The Historical Jesus

[Ferrocyanide]

It sounds like you are saying that gender is based on an individual claiming to be male or female with no reason.

I'm not sure that "no reason" is correct. Probably there is a reason. But the reason is NOT anatomical. 

If a person who has all the anatomical characteristics which we used to associate with maleness (chromosomes, genitalia, hormonal balances) identifies as a female, then the current consensus among right-thinking people is that she is in fact a woman. 

If someone objected and said, "I don't care how you 'identify,' you have a dick and a beard and XY chromosomes, therefore you're a man, like it or not," this person would be labelled a transphobe. 

In that case, the words male and female lose meaning.

They appear to have lost the meaning they used to have. But I'm told that people who hold to the old meanings, and deny that trans women are women, are no longer on the right side of history.

I agree that it is not chromosomes, genitalia, hormonal balances that absolutely and definitely determine if a person feels like a male or female.
They probably play a role in shaping up the brain (the neural circuits) but probably there are some other factors that effect the neural circuits as well.

I was confused when you said

And I am saying that even if a person has a "female brain" (whatever that is) it would not be determinative of that person's gender.

Because brains are anatomical organs, and we no longer believe that gender is determined by anatomy.

Because if it isn't the brain that determines this, then we are left with what?