To suppose that the eye, with all its inimitable contrivances for adjusting the focus to different distances, for admitting different amounts of light, and for the correction of spherical and chromatic aberration, could have been formed by natural selection, seems, I freely confess, absurd in the highest possible degree. Yet reason tells me, that if numerous gradations from a perfect and complex eye to one very imperfect and simple, each grade being useful to its possessor, can be shown to exist; if further, the eye does vary ever so slightly, and the variations be inherited, which is certainly the case; and if any variation or modification in the organ be ever useful to an animal under changing conditions of life, then the difficulty of believing that a perfect and complex eye could be formed by natural selection, though insuperable by our imagination, can hardly be considered real.
Darwin, Origin of Species, Chapter VI. I've always liked this quotation from Darwin, and since it peaked its head up in a post (very indirectly through a horrible misquotation) at Doing Things With Words, I thought I'd post it. The book is actually a very good read; unfortunately the remark Chesterton made decades ago about it is still true - just as many people are under the mistaken impression that evolutionary theory has explained things that it actually hasn't, so many people are under the mistaken impression they've read the Origin of Species when they actually haven't. I suppose that's the imagination's revenge on Darwin; there are all types of people who confuse strong imaginative association with rational conclusion, and Darwin has suffered a lot from it. I strongly recommend you read it if you haven't; Darwin is philosophically a much more consistent and powerful (and often cautious) reasoner than many of his pop-sci defenders have been, despite the fact that they could probably run circles around him in issues of fact. (Here and there one can find annotated OS's, in which some biologist or another has footnotes updating some of the facts - I recommend this sort of edition if you can find it.) Darwin has the same feature he attributed (rightly) to Paley - logic almost like Euclid's. (The Descent of Man is not as good in this regard, but isn't bad, and is in some ways more philosophically interesting.)
I think one of the most serious philosophical issues that is raised by scientific popularization is precisely this trouble with the continual flux of cooperation and competition between imaginative association and rational inference; and one of the reason so many scientific popularizations are so horrible is that they fail to navigate this flux properly - they either confuse imaginative association with rational inference, or they fail to recognize the flux at all. It takes a surprising amount of talent to convey science correctly to the public; and perhaps a bit of luck, too. (This is the aspect of philosophy of science that really interests me; it's hard to find anything on it, though, since it's just a poor country cousin of most of what interests people who actually go into philosophy of science.) One thing I like about Darwin is that he raises the bar beautifully; a sterling standard when it comes to careful argumentation that doesn't dumb things down and yet conveys things clearly and rationally.