Just in time for his new book "Why Evolution is True" Jerry Coyne has written an excellent article which examines attempts to forge a link between the scientific worldview and the religious worldview. With every point Coyne hits the nail on the head. The scientific way of thinking and the religious way of thinking could never be reconciled precisiely because science allows for the possibility of being in error and bases its understanding of the world on observation. Religion, however, is not open to change and does not base its understanding of the world in reason or evidence. These two ways of thinking can never be reconciled. Even if science proved that God exists, it would never be dogmatic about its assertion, and its discovery of God would be based on honest and objective observation. This is obviously nothing like the "faith" espoused by believers, or "the personal relationship with Jesus" espoused by the more lovey-dovey Christians.
The only way that any religion could avoid overlap with science is by making absolutely no claims about the observable world. And as we have seen, the religions of Abraham, as well as the vast majority of religions, do not abstain from making claims about the world we live in.
I also found Coyne's explanation of contingency in evolution to be superb. He points out that current evidence indicates that the human race was a fluke. If everything but one celled organisms were wiped out in atomic bomb, it is grossly unlikely that anything even resembling our species would evolve a second time. This poses a problem for the Abrahamic faiths because it shows that we were nothing special. We were not the intended outcome of the evolutionary process, as some theistic scientists like to think.
The only way out of this conclusion is for theists to turn to hardcore determinism: that everything around us inevitably followed from the Big Bang. This way theists could claim that God set everything up to lead to us, but this suggestion comes at a very steep cost. In Finding Darwin's God, Kenneth Miller discusses why such a deterministic universe would undermine theism. His answer? It is very hard to see how a deterministic universe could allow for free will, a concept very near and dear to believers. To resolve this problem he turns to quantum randomness, which only undermines his position: If things are random at the quantum level, they are somewhat random at the atomic level, and fairly random at the molecular level, which means so many mutations really are purely random, meaning that contingency comes back into evolution and we no longer have a loving God that predetermined us as the outcome.
I suppose one could argue that the universe was purely deterministic until humans came on the scene and God gave man free will. But this only serves, once again, to undermine the theistic position. If human beings are truly distinct from animals in having a soul, then this means that the choices animals seem to make, and the consciousness they seem to have, is nothing but an illusion. If this is true then it raises some troubling questions for the theist: If he can say that animals are not conscious and don't have free will (despite the appearance that they do), how does he know that other minds exist? If animals are conscious, then this means that God left the possibility of human evolution in the hands of animals (our ancestors) who could have cared less about whether humans evolved, and certainly did not have our evolution in mind. If animals are not conscious, then God was not only deceptive in creating them to seem like they are, but the entire explanation is just ad-hoc and not truly representative of reality. If you think animals are not conscious, they only seem like it, you are inventing this explanation to keep God in the picture. This, as most of us know, is utterly unscientific.