Without rational thought, if a situation requires an immediate reaction, we will search our memory for a similar already-learned experience as a guide: if one is found, our emotional reaction to that will decide our actions, and if there is none, a panic ('fight or flight') reaction ensues.
Yet with rational thought, almost in parallel with the above process, we are able to 'calculate' the situation beyond 'knee-jerk' instincts of self-preservation: our brain can compare how one remembered course of action may be better than another, it can consider an action's effects on the surroundings, on other people and even what future consequences those actions will have. Neuroscience shows us that, if our brain decides that the rational conclusion is 'better' than the instinctive one, it will override it.
Yet many in a religious or totalitarian regime, at least the followers, have no use for rational thought: their actions are based on a 'punishment or reward' reaction to situations shown (and often only 'explained') to them by someone else, usually a 'trusted leader'.
In everyday interactions, if a situation or someone's answer 'matches' with something a follower was taught, the emotion attached to that memory (what he was 'taught to feel') will dictate their action: if they get a match with something in the 'good' category, their brain will give them a chemical reward and permission to continue the action; if it is in the 'bad' category, they will 'reject' the situation or their (instinctive) defense mechanism may be activated; if there is no match at all (and they don't feel in danger) there most likely will be no reaction at all - that 'deer in the headlights' look.
What the above paragraph really describes is our childhood learning process. When our frontal lobes (where neuroscience shows us that rational thought and 'morality' are seated) have reached maturity in late adolescence, our brain (well, the model of it promoted by evolution) normally expects us to start using it, but somehow, in many, this 'switch' never happens.
Mimicking lessons that promote self-preservation and/or personal reward is not 'morals'.
