The prior posters are correct about the primamry colour gene being on the X chromosome. One of these is shut down fairly early in development (in females), and it is random which it is, so that a heterozygote for this pigmentation will show both black and brown (or grey and tan) colourations in different parts of the body. Males, having only one X, will be monocoloured. Once one of the chromosomes have been shut off in a cell, the descendants of that cell will also have the same one turned off. The thing that makes the difference between the fine mottling of the tortoise shell and the patchiness of the calico is the time at which this happens. If it happens earlier, the size of the resultant descendant cell clusters will be bigger, and the colouration patchier.

Several other genes influence colouration as well (you'll note that you don't see a tan and orange calico, or a black and grey one; if you think you are seeing this, look closely, and the variation will be like the lighter and darker striping of a tiger tabby); the genes operate independently of the primary colour gene on the X chromosome.

In fact, the colour is modified so that in patches of a calico cat, you will also see some tiger-stripe variation of the basic colour, just as you would see this in a standard tabby. In addition, there's another gene that influences the white colouration; in calicos as in other monocoloured cats, the extemities ("socks") and belly are often white, where neither primary colour is apparent; for some cats, about the only spot of white is a little dot on the front of the neck, (this is true of both males and females).

Siamese cats (and similar ones such as Himalayans) have a gene that codes for a mutant protein that is temperature sensitive; at higher temperatures this protein denatues and there is no melanin colour pigment. Thus in these cats, the extremities, being cooler, show colour while the body and head is lighter. But as above, other genes can turn this off, so that I've seen part-Siamese who have the white "socks" seen in other varieties.

Siamese also have brain miswiring (an abnormal contralateral crossing of the nerves going from the eye to the brain), so that their vision is in most cases somewhat impaired (and they are often cross-eyed). This phenomenon also shows up in other albino animals, such as rats, and even one albino tiger. In this sense, Siamese are "albinos" except for their extremities. Because of this, they have no tapetum (the reflective layer at the back of the eye which makes cat eyes glow green in a direct light), and their eyes reflect red (as do humans, who have no tapetum at all).

Probably too much information. . . . Sorry.

Cheers,

                              -- Arne Langsetmo