Nineteenth and twentieth century philosophies of science have consistently failed to identify any rational basis for the compelling character of scientific analogies. This failure is particularly worrisome in light of the fact that the development and diffusion of certain scientific analogies, e.g. Darwin’s analogy between domestic breeds and naturally occurring species, constitute paradigm cases of good science. It is argued that the interactivist model, through the notion of a partition epistemology, provides a way to understand the persuasive character of compelling scientific analogies without consigning them to an irrational or arational context of discovery.