Carl Zimmer's terrific blog The Loom has a number of very interesting posts from the last few weeks. His post, entitled The Whale and the Antibody , illustrates an historical fact about Darwin's theory of natural selection: sometimes the biological observations which seem to pose the greatest challenge to Darwin turn out, after investigation, to confirm his ideas even more solidly.
The Whale and The Antibody addresses one such challenge to the idea of natural selection, namely, where are all the missing links? If apes and humans share common descent, why aren't there apemanzees (or hurillas?) This problem becomes acute when you consider animals like whales, who, when first investigated, seemed literally related to nothing else on earth. On the face of it, it would be easier to explain such a phenomenon using instantaneous creation, or at a minimum, a blind watchmaker. Carl had a whole book showing that, in fact, the fossil record is full of transitional forms between the bearlike ur-ancestors of the whale lineage, and increasingly aquatic and successful intermediates.
Carl uses this analogy to tackle a similar paradox occuring on a different level of life. The immune system of gnathosomes (fish, mammals, etc.)involves a very complicated set of cells, organs, and signals, which do not occur at all in lampreys. This seems to be a case of de novo creation of a new capability within a set of species. Recent work, however, makes clear that each of the components of the gnathosome immune system do in fact exist in lampreys-- just not in assembled, coordinate form. So not only for species, but also for capabilities, natural selection seems to be the absolute rule by which life rolls on.
I've seen this type of anecdote most thoroughly examined in Daniel Dennett's book Darwin's Dangerous Idea . Possibly no scientific notion has been as rigorously tested, by so skeptical a cohort of opponents, as Darwin and natural selection. It's just hard to believe that Darwin's simple rule can explain all the vast complexity of life! But time after time, tests of these principles, when designed to be falsifiable, confirm Darwin's ideas, past even his relatively modest assertions.
There's lots more like this on Carl's site!