I don't like the expression "carve reality at the joints", I think it's very vague and hard to verify if a concept carves it there or not. The best way I can imagine this is that you have lots of events or 'things' in some description space and you can notice some clusterings, and you pick those clusters as concepts. But a lot depends on which subspace you choose and on what scale you're working... 'Good' may form a cluster or may not, I just don't even know how you could give evidence either way. It's unclear how you could formalize this in practice.
My thoughts on pleasure and the concept of good is that your problem is that you're trying to discover the sharp edges of these categories, whereas concepts don't work like that. Take a look at this LW post and this one from Slatestarcodex. From the second one, the concept of a behemah/dag exists because fishing and hunting exist.
Try to make it clearer what you're trying to ask. "What is pleasure really?" is a useless question. You may ask "what is going on in my body when I feel pleasure?" or "how could I induce that state again?"
You seem to be looking for some mathematical description of the pattern of pleasure that would unify pleasure in humans and aliens with totally unknown properties (that may be based on fundamentally different chemistry or maybe instead of electomagnetism-based chemistry their processes work over the strong nuclear force or whatever). What do you really have in mind here? A formula, like a part of space giving off pulses at the rate of X and another part of space at 1 cm distance pulsating with rate Y?
You may just as well ask how we would detect alien life at all. And then I'd say "life" is a human concept, not a divine platonic object out there that you can go to and see what it really is. We even have edge cases here on Earth, like viruses or prions. But the importance of these sorts of questions disappears if you think about what you'd do with the answer. If it's "I just want to know how it really is, I can't imagine doing anything practical with the answer" then it's too vague to be answered.
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Life, sin, disease, redness, maleness and indeed dogness "may" also be like electromagnetism. The English language may also be a fundamental part of the universe and maybe you could tell if "irregardless" or "wanna" are real English words by looking into a microscope or turning your telescope to certain parts of the sky, or maybe by looking at chicken intestines, who knows. I know some people think like this. Stuart Hameroff says that morality may be encoded into the universe at the Planck scale. So maybe that's where you should look for "good", maybe "pleasure" is there as well.
But anyway, research into electromagnetism was done using the scientific method, which means that the hypothesis had to produce predictions that were tested and replicated numerous times. What sort of experiment would you envision for testing something about "inherently pleasurable" arrangements of atoms? Would the atoms make you feel warm and fuzzy inside when you look at them? Or would you try to put that pattern into different living creatures and see if they react with their normal joyful reactions?
Although life, sin, disease, redness, maleness, and dogness are (I believe) inherently 'leaky' / 'fuzzy' abstractions that don't belong with electromagnetism, this is a good comment. If a hypothesis is scientific, it will make falsifiable predictions. I hope to have something more to share on this soon.