John Wilkins has an interesting post on the problems that philosophers have had with evolution:
The odd thing about this is that as people were asserting that essentialism is dead (see the article on species linked above), they were being essentialists about concepts and units and ranks. Ernst Mayr, for example, who asserted that species individually (the species taxon, as he put it) have no essences, nevertheless asserted that the concept of species (the species category) did so. He was an essentialist about the species concept. Likewise, the gene centrism of a Dawkins is essentialist about the replicator concept. And so on.