In the context of the brain, we look at various views on how biology and consciousness may be linked, then look at possible correspondences between physical processes and mental practices.
In general we could say that the brain plays a role in mediating between the physical world and consciousness.
Strict materialists would say that intelligence, self-awareness and consciousness in general is a byproduct of a biological system. When a system is complex enough, some form of consciousness emerges by itself, then is shaped by processes of adaptation.
The reverse view would be that the brain is only a receiver and that any animating intelligence or consciousness is external to it.
The materialistic view has problems accounting for psychic occurrences such as reports of near-death experiences, probable cases of reincarnation with checkable memories of would be past lives etc.
Consciousness is not independent of the brain either. The fact that personality changes take place as a result of brain damage, that drugs affect mental processes, that mental states reflect in metabolic and electrical activity of the brain offer ample evidence of tight coupling between brain and anything we could call consciousness.
So, if consciousness is both within and without the brain, something must mediate between these states. Heimerov and Penrose have proposed that quantum level processes inside neurons would provide a gateway between the physical world and an 'implicate order' which guides the apparent randomness of single quantum events. Cells contain hundreds of thousands of so-called microtubules which form a sort of receiver sensitive to quantum effects. The quantum nondeterministic motion of an electron inside the microtubule can affect the chemical and electrical brain activity.
So, 'spirit' would tweak the functioning of matter by playing on probabilities of detecting an electron in one place or another. Matter would conversely inform spirit by a 'back action' through this same gateway.
Another proposed link between matter and a world of information is the morphogenetic field proposed by Ruper Sheldrake. In Sheldrake's model, similar structures of matter are linked through time and space by virtue of their similarity. The reason why the human perceives time as a continuous sequence is the fact that its immediate past is the closest thing in terms of structure to its present. But forms exist outside of time and space and by having a certain structure one can 'tune in' to these forms and receive information. The link between 'soul' and body could be seen as a special case of such a process. The morphogenetic field gives a nice conceptual model for events such as apparent species level learning by animals, independent emergence of similar ideas, even phenomena in formation of crystals etc but fails to make testable predictions.
Attempts at formalizing a link between the different levels of existence intuited by humans throughout the ages has thus far not been successful.
Psychic research and the experience with the so-called spirit attachment phenomenon give us more ideas about the survival of consciousness and its relation with matter. We cannot however reconcile these with laws of physics as we generally understand these. The spirit attachment phenomenon takes place when a recently deceased soul attaches itself to a living body occupied by another soul. There are numerous cases of making contact with such attached disincarnates through hypnosis of the subject of attachment. The attachments often say that the host must have a certain 'frequency,' be somehow structurally compatible with the attaching spirit.
Anyhow, if the brain is a receiver, as this phenomenon would suggest, then we need to explain why it primarily receives the incarnate 'soul' and not every other one. Genetics may form a sort of tuner for this but are not in themselves sufficient for explaining all. Identical twins for example are not the same entity, even though they often have a certain psychic affinity.
many occult practices assign importance to genetics as a link between physicality and spirit. Also, psychic sensitivity seems in large measure to be a hereditary trait.
In terms of work on the self, we may first look at learning in general. The brain seems to form connections between things which occur together. Even the simplest animals can be conditioned. If a dog gets an electric shock when hearing a sound, the dog will react to the sound as if shocked even if there is no electric shock. The effect wears slowely off with time. Dissensitizing occurs more slowly than sensitizing. The same can be observed with very primitive animals.
We can begin to draw rough parallels between what we know of the brain and the various concepts of the 4th Way and other methods of self-development. We do not expect to find precise correspondences between phenomenology and physiology or anatomy but can make some general observations and identify special cases.
The little I most likely corresponds to a set of neural circuits. Different I's are associated to different aspects of different centers. The centers (thinking, feeling, moving) clearly have a rough representation in the brain anatomy but the concept of center is somewhat broader and encompasses more than the neural circuits associated with some area of functioning.
We could imagine the little I as a frequent pattern of simultaneous activation of groups of neurons. Such a pattern could be seen in a PET scan of the brain as increased metabolic activity in the areas concerned. Such frequent joint activation causes information paths to be strengthened between the parts concerned. In this way, a pattern of habit can acquire an electrochemical and maybe even anatomical representation.
A buffer on the other hand could be represent as relative scarcity of connections between such connected islands. Also the phenomenon of state dependent recall may play a role in this process. Certain memories may only become accessible when the brain chemical state is similar to the state in effect when the memory was formed. Thus emotional states may block and enable entire areas of memory. Emotional states have a rough correspondence with levels of dopamine, serotonin and other neurotransmitters. The concept of repressed memory is a special case of a strong buffer and is likely represented by severing connections between frontal cortex cognitive functions and the structure of long term memory corresponding to the experience. The experience may however be stored as a second copy in the amygdala, thus activating generalized anxiety, fear or aggression when exposed to some stimulus of which there is no conscious recall. Consciously reprogramming this is not possible if there is no link to conscious function to start with, so new connections cannot be drawn if the thread is lost.
The practice of self-remembering consists of being simultaneously aware of the state of self and of environment. As a constant practice, this may increase connections between the sensory, thinking, emotional and motor areas of the brain. Learning at the physiological level is after all based on things occurring together. By observing the body, emotions and environment, the functions corresponding to self-awareness get exercised and the connections to other functions strengthened. Self-awareness becomes physically more rooted in reality, so to speak.
Still, such work is only seen as preparatory and is not the same thing as connecting to the real I or 'higher centers.' Still, even if these processes are not physical per se, to the extent they involve an incarnate human being, they most likely have some sort of neurological representation and do not occur independently of it.
We could think that exercise of self-remembering reduces the fragmentation of the brain, even in a physical sense. If the brain is then seen as a receiver for contents of a sort of idea world, then a minimum coherence should exist in the brain before such contents can be received and picked out from the noise. Work on the self may thus open doors to new possibilities by preparing the ground.
It is conceivable that there exist two possible but in a sense opposite ways of creating a certain coherence in the brain. The way discussed here which has to do with seeking multifaceted and within limits of possibility objective understanding of self and the world and another way which has to do with single-minded focus on belief and shutting out all which does not conform to this. Practices of magic or 'you create your own reality' may for example fall in the second category. These ways correspond with objectivity and subjectivity in their more focused forms, which both may open doors to 'higher' states of consciousness but then for a fundamentally different purpose.