Human Spiritual Structure: The Brain
Notes in progress © 1998-2002 Alan McAllister  

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The Evolution of the Brain

The human brain is a collection of some 30 billion neurons.

As animals have become more complex, in order to express an increasingly complex mind with more vrttis, the brain has developed in three main stages. The earliest part is the brain stem, at the top of the spin, and is present in reptiles. The second stage, which appears in mammals is the limbic system. The third layer, which has developed mainly in humans is the cortex.

The physical brain is made up of three gross parts which have developed sequentially, one on top of the other. The oldest is the "reptilian brain" which is the brain stem, and evolved more than 500 million years ago. The brain stem manages the basic biological stability of the body and the basic life support systems, e.g. breathing, the heart, sensing of other animals (prey or predator). These functions were necessary in the oceans. On land several new factors had to be dealt with, e.g. gravity, temperature changes, and the uncertain availability of food and water. Some 200 to 300 million years ago the limbic system developed in the center of the brain, on top of the brain stem. The limbic system is mainly responsible for the stability of the basic conditions of the body, e.g. heart rate, temperature, blood pressure, blood sugar level, etc. In mammals it is also involved with the basic emotions (hypothalamus). About 50 million years ago the cerebral cortex developed. This thin folded layer is where decisions are made, models of the external and internal worlds are formed, memories are accessed, language is produced, and sight and sound are appreciated. [HB]

It is pointed out in The Healing Brain that the primary function of the brain is to keep the body out of trouble, to manage and tend to its needs, keeping it free from injury or disease. Most of the brain is taken up with these processes. The thinking and "rational" functions are a very recent development and involve a relatively small portion of the physical volume of the brain. Even the higher functions, such as speech and communication have the primary goal of keeping the body safe, healthy, and happy. It creates both external and internal models against which new sensory data is constantly compared, and which are adjusted as conditions and experience changes. The brain therefore is the vehicle for adapting to change. There is also a prioritizing system that ranks which aspects of the world to deal with or to respond to first. The physical and psychological needs are ranked, with the most basic generally the strongest. These are all balanced by the brain.[HB]

The brain is said to be many small brains combined into one, each with its own functions and preferences. This is part of the reason that we may have mixed feeling, emotions etc. It can also happen that one will suddenly override another, or come to the fore due to an external trigger. In its more extreme forms we may do things we hadn't intended, or apparently change personalities quickly, as a different component comes to the fore. This is not a signal that we are possessed by beings.In general not all sub-systems are active at the same time, but turn on an off as necessary. The number of these units that are involved with conscious awareness at any one time is even smaller.[HB]

It seems probable that these regions develop as the brain of the infant and child becomes more complexly interconnected in its early years. [AHM, evidence?] I.e. the mind creates a brain that will carry out certain functions.

The brain is directly sensitive to light (at least the pineal gland is). Many people suffer a cycle of depression in the fall and winter, which switches to an almost manic state in the spring. [HB]

Baba says that cerebral nerve cells are necessary for the experience of pleasure and pain.

The Reptilian Brain: the Brain Stem

The oldest part of the brain is the brain stem which sits at the top of the spinal column, or the base of the brain. The brain stem manages the basic biological stability of the body and the basic life support systems.

The stimulation of the portions of the brain stem around the cerebral ventricles results in the production of large numbers of endorphins. The regions with the most opiate receptors also produced the most endorphins when stimulated. This is part of the body's natural pain control system. [HB]


A portion of the brain stem, the Reticular Activating System (RAS) helps to filter the incoming sensory impressions. This filtering is different in each of us and can change over time even within the individual. This means that we all experience our own individual reality. This is a feedback loop, the more individual we are, the more also is our experience.

This filtering system can be qualitatively different, but also quantitatively, i.e. the RAS of different people may pass more or less of the incoming stimuli. Example of someone like Van Gogh who probably was relatively flooded with input, particularly visual. This effect is also found under the influence of some psychotropic drugs which may reduce the filtering, leading to `heightened sensory awareness. An interesting question is what the other extreme is, are there people who have overly strong filters?

The RAS then passes its output to the Thalamus, which is the secretary or answering service of the brain. This center routes the various signals to the different regions of the cortex which interpret them, or bring them into consciousness. When the thalamus is damaged or destroyed the person loses sensory awareness, and enters a vegetative state. The thalamus is the physical aspect of the Manas Chakra, which is in the center of the brain and controls the indryas (the sense organs).

