Interesting thread, paraphrased from @Zoe_Brain elsenet, explaining how sex and gender are loads more complex than many folk think....
In 1890, X and Y chromosomes were discovered. Seemingly the men who were tested had 46 chromosomes, including an X and a Y, while women who were tested also had 46 chromosomes, including 2 X chromosomes.

So obviously Y => male. A reasonable conclusion. 1/
50 years or so later, it turns out that some men had 47 chromosomes, including 2 X's and a Y, while some women had 45, including only one X. Still fits the "Y chromosome => male" idea.

Except... it was found that fully 1 in 300 men weren't 46,XY. Some women were.

Oops... 2/
Once individual genes could be detected, it was found that the SrY gene, usually found on the Y chromosome, sometimes was missing. And sometimes had been translocated to another chromosome, hence 46,XX men and 46,XY women. So SrY defined masculinity. 3/
Then.. it was found out that some men didn’t have an SrY gene, not anywhere. Some women did. Other genes were involved. Worse, other factors, such as androgen insensitivity made 46,XY people female, and Congenital Adrenal Hyperplasia masculinised 46,XX people. 4/
Then in the 70s, other syndromes, such as 5alpha-reductase-2 deficiency were identified, which caused babies to look like one sex at birth, then the other at puberty. Worse, in some places 1 in 50 infants had this natural sex change, it was not rare there. 5/
(In part of the Dominican Republic in the 70s, 2% of children were "guevedoces". They'd appear to be girls at birth, but at puberty they would appear to turn male and for the rest of their lives they'd be men in nearly all respects.

Science 1974 Dec 27; 186 (4170): 1213-5) /6
In the 90s, it was found that hormone variations in the womb could cause parts of the body to develop as one sex, and others as as the other, regardless of genetics.

Some male to female transsexuals have been found to have female neuron numbers in a limbic nucleus. /7
(Kruiver et al, in J Clin Endocrinol Metab (2000) 85:2034–2041: "neuronal sex differences in the BSTc and its sex reversal in the transsexual brain support the paradigm that in transsexuals sexual differentiation of the brain and genitals may go into opposite directions") /8
It's a matter of timing during foetal development. Sometimes a boy is born looking like a girl, sometimes a girl is born looking like a boy, regardless of chromosomes. /9
Everyone knows that you don't teach relativity or quantum mechanics in primary school. Similarly, "XX => female" and "XY => male" is fine up until college or university - but it's only a generalisation /10
The exceptions are only relevant when talking about trans or intersex people, just as relativity is only relevant on the cosmic scale.

People don't need psychiatric help with relativity. So why should they need it if they find their sex is different from their genetics. /11
Intersex people exist. Trans people exist. They are unusual, so trying to apply the usual approximations is like applying Newton's laws to things moving near the speed of light. Legislating such things is as insane as legally ruling that Pi=3 (which also happened) 12/12
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