Mapping Evolution of Molecules Across Biochemistry with Assembly Theory

TL;DR

This paper introduces Assembly Theory to analyze the evolution of complex natural molecules, offering a new perspective on molecular evolution beyond genetic mechanisms and aiding drug discovery.

Contribution

It applies Assembly Theory to map and measure evolutionary forces in natural products, extending evolutionary analysis beyond genetic information.

Findings

Assembly Theory reveals how natural products are selected for complexity and improbability.

Comparison with molecular databases assesses evolutionary contingency and molecular novelty.

The approach offers new insights into molecular evolution and potential drug discovery pathways.

Abstract

Evolution is often understood through genetic mutations driving changes in an organism's fitness, but there is potential to extend this understanding beyond the genetic code. We propose that natural products - complex molecules central to Earth's biochemistry can be used to uncover evolutionary mechanisms beyond genes. By applying Assembly Theory (AT), which views selection as a process not limited to biological systems, we can map and measure evolutionary forces in these molecules. AT enables the exploration of the assembly space of natural products, demonstrating how the principles of the selfish gene apply to these complex chemical structures, selecting vastly improbable and complex molecules from a vast space of possibilities. By comparing natural products with a broader molecular database, we can assess the degree of evolutionary contingency, providing insight into how molecular novelty emerges and persists. This approach not only quantifies evolutionary selection at the molecular level but also offers a new avenue for drug discovery by exploring the molecular assembly spaces of natural products. Our method provides a fresh perspective on measuring the evolutionary processes both, shaping and being read out, by the molecular imprint of selection.