Conscience As a Guide to Truth

Victor Reppert made an interesting post that raises the issue of reliability of our moral intuitions.  Since it is brief, I'll repeat his post here in its entirety:

A common atheist retort: "Would you rape, pillage, and plunder if you did not have the Bible to tell you not to?"
The implication is that this would be a superficial morality. And it would indeed.
Reply: Theists and atheists alike refrain from such acts because conscience tells them that it is wrong. The question is whether they have equally good explanations for why we should suppose that conscience is a reliable guide to truth. - Reppert

The first question it raises in my mind is what kind of statement is this retort from atheists responding to?  It seems to be an answer to the common trope from religionists that atheists lack the moral guidance that comes from God, which is often stated as Dostoyevsky's famous line from The Brothers Karamazov: "If God does not exist, everything is permitted."  Many religionists take this claim at face value, and assert that atheists are devoid of any morality at all.  To such an assertion, a retort like the one Victor cites might be appropriate.  But Victor's view is slightly more sophisticated than that.  At least he doesn't deny that atheists have some kind of morality.  He just denies that the morality of an atheist is a truly worthwhile or effective way of guiding human behavior.

If I understand Victor's beliefs about the morality of atheists correctly, he is convinced that if naturalism is true, then there would be no moral behavior at all.  This is evident in one of his posts, where he says that self-interest would be the only guiding force under naturalism.  That is based on a poor understanding of evolution.  But obviously, Victor doesn't think that's the case.  In another post, he recognizes that even atheists have a conscience, and according to theistic beliefs, that sense of conscience comes from God, whether atheists think so or not.  But it can still be ineffective in atheists, because they think they don't have to answer to anyone for their transgressions.  So we see atheists who exhibit "everything is permitted" reasoning, like Woody Allen.  And how does he respond to the problem of theists who are not always guided by their conscience?  He ducks the question, noting that in many cases, they are restrained from evil, but good behavior doesn't make the headlines.  Victor fails to mention that good behavior by atheists doesn't tend to make the headlines, either.  In fact, there is no clear difference in moral behavior between atheists and theists, and Victor's idea about atheists reasoning that they have nobody to answer to doesn't fit observed reality

So rather than taking an objective look at the actual ethics and behavior of theists and atheists, Victor now prefers to couch the whole issue in somewhat different terms.  It isn't a question of who actually behaves better, because I don't think he'd have any significant advantage on that one.  It is a question of which belief system offers a better explanation for the sense of conscience we all share.  Does atheism or theism provide a more "reliable guide to truth" through conscience?  And of course we already know what his answer to that question would be.  Because as we have seen, he doesn't think evolution can explain anything but self-interest.  So Victor thinks he has a defeater for naturalism by asking whose explanation works better.

I almost have to give him credit on this one, because as a naturalist, I concede that conscience isn't a guide to truth - it's a regulator of human behavior.  But I also notice that he has turned the question from who has the better explanation of morality to whose morality is better able to reveal the truth of what's right and wrong.  And the answer to that depends entirely on whether you think such a truth exists in the first place, and whether conscience is a means to reveal that truth.  One of his commenters puts the question this way:

Atheists think conscience is reliable because conscience evolved in us. Reliability means we can rely on it to help us survive in the future. Something that evolved is likely to be in tune with evolutionary fitness.

Religious people think conscience is reliable because God gave it to us. Reliability means we an rely on it to guide us in doing God's will. Something that God gave us is likely to be in tune with God's will. - John Moore

This comment was well-received by Victor, because it seems to play into his formulation of the question by agreeing (on behalf of naturalists) that we should see conscience as a reliable indicator of some purpose.  And I think John Moore was trying to make a fair representation of the naturalist's position, but he still gets it wrong, because there is no message imparted to us by conscience, and no enduring purpose revealed.  In general, there's no guarantee that evolved mechanisms will continue to work under changing conditions.  Evolved mechanisms are not reliable for any enduring purpose.  They cope with conditions that affect survival.  When conditions change, so do the mechanisms that have evolved to cope with those conditions.

Conscience is an accident of nature that manifests itself as a regulator for human behavior.  What we perceive as "good" is the behavior toward which our instincts drive us.  As an evolved behavioral mechanism, we can infer that it developed in the past under conditions where it enhanced survivability.  If it had been the case that killing the second son would usually lead to enhanced survivability of the family, then that's what our conscience would guide us to do, and today's theists would be declaring that killing the second son is an "objective moral good".  As it happens, cooperative behavior has been a successful survival strategy, and that's what our conscience directs. 

And from a naturalist's perspective, there's no reason at all to think that conscience gives us some kind of revelation about the truth of God's will, as Victor wants to believe.  Our belief in God is also an outcome of evolutionary processes, but that doesn't imply that that religious belief is in any way reliable.  It only means that belief has been beneficial to survival at some time in our evolutionary past, and possibly, but not necessarily, that the survival advantage persists to the present.  And that's exactly what we can say about the existence of human conscience.

Victor thinks that by couching the question in terms of how conscience reveals God's truth to us, he can maneuver atheists into conceding the issue, because they have no answer for how conscience reveals the truth.  But that assumes that there is a God who communicates to us by means of conscience.  The naturalist certainly doesn't share that assumption - either by accepting the existence of a God, or by accepting the notion that human conscience serves to communicate some kind of truth to us.  Sorry, Victor, but there is a better way to explain conscience than simply saying "God did it."  And as usual, science leads us to the the more realistic answer.