One objective of science is to unlock Nature's 'secrets', and there is a natural hunger to be among those who see most deeply what others have not seen before. That's why our culture properly respects our Newtons and Darwins (and why there are priority squabbles). But (and as priority squabbles show), we have to lobby and promote our ideas to get them both recognized and accepted.
When we do that, especially if there has been financial investment in our ideas, we naturally tend to be defensive about them. We can easily back ourselves into a conceptual corner in doing so. Being wrong is not what our ethos is all about. Defending dated ideas is not good for science, but it is largely the way science actually works, until a better idea forces earlier ones off the stage. This was a central point in Thomas Kuhn's analysis of scientific 'revolutions' (like the Darwinian one of which we're the beneficiaries).
But being wrong and having only imperfect knowledge is part of the game. As put in a cogent quote in a very fine recent biography of Ernst Haeckel by Robert Richards (The Tragic Sense of Life, 2009, U Chicago Press), 'every scientist since yesterday' has been wrong. If there's a lesson here for all of us, it would--or at least should--be to be more humble in promoting our favorite ideas. They are all wrong, in one way or another.
Unfortunately, imperfection is the gap that opponents of science itself often use as a wedge to dislodge an understanding of the world from its empirical foundations. In this case, I've been barraged with a listserv of messages from a group of people (mainly scientists of various kinds) who support a theological interpretation of life by hammering away at the imperfections, and excessive claims, of evolutionary biologists. They use various arguments, but mainly the false syllogism that because evolutionary biologists don't know everything, they must be wrong about evolution....and therefore some God-based explanation must be right.
In genetics and evolution there are many unknowns, and we tend to minimize them (except those that help us in a grant application), and overstate or oversimplify our own particular worldviews. We are doubtlessly wrong in many ways, but it is not true that every scientist since yesterday was completely wrong, and there can be little doubt that we understand Nature much better today than we did yesterday.
Life is a tough subject to study, and we should be more careful about what we don't know and the range of plausible explanations for our phenomena. But it is also true that what we don't know is not evidence for some specific alternative theory, religious or otherwise. Scientific theories may always be underdetermined--more than one explanation being consistent with the available facts, but there is nonetheless likely to be some truth out there, and it must be compatible with those same facts. We should do our best not to shun or exclude alternative ideas, while at the same time defending the nature of science as an imperfect attempt to understand Nature that needs to have a coherent operating framework.
It is, in fact, remarkable that blobs of protoplasm, called 'humans', could have evolved to have even the level of ability to understand Nature that we have. Since every scientist since yesterday has been wrong in one way or another, the Aristotelian kind of argument that we evolved to have a correct intuitive understanding of Nature does not account for our species' abilities. Indeed, we evolved by doing what we needed to do, so it is likely that we would have cognition at least consistent with the relevant subset of the nature of Nature. Beyond that is the remarkable fact that, fallible though we are, the evolution of general problem-solving ability has led us to go so deeply beyond the specifics of our past survival challenges.