That's right. Scientific ethics assumes that we want to have productive science. Similarly, Harris's assumption is that we want human beings to flourish. Harris is saying that all sciences have assumptions at the heart of them and he wants this "scientific morality" to start with this "flourishing" assumption. After reading his rebuttal, it doesn't seem like a bad argument. But I'm of two minds on this issue.
That "flourishing" assumption is just utilitarianism. It beats me how Harris managed to stagger through a philosophy degree without picking up that point but maybe he skipped ethics.
Once you figure that out, Harris' point is utterly banal. The fact that science is useful to utilitarianism is not news and never has been news.
Of course it can tell us why we ought to bring about such things.
Or, to be more accurate, it can help us to answer the question of whether we should or should not.
Science can help us to predict potential outcomes, to understand why we want what we want (e.g. why extended confinement and isolation causes stress to a calf but not to a rockfish), and so forth.
Those are brute facts, not moral judgments.
"If I shoot you with this gun you will be in pain, and experience terror, and then die" is a factual claim.
It has absolutely no moral content until you pair it up with some kind of non-evidence-based moral claim, such as "you should not cause pain" or "you should not frustrate a person's preferences by killing them".
"Extended isolation causes a calf or a human infant stress" is a factual claim. It has no moral content until you pair it up with some kind of non-evidence-based moral claim, such as "you should not cause stress".
Science can only tell you what the outcomes will be as a matter of brute fact. It cannot tell you which outcome you should prefer from a moral perspective until and unless you establish some criteria for which outcomes are morally preferable.
Science cannot establish those criteria. It can only tell you what actions will bring about situations that meet those criteria.
And it can help us remove the question of "Why is it better?" from the black hole of pure relativism and provide some more concrete answers, such as "It is better because evolution has shaped us so that we want it and we thrive when we get it, and thwarting it has eventual repurcussions which serve up consequences that evolution has shaped us to dislike."
Before you were being a utilitarian, and utilitarianism is a fairly useful moral theory. It's imperfect but it's pretty decent.
Whereas now you're wallowing in the Naturalistic Fallacy. Something is not better just because we have evolved to like it. We've evolved to like kidnapping women from neighbouring tribes and raping them, yet rape is almost universally held to be immoral. We've evolved to like hitting people who annoy us in the face, but that too is generally held to be immoral.
You can't pick and choose some evolved preferences as moral preferences, and some as immoral preferences, without first adopting some kind of non-evidence-based moral assumptions.
Of course, evolution produces maladaptations as well, so that, for instance, we get people like Larry Bittaker and Dean Corll who simply get off on watching other people suffer. They're going to come to their own conclusions, and that's just the way it is.
It's not a maladaption from an evolutionary perspective unless and until it limits their chances of passing on their genes.
Personally, I hold moral views such that I think that behaviour is immoral regardless of whether it helps or hinders the transmission of their genes.
I simply don't see any place in the process of moral reasoning where it's justifiable to build a wall of exlusion to the participation of science, and to declare "There be dragons".
You and Harris, it seems to me, are both making the same fundamental error and attacking the same straw man.
The straw man is the imaginary position that holds that nothing science says can ever be relevant to moral evaluations. That position is straightforwardly daft if you give any weight to consequences at all, and almost all sane people place at least some weight on consequences when evaluating the morality of an action. (Kant would not do so, but Kant was a bit nutty that way).
The fundamental error is sneaking in utilitarianism (broadly, utilitarianism is the position that "good" is maximising desirable outcomes) without acknowledging it as a non-evidence-based moral assumption, and then claiming that your utilitarian moral philosophy is purely scientific with no non-evidence-based moral assumptions at all.
That just makes you a confused utilitarian, and a bad scientist. It's greatly preferable to be an honest utilitarian and a good scientist - at least according to my non-evidence-based moral assumptions.