The Theory of Evolution explains embryological quirks, vestigial organs, and other bad designs.  It also explains how order and complexity (like eyes and new enzymes) can grow from simplicity.  Over billions of years, evolution has resulted in the vast array of species on our planet, with their many complex organs and traits.  We understand how biological patterns emerge.  Climbing Mount Improbable, by Richard Dawkins, shows how highly intrinsically improbable features of organisms can come about thru very small (and possible) evolutionary steps.  Daniel Dennett explains, in Darwin's Dangerous Idea: Evolution and the Meanings of Life, how evolution is the central organizing natural process that gives rise to complexity.  Evolution doesn't require a top-down designer; it is a bottom-up process that results in complexity and order naturally emerging from simplicity.