Dang! You killed that one VnutZ. Beautifully executed.
I think you got it pretty close Vnutz; there is a time differential between the pre-frontal cortex (the part of the brain responsible for conscious action), and the amygdala (the part of the brain that decides fight or flight and anxious responses). The thing is, the prefrontal cortex takes a lot longer to make decisions, because it processes information so deeply, whereas the amygdala has to make snap judgements geared toward our basic survival in an evolutionary context.
So, when confronted by an emotionally charged situation, you have about a quarter of a second before your amygdala takes over and drives you to do something that might not otherwise do if you had time to reason the situation through.
This comes up often in psychological studies of Buddhist meditation--the idea being that meditation increases your likelihood of "catching" yourself before the amygdala takes over--thus leading to a calmer assessment of a situation and more consciously directed actions. Of course, there are still situations where a fight or flight reaction is called for, but the hope is you'll have more conscious choice in what you do without sacrificing reaction time. This is the "no mind" state talked about in the Zen tradition and in the martial arts, but which comes in handy in any emotionally charged situation--like in preventing you from saying something hurtful when you have a fight with your wife, etc.
That's the bit about the "monk" class that never made it into the Player's Handbook...

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Some Thoughts
For simplicity (because I don't want to keep typing the word), lets call the conscious mind the C engine and the subconscious mind the S engine. Using their findings, you could define the S-Decision as f(S) and the C-Decision as f(C) where f() is some function of experience, memory, teachings and instinct. The overall decision is then Decision = f(f(S) + f(C), t). "t" will be a time factor that I'll discuss further down. So let's use that framework to establish common language reference points to think about it a little.
Let's make the scenario such that Bob is threatening to rape Alice in a dark alley, but she has just enough time to reach into her purse and pull out a gun. What does Alice do?
Looking at her S-Decision, let's imagine that her fight or flight instinct leans 75% fight and 25% flight. Her f(S) function quickly evaluates what she knows about her environment and deems escape not only difficult but not likely of success either. Combine her innate tendency towards fight and its clear f(S) resolves to shoot Bob.
Let's look at her C-Decision. This could go all kinds of ways so we'll establish her background as having been raised in a very peace-loving, nurturing environment by loving parents and a heavy Christian background (a practicing one ... not a generic, hey I go to church on Sundays but can't wait for it to be over one). Soooo, given that, her f(C) function would be very different than someone that grew up in an abusive household, locked in an incestuous dungeon, etc. etc. Her f(C) function actually might lean towards not shooting Bob but say it creating a response to scream loudly for help, fire the gun in the air followed by pointing it at Bob and reasoning with him to "not do this and just walk away".
Now, for this practical example, it's obvious f(C) and f(S) are creating different responses which lend themselves well for your question. What drives her final decision? Are her actions the sum of what's in the physical brain?
I'm speculating, but I think the t I alluded to in f(f(S) + f(C), t) is the factor. The more time she has before being forced to act, the more likely she is to go with f(C). But I think the smaller "t" is, the more likely she is to go with f(C). So the final decision is a sliding function of time where the % weighting on either source function begins to tip towards the conscious decision the longer she has to think about it.
So what differentiates two people? I think the experientially learned attributes of behavior and instinct drive f(S) and ultimately affect how strongly it's weighted at small values of t. For example, somebody that's been burned on a stove as a child will have a strong f(S) aversion to hot things and will be virtually 99% likely to act as f(S) for even large values of t. Whereas someone who's only been told they'll be burned by a stove and has never felt a burn will have an instinctual f(S) avoidance of hot things, but ultimately might weight that evaluation as 50% against f(C) and for short durations of "t" will quickly value the determination of f(C).
So I think who we are is almost entirely driven by the brain as a function of experience, teachings and time to react. Then again, I might simply be a level 50 paladin whose dexterity, intelligence and THAC0 were determined by a 20-sided die whose f(S) and f(C) functions are driven by subsequent rolls of the dice.
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