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scientism comments on Transsexuals and otherkin - Less Wrong Discussion
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I'm aware of the research but I don't find it compelling. There are, of course, neurological differences for all types of behaviour, regardless of origin (learned, unlearned, innate, etc). These studies tend to draw conclusions that don't follow from the data. For example, in the first study you link to there's no evidence for the claim that the difference is present at birth and in the second study they are, for some reason, claiming that neurological differences imply that something is not learned.
"some reason" is that even people who are otherwise not susceptible to supernatural beliefs often picture human volition as being composed of a material brain being "driven" like a car by a disembodied mind. So if you can't tell the difference between two brains making different decisions then it must be because those decisions came from the mind, and if you can tell the difference between those two brains then it must be because those decisions were mandated by the brain.
As you say, every difference between human decisions is going to be due to some combination of random chance and preexisting physical differences, and it will merely be up to the quirks of human biology and the advancements of human biologists to determine which internal differences become diagnostically detectable when. So there may be many decades of public confusion ahead of us.
One also sees the opposite, especially in rationalist, materialist circles, including LessWrong. Even people who are otherwise not susceptible to supernatural beliefs often picture human volition as being composed of a disembodied mind being "driven" like a car by a material brain.
ETA: Correction: the view is more that the disembodied mind is being "driven" like a car passenger by the material brain.