One frequently employed argument against the theory of intelligent design is that if living things are indeed the product of intelligent agency the designing agent must not be all that competent since some biological structures appear to be quite poorly designed.
The argument goes back at least to David Hume (d. 1776) in his Dialogues Concerning Natural Religion, and modern skeptics point to the human eye as an almost paradigmatic illustration of Hume's claim. The light sensitive cells in the eye's retina, it has long been thought, are facing the wrong way. This would seem inexplicable if the eye were engineered by an omniscient, omnipotent designer.
Yet, as research on the eye continues it looks more and more as though the skeptics have been wrong. These light receptors in the retina appear, in fact, to be optimally designed and oriented for the role they play in vision.
Here's a short video which makes this point quite well:
The optimality of the eye's design, coupled with the fact that complex eyes have been around since the Cambrian era and seem to have no fossilized ancestral predecessors, leads to the conclusion that this very complex structure arose with relative suddenness in the history of life and apparently de novo.
That's pretty hard to explain on any naturalistic theory of origins.