Unlocking the Secrets of Autocatalytic Sets: How Bit Strings and Reactions Shape Molecular Evolution

Table of Links

Abstract and Introduction

Part I. A Definition of Life

Part II. The first Miracle: The emergence of life is an expected phase transition – TAP and RAF.

Part III. The Second Miracle: The evolution of the biosphere is a propagating, non-deducible construction, not an entailed deduction. There is no Law. Evolution is ever-creative

Part IV. New Observations and Experiments: Is There Life in the Cosmos?

Conclusion and Acknowledgments

Figures and References

FIGURES

A simple collectively autocatalytic set. The model molecules are bit strings acting as substrates and products of reactions. Black solid arrows are drawn from the dots representing substrates of a reaction to a box representing the reaction. Black solid arrows are drawn from the reaction box to the dots representing the products of the reactions. The actual direction of flow of the reaction depends upon displacement from equilibrium. Dashed lines from dots representing molecules to the boxes representing reactions depict which molecules catalyze which reactions.

The exogenously supplied food set of monomers and dimers is shown in the grey oval. Derived from (28).

A collectively autocatalytic set of linear polymers derived from reference (3). Ovals contain polymers of two monomer types, A and B. Allowed reactions, shown as dots, are cleavage and ligation reactions. A dotted arrow from a molecule oval to a reaction dot indicates that that molecule catalyzes that reaction. Derived from (3).

The nine peptide collectively autocatalytic set discussed in reference (9). The ovals show the molecules, the arrows show the transitions among the molecules and the relative rates.

A small molecule collectively autocatalytic set with no DNA, RNA, or peptide polymers in a prokaryote. Similar small molecule autocatalytic sets are found in all 6700 prokaryotes. Presumably the phylogeny among these is part of the evolution of metabolism.

The Theory of the Adjacent Possible (TAP) equation and its dynamics. Thanks to W. Hordijk.

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