In the analysis of the dynamics of the brain there is a pattern that shows a 'fractal' element at work in that the generic dynamics of the neuron are repeated, if but in more complex forms of expression, at the level of the neocortex and so 'hemispheres' of the brain.
The general dynamics of the neural networks show patterns of differentiating/integrating as information is processed. From an electronics perspective we detect a dynamic operating around the notions of FM (frequency modulation - differentiating, pulse focus) and AM (amplitude modulation - integrating, wave focus). What is essential to recognise here is a development process of FM FROM AM, differentiating develops from integration - a whole is broken down into parts, the analogue is digitised. However, the output of FM (axon dynamics) to the input of other neurons and so their realm of AM (dendrite dynamics) shows a dynamic in the form of a hierarchy where what as 'differentiating' at one level becomes a feeder of the agent of 'integrating' at the next level.
If we zoom-in on these general dynamics to the immediate particular dynamics of a neuron we find two basic neurotransmitters at work - GABA and Glutamate. GABA acts to inhibit and so regulate the excitation nature of Glutamate and interestingly GABA is only synthesisable from Glutamate - in other words the main excitor of the neuron elicits its own regulator.
If we zoom up to the hemispheres of the brain, reviewing them both in their path of back-front development, the rear of the brain (moving down through neocortex, limbic, and 'reptillian' areas) is more 'primitive' and functions emotionally with the front, the frontal lobes, acting to suppress emotional expression and so regulate that expression. Now since the frontal lobes develop after the more emotion-focused parts (e..g. the limbic system) and yet act to regulate it so we see here a repeat of the basic dynamics of Glutamate/GABA. (the hierarchy here is that the limbic system acts as a regulator to the 'reptilian' areas but is, from the neocortical position, more excitory through its strong influence on emotion dynamics).
In addition to neurotransmitters we also find neuromodulators that are more global in their affect on information processing where they act to excite/inhibit the excitors/inhibitors of the local neural networks - e.g. Serotonin as a neuromodulator acts to excite GABA and so ultimately to increase inhibit activities (or more so 'integrate' and protect rather than differentiate and exploit)
This dynamic of the excitor eliciting its own regulator shows us self-referencing at work through use of positive and negative feedback and so the development of control mechanisms that can overide genetically-determined responses to stimuli and so be more precise in responses as well as imposing a delay on that response to allow for more data to be collected.
If we move to the level of the neocortex so the dynamics of frontal lobes and emotions shows us the hard-coding of reason as an agent of regulation on emotion. In other words the realm of the rational serves as a regulator of the irrational from which the rational has emerged and as such the realm of the rational is a 'part' of the whole that is more emotional in manner.
Brain damage to frontal lobe areas show us the price of losing 'reason', of losing regulation, in that a reasonable person becomes highly irrational in behaviour, animal-like, primate-like, pushed by emotion-driven instincts.
As such, the dichotomies of reason/emotion or of rational/irrational are not 'opposites' but more so representations of a basic dynamic that allows for the regulator to develop from the excitor as an act of increased precision, control, in expressions. This emergence reflects a translation from a holistic, immediate, organic but general expression to a more partial, delayed, mechanistic but precise form of expression. The short-term cost being in energy outlay, the long-term benefit being the creation of a precise instinct suitable for a range of stimuli and so conserving of energy in the long run; our 'mindless' emotions develop discernment, quality control and so a more refined set of responses to stimuli. There are of course physiological issues here in that high precision means high frequency management, the issue of which is that high precision is unstable in that 'blue light' is easily scattered and so works best at short range (and so FM is local, clear, precise, but short range - the ease in scattering also bring us to issues of attention deficit issues and their relationship to frontal lobe dynamics).
Where does this lead us? An essential feature of social development is in the process of learning local social 'rules' and so it is no coincidence that the area of regulation in our human brains, the frontal lobes, is the last to complete development - showing an essential need for frontal lobe 'training' rather than depending on generic frontal lobe dynamics sourced in our genes only.
The focus on regulation takes us into a focus on freedom and the "Science of Freedom" is present in the form of issues of Ethics/Morality (as compared to "Physics" etc being the "Science of Nature")
Implicit in this understanding is that emotions lack ethics/morality or more so are self-centered, self-serving, corse, and so regulation is required (or was found to be of 'benefit' and so favoured in selection - a developed frontal lobe allowed for planning, delay in process, and on imposition of control on the irrational in a social context)
Given this focus on regulation and issues of freedom so emerges a focus on mediation and so on consciousness, where the main elements of consciousness appear to be developed from frontal lobe dynamics and as such consciousness is emergent from regulation in that it offers choice in regulation rather than 'mindless' regulation that operates on a stimulus/response, heuristics-driven, dynamic. (Of note is the delay factor present in learning where once we have learnt, and so created a response to a stimulus so the delay, the awareness factor, the self-referencing, self-monitoring agent, and so a mediating agent, dissapears).
Since the realm of emotions appears prior to its regulator so that realm has a degree of autonomy in its dealings with reality where reality is 'painted' with emotions to enable a form of interpretation of the immediate context through emotional resonance. If we then add-on a regulator (frontal lobes learning of social rules) together with a mediator (extending 'mindless' regulation into mediated regulation) so it is possible for emotional dynamics to elicit vague sensations of being 'uncomfortable' in some context without consciousness being able to determine what that uncomfort is, all due to the regulator 'filtering-out' information it finds taboo or not appropriate for expression 'at this time'. (Note here another example of differentiating emerging from integrating is the left hemisphere behaviours being less developed than the right hemisphere pre and just post birth. As precision develops so this precision comes to allow for increased control of behaviours and so their regulation/management with the precision of the left taking over from the 'instinctive', 'as is' nature of the right. This precision moves to a level of being universal and so biases in such behaviours as handedness and the left bias to control of precise language (highly differentiated language) etc).
It is possible through analysis of the dynamics of the brain as it deals with novelty to 'bypass' the regulator and 'speak' to the emotions to elicit a general representation of what in the context is "pushing one's buttons". This can be surprising or upsetting at times in that it brings out the 'true' feelings for some event where those are self-centred and so at odds with social regulations. The surprise being in consciousness having this regulatory element brought to its attention and so the recognition of consciousness of the incongruency present - however the experiencing of discomfort by consciousness caused by the emotions indicates that there is a serious issue at hand in need of understanding and resolution.
In the context of frontal lobe training, since the focus is on the "Science of Freedom" and so the rational and use of reason to work in principles of Ethics, the discipline best suited to this focus is that of Philosophy. However the regulator of this discipline has to be Science where the abstractions of reasoning allow for self-referencing of the general and more emotion-based aspects of Philosophy, rooted in pure rhetoric (and so 'oneupman-ship', argument for the sake of argument) and ensure that the reasoning is grounded in empirical studies. Without this grounding and so lack of such regulation we allow for 'unrestrained' philosophy to confuse the imagined and the real to give us 'interesting' interpretations of experiences where the interpretations are all grounded in fantasy. As such, we see in frontal lobe dynamics the same relationships as we see in reason/emotion in that with consciousness comes mediated regulation, guided reasoning (and so capable of detecting false reasoning), such that the excitory (consciousness) feedsback on the inhibitory (reason) that feeds back on the instinctively excitory (emotions) that in turn regulate the mindless nature of the neurology to form into elements of communication.