First, thanks for your post. It’s reasonable and thoughtful and maybe worthy of a thread on its own. The topic is not new here at PS, not hardly, but IMO it’s important and valuable to explore regularly.
Re the comments about amino acids, I do think that was a mistake that is mostly due to this medium (quoting snippets from previous posts and responding to them). Nevertheless, IMO John was nitpicking and was careless, and I think there has been an overall failure to try to address simple comments (from @theaz101) in the spirit in which they were made. I might ask you to note that John corrected the mistake, and to further note that error correction is a theme of this part of the thread. The major mouthpieces of the ID movement seem never to do this. A discussion of that specific topic, which might include examples that show my impression to be wrong, would be valuable IMO.
Still, you are right that to whatever extent the discussion is “us” vs “them” with “sides,” there will automatically be barriers to “productive dialogue.” You can call that “ideology” but I think it’s more basic, more animal, than that. It’s human tribalism and it requires effort to negate. Is such dialogue “nearly impossible”? Call me naive and romantic (it happens a lot actually) but I disagree. Maybe one first step is to refuse to see another person as a member of a side or tribe, and to engage them as a human. Maybe a second step is to all agree that ideas are not protected or worthy of special respect, but that people are. And then maybe an additional critical step is to acknowledge and even expect people to fail, even spectacularly, and then expect them to apologize.
Sorry for the long response; FWIW I thought you deserved one.