Origins of life: first came evolutionary dynamics

Kocher, Charles; Dill, Ken A.

doi:10.1017/qrd.2023.2

Cited by 4 publications

(9 citation statements)

References 107 publications

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“…It is worth noting that UCA is the ‘most recent’ UCA or the ‘last’ UCA of a lineage of cellular species since the origins of cells; evolutionary telescopes cannot peer into pre-UCA or pre-cellular epochs of evolution (Kurland and Harish, 2015a ). However, plausible models of pre-UCA and pre-cellular evolution can be developed based on our knowledge of the biophysical and biochemical constraints that govern protein folding and protein evolution, independently of the use of evolutionary telescopes (Abroi and Gough, 2011 ; Norden, 2021 ; Kocher and Dill, 2023 ).…”

Section: Farsightedness and Nearsightednessmentioning

confidence: 99%

Protein structures unravel the signatures and patterns of deep time evolution

Harish

2024

QRB Discovery

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The formulation and testing of hypotheses using ‘big biology data’ often lie at the interface of computational biology and structural biology. The Protein Data Bank (PDB), which was established about 50 years ago, catalogs three-dimensional (3D) shapes of organic macromolecules and showcases a structural view of biology. The comparative analysis of the structures of homologs, particularly of proteins, from different species has significantly improved the in-depth analyses of molecular and cell biological questions. In addition, computational tools that were developed to analyze the ‘protein universe’ are providing the means for efficient resolution of longstanding debates in cell and molecular evolution. In celebrating the golden jubilee of the PDB, much has been written about the transformative impact of PDB on a broad range of fields of scientific inquiry and how structural biology transformed the study of the fundamental processes of life. Yet, the transforming influence of PDB on one field of inquiry of fundamental interest—the reconstruction of the distant biological past—has gone almost unnoticed. Here, I discuss the recent advances to highlight how insights and tools of structural biology are bearing on the data required for the empirical resolution of vigorously debated and apparently contradicting hypotheses in evolutionary biology. Specifically, I show that evolutionary characters defined by protein structure are superior compared to conventional sequence characters for reliable, data-driven resolution of competing hypotheses about the origins of the major clades of life and evolutionary relationship among those clades. Since the better quality data unequivocally support two primary domains of life, it is imperative that the primary classification of life be revised accordingly.

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Section: Farsightedness and Nearsightednessmentioning

confidence: 99%

Protein structures unravel the signatures and patterns of deep time evolution

Harish

2024

QRB Discovery

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“…We now give a model at the micro level. The Foldcat Mechanism, described previously [36,38,40,69], postulates that the synthesis of random short-chain peptides leads to small populations of longer protein molecules that can both fold and catalyse chemical reactions [28,48,[70][71][72][73]; see figure 2. Short random HP (hydrophobic/polar, referring to the two types of monomers) peptides are synthesized, catalysed at first through some macroscale object, like clays or minerals which, as shorthand, we call the Founding Rock.…”

Section: The Foldcat Mechanism and Its Emergent Evolutionary Dynamicsmentioning

confidence: 99%

“…We reason instead about what driving forces and dynamics would have led to sustained bio-like propagation [36][37][38][39][40][41]. Why was there any tendency at all to create biology?…”

Section: Introductionmentioning

confidence: 99%

“…Life cannot originate until it can propagate. This prebiotic evolution-like process could then act as the driving force that steered prebiotic chemistry toward biology [38,40,43], instead of toward 'asphaltization' or other dead-ends [44][45][46][47]. The question of the origin of life then becomes a search for the origin of some dynamical evolutionary mechanism or process.…”

Section: Introductionmentioning

confidence: 99%

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The prebiotic emergence of biological evolution

Kocher,

Dill

2024

R. Soc. Open Sci.

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The origin of life must have been preceded by Darwin-like evolutionary dynamics that could propagate it. How did that adaptive dynamics arise? And from what prebiotic molecules? Using evolutionary invasion analysis, we develop a universal framework for describing any origin story for evolutionary dynamics. We find that cooperative autocatalysts, i.e. autocatalysts whose per-unit reproductive rate grows as their population increases, have the special property of being able to cross a barrier that separates their initial degradation-dominated state from a growth-dominated state with evolutionary dynamics. For some model parameters, this leap to persistent propagation is likely, not rare. We apply this analysis to the Foldcat Mechanism , wherein peptides fold and help catalyse the elongation of each other. Foldcats are found to have cooperative autocatalysis and be capable of emergent evolutionary dynamics.

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“…Peptides may have also played a role in the formation of the first cell membranes ( 18 , 19 ). Therefore, the major role of peptides in the origin of life was suggested ( 2 , 20 , 21 ). On early Earth, peptide synthesis typically considers occurring through the polymerization of amino acids.…”

Section: Introductionmentioning

confidence: 99%

Formation of extraterrestrial peptides and their derivatives

Krasnokutski,

Jäger,

Henning

et al. 2024

Sci. Adv.

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The formation of protein precursors, due to the condensation of atomic carbon under the low-temperature conditions of the molecular phases of the interstellar medium, opens alternative pathways for the origin of life. We perform peptide synthesis under conditions prevailing in space and provide a comprehensive analytic characterization of its products. The application of 13 C allowed us to confirm the suggested pathway of peptide formation that proceeds due to the polymerization of aminoketene molecules that are formed in the C + CO + NH 3 reaction. Here, we address the question of how the efficiency of peptide production is modified by the presence of water molecules. We demonstrate that although water slightly reduces the efficiency of polymerization of aminoketene, it does not prevent the formation of peptides.

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Origins of life: first came evolutionary dynamics

Cited by 4 publications

References 107 publications

Protein structures unravel the signatures and patterns of deep time evolution

Protein structures unravel the signatures and patterns of deep time evolution

The prebiotic emergence of biological evolution

Formation of extraterrestrial peptides and their derivatives

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