Mapping Evolution of Molecules across Biochemistry with Assembly Theory

Evolution is often understood through genetic mutations driving changes in an organism's fitness, but there is potential to extend this understanding beyond the genetics. 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 evolution 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.