Robert M. Sapolsky has degrees from Harvard University and Rockefeller Universities. He is currently a Professor of Neurology at Stanford University, and a Research Associate at the Institute of Primate Research in Kenya. Behave: The Biology and Behavior of Humans at Their Best and Worst is his most recent book.
Robert Sapolsky: How can we think best about the brain? It's crazy complicated. Everything connects to everything. It's easy to see the brain in three functional layers despite all its complexity. This simplifies aspects of brain behavior and functions. The brain doesn't really have three layers. This diagram is extremely schematic.
However, one could think of the oldest, the lowest, and the first most as what is most often.
The reptilian brain is also known. The wiring in our brains is the same as that of a lizard or any other ancient creature. The brain's base is covered in ancient, ancient wiring. What does this region do? All the regulation stuff. It senses when your body temperature changes and sends you a signal to either sweat or shiver. It monitors your blood glucose levels and releases hormones essential for everyday shopkeeping. It is merely keeping regulatory stuff in check.
The limbic system, which is the emotional part the brain, sits on top. This is a mammalian specialty. You can see them out in the grasslands arguing with another mammalian with antlers. Your limbic system is heavily involved in fear, arousal and anxiety.
The cortex is then at the top. The cortex is the most recently developed part of the brain. This is the part of your brain responsible for impulse control, long-term plan, and emotional regulation. It is the part of your brain that whispers to you, "Do you really want to do that right now?"
This flow of commands is very simple functionally. Layer two could be the limbic system, which could activate layer one of the reptilian brain. What is this? Your heart beats faster than normal, and it's not because of some regulatory reptilian thing. Ooh! You've been cut. This is not something that hurts, but rather an emotional state. Your heart rate increases because you're a wildebeest, and you have some menacing wildebeest in your path. You have a stress response. It is not because you are being regulated.
Change occurred in your body but for an emotional reason. It's easy to see this layer as the cortical area commanding your second layer, the limbic system, to produce an emotional response. Here's something more than an emotional scene. A movie that is emotionally disturbing appears before you. These characters aren't real, they're pixels. Your cortex is what transforms that abstract cognitive state into an emotion.
Your cortex, layer three, could also influence events in layer 1. This is a purely cognitive state. Ooh, I see people on the other side of this planet who are going through a traumatic event. My reptilian brain reacts by feeling upset. It's easy to see how a three-to-two scenario can be. As easily, however, you can think of one talk to two talks to three.