The very existence of a discipline called "cognitive science", based upon the idea that minds can be equated with computer programs. The whole idea was philosophically-backwards from the start, but it has taken 40 years for this problem to become large enough to provoke an identity crisis in cognitive science.
Perhaps we have rather different opinions on the importance of a proper dialogue between science, philosophy and religion. I think there are lots of serious problems in this world which are unfortunately unsolvable. The failure of science to communicate/integrate properly with the non-scientific world isn't one of them. This problem is actually solvable. Our difference in opinion may be down to the fact that you believe that religion and philosophy have nothing of relevance to say about anything (others here believe this). If so, then you are just demonstrating why it's a problem, because both religion and philosophy have things of relevance to say - things which science cannot.
There is a historical problem which goes right back to Newton and Galileo. When science took the path of objectivisation, it lost something at the same time. What it lost was the capacity to acknowledge/understand/explore subjectivity. This was quite deliberate, of course. The whole point in Galileo's revolution, from his point of view (and Newton's) was to eliminate the profanity of human subjectivity and get closer to the objective mind of God. Objective science then became a raging success, answering objective question after objective question - and remaining absolutely silent on subjectivity. And here we are in 2006 with a bunch of scientifically-biased people trying to claim there is no reason why objective science cannot explain subjectivity. Those people do not seem to understand where science came from, what it does best, what it does not do, why it can't cope with subjectivity..... And when it comes down to it, what, exactly are we talking about when we say "subjectivity"? Well, we are talking about the subject of conscious experiences - that is you and me. We are asking the question "What am I?, ontologically?" This is no small scientific loose end. This is a question about the identity of the self, the meaning of life and the nature of Being - the ultimate questions that human beings ask.