Notions of function and dysfunction are fundamental for neuroscience, psychology and psychiatry, but remain contentious. We propose that some of these controversies arise from tacit creationism, which incorrectly views aspects of evolved systems as if intentionally designed. Many philosophers agree that “failure to perform a normal function” is fundamental to the concepts of physical disease and mental disorder. However, unlike machines and computers, bodies and brain-minds are variable in multiple respects, and these variations may have advantages and disadvantages in different environments. Indeed, in the case of bodies and brain-minds it may be difficult to draw a bright line between normal and excessive activation of an adaptive defense in a particular context. The metaphors of body as machine, or the brain-mind as computer, encourage the notions that components of bodies and brain-minds have specific functions like those of the parts of machines, and that disorders have clear boundaries. Rejecting tacit creationism, and accepting the messy reality of organic complexity, as well as the fuzzy boundaries of disorder, offers a better way forward for neuroscience, psychology, and psychiatry.