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This is a super informative. It’s very hard to find non-partisan reviews of this literature. Thank you for this!

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I know I'm coming to this pretty late, but I'm in a discussion/debate with a trans friend of mine who's quite dismissive of the desistance literature for exactly the issues that you cite, so this has been immensely helpful. I've been reading into some of Zucker's literature from the 2000s to try and see if he's trying to address this, and it does seem that he spends a lot of time addressing it. Seeing as he was the head of the working group that, among other things, crafted the DSM-5 criteria for GD, I'd say that him and those who associate with him (also in working group) have heard the criticism and are trying to make further research more robust by tightening up the criteria. I wouldn't be surprised if the desistance rate was still around 60%, but hopefully we'll see in future studies.

Also an issue with tightening up the criteria is denying more genuinely trans kids recommendations for their insurance to cover costs associated with transition pre-puberty, so there is a trade off between getting more accurate desistance measurements and delivering trans healthcare to those who need it which we may or may not hear about. But seeing as I'm a watchful waiting type person myself, perhaps this isn't that bad.

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