A great challenge in modern biology is understanding the origins and evolution of new molecular functions. Research in the lab addresses this challenge through the genetic dissection of regulatory differences between distantly related species. Because genetic approaches are often difficult or impossible to implement between most species, we focus on the genetic, phenotypic, and methodological diversity of the Saccharomyces yeast, allowing us to see through the ‘Mendelian blind spot’ and perform inter-species genetics. We both develop and use high-throughput genetic approaches as well as novel molecular and statistical tools to experimentally evolve historical changes in gene regulation within the laboratory. By ‘replaying the tape of life’ and placing these ancient regulatory changes within a framework of ‘what might have been’, research in the lab determines not only the historical genetic basis for new molecular functions, but also the broader genetic mechanisms underlying how these functions emerged and have evolved.