The Mammalian Brain and the Limbic System

It is a group of neural structures that form a border (limbe) deep in the brain. It is widely connected through out the brain and is involved in maintaining (along with the hypothalamus) the stability of the physical parameters of the body, e.g. heartbeat, respiration, temperature etc. It is also involved in the emotions (particularly their physical manifestation) through communication with the hypothalamus. [SFF]

The frontal lobe limbic system is the center of the emotional "selfish" brain, which is primarily responsible for the integrity of the body. While this center can be overridden, it tends to be the most powerful director of action, when it feels the need to act. There is an emotional interpretation that is overlaid on all sensory perception, which is a primary means for judging the appropriate reaction. While it is impossible to pinpoint the seat of the "self" in the brain, many of the functions that are involved in defining and maintaining the "self" are located in the frontal lobes.[HB]

Destruction of parts of the limbic system in monkeys lead them to become tame, lacking in fear or anger, but hypersensitive to sensory input, sexually overactive and to place all objects into their mouths. In people it is involved in the emotions and memory, being generally active whenever memory is active. [SFF] [Perhaps this is the physical link between memory and emotion, i.e. that involvement of emotion in providing meaning to perception].

The Hypothalamus

The Hypothalamus controls the basic physical desires, hunger, thrist, sleep, and sex, and is involved in many of the basic emotions. It also regulates temperature, blood pressure, the heart and the lungs, etc. This operation is via a feed back mechanism, in which sensory input from the body, via the nervous system and from the organs via hormones in the blood, is used to determine adjustments that will keep the parameters within desired bounds. It also balances hormone levels through chemical and electrical control of the pituitary gland, which in turn controls all the other endocrine glands . [HB]

Although the hypothalamus is mainly a neural structure it produces various controlling hormones, and may serve as a key juncture between the neural and neurotransmitter communications systems. Its control over the pituitary allows it to switch the body on and off, disconnecting it from conscious awareness for meditation and sleep.[Bp] Note the use of the hypothalamus in exactly this way in some psychic meditations [AHM].

There are specific temperature cells in the hypothalamus which change their rate of firing when the body temperature (the blood through the brain) deviates more that 1 C from the nominal value. This changed rate of firing activates mechanisms to either heat or cool the body. The mechanism for regulating body fluids is more complex, beginning with sensitive pressure sensors in the blood vessels which react to a rise in pressure due to the release os cellular water into the blood, itself a reaction to increased salt content in the blood stream. Communications via the sympathetic nervous system to the kidneys, results in the release of renin. This reacts with a blood protein to form a "thirst substance" which activates certain receptors in the hypothalamus and the rest of the limbic system. At night a hormone (ADH) feedback system is used to signal the kidneys to remove water from the urine and dump it into the blood stream. [HB]

The regulation of hunger is even more complex, and is that only one of the three that is prone to serious imbalances, (absent physical damage to the hypothalamus). It involves external cues as well as internal ones. Absence of the lateral hypothalamus causes a complete loss of appetite, and of the ventromedial nuclei (VMN) a tendency to overeat, but only preferred foods. These regions of the brain have an established "set point" for body weight, which they tend to maintain quite closely, irrespective of the actual intake of food. The number of fat cells in the body is determined in the first two years of life. Once formed they do not go away, they can only be emptied out, but remain waiting to be filled. These help to fix the set point, and changing that can be very hard, however exercise does help in this way, by raising the rate at which calories are burned throughout the day, not just during the exercise. [HB]

The hypothalamus apparently is necessary for proper immune system functioning, probably through its control of the thymus gland. Information is also received here from the immune system, as shown by increased activity when antigens are present. The greater the immune response the greater the activity.

The Thalamus

Sensory signals from the eyes and ears come first to the thalamus. They are then routed to the amygdala and the neo-cortex.

The Amygdala

This region is a key player in the emotions.

A pair of almond shaped clusters of interconnected structures, perched above the brainstem, near the bottom of the limbic ring, one on either side of the brain. Along with the hippocampus it formed the primate "nose brain" that evolved into the cortex and neo-cortex. Main seat for emotional memory, significance, and personal meaning. Plays a key role in all passions, emotions, sense of social structures, etc. With the cingulate gyrus controls tears.[EI]

The amygdala scans incoming sensory signals, coming over a single synapse from the thalamus, for survival level patterns. If these are recognized it sends out alarm signals to every part of the brain. The body and brain are alerted, placed in emergency modes, and focused on the source of the alarm. This state of emotional emergency will override the cortex and any rational, conscious processes, which are processed by the neo-cortex producing a more refined, but slower (by a factor of roughly 2) response. This is the main brain system for non-mammals. [EI]

