Natural selection has played an important role in establishing various phenotypes, but the molecular mechanisms of phenotypic adaptation are not well understood. The slow progress is a consequence of mutagenesis experiments in which present-day molecules were used and of the limited scope of statistical methods used to detect adaptive evolution. To fully appreciate phenotypic adaptation, the precise roles of adaptive mutations during phenotypic evolution must be elucidated through the engineering and manipulation of ancestral phenotypes. Experimental and quantum chemical analyses of dim-light vision reveal some surprising results and provide a foundation for a productive study of the adaptive evolution of various phenotypes.