I’ve read Diamond’s response to your first part and I had a look at his book to see where he’s coming from. The disagreement here seems largely epistemological. As is often the case, we have different views of what counts as knowledge. In this case, you’re disagreeing about how science works and about the value of scientific explanations.

I agree that overspecialization can be a problem in science and elsewhere. But I don’t think scientists are obliged to be entirely open-minded, as though they were blank slates that mindlessly absorb the data and only afterward start formulating explanations. Present-day science rests on all established science. Plus, the special sciences rest on the more universal ones like physics, chemistry, and cosmology. On top of that, scientists do have philosophical assumptions even if they prefer not to contemplate them. For example, scientists presuppose a philosophy of science which includes concepts of causality and natural law. Most importantly here, I think, is methodological naturalism, which scientists assume on a professional basis, meaning that this is an institutional framework for the business of science.

Thus, evolutionary biologists discount the supernatural at the outset, on philosophical grounds. If that’s your primary disagreement, since you prefer to leave open the question of whether gods are real or whether psychedelics provides us access to them, your real disagreement with Diamond isn’t scientific but philosophical. Diamond would have to defend methodological naturalism, a skeptical sort of epistemology, and a type of critical thinking that support science and rule out theism, superstition, and certain paranormal possibilities.

You can say the evidence itself points to this or to that, but no one comes to the evidence as a blank slate. In particular, we presuppose answers to certain philosophical questions. You’ll approach the data with some ideas about how properly to assess them; that is, you’ll have an ideal of rationality in mind as you try to make sense of what you’re observing. (Terence McKenna talks about this in the context of “dying from astonishment,” from the psychedelic experience; we grapple with the bizarreness of the experience, because our rational mind is left intact by DMT.) Scientists likewise have an epistemic ideal, based largely on their experience of doing scientific work.

Diamond connects technological advances to the scientific method and the naturalistic worldview. That’s not entirely out of line, since the workability and testability of scientific explanations are signs of the value of scientific methods of inquiry. If those methods are valuable because they evidently work, the scientist is hardly going to be so open-minded as to approach the evidence like a blank slate, dismissing the philosophical underpinnings of those methods and of the resulting naturalistic worldview.