Emotional responses can be learned completely subconsciously via the direct link from the thalamus to the amygdala, as well as via the conscious analysis of the cortex. It is possible for the unconscious and conscious emotional reactions to be different. Thus there is a storehouse of unconscious emotional memories and opinions in the amygdala. The emotional (hormonal) state of the body and brain affects the strength forming memories via the amygdala.[EI]

The amygdala's processing of inputs is associative, and often somewhat sloppily so. This is partly due to the limited signal that is passed by the thalamus, while the full sensory input goes only to the neo-cortex. This memory center is fully functional early in life, before the hippocampus and neo-cortex are fully on line.[EI]

When circuits between the amygdala and the neo-cortex are damaged people have difficulty making good decisions, or sometimes in making any decision at all. Access to emotional memory and learning appears to be an important contribution to reasoned decision making. [EI]

Timidity and general fearfulness, including major traumatic reactions (post traumatic syndrome), is correlated with over activity in the amygdala and the locus ceruleus, which regulates the secretion of adrenaline and noradrenaline. In PSTD Vietnam veterans there were fewer receptors for stopping these hormones. The hippocampus, hypothalamus, and cortex are all linked in the circuitry that regulate these hormones. Changes also appear in the nerves linking the limbic brain with the pituitarygland which controls the release of CRF (the major stress hormone). [EI]

The Hippocampus

Curved ridges on the floor of the lateral ventricles. This is part of the limbic system? It is certainly associated with it.

It is involved in regulating heartbeat, digestion, and respiration. Also appears to be essential to the processes involved in short and long term memory. [SFF] In one case it seems that the destruction of the hippocampus impacted the ability to form new long term memories, but not short term memories. It also did not affect memory related to music, geometry, physical procedures, etc. [AM]

Along with the amygdala it formed the primate "nose brain" that evolved into the cortex and neo-cortex. A main seat for learning and memory. It appears to play its main role in providing contextual memory, recognizing patterns that provide a context (is the tiger in a cage or not), while the amygdala handles the emotional aspects. Provides recognition, remembers sensory detail. [EI]

The Diencephalon, or Forebrain

This is located deep below the cortex. It is involved in the production of memories. It is also involved in the basic basic desires for sleep, food, and sex. When it is not functioning a person tends to respond only to presented external stimulus, the internally generated impulse is lacking. [AM]

The Rhinencephalon

This is the region that processes smell.[AM]

The Human Brain and the Cortex

The cortex is the seat of sensory organs of the brain, the indryas and corresponds to the kamamaya kosa. This is the third and latest part of the brain to develop. It is mainly present in human beings. It is also the center for decision making, memory, and model building (functions of the manomaya kosa).

The cortex is divided into lobes, the frontal, temporal, parietal, and occipital, though the divisions of functions occur on a smaller scale.

The cells of the cortex are arranged in columns, which have specialized functions, such as recognizing edges or corners in images. They are hardwired (surely after birth) as modules that preform specific analysis tasks, and which can be combined for more complex tasks. The different senses and body abilities (such as balance or coordination) each have their own area for analysis and processing. The development of these areas varies from person to person, as does the talent that depends on them. [HB]

The cortex receives sensory signals from the thalamus, compares them to prior experience (memory), makes decisions, and sends signals for action to the muscles, glands, etc. From the cortex signals are sent to the amigdula and the limbic brain, the seat of feelings. From here the signals to the motor organs are sent out. There are cases in which the cortex is by-passed, a backdoor nervous path that allows direct reaction to perceived danger, before the input has time to come into consciousness.

In processing the input from the eyes, the signals apparently go first to the "blobs" of V1 cells, which interpret intensity, and then via the "stripes" of V2 cells are passed to the V4 cells which seem to help form the sensation of color. The V4 cells are then widely connected throughout the brain, sending their output on to all the areas the interpret and give meaning and emotion to the images in the limbic system and the amygdala. They also go the hippocampus which is involved in memory.[AM]

Other areas of the cortex involved in primary visual processing are the M system, which handles motion and depth perception, and the P-interblob system which may probably produces fine-scale form perception. Including the regions that add meaning, or create a stable visual world for us, roughly half the cortex is involved with sight. [AM]

The Frontal Lobes

These are a crossroads in the brain, being at the intersection of the nerve paths from the emotional limbic system carrying information about the state of the body, and the parietal areas which contain information about other people and external conditions. They also contribute to basic functions like the heart rate. They are very closely connected to the limbic system (and are sometimes classified as a part of it). [HB]

