Actually, various forms of this argument have been in circulation for quite some time.
Notre Dame philosopher and Theist Alvin Plantinga has written extensively on the epistemological problems with reconciling the Theory of Evolution with Scientific Naturalism. In short, Plantinga has extensively argued that The Theory of Evolution negates, by logical necessity, the common notions many hold regarding naturalism.
Plantinga does not oppose Evolution. His argument is that Evolution and Philosophical Naturalism cannot be reconciled from an epistemological standpoint. There have been numerous rebuttals to his arguments and they are still hotly debated. Agree or disagree, Plantinga does present many arguments that have yet to be sufficiently addressed by the opposition.
Here are a few papers:
An evolutionary argument against naturalism:
hisdefense.org | DNS_PROBE_FINISHED_NXDOMAIN
Naturalism Defeated: (In this paper, Plantinga also replies to the counter-arguments.)
http://philofreligion.homestead.com/files/alspaper.htm
If you would like to know how these arguments are rebutted, here is an example:
http://fitelson.org/plant.pdf
More Plantinga Papers :
http://philosophy.nd.edu/people/all/profiles/plantinga-alvin
p.s. I am not arguing for or against any position. I am simply presenting, for those that are interested in this line of reasoning, some scholarly material on the subject.