You are part of the mammal tree of life. You are warm-blooded, you normally don’t lay eggs, and you like to provide nutritional snacks to little versions of you. On the primate branch of the mammal tree, your gang hangs out — the homindae, or the great apes. There are not many of you in that neck of the woods, just the chimpanzees and bonobos, humans, gorillas, and orangutans. Now your family, the great apes, share many physical features. One noticeable feature is that male great apes are generally bigger and stronger than female apes.
Given the general physical characteristics of adult apes, it had been traditionally assumed that the male sex was the dominant sex and female the inferior. Yet, at the microscopic level, the Y chromosome — that chromosome that defines mannishness — is not all that impressive.
The Y chromosome is about 1/6th the size of the X chromosome and consists of less than 80 genes. Much of the Y chromosome is full of genetic leftovers, stuff that hangs out because it has nowhere else to go. Of those remaining active genes, they appear to be solely related to male sexuality and tend to code for proteins that exist primarily in the testicles. It would seem that the Y chromosome’s only job is to say, “Hey! Over here! Look at me, I’m a guy!” Genetically, not a whole lot is going on over at the Y chromosome party.
The X chromosome, on the other hand, is pretty robust and contains a healthy package of approximately 1000 genes, many that are important for reproduction and intelligence.
At one point in our evolution, the X and Y chromosomes where identical. Then, around 160 million years ago, the Y chromosome began to diverge. Time passes and 6 million years ago, humans and chimpanzees split, eventually leading to modern humans. During this slow process, the X chromosome stays roughly the same. The Y chromosome, however, goes through a gradual decay with most of its genetic material damaged or lost.
In a very real sense, men are genetically mutated women.