It's too late to change my entry to Sam Harris' Moral Landscape Challenge, but I've just thought of a pithier way to put part of my argument: Science does not lead to values; values lead to science.
Let me give some background to that first. Sam Harris argues in his book, The Moral Landscape: How Science Can Determine Human Values, that the fact/value distinction is illusory, and that the naturalistic fallacy, that one cannot derive an 'ought' from an 'is', is therefore also invalid. In short, Harris believes we can derive our morality from science.
In his argument he also points out that science already includes certain values, such as a respect for evidence and logical consistency. But this is where I think he goes wrong, because those values are prior to the choice to use science in the first place. That is, one does not find oneself suddenly valuing logic and evidence because one happens to be a scientist; rather, one becomes a scientist because one already values evidence and logic. You can look at science, sitting there on the shelf among various alternative ways of dealing with the world, read the label and see that it offers reproducible results and reliable predictions, but you won't buy it if you don't care about those things.
A recent exchange with one of the anonymous commenters to this blog has helped to dramatize this point for me. He or she castigated me for referring to evolution instead of attributing everything to God's will, and I replied that the latter approach was literally stupid.
Now, as I've written before, the word "stupid" has unfortunate pejorative connotations, and so I tried in my comment to stress that I was using the word in a clinical rather than moral sense. "Clinical" stupidity I define as a deliberate preference of ignorance over understanding. I do not mean it as an expression of contempt or condemnation in and of itself.
Obviously, of course, given my value system, I see stupidity as something to be avoided, but that's based on my value preferences. I can only persuade you that stupidity is something you should avoid by appealing to shared values of logical consistency and objective truth; if you just don't care about logical consistency and objective truth, there's nothing I can say to make you value them, and your proper response to my calling your beliefs stupid is, "So what? What's wrong with stupid?"
(This is a symmetrical relationship, of course. If someone values something other than logical consistency, and appeals to me to embrace some paradoxical belief system because it is paradoxical, my proper response is "So what? What's wrong with not being paradoxical?")
In the real world, there aren't a lot of people who explicitly value stupidity, at least not in themselves. Where I say I value "objective reality", they aren't going to say, "What's so great about objective reality?" (unless they're maybe Karl Rove); rather, they're more likely to offer an alternative definition of objective reality. In the present instance, they'll say that the Bible just is objective reality, and that any belief system that doesn't recognize it as such is, as I have put it, clinically stupid.
Yet the problem is still basically the same: we have fundamentally different values, even if we assign them both the same name of "truth". When I appeal to rationality and empirical evidence as part of the value of "truth" to argue for why I believe we're very probably the products of an evolutionary process, the creationist doesn't just disagree about my conclusions; he literally does not care about my standard of "truth"; I could only conceivably persuade them by showing how the Bible supports my view. And my anonymous critic cannot convince me to accept the Bible as literally true without appealing to the particular set of truth values I happen to hold. My response to "but the Bible says..." is necessarily going to be "So what?" To them, rejecting the Bible is clinically stupid, but so what? I do not -- indeed cannot -- care about their definition of stupid if it has no connection to mine.
The point of all this is not to argue for my particular conception of Truth. If you happen to share it, then great, we can have a meaningful discussion and maybe some of what I have to say will be useful to you, and I can learn from your comments. If you don't, then it's pretty much a waste of your time and mine to try to persuade me to abandon it.
No, the point of all this is my argument with Sam Harris about whether or not science can lead us to moral truth. It can certainly help us to answer moral questions about how we ought to behave in accordance with our values, but it cannot tell us what those values ought to be. True, almost any person who has any respect for science will probably have values that include a respect for objective truth, but that's a sort of selection bias; people who don't care about this conception of objective truth also won't have any interest in science. (It's actually a variation of the anthropic principle; the fact that everyone who values science also values truth is no more a coincidence than the fact that we happen to live on a planet that has just the right conditions for us to live here; if it didn't we wouldn't be asking the question here.)