I'll preface by saying that we are letting Hume become to morality what Aristotle (and subsequently Newton) became to science- they contributed so much to scientific thinking that they stood in the way of prospective advancements beyond them, because before we allowed ourselves to stand on their shoulders and look with them at the natural world, we had to spend several centuries groveling below them, elevating them to the status of (quite unmovable) monoliths.
Sam Harris notes that one is making a factual claim when one notes that capacities for conscious experience, and therefore suffering, varies amongst rocks, ants, and apes. Sean Carroll replies:
Let’s grant the factual nature of the claim that primates are exposed to a greater range of happiness and suffering than insects or rocks. So what? That doesn’t mean we should care about their suffering or happiness; it doesn’t imply anything at all about morality, how we ought to feel, or how to draw the line between right and wrong.
Let's note, right from the start, what Carroll's complaint isn't.
Carroll is not disputing Harris's point that humans and other living creatures have experiences of suffering and pleasure. Carroll not disputing Harris's point that the existence of sufferings and pleasures are biological in basis. Carroll is not disputing Harris's point that there are facts of the matter about whether and how these pleasures can be promoted and pains suppressed. He's not disputing Harris's point that science can inform us as to which facts are relevant in these matters, he's not disputing that cultural dispositions may encourage acts that truly cause suffering. Carroll is not even objecting to Harris's observation that almost every instance in every culture where the concept "moral" is invoked its with reference to entities that can have conscious experience.
No, he disputes none of this. So Carroll's rebuttal, such as it is, fails to even interact with 95% of Harris's talk.
Carroll thinks Harris has failed to get around the is/ought problem:
Harris is doing exactly what Hume warned against, in a move that is at least as old as Plato: he’s noticing that most people are, as a matter of empirical fact, more concerned about the fate of primates than the fate of insects, and taking that as evidence that we ought to be more concerned about them; that it is morally correct to have those feelings. But that’s a non sequitur. After all, not everyone is all that concerned about the happiness and suffering of primates, or even of other human beings; some people take pleasure in torturing them. And even if they didn’t, again, so what? We are simply stating facts about how human beings feel, from which we have no warrant whatsoever to conclude things about how they should feel.
One ought to recognize where oughts come from. If you want to make caramelized onion quiche, you "ought" to have 3 large eggs, 6 ounces grated Gruyère cheese, 1/2 cup heavy cream, 2 onions etc. You "ought" to french the onions and you "ought" to pre-bake a pie crust.
These oughts vanish if you don't intend to do anything particular with the ingredients. A moral "ought" is only an "ought" if there is morality. There exists a distinction between moral "ought" and a factual "is" only if you believe the stuff of morality isn't the kind of stuff to be met with in experience.
To say is/ought is a "problem" is only true to the extent that you subscribe to this division in the first place. Carroll hasn't denied that any of the things Harris refers to (suffering, differences in cognitive capacities) exist, and no one does in these arguments. The objection is whether you can call those things morality.
But what if I believe that the highest moral good is to be found in the autonomy of the individual, while you believe that the highest good is to maximize the utility of some societal group? What are the data we can point to in order to adjudicate this disagreement? We might use empirical means to measure whether one preference or the other leads to systems that give people more successful lives on some particular scale — but that’s presuming the answer, not deriving it. Who decides what is a successful life? It’s ultimately a personal choice, not an objective truth to be found simply by looking closely at the world. How are we to balance individual rights against the collective good? You can do all the experiments you like and never find an answer to that question.
Who decides what a chemical is? It depends on the person. Alonzo Fyfe proved this:
... no scientist can give any type of objective argument showing that six proton atoms have to be called 'carbon' and cannot have any other name. The decision to call six proton atoms 'carbon' is arbitrary and subjective. So, chemistry itself is subjective. [...]
Not only is it the case that the scientist cannot objectively prove that six proton atoms must be called 'carbon' - that this choice is not arbitrary - but can give no objective answer to the question of why he has decided to write about 6-proton atoms.
There are over a hundred different atoms that the chemist could be talking about - hydrogen, oxygen, iron, uranium. The decision to talk about carbon atoms, as opposed to one of these other types of atoms - is entirely arbitrary. It is up to the whim of the chemist what atoms he is going to write about. That is to say, the choice is totally subjective. Therefore, chemistry is totally subjective.
I am going to make a noise with my mouth. If I try to spell this noise out using latin alphabet, I guess I would spell it "m-o-r-a-l". I am going to decide that this noise is a word. I am going to decide that this word is about pleasure and suffering of creatures. Now that you know what I mean by it, we can use it to more easily discuss the pleasure and suffering of creatures.
But even Carroll's feeble objection about the definition of 'morality' isn't problematic. No one holds a copyright on the word morality. If I decide it is a useful concept to explain certain facts, it doesn't make the term "incorrect" because other people use it differently than I do in contexts independently from me. Carroll has made the mistake of making the term "moral" so sacred that he would refrain from staining it with any meaning at all. So long as you are aware of the real things in the world I am pointing toward whenever I use the word, we can get to work.
Far from a penetrating insight, Carroll is offering nothing but a flat-footed reassertion of the very concept Harris spent his presentation criticizing, and telling Harris he doesn't subscribe to a conception of morality when Harris is arguing that he doesn't subscribe to that conception of morality does not represent forward progress in a conversation of any kind, much less a rebuttal.