Re: why do people have different eye colors?

Eye color is a very interesting subject. People have studied the genetics and biochemistry of eye color for a long time, because it can teach us a lot about biochemistry and genetics. For one example, many people who study genetics use the fruit fly, Drosophila melanogaster, because it has a very short life span, produces hundreds of offspring per generation, lives simply in a laboratory, and has interesting features to look at such as eye color, which are genetically determined.

Here are some non-technical web sites on human eye color:
The Genetics of Human Eye Color
A 3-gene model for eye color in humans
Structure of the Human Eye
MadSci Eye Color Genetics Page.

There are many web sites and books that explain eye color. But you can't always trust everything that you read. For one example, this page about eye color:
Everyone wants to Know about Eye Color
is a pretty good description, except that it claims that melanin is a protein. Melanin itself is not a protein, it is more like a hormone, a complex chemical which is made by proteins. In the case of melanin, which is the major eye, hair and skin pigment, there are protein enzymes, and regulatory proteins, that control the production of melanin from tyrosine. There are also other proteins (and therefor genes, because all proteins are coded by genes), involved in transport and storage of melanin crystals within cells.

An on- line encyclopedia has this to say about melanin:
melanin[melŽunin] Pronunciation Key, water-insoluble polymer of various compounds derived from the amino acid tyrosine. It is one of two pigments found in human skin and hair and adds brown to skin color; the other pigment is carotene, which contributes yellow coloring. The synthesis of melanin reactions is catalyzed by the enzyme tyrosinase; an inherited lack of tyrosinase activity results in one of the forms of albinism. Tyrosinase is found in only one specialized type of cell, the melanocyte, and in this cell melanin is found in membrane-bound bodies called melanosomes. Melanosomes can be transferred from their site of synthesis in the melanocytes to other cell types. The various hues and degrees of pigmentation found in the skin of human beings are directly related to the number, size, and distribution of melanosomes within the melanocytes and other cells. Besides it role in pigmentation, melanin, which absorbs ultraviolet light, plays a protective role when skin is exposed to the damaging rays of the sun.

It turns out that almost everyone has the tyrosinase enzyme, only albinos lack a functional tyrosinase. So the genetics of eye color is mostly about the genes that control how much melanin is produced, exactly which type of melanin, and exactly how the melanin is conceentrated and stored in granules within cells. The eye color of most people is determined by at least 3 genes (not including tyrosinase because everyone except albinos have at elast one functioning copy of that gene), but there are dozens of alleles of each of those genes, so we can get hundreds of different shades from blue to green to light brown to dark brown to almost black irises from them. In addition to those three genes and their normal alleles, there are then very rare genes or conditions, such as albinism, that also can affect eye, skin and hair color. Eye, skin and hair color are all produced by melanins in addition to other pigments, so eye color is linked to skin and hair color and a blue eyed person with very dark brown skin and black hair would be very rare, involving some gene specific to the transport of melanin in the iris.

This page on Melanin has a picture of the chemical structure of various types of melanins.