Autocatalytic Sets and Biological Specificity

TL;DR

This paper extends RAF theory to more realistic models of catalysis in biochemical systems, analyzing their structure and properties, and comparing them to simpler models to understand autocatalytic set behavior.

Contribution

It introduces refined models of catalysis reflecting actual biochemical reactions and analyzes their properties, advancing the understanding of autocatalytic sets in biological systems.

Findings

Certain properties are similar to simple binary models

Some properties lead to different estimates

New results on the structure of RAFs

Abstract

A universal feature of the biochemistry of any living system is that all the molecules and catalysts that are required for reactions of the system can be built up from an available food source by repeated application of reactions from within that system. RAF (reflexively autocatalytic and food-generated) theory provides a formal way to study such processes. Beginning with Kauffman's notion of "collectively autocatalytic sets", this theory has been further developed over the last decade with the discovery of efficient algorithms and new mathematical analysis. In this paper, we study how the behaviour of a simple binary polymer model can be extended to models where the pattern of catalysis more precisely reflects the ligation and cleavage reactions involved. We find that certain properties of these models are similar to, and can be accurately predicted from, the simple binary polymer model; however, other properties lead to slightly different estimates. We also establish a number of new results concerning the structure of RAFs in these systems.