Then that would be the wrong way to go about it, and part of (I suspect) why anti-reductionist ideologies become popular among human minds. From the fact that atoms (or quarks) govern social interaction and preferences, it does not follow that the best explanation/model directed at a human will speak at the level of atoms, or explicitly reference them.
Rather, it need only use higher level regularities such as emotions, their historical basis, their chemical mechanisms, etc. The mechanisms for moral intuitions almost certainly act in a way that is not dependent on the particulars of atoms, in the same way that the mechanisms behind a heat engine do not depend on any particular atom having any particular velocity -- just that, in the aggregate, they produce a certain pressure, temperature, etc.
The constraint of reductionism (which correct reasoning quickly converges to in this universe) is not that every explanation must reference atoms, but rather, that it could ultimately be connected to an atom-level model, even if that adds no further insight on the particular problem under investigation.
So asking for an atom-level explanation is asking for far too fine-grained of a model.
Sorry, I was unclear. I didn't mean that cousin_it was looking for atom level explanations specifically, I meant that cousin it wanted the questions explained in terms of questions involving already understood phenomena or at least questions that are obviously in-principle reducible (like 'what is the cognitive algorithm that makes humans think then experience X?').
lukeprog gave a list of metaethics questions here:
Most of these questions make no sense to me. I imagine that the moral intuitions in my brain come from a special black box within it, a "morality core" whose outputs I cannot easily change. (Explaining how my "morality core" ended up a certain way is a task for evo psych, not philosophy.) Or I can be more enlightened and adopt Nesov's idea that the "morality core" doesn't exist as a unified device, only as an umbrella name for all the diverse "reasons for action" that my brain can fire. Either perspective can be implemented as a computer program pretty easily, so I don't feel there's any philosophical mystery left over. All we have is factual questions about how people's "morality cores" vary in time and from person to person, how compelling their voices are, finding patterns in their outputs, etc. Can someone explain what problem metaethics is supposed to solve?