My problem with the theory of evolution is that it is born purely out of the scientific method which conveniently chooses to ignore, and in fact *must* ignore, any philosophical, mathematical, or other kinds of non-empirical facts or truths in the process of theory-making.  And it does this despite absolutely depending upon certain philosophical and mathematical truths to have any kind of consistent methodology at all.  In other words, the same philosophical and mathematical foundation upon which science is built is not permitted in the actually process of scientific theory-making.  Hence, science is an incomplete methodology.