Robert Wright interviews evolutionary icon John Maynard Smith on the mystery of consciousness and seems driven toward the conclusion that perhaps there is a God after all. Smith demurs. Their exchange can be viewed here.
Consciousness poses a challenge to materialism in that it's very difficult to conceive of an explanation for how matter could produce sentience, self-awareness, and abstract thought purely by chance and the laws of nature. The materialist believes that consciousness is just a product of the chemical and electric phenomena occuring in the brain, and it may be, though I doubt that it's that simple, but the salient question is not just what consciousness is and what generates it, but how did it ever emerge.
It is as if, the materialist would have us believe, an ocean of computer parts was somehow, through the action of blind physical forces, able to gradually construct a machine that was aware of itself and of its environment. This, if it happened, would be a feat every bit as miraculous, if not moreso, than turning water to wine or parting the Red Sea, events at which materialists are generally given to scoff.
The origin of consciousness, along with the origin of life itself, may well be the two greatest mysteries confronting human understanding today and are certainly two of the greatest difficulties with a materialist worldview.