Sex? What's the Difference? It's not binary; it's complex.

Claire Ainsworth in Nature, from February 15, 2016:

Sex can be much more complicated than it at first seems. According to the simple scenario, the presence or absence of a Y chromosome is what counts: with it, you are male, and without it, you are female. But doctors have long known that some people straddle the boundary — their sex chromosomes say one thing, but their gonads (ovaries or testes) or sexual anatomy say another. Parents of children with these kinds of conditions — known as intersex conditions, or differences or disorders of sex development (DSDs) — often face difficult decisions about whether to bring up their child as a boy or a girl. Some researchers now say that as many as 1 person in 100 has some form of DSD2.

When genetics is taken into consideration, the boundary between the sexes becomes even blurrier. Scientists have identified many of the genes involved in the main forms of DSD, and have uncovered variations in these genes that have subtle effects on a person's anatomical or physiological sex. What's more, new technologies in DNA sequencing and cell biology are revealing that almost everyone is, to varying degrees, a patchwork of genetically distinct cells, some with a sex that might not match that of the rest of their body. Some studies even suggest that the sex of each cell drives its behaviour, through a complicated network of molecular interactions. “I think there's much greater diversity within male or female, and there is certainly an area of overlap where some people can't easily define themselves within the binary structure,” says John Achermann, who studies sex development and endocrinology at University College London's Institute of Child Health.

These discoveries do not sit well in a world in which sex is still defined in binary terms. Few legal systems allow for any ambiguity in biological sex, and a person's legal rights and social status can be heavily influenced by whether their birth certificate says male or female.

The final two paragraphs:

Yet if biologists continue to show that sex is a spectrum, then society and state will have to grapple with the consequences, and work out where and how to draw the line. Many transgender and intersex activists dream of a world where a person's sex or gender is irrelevant. Although some governments are moving in this direction, Greenberg is pessimistic about the prospects of realizing this dream — in the United States, at least. “I think to get rid of gender markers altogether or to allow a third, indeterminate marker, is going to be difficult.”

So if the law requires that a person is male or female, should that sex be assigned by anatomy, hormones, cells or chromosomes, and what should be done if they clash? “My feeling is that since there is not one biological parameter that takes over every other parameter, at the end of the day, gender identity seems to be the most reasonable parameter,” says Vilain. In other words, if you want to know whether someone is male or female, it may be best just to ask.