Amygdala

I never even knew I had one. Like most folks, my knowledge of the grey lump inside my skull was limited to some pretty basic divisions: cerebrum, cerebellum, etc. I never stopped to think that there was a lizard in there.
Most folks that have had the basics know that the cerebellum or hindbrain controls the autonomic functions like breathing and basic muscle controls. It's the oldest part of the apparatus. That section, and the midbrain control most of our "instinctual" behaviors.
The newer part, the cerebrum, contains the main cognitive stuff; 60% is dedicated to associative thinking, making connections as it were. The remaining 40% has been related to processing specific motor and sensory activities. Where are those pesky memories and such? Are they controlled by these "new parts" of the human brain?

In the core of the cerebellum is a leftover reptilian, or perhaps lizard-type brain. That's where memories are processed. Research has shown that the hippocampus is responsible for processing conscious, declarative, explicit recollections of events. It seems to sort out the autobiographical memory.
The hippocampus is not well developed at birth, but the neighboring area, the amygdala is. Research suggests that the emotions are first processed by the aymgdala, which gives them their significance first before the cognitive process takes over. From an evolutionary standpoint, this makes good sense.
Fight or flight? We don't have time to think it over and cogitate on it. Especially when we are newly born! Our emotional responses to stimuli govern our very survival. So with good reasons, our emotions are processed separate from our rational selves. They bypass the normal associative structures that our brains dedicate so much real estate to. Emotions are relayed to our cognitive machine, but only after they have impacted our core limbic system. They are placed in memory before we get the chance to think about it.
This is big stuff. I'm still processing it, but I wanted to sketch a rough outline while it was still fresh. You can't reason yourself out of feeling things, and it seems that way by design. This has broad implications, to think that there is a completely separate area that makes us feel— and that we feel before we think. The initial stages of memory are non-declarative, implicit, and unconscious. We can't stop them, or process them away. Emotions matter, and they begin even before we are able to think about them. Memory begins before rationality can make any sense of it, in a tiny little almond shaped place called the amygdala.
Another interesting thing about the differentiation in real estate is that the hippocampus deals with temporal ordering, whereas the emotional center, the amygdala, is largely atemporal— emotions are not memorized in a narrative form. They are processed without temporal ordering. They are imagistic, abstract, and not organized in the same way as other information.
Oh, and one more thing— notice that all these structures are buried deep, away from the surface that might be damaged. We can survive without our reason, but not without our instinctual mechanisms and feelings!

Nice to see this on your page. It becomes even more interesting, for me anyway, when the yogic metaphor gets added into this western psych and disect model. And the Newsweek article of last May is way too superficial, had the cart before the horse. Here in India is a fair amount of info relating east to west in terms of the brain and mind. Meditation amazes me more and more as the years go by, and if one thinks of the body and brain as merely (!) a gross-level coagulation of an ever more ephemeral collection of energies, going all the way back, in, to purely consciousness, well, then it's really big stuff.