cousin_it comments on Transsexuals and otherkin - Less Wrong Discussion
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I don't see any special mystery here. Some people are also unhappy until they "find God". Other people earnestly believe that their arm is missing. Human brains can act in all sorts of ways! You could go LW-extreme and say that delusions are always bad (i.e. a man who thinks he's a woman isn't any better than a man who believes in god, no matter the emotional implications of either belief). Or you could apply the reasoning Yvain used in his "diseased thinking" post, and ask whether society is better off accepting this or that deviation from the mean, or trying to "cure" it.
The neurology involved in finding god is very real and useful and happiness-inducing. It is also completely independent of the actual existence of a god to be found. (It's actually better for people who try to find or have found god to become atheists. Once you know how god works, you can have more of it.)
Believing in the existence of god, or that your arm is missing, involve wrong beliefs. The ideal (possibly forbidden by brain bugs) resolutions are learning that god isn't a dude in the sky but a perfectly ordinary oxytocin-secreting circuit, and that your arm works and you can use it. I'm not seeing the analogy to gender and species. If told "The reason you go around saying you're trans is a bug in your brain similar to believing your arm is missing.", I expect most transpeople would be able to believe it, in the sense of exhibiting verbal behavior like "Yeah, I was wrong." rather than "No, actually it's my daughter's brain. The spirits spoke to me in my heart.". Yet they wouldn't stop being miserable.