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Stupid Questions May 2015

Presumably most people would agree that there are people who are confused about their sexuality.

"Confused about their sexuality" is a particularly uncharitable characterization of a transgender person. Many are not confused, rather absolutely certain. Unless you're using the term "confused" as a polite way of indicating that you believe such a person to be mistaken or delusional, in which case you would be begging the question.

By the way, gender is not the same thing as sexuality.

It would only be a counterexample to that model if the student was correct, but whether or not the student is correct is precisely what we are discussing.

If one models gender as a boolean switch that can be set to either "male" or "female", and encounters an individual who has a combination of "male" and "female" characteristics, their model may not accommodate the new observation. I have watched people (who I previously considered fairly sane) break into a yelling fit when confronted with someone undergoing a gender transition, demanding to know their "real" gender and hurling insults when the response was not what they expected.

Stupid Questions May 2015

I don't know the LessWrong-like answer, so I can only offer you the human, empathic answer.

Based on the phrasing of your question:

whether someone born a male but who identifies as female is indeed female

and the fact that you have posted it to LessWrong, I understand it to be a question about constructing a useful and consistent model of the human condition, rather than about respecting an actual or hypothetical human being. If so, I think you are asking the wrong question.

Your students want to learn from you, but on a more basic level, they want to feel safe with you. If you have a trans student, or a student with a trans friend/relative, she is likely to take your answer to this question very personally. Your choice boils down to whether you offer a personal welcome (by recognizing your student's identity) or a personal affront (by implying that you have more authority than she does to determine who she "really is").

I should add that it is a common failure mode for humans, when confronted with a counterexample to their existing model of the human condition, to insist that their model is correct and that the fellow human they are dealing with is a bad data point. As well as rude and demeaning, this approach is irrational and intellectually dishonest.

Random LW-parodying Statement Generator

LessWrong updates the truth to fit its priors.

Them's fightin' words, Random Profound Deep Wisdom Generator!