One of the greatest challenges faced by modern biologists is understanding the origins and evolution of new molecular functions. My research exploits the genetic, phenotypic, and methodological diversity of the Saccharomyces yeast to dissect the genetic and biochemical mechanisms underlying the evolution of gene regulation. I use a combination of novel molecular and statistical approaches to experimentally determine the historical mechanisms responsible for changes in gene regulation, the role the mutational process plays in shaping the outcomes of evolution, and the alternative paths and mechanisms by which historical functions could have evolved. I use this information to formulate and test hypotheses about the molecular origins of novel functions.