A good point from Stephen Barr, a particle physicist:
The philosopher Daniel Dennett visited us at the University of Delaware a few weeks ago and gave a public lecture entitled "Darwin, Meaning, Truth, and Morality." I missed the talk -- I was visiting my sons at Notre Dame and taking in the Notre Dame-Navy football game. Friends told me what I missed, however. Dennett claimed that Darwin had shredded the credibility of religion and was, indeed, the very "destroyer" of God. In the question session, philosophy professor Jeff Jordan made the following observation to Dennett, "If Darwinism is inherently atheistic, as you say, then obviously it can't be taught in public schools." "And why is that?" inquired Dennett, incredulous. "Because," said Jordan, "the Supreme Court has held that the Constitution guarantees government neutrality between religion and irreligion." Dennett, looking as if he'd been sucker-punched, leaned back against the wall, and said, after a few moments of silence, “clever.” After another silence, he came up with a reply: He had not meant to say that evolution logically entails atheism, merely that it undercuts religion.
Jeff Jordan’s question underlines how the self-appointed defenders of the scientific method are trying to have it both ways. Don’t allow religious philosophy to intrude into biology classrooms and texts, they say, for that is to soil the sacred precincts of science, which must be reserved for hypotheses that can be rigorously tested and confronted with data. The next minute they are going around claiming that anti-religious philosophy is part and parcel of the scientific viewpoint.