[TeMPOraL]

If you believe "the moving bits in organisms came about through an unguided process" - remember, some people don't, and I suspect a lot of people just sort-of believe - it's still fine to ask what functions those bits perform well and which they don't. It's building a model, just like we build models in physics or chemistry. The function of free electrons in an atom is to let many atoms stick together. In science, it doesn't imply that they were explicitly designed that way.