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This is fundamentally just a really bad way to judge whether a treatment works, one that we rightly dismiss for other treatments. There are also countless anecdotal reports of people who recover from cancer after faith-healing. And unlike spontaneous remission of cancer, which is rare, regression to the mean in mental health is the norm. "My mental health got so bad that I sought out X treatment, after which I got better" is the default result.
Go read Scott's Alcoholic Anonymous post (another treatment that a lot of supposed beneficiaries swear by that some critics accuse of being cult-like). Notice both how the evidence base is a complete mess (because it's really hard to test these things) and how the ultimate conclusion seems to be that AA (and pretty much all other treatments tested) is similarly effective to your doctor spending a few minutes telling you that alcoholism is bad and you should stop. Well, the evidence regarding gender transition is even worse. If it turns out outcomes for gender transition are equal or worse than your doctor spending a few minutes telling you "puberty can be scary but you'll be fine" or "accept yourself", that's something we really want to know rather than continuing with a standard treatment with so many downsides. Really it's something we should have known before establishing it as a standard treatment, but instead it went from "so rare you can't do decent studies" to "so common and standard that it would be unethical and difficult to have a real control group" without the step where we actually find out if it works.
A lot of arguments regarding gender transition research seem similar to other arguments that you pick up reading about medical research from people like Scott or Derek Lowe, just with the additional politicized element.
A lot of treatments are based on popular theories on how things work that make the effectiveness of the treatment seem like an inevitability, then crash and burn in randomized control trials. Suggesting a biochemical pathway is bullshit is less likely to get you fired than suggesting "inborn gender identity" is bullshit, which makes it even worse.
"The trial doesn't look good but maybe it works in a subgroup" is the sort of dubious cope you see all the time. At least the p-hackers saying "efficacy was shown in middle-aged hispanic women" have some sort of evidence, saying "okay but assuming the treatment works we just need to do a better job of diagnosing the people it'll work on" is even worse. The only saving grace is that the negative studies on gender transition aren't high-quality randomized control trials because none of the studies on the subject are.
Most fundamentally, everyone knows that the vast majority of prospective treatments fail and the burden of proof is with the people who think they'll succeed. You can have a clear mechanism, anecdotes, observational trials pointing the right direction...and people know not to get too excited. Yes there are standard treatments that are grandfathered in without going through the FDA or equivalent, but the reason why that works isn't really "standard of care", it's "so incredibly obviously effective that the result was clear with much lower standards of evidence". The argument would be that gender transition is such a case, but the various negative studies (and "positive" studies that are pretty negative on closer examination) seem to show it's not really that obvious.
Because it calls into doubt both the advisability of the current standard of care and the theoretical framework the treatment is based on. If "diagnose people with gender dysphoria if they say they're trans" is an effective diagnosis method, why is it getting so many apparent false-positives? If "gender identity" is an inborn trait that people have an internal sense of, how are all these people getting it wrong? Why don't they just feel "gender dysphoria" the first time someone calls them "he" and immediately stop? For those who think they're not false-positives, why does it seem to so obviously spread socially? If the answer is something like "because the born-trans members felt more comfortable coming out", how does it get such absurdly high rates among not-very-selected subgroups? If 40% of a classroom in a private girl's high-school comes out as trans, does that mean we should believe 40% of all women throughout the world and all of history are closeted transgender people? I don't think you have be certain about whether you think "inborn transgenderism isn't real" or "inborn transgenderism is real but 99% of post-surge ones are false-positives" or "more than 1% are real but there's a large fraction of false-positives" to point out the ways the dominant theoretical framework and treatment methodology doesn't really make sense. Nor is there going to be a lot of a agreement on those among critics. Also "Are there a group of people with an inborn 'wrong gender identity' disorder that is best treated through gender transition?", "Are those people 'really' the other gender?", and "Would it be best if society did X to encourage or enforce classifying them as the other gender?" are three different questions.
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