But there seems to be a third category; emotional motivations that are not understood by the conscious mind. — EnPassant
True. So habits are the mid-brain doing its thing of automating responses so "you " don't have to think about them, or attend to them. That is one aspect of what people label the unconscious, or subconscious, or preconscious.
And as well as this "how" of unconscious, or rather non-attentive, behaviour, there is the "why" - the motivation or valuing that gets labelled as emotion, in opposition to "conscious reasoning".
So now the neurological basis of that is about the brainstem and limbic system - amygdala, hypothalmus, etc. And that is its own complex story.
But primarily, the emotions can be understood as perception of the internal state of your own body and physiology. Are you hungry, thirsty, excited, tired, in pain, etc. So it is hardly unconscious. Like all perception, the question is whether you are attending and so focused on how to respond to the signals.
I could just as well be staring out the window and not seeing what my eyes are seeing because my mind is far away concentrating on something else. But seeing isn't then part of the subconscious mind. It just means attention blocks out awareness for what doesn't currently matter.
All the sensations - internal or external - are "there". But attention acts as a filter that focuses on a foreground by blanking out a background. Whether some aspect of what is going on is conscious or unconscious is down to a dynamical balance of selection/repression.
But a second aspect of this emotion story is the habit/automatism one. Emotions do seem to break through unbidden because the brain does have to know when to jerk attention towards significant events. And as importantly, our physiological state has to start reacting as soon as possible to deal with whatever is about to happen.
So if we hear heavy footsteps coming up behind us on a dark night, we instinctively get all the right reactions starting up as soon as the possible significance of this is realised at an automatic level - heart beats faster, digestion slows to divert blood to the muscles, cold sweat begins, nor-adrenaline pumps in the brain to create an aroused alertness.
Conscious or attentive awareness of the world takes about half a second to develop. It takes that long to focus and work out what is going on in an intellectual fashion. But habits - as learnt response - can simply be emitted in reflexive fashion. We can react in a simple startled fashion in about a tenth of a second, and in quite a well-honed smart fashion - the kind of skilled moves involved in sport - in a fifth of a second.
So the brain is set up to respond fast in learnt habitual fashion - to generate an appropriate flood of emotional feelings - and then let lagging attention swing into place to check whatever it was that just gave us a surprise. We might either then start to calm down, or decide we really need some kind of conscious action plan.
Thus the key dynamic in neurobiology is the divide between attention and habit. Do we need to focus on something in a whole brain reasoning fashion, or do we basically understand exactly how to react from a lifetime of experience? The brain is set up so that everything first goes through the fifth of a second loop that pretty much equates to an unconscious level of processing. Then only if it matters does it break through to become the subject of slower reacting, but far more explorative and remembered, attentive processing.
Emotions, as perceptions of internal state, are just like perceptions of the external world in being new information filtered in this two-stage fashion.
And then emotions as orienting responses - or appropriate shifts in physiological state to match the level of challenge in the world - is about what happens down at a reflexive or habitual level of response without waiting for attention to catch up and say it is the proper thing to do.
So emotion becomes attached to the events of the world as judgements about how aroused or relaxed we need to be in the next moment or so. And emotions are also news about our physiological needs - hunger, thirst, lust, etc - that are drives that need satisfaction. If habit isn't already delivering and the need is growing, then time for attention to be interrupted and focus on the fact.
Sometimes people act without understanding their motivations. That seems to be a kind of unconscious mind. — EnPassant
Now we are into yet another different level of explanation - one that ain't strictly neurobiological but linguistic and socio-cultural.
Humans have narrative consciousness, or language-structured self-consciousness. A good way to direct attention is to speak to ourselves in our heads as if we are addressing a person - our self.
So this is another habit(!) we learn. We construct an integrated tale about who we are, what we are about. There is this whole life story about the reasons we would do this or that which is all part of the learnt apparatus of being a self-regulating member of a human society.
So we are meant to be able to explain the reasons for our behaviour to others at all times. It is just part of the routine. And yet the neurological truth is that much of the reason we do things are down to habits and instincts we have learnt as our reliable ways to deal with the world with minimal attentive effort.
The neurological level need is to be efficient and think as little as possible about life. If you know the right kinds of things to do, just do them without stopping to think and debate. Focusing attention on any skilled action - even climbing the stairs - and you can set up the kind of wrestle between two processes with different basic rates (a fifth of a second vs half a second) that causes you to stumble and misfire. When it comes to action or output, one or other level of processing has to be in charge for the moment.
So on the whole, as a general rule, neurobiology will be wanting to respond to everything at the most habitual and automatic level first. We get a big tick from our biological self if we are successfully "unconscious" when getting stuff done. That is what an efficient and well-adapted brain looks like.
But then we get a conflicting socio-cultural message as, at that level, we are meant to be self-conscious selves, completely in charge and attentively regulating every action that issues from us. We are held responsible. And we better be ready with articulated reasons for everything.
If we do stumble even on something so trivial as climbing a flight of steps, blame has to be assigned for the failure. Maybe a dog barked and distracted us. Maybe the step wobbled. Maybe - if we are really forced to confess our guilt - we were being "inattentive".
Society is built on this kind of expectation. We are all selves, and that entails a conscious level responsibility for every action that results. That in turn sets up this great social concern and mystery when it comes to "unconscious" behaviour or thought. We have this dangerous inner world with its own mind. Mostly it seems to go with the flow, obey our narrative about our motivations. But there is lurks, always ready to betray us.
Again, it all comes back to a natural division of labour - the dichotomy of attentive-level and habit-level processing. And neurology celebrates the efficient brain that learns to get by as inattentively as possible, while sociology demands the impossible thing of a brain that is attentively responsible for every single detail of its behaviour. The unconscious thus looms large and mysterious in the popular imagination.