid World”: A Fertile Partnership with David Deamer

Lancet,

Segrè,

Kahana

2019

Life

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“The Lipid World” was published in 2001, stemming from a highly effective collaboration with David Deamer during a sabbatical year 20 years ago at the Weizmann Institute of Science in Israel. The present review paper highlights the benefits of this scientific interaction and assesses the impact of the lipid world paper on the present understanding of the possible roles of amphiphiles and their assemblies in the origin of life. The lipid world is defined as a putative stage in the progression towards life’s origin, during which diverse amphiphiles or other spontaneously aggregating small molecules could have concurrently played multiple key roles, including compartment formation, the appearance of mutually catalytic networks, molecular information processing, and the rise of collective self-reproduction and compositional inheritance. This review brings back into a broader perspective some key points originally made in the lipid world paper, stressing the distinction between the widely accepted role of lipids in forming compartments and their expanded capacities as delineated above. In the light of recent advancements, we discussed the topical relevance of the lipid worldview as an alternative to broadly accepted scenarios, and the need for further experimental and computer-based validation of the feasibility and implications of the individual attributes of this point of view. Finally, we point to possible avenues for exploring transition paths from small molecule-based noncovalent structures to more complex biopolymer-containing proto-cellular systems.

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“…3 The problem of a simple mechanism for RNA synthesis remains unanswered. In response some markedly different catalytic systems have been proposed for the origin of life including stacking of heterocyclic bases in the absence of a backbone, 11,12 compositional catalysis by assemblies of lipid molecules, 13,14 and catalysis by mixtures of random oligomers formed from prebiotically available molecules. [15][16][17] Proposals that do not include linear replicating polymers have to explain the eventual synthesis of RNA together with the metabolism needed to support it.…”

Section: Rna Has An Evolutionary Historymentioning

confidence: 99%

An alternative to the RNA World Hypothesis

Francis

2011

Trends Evol Biol

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The RNA world hypothesis for the origin of life is widely accepted in spite of the complexity of RNA synthesis. An alternative hypothesis is advanced for the origin and evolution of protein and nucleic acid synthesis. From an early stage synthesis of the evolutionary predecessors of nucleic acids and polypeptides was coupled. This evolved into an RNA replication process that used 3'-aminoacyl-NMP monomers (N= pyrimidine or purine) with a singlet coding system in which the four bases coded for glycine, alanine, valine and aspartic acid. Ribosomal protein synthesis (RPS) evolved from coupled replication by using tRNAs and separating fidelity checking and peptide bond formation functions into small and large ribosomal subunits. Continuity was maintained during the transition to the triplet process by using the same catalysts that aminoacylated NMPs to aminoacylate four different bases at the 3' ends of the original tRNAs. Four GNC codons used the central base to designate the same four amino acids that were coded in singlet replication. Triplet-coded protein synthesis had the advantage of producing multiple copies of protein from a single copy of RNA, and eventually replaced protein synthesis via singlet-coded replication. Evolution of the simple triplet-coded process into RPS is described.

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Compositional Inheritance: Comparison of Self-assembly and Catalysis

Cited by 15 publications

References 42 publications

Excess Mutual Catalysis Is Required for Effective Evolvability

Excess Mutual Catalysis Is Required for Effective Evolvability

Twenty Years of “Lipid World”: A Fertile Partnership with David Deamer

An alternative to the RNA World Hypothesis

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