Either we dispense with all morality as an unscientific superstition, or we find a way to reconcile causation (genetic or otherwise) with responsibility and free will. . . . Like many philosophers, I believe that science and ethics are two self-contained systems played out among the same entities in the world, just as poker and bridge are different games played with the same fifty-two card deck. . . . Free will is an idealization of human beings that makes the ethics game playable.
Pinker's discussion is at greater length, and he would undoubtedly claim I oversimplify, but I don't think it's entirely unfair to say that he tries to duck the challenge cognitive science poses to morality by proposing non-overlapping magisteria, as Stephen Jay Gould did to evade the conflict between science and religion. I think it's a cheap trick, and it doesn't work.
The abolition of Cartesian dualism, and the recognition that free will is an illusion (albeit a very compelling one, which I fully embrace as my own experience), requires us to reason about morality differently than we once did, and hence to adopt a somewhat different moral stance. We understand that moral intuition is a feature shaped by the evolution of intelligent social beings. Morality makes society possible, in other words. It is inherent in our nature, though not anywhere else.
We therefore honor it as human beings, but we also recognize that the very general basic intuitions with which we are endowed -- non-maleficence, benevolence, respecting the autonomous personhood of others -- are shaped by culture and circumstance into much more specific and elaborate sets of rules that can vary enormously. We also recognize that these intuitions can be manipulated by self-interest, including the self-interest of powerful people who impose rules that may be internalized by the weak; and that what seems to make sense in one time and place may not make sense in another. Finally, we recognize that elaborations of rules are in part a response to the frequent conflicts among moral principles.
These realizations compel us to think about morality pragmatically. We sanction wrongdoing, not because God commands us to do so, or because right and wrong contend metaphysically and we are soldiers in the battle, but because it is necessary to maintain the social order. It seems to me that it is much easier to hate the sin but love the sinner when we reject religion and the ghost of free will, and understand that people do not create themselves or bring themselves to where they are. This recognition would eliminate retribution from the practice of correction, and profoundly change how we deal with crime, and the rules that we write.
I think particularly of sexual morality -- all that ought to matter is that we not coerce, hurt or betray people, and that we protect the public health -- of drug policy, obviously; and of the kind of environment we create in prisons, which ought to contain far fewer people. Also, I think of how we raise our children, interact with our peers, and govern ourselves. It seems to me that integrating science and morality, rather than proposing that they are separate realms, is the straight path to a more humane and free society.
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