There are really a few causes.
The oil becomes contaminated by "particulates", which are microscopic bits of metal from wear.
The oil also gets contaminated with combustion byproducts from "blowby", a term that includes the combustion gasses (including carbon) that pass by the rings during the combustion process. This happens in all engines. In addition to the rings' seals not being perfect, there are gaps in the rings (necessary to allow expansion and contraction) that allow tiny amounts by.
There can also be some "coking", a process describing basically the cooking of the oil. Remember that it gets really hot in those cylinders.
I'm guessing, but I think the carbon from the combustion process is probably the biggest blackening agent.
www.carbibles.com has a good primer on oils. I suggest a visit.