Okay, I found that link both interesting and disputable.

First of all, my question:

What I don't really get is, what do transpeople associate with gender? What does it mean for a trans-man to have male gender? What defines male for them - they certainly don't aspire to behave and feel like cis-men, or do they? This is what I don't totally understand, the rejection of the assigned gender and rejection of the behavior of the stereotypical cis-gender, but at the same time they... - what is it that makes a trans-man feel like a man, what's the defining characteristic of man for them? It cannot be what most of the society regards as typically "cismale", because that attracts downright disgust from the trans community (or at least that's what I witnessed). (This obviously disregards the community which feels as neither male or female).

Please regard that when I say male and men in the paragraph above, I mean the gender and not the sex (as you may have noticed, I'm not totally familiar with the terminology).

Now come the parts I disagree with:

Whether the baby is intersex or not, the child is then raised as whatever arbitrary gender the doctor saw fit to assign.

At least where I live this decision is not made immediately and not solely by the doctor, at least the parents are involved, usually more people.

For whatever reason, they are able to live somewhat comfortably within the gender in which they have been cast. No one really knows why so many people are capable of fitting into such arbitrary categories.

I find this paragraph surprising; while I can understand why someone who does not agree with his assigned gender might wonder why everybody else seems to have such an easy time with it, there is without doubt a complex interplay between sex, karyotype and neurology; there are differences in the brains of men and women (sex) and you cannot completely decouple sex from gender. If we would follow the train of thought of the author, we would have to ask ourselves: why the hell would bulls behave like bulls and not like cows; why do male lions behave like male lions and not like females? Certainly there are exceptions to the rule, but it simply seems to be the norm in nature and it seems as if there is a strong causal relation between genetics and behaviour (and thus gender). Correlation does not imply causation, but it heavily implies it. And don't disregard this as an "appeal to nature", as this is not a statement about which state is preferable, it's merely an observation. This is NOT to say that the question is not quite interesting from a (neuro)biological point of view, it's just that the observed behavior is not surprising nor that it is hard to imagine a causal relationship between the two.

The entire concept of “sex” is simply a way of attaching something social– gender– to bodies.

Tell me, a biologist sorting a bunch of Drosophila in males and females, in what way does he assign any social value to the fly? The statement that the "entire concept of sex" is a social construct to assign some personal, or predefined by society, value to something strikes me as quite detached from reality.

The fact is that the concept of binary sex is based on the fallacious idea that multiple sex characteristics are immutable and must always go together

There's male, female and intersex (plus a wider variety for words to better describe intersex). It's largely used binary, which is not precise.

There are people with hormonal anomalies. In fact, hormone levels vary wildly within the categories of cis male and cis female

Yes, but usually there is still quite a clear difference in the levels, almost in orders of magnitude. If a women has the progesterone and testosterone levels of a man, several tissues will stop working - this is considered a disease (and correctly so usually, otherwise you can say that diabetes or pancreatic insufficiency is a disease too).

In addition to variations like XXY, XXYY, or X[0]

Yes and some of those come with serious problems. Dysplasia, hypogonadism, etc. While I don't think these karyotypes can be called diseases, they certainly are anomalies - and usually require to something go not as expected in spermatogenesis/oogenesis/embryogenesis.

Also the mentioned XX males are most likely the product of a translocation of the sex-determining region of Y, but due to the genetic configuration they suffer (afaik) from azospermia. In this regard the author is right, it's not strictly the karyotype, but the translation of the genetic information - it's just that if no anomalies occur, this - at least in regards to sex-specific traits - is influenced pretty strong by karyotype.

Yet it is possible to isolate, alter, and remove many of these traits. Many of these traits do not always appear together, and before puberty and after menopause, many of them do not apply.

It is not possible to change the histologic type of many tissues, a sex-changed person will not (yet) produce sperm instead of ova and vice-versa, there's no way to give a man a uterus complete with endometrium and a vagina and penis are not basically the same thing. They have to some degree the same roots, but they both contain cells that differentiated to a type that is not found in its counterpart and they cannot differentiate into their counterpart (to claim they are still the same because they have the same roots would mean that you could claim that your brain is the same as your toe-nail, since they both came from the same zygote). A table and a stool are not the same thing, even if both are made out of wood.

This being the case, I believe the most sensible way to look at the question of sex now is this: a male body is a body belonging to a male– that is, someone who identifies as male.

Females suffer from different diseases, have different risk-factors, even different lab values (i.e. Hb, hematocrit,etc.) than males, male and female anatomy differs not only on an internal but also on an external level and even on smaller levels (histology/neurological functionality). Again, there is a strong correlation between the gender and certain traits, traits that range beyond behavior (i.e. traits not influenced by society).

I somehow feel that this article gets the directions wrong - it says "why do we understand sex as biological traits???" when, at least in biology, the term was meant to describe individuals that produce ova or sperm. It's like wondering, why do we call light with 720nm wavelenght red and not blue - when the reason is that we assigned the wavelength 720nm the term "red". There's also room for improvement, no doubt - do men with azospermia don't count as men because they can't produce men? Or is the ability to produce sperm on a principal level (i.e. the production of tissue which is predisposed to produce sperm, but may not be able to)...

I don't want to question that the term sex is often misused when gender is meant, but I don't regard the misinterpreting/abolition of the term sex as the correct solution. The concept of sex is not a social construct, it's a concept to describe a certain phenomenon in biology and is extremely useful, not only for biologists, but also for medicine.

I hope I found most typos and grammatical errors, if not excuse them please - writing this took longer than excepted and I have to stop procrastinating now (or never).