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We could maybe give people like her a glimpse into the sheer defiance that nature has against all attempts to fit into tiny categorical boxes.
It's not just the topics that she doesn't understand (especially the intersection of gender with endocrinology and neurology), but everything.
If you are a biologist and think you have found a rule that applies to some part of biology, you will feel deeply uncomfortable until the inevitable exceptions start cropping up that tell you that while the theory is still statistically sound, it's not unnaturally strict and therefore plausible.
Obviously trans people exist and are valid. Thinking otherwise would be ignoring mountains of biological patterns and data that tell us that every binary in biology isn't actually clean-cut.
To be clear I'm asking what you think a biologist could tell Rowling that would challenge her. You seem to be saying that a biologist could tell Rowling that biology is fuzzy at the edges. What makes you think this would challenge Rowling?