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On what purely naturalistic grounds can an atheist judge something as either morally good or evil?
The question carries several hidden assumptions. First, that atheistic morality is grounded on some sort of “naturalistic” inference. This is the naturalistic fallacy, that “is” cannot tell you about “ought.” And second, that “non-naturalistic grounds” leaves you any better off.
As I stressed in the NOMA posting, all moral, ethical and esthetics judgments fall in the “undecidable” realm of philosophy, and while naturalistic observations about the practical consequences of a particular moral belief may be of relevance to note, that cannot settle the initial belief.
Reciprocity plays a role as foundation here: do or do not do unto others as you would want to be done unto. Do no harm, and be kind, would be further elements to consider. But even if it were the case that cultures that behave that way fail more than ones that do not (and is North Korea a “successful” culture here or not?) that naturalistic aspect would still have no bearing on the morality of doing or not going that act.
Turn the argument around: by what non-naturalistic grounds can a religious believer judge something as either morally good or evil? Because the rule book says so, no further thought required? In the case of the Old Testament, apart from things like worshipping graven images, for every absolute there seems to be an exceptional loophole. So thou shalt not kill … except in the case of witches (when you are commanded to kill them) … or the Amalekites in the case of King Saul.
One could argue that witch killing was absurd because there were no real witches capable of supernatural malevolence (a naturalistic observation) but even with witches certain of their magical powers the rule would still be wrong if you hold that killing is inherently wrong (a moral judgement having nothing to do with naturalistic or non-naturalistic presumptions).
The reason why moral reasoning is fraught with peril is because any “absolute” rule will inevitably collide with exceptions, but the collision is not taking place in the realm of naturalistic inference.