From messy chemistry to ecology: Autocatalysis and heritability in prebiotically plausible chemical systems

A key question in origins-of-life research, is whether heritability, and thus evolution, could have preceded genes. Out-of-equilibrium chemical reaction networks with multiple autocatalytic motifs may provide chemical "memory" and serve as units of heritability, but experimental validation is lacking. We established conditions that may be conducive to the emergence of heritable variation and developed methods to search for heritability and autocatalysis. We prepared a food set (FS) of three organic species, three inorganic salts and pyrite. We conducted a serial dilution experiment where FS was incubated for 24 hours, after which a 20% fraction was transferred into freshly prepared FS that went through the same procedure, repeated for 10 generations. To serve as controls, we also incubated the fresh solutions in each generation. We compared the chemical composition of transfer vials and no-transfer controls using liquid chromatography-mass spectrometry (LCMS), with metrics adapted from ecology and evolutionary biology. While variability was high, focusing on a subset of chemicals with more consistent patterns revealed evidence of heritable variation among vials. Using rule-based chemical reaction network inference, constrained by the LCMS data, we identified a plausible FS-driven chemical reaction network that was found to contain numerous autocatalytic cycles.

Methods
This is the supplementary data for a biorxiv preprint https://doi.org/10.1101/2024.08.03.606486. It is split into 3 folders:

1) python and R code to process LCMS data in ways described in the article;

2) raw outputs of CompoundDiscoverer software on the LCMS data from the two replicate 10-generation experiments and incubation tests described in the article and the Appendix A;

3) inputs and outputs for the computational pipeline using Rule-it and autocatalyticsubnetworks software described in the article and Appendix C.