Ramesh Ponnuru, of the National Review, says this:
What renders atheism incompatible with a coherent account of morality, when it is incompatible, is physicalism (or what is sometimes described as reductive materialism). If it is true that the universe consists entirely and without remainder of particles and energy, then all human action must be within the domain of caused events, free will does not exist, and moral reasoning is futile if not illusory (as are other kinds of reasoning).
Will Wilkinson offers up an astute reply:
This is a stupefyingly widespread view that flows from an elementary error in thinking. Suppose you know that there is free will or that moral reasoning is not futile. Next, suppose you find that the universe is made out of only whatever the universe is made out of. What do you infer? You infer that free will and moral reasoning, which occur inside the universe (or as aspects of the universe), whatever they may be, are made possible because of whatever it is the universe is made out of. And there you are.
Here is what you do not do. You do not start with a mystifying conditional like “If the universe is only physical (or whatever), then there is no free will,” because how do you know that? You don’t. But you may think you do and so you get caught in a retarded ponens/tollens showdown: the universe is physical, ergo no free will, or… free will, so the universe is not physical. But, again, through what method of divination do we validate this conditional? None. Because we already know it is false.
I think that’s exactly right. Looking at the neural anatomy of morality didn’t undermine morality, or disprove its existence. On the contrary, the “reductive materialistic” approach simply showed us where, approximately, moral questions are processed inside the brain. I think a similar thing will happen with the concept of free will. Although many commenters will claim otherwise, I’m very dubious that neuroscience or physics will ever “disprove” free will. Free will is such an elemental part of human experience that disproving free will would literally require some sort of Laplacean demon. Until we obtain that level of omniscience – and I’m not holding my breath – I’ll continue to assume that free will is a natural side-effect of some element of the material universe. Quantum indeterminacy sounds about right.