Self-organization is sometimes presented as an alternative to natural selection as the primary mechanism underlying the evolution of function in biological systems. Here we argue that although self-organization is one of selection's fundamental tools, selection itself is the creative force in evolution. The basic relationship between self-organization and natural selection is that the same self-organizing processes we observe in physical systems also do much of the work in biological systems. Consequently, selection does not always construct complex mechanisms from scratch. However, selection does capture, manipulate, and control self-organizing mechanisms, which is challenging because these processes are sensitive to environmental conditions. Nevertheless, the often-inflexible principles of self-organization do strongly constrain the scope of evolutionary change. Thus, incorporating the physics of pattern-formation processes into existing evolutionary theory is a problem significant enough to perhaps warrant a new synthesis, even if it will not overturn the traditional view of natural selection.