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It’s not a bad thing if we decide bodily autonomy isn’t the highest standard and that it’s significantly more accurate than self decision.
The trans community is rightfully nervous about diagnostic criteria because they’ve been used really badly against us. Like 15 years ago it was common to not be allowed to transition if you had the wrong sexual orientation (we’re pretty evenly split between straight, bi, and gay, so between 1/3-2/3 were rejected) as well as real life experience which didn’t help anyone but was/is extremely uncomfortable. And going further back you get stuff like transition being denied because a psychologist doesn’t think you’ll be attractive enough.
I get the sentiment, but I could use the same arguments against HRT, which isn't exactly what you want.
Bodily autonomy is fine, as long as it's not harming anyone (including oneself). If this tool is accurate (again, big if), it could actually increase bodily autonomy, since you could distinguish between real cases and those who really have other problems. That takes the burden of proof away from trans people.
Think about how long it takes today from the first visit at a doctor's office until actual treatment or legal processes can start. Using diagnostics like this, this could be shrunken down to one MRI.
Who decides what is "real" though, if it's not the person in the body? So someone says they are a boy, but the MRI says nope, you are wrong, you are a girl through and through.
What if I am a cis woman and have a mind that works more like a guy's mind? But if I still am comfortable and happy in my woman's body, who cares how my mind works? Nobody, that's who. Why would trans people not get the same consideration?
I just don't think it makes sense to use tech to invalidate someone's experience, and it's just not anyone's business if someone wants a different body. My sister got big fake boobs, nobody said "well, you don't have a body that matches the boobs" they just gave her what she asked for and paid for. Why can't a man do that if he wants? Why does he have to prove he's a woman first?
None of that makes sense to me.