[glacier5674]

I'm guessing it's passages like this one regarding transitional forms:

Why then is not every geological formation and every stratum full of such intermediate links? Geology assuredly does not reveal any such finely graduated organic chain; and this, perhaps, is the most obvious and gravest objection which can be urged against my theory. The explanation lies, as I believe, in the extreme imperfection of the geological record.

[ceejayoz]

Fun fact: Archaeopteryx - a transitional fossil between dinosaurs and birds - was discovered two years after Origin of Species.