Fear is perhaps the most fundamental emotion. It's at the core of anxieties as global as those stirred up by nuclear sparring between India and Pakistan, and as narrow as those triggered by a dog's bark if you've been bitten in the past.

New research on the brain is beginning to explain just how this extraordinarily important and utterly primitive emotion works. In simple terms, there's an emotional computer in your brain called the amygdala. It rests quietly until it perceives a threat. When the amygdala determines that danger is present, it shifts into high gear, marshalling the resources of the brain in an effort to protect you and yours from harm.

This system was designed by evolution to detect and respond to predators and other kinds of natural dangers that threaten survival or territory, and it governs both innate and learned fears. For example, a laboratory-born rat, upon encountering a cat for the first time in its life, will freeze and its fur will stand on end. On the other hand, a rat will also respond fearfully if it hears a sound that occurred previously in association with an unpleasant experience, like a mild shock to its feet. It only takes one such pairing in order to make a particular sound a warning signal for danger. Although much of what we know about the amygdala has come from studies of rats, we've learned that the human amygdala works the same way.

The key to the amygdala is its neural wiring. It receives nerves that carry messages from all the senses: sight, hearing, smell, touch. If there's danger lurking in the messages carried by any of these, the amygdala is activated, and quick as a flash nerves coming out of it send messages to bodily organs that respond in ways to keep you safe. The amygdala works automatically, without "you" having to get involved in the act. If you saw the home video of the bombing at the Atlanta Summer Olympics, you'll remember that the crowd collectively froze immediately after the bomb exploded. Freezing occurs not because it's necessarily the best thing to do in this situation, but because it was often beneficial when our ancestors and theirs were threatened by predators. Evolution's calculation works for most animals most of the time, because motionless prey often elude detection. But when a deer freezes as your car speeds towards it, it's paying the price of having a decision-free initial response to danger.

Freezing is just one of a variety of things that happen once the amygdala is turned on. Blood pressure rises, reflecting the shift of blood towards body organs that are going to be actively involved in fight or flight (the muscles) and away from organs that won't (digestion, for example, can wait). It's well known that wounds are ignored by soldiers in battle, and this too is controlled by the amygdala. In addition, the amygdala regulates the release of a variety of hormones from bodily organs, like the adrenal gland. These then return to the brain and improve the efficiency of neural function and thus facilitate survival.

There is strong evidence that the amygdala never forgets. The indelibility of fear is very useful; once we learn that something is dangerous, we don't have to relearn it. However, we pay a penalty for this luxury. Many people carry fears and anxieties around with them that they want to get rid of but can't. Part of the reason for this is found in the nature of the connections between the amygdala and the cerebral cortex, where our thoughts, hopes, and plans occur, and through which we exercise control over our emotions (to the extent we can). It turns out that the amygdala is in a much better position to influence the cortex than the other way around. This explains why it is so hard to control our emotions, and why, once fear is learned, therapy is such a difficult and prolonged process.

Joseph LeDoux is the Henry and Lucy Moses Professor of Science in the Center for Neural Science at New York University. He is author of The Emotional Brain.