"Amygdala" is not the name of Natalie Portman's sister in the Star Wars prequels.
The Amygdala is the part of the hind-brain that parses sensory input, combing it as quickly as possible for anything that looks like might impact the organism's immediate chances of survival, and when necessary triggering a cascade of physiology-altering hormones in response. Those bursts of hormonal nitrous are what kick a human into immediate life-saving action, many times faster than conscious thought could. They're also what we perceive in ourselves and others as emotions.
Emotions are the body's way of processing information: Physical reasoning. In other words, the classic dichotomy between emotion and reason isn't accurate. The dichotomy is really between physical reasoning carried out at the hind-brain fast-twitch level, and intellectual reasoning carried out by our great big hypertrophied primate forebrains. Hindbrain quick, forebrain not so much. In fact, when the Amygdala kicks in, what we're really feeling, aside from the obvious flutter of adrenaline coarsing into our cardiac muscle, is a kind of chemical palace coup taking place in the central nervous system as our ancient animal reactions assert themselves, silencing our more recently-evolved talents for equivocation and thoughtful analysis like a Roman chamber full of murdered Senators.
Emotions scream "Enough talk! This means WAR!", which is probably why they often feel so inappropriate at the time. It's almost never, actually war.
If humans were like lizards or birds our reasoning would typically begin and end at the hindbrain; but we're not. Thanks to our binocular-eyed mammalian ancestors, we've inherited a midbrain legacy optimized for tracking moving prey at a distance and discerning variations in the visual field. That development required an upgrade in brain volume and connectivity. Out of that complexity emerged the early threads of cognition. That, plus a few hundred thousand years, led to abstraction.
Our evolutionary advantage comes from our (possibly unique) ability to abstract analogues of our world and the rules that govern it, then use those analogues to make educated guesses about cause and effect. We build those analogues out of painfully-won chunks of past experience. Our ability to point to analogues of our own experience automatically is, in a sense, a type of compression; tightly connected to the way in which humans process language and ideas. This enables us to make assumptions and predictions about the world without having to run a pixel-perfect simulation of it in our oversized heads.
Applying an accumulation of life experience, every choice - from the small stuff like how to put one foot in front of the other, to the big, like what time of year to plant crops (to the byzantine, like which supermarket lineup is probably going to move fastest) - is first tested out in this low-fidelity virtual world of the individual's own making. We maintain from birth a crudely-drawn map of the world, with very little detail about the actual physical, chemical or even spatial properties of things, but LOADS of data on causation and risk.
It shouldn't be surprising then that humans need such a big, complicated neuron-loaf packed into their skulls. The way we store memories is through a fuzzy process of association, a strategy that makes us very adept at pattern recognition and the ability to perceive similiarities between both things and situations. When we learn, or are trained through both repetition and attempted synthesis, we are adding greater and greater precision to our crude world map, layering in detailed notes and carefully plotted lines over top of older crayon doodles, overwriting some of the early mental picture but never really erasing it.
Over time, we become so reliant on this mental map, so conditioned to put our faith in its predictive power, that we find it difficult or even impossible to make choices that contradict its logic.
Which is exactly why survival situations are so stressful. Years of training and conditioning, of refining our mental map - collides all at once with 50 million year -old tadpole instinct. And frequently they point to different conclusions. The soldier's hindbrain screams "Someone's shooting at you... RUN!" while the mental map calmly, relentlessly intones "Hold your position. Cover the man to your right. Confirm your target. Three-round bursts." When this works, it's called training and discipline. But when it fails... thus follows talk of deer, headlights, etc.
The final point to take away from all this blathering about evolutionary neuroscience is that when humans encounter a situation in which their emotions and their mental map are in conflict, they really only have two ways out: They can freeze up and hope that God or luck or Brownian motion will save them at the last second; or, they can step outside of the deadlock in a willfull act of concious thought. If they have the mental toughness, the nerve if you will, they can force themselves to process the sensory data bombarding them the slow way, the scary way. They can assess the threat to their existence without the benefit of either animal instinct or conditioned response and make a deliberate choice, putting faith only in their smarts. They can take a gamble and bet on their brains.
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