Barry Arrington at Uncommon Descent highlights the problem when he writes:
Consciousness could not have evolved from “simpler” states of matter, because it is not a state of matter. To say that consciousness evolved from matter is like saying Newton’s theory of gravity evolved from apples.Naturalist philosophers, of course, don't regard the mind as "a thing" like the brain. Rather they think of "mind" as simply a word we use to describe one of the functions of the brain, sort of like we think of digestion as the function of the stomach.
Even if for the sake of argument one concedes that natural selection might account for the development of a material body, consciousness remains a mystery. There is still a vast uncrossable gulf between the physical body and mind.
In other words, the difference between body and mind is qualitative, not quantitative. You can’t get an immaterial mind no matter how many slight successive modifications of the body there may have been.
The brain itself is regarded as a computer made of meat, but the problem with this is that there are so many mental characteristics that are completely inexplicable as products of a lump of material neurons.
If we entertain for the sake of discussion the claim that the brain is analogous to a computer we might ask what computer can give meaning to the words it generates on the monitor? Can a computer convert electrochemical impulses into the sensation of color, or flavor, or sound or pain? What exactly are these sensations anyway?
Does a computer experience boredom, frustration, pleasure, guilt or regret? Does it have wishes and hopes, beliefs and doubts? Do computers understand what they're doing?
The fact that human beings do all these things is a serious problem for naturalism because most naturalists hold that naturalism entails physicalism (i.e. the view that physics fixes all the facts about the world), as well as materialism (the view that all of reality is reducible to matter).
Conscious experience, however, does not seem to be something explicable in terms either of physics or matter, which means that it is a prima facie defeater for naturalism.
Naturalists can avoid this unpleasant implication of their metaphysics by conceding that both physicalism and materialism are false and trying somehow to enfold consciousness into a naturalistic ontology, but this would be an accommodation most naturalists would find devastating and repugnant.
To grant that there's more to reality than just physical matter and energy is to open the door not only to the existence of immaterial, non-physical human minds, but a forteriori to the possibility of a transcendent Mind and that's a possibility that most naturalists want to avoid at all costs.
Naturalism dominated philosophy for the two centuries from about 1790 to 1990, but it appears that work being done in the last couple of decades in both neuroscience and the philosophy of mind is bringing an end to the hegemony it once enjoyed and making it increasingly difficult to be an "intellectually fulfilled atheist," as atheist biologist Richard Dawkins once put it.