One key thing we’ve learned about the human brain is that it’s just like the rest of the body: every part of it can go wrong, in a million different ways. It’s unlikely that the gender identity part is the one special case that always works perfectly and is 100% male or female.
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(“go wrong” and “works perfectly” are bad framing here. The point obviously isn’t that trans and non-binary people’s brains have gone wrong – they haven’t, of course! – but that the default expectation is a range of neurodiversity across all function, gender identity included.)