What are the neural substrates of racism?
Many animals have a way of identifying family members, to avoid breeding with them; and a way of identifying things which are too different and thus that they shouldn't try to breed with (like other species). Racism is just the latter such mechanism being triggered.
If you look at the thin slice research of Ambady et al you will see that there is tons of evidence supporting this. Seeing just a split second video of someone can allow you to make good predictions about their behavior, and engage in automatic stereotyping.
And it works.
The thing a lot of people hate the most, but can't argue their way out of, is these heuristics have a very high accuracy. Even if someone rejects their validity, they work, and down the line one cannot help but slowly see how right they were all along.
The brain is doing a lot at any given time, and not all of it is fed into or readily accessible to the conscious mind. A lot of learning throughout your life is indirectly unearthing what happens in the background. Complex pattern recognition is one such thing.
Absolutely. The brain doesn't concern itself with what it ought to do. Many bigots don't realize they're bigots and even good liberals have these automatic reactions to people of othet races.
To answer OPs question, this experiment found differential amygdala activation. http://www.mitpressjournals.org/doi/abs/10.1162/089892900562552
Racism is more a Psychological thing than Neurochemical.
i mean, when your a 17th century Spaniard who is exploring Africa for the first time, and you see a bunch of tribal black people, are you honestly gonna believe they are equals let alone human?
modern racism is just built upon this, plus your white with a 3 digit IQ and lived in a black Detroit neighborhood for a week you become racist pretty fast