 Kimura predicted that silent substitutions would evolve more rapidly than replacement substitutions before sequence data were available to test his neutral theory of molecular evolution. Molecular genetic studies have confirmed his prediction: silent sites evolve several times faster than replacement sites. These studies clearly show that the primary mode of action of natural selection at the level of the DNA sequence is purifying selection. It is this highly conservative aspect of natural selection that permits comparative molecular evolutionary studies of developmental processes across species as diverse as humans and flies. At the molecular level, most genes, though polymorphic in sequence, do not display evidence of balancing selection and instead manifest patterns of variation that accord well with neutral theory.