Understanding Molecular Evolution

Humanity has harnessed evolution to sculpt domesticated animals, crops, and molecules, but the process remains a black box. Which combinations of evolutionary parameters will enable us to discover the best solutions? We plan to answer this question by performing massively parallel directed evolution experiments. Our system will use phage-assisted continuous evolution (PACE), a method of building synthetic ecosystems in which billions of fast-replicating viruses compete to optimize a molecular function of our choice. We are developing methods of running many experiments in parallel, each with real-time fitness monitoring and customized evolutionary conditions such as mutation rate, selection stringency, and evolutionary goal-switching. We will use these methods to systematically characterize the relationship between evolutionary parameters and outcomes.