His sex was innate. This case does not demonstrate that there is something different and seperate from the material reality that he actually was male, and that this was not changed by the abuse done to him.
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We get better at it as we approach the usual age of puberty for obvious reasons.
I don't know. How do mice sense their sex? How do beetles sense their sex? How do fish sense their sex? Its not a great mystery that sexually reproductive animals would have a hardwired instinct for this.