The frontal lobe limbic system is the center of the emotional "selfish" brain, which is primarily responsible for the integrity of the body. While this center can be overridden, it tends to be the most powerful director of action, when it feels the need to act. There is an emotional interpretation that is overlaid on all sensory perception, which is a primary means for judging the appropriate reaction. While it is impossible to pinpoint the seat of the "self" in the brain, many of the functions that are involved in defining and maintaining the "self" are located in the frontal lobes.[HB]

Decision making, memory, and model building are controlled by the frontal lobes. These are involved in the construction of all higher level concepts, including ego formation, language, judgement, imagination, and emotion. These are highly developed in humans (only reaching full development around age seven), much less so in other primates and hardly at all in other mammals. These are also responsible for conscience and the sense of duty, from which we need an occasional break. [AM]

The prefrontal lobes, behind the forehead, appear to play a role in shutting down immediate emotional responses from the amygdala. These secondary responses are more calculated and are generally based on more accurate information. They serve to amend or correct limbic responses. In the normal course most sensory input goes here first and after analysis responses are sent out, including emotional responses, to the amygdala.[EI]

Strong emotional signals from the amygdala to the neocortex can interfere with rational thought and "working memory" which is another prefrontal function. On the other hand, positive emotions can enhance thinking and provide a boost to concentration. [EI]

Removal of one or the other lobe has drastic effects on personality. Inter and intra-personal intellegences. Loss of the left lobes produces anti-social and uncontrolled behavior dominated by fear and aggression (e.g. Phineas Gage). Loss of the right lobes produces eternally happy emotional states, no responsibility. In experiments where shock therapy rendered one side temporarily inoperative there were similar results. When the left side was shocked the patients where very unhappy, while the shocking of the right side made them very happy [HB]. This is compared to the two petals of the ajina chakra, the right controlling mundane and the left spiritual vrttis in the lower chakras. When the left lobes are gone only the mundane vrttis remain and visa versa?[DAM]

There is a strong correlation between which lobe is generally more active in a person and that persons overall mood. If the left lobe dominates they tend to be cheerful and up beat. If the right lobe dominates they tend to be more gloomy and fearful. [EI]

When both lobes are damaged, there is a general lack of control, a disintegration of the coherence of the ego, a lack of "psychological distance" between the person and his or her environment. Most incoming stimuli are treated equally, without judgement or weight. [AM]

In serial killers, there is no measurable frontal lobe activity. I.e. no emotional connection.

The prefrontal lobes, behind the forehead, appear to play a role in shutting down immediate emotional responses from the amygdala. These secondary responses are more calculated and are generally based on more accurate information. They serve to amend or correct limbic responses. [EI]

The Temporal Lobes

The medial temporal lobes are necessary for conscious (explicit) learning, long term memory. [AM]

Right and Left Brains

The brain is nearly completely divided down the middle into a left and a right side, which physically are roughly mirror images. They are connected through the corpus collasum, a thick bundle of nerve fibers in the middle of the head. Starting with observations of people suffering traumatic brain injuries and more recently those who have had their corpus collapsum severed to prevent epileptic fits, it has been determined that some mental functions are normally performed on one side if the brain or the other.

It is important to note that work by Japanese surgeons has indicated that the allocation of functions to the right and left brains depends on the first language spoken by an infant. While most languages produce a structure similar to English, a handful of others including Japanese ... produce a different structure. [Omni??..circa 1978?]

In left-handed persons, the distribution of functions may be reversed from the normal (see below), or a mixture. [HB]

The symbolism of body right and left (brain left and right) representing male and female, or yang and yin in general is common to nearly all cultures and ages.

Neural Synchronization

This occurs in the visual cortex and the associative cortex in preparation for perceiving a familiar sight, or object. Thousands of cells generate high frequency gamma waves by synchronizing their firing. The rate of firing appears to be a separate parameter, and has more to do with the incoming sensation, while the synchronization is related to the actual perception. If the perception is followed up by an action, the waves shift to the motor cortex and to other parts of the associative cortex.

Change and Stress

The brain likes an optimum throughput of new information. Too much information or change is stressful, but so is too little. The quality of the change is also important (i.e. good vrs bad stress). The brain, from that of an infant, balances increased access to information with simplification and organization of information. The older we get the more familiar things become and the more we have to expand or explore to find something new. When sensory input is reduced, or prevented we become disorganized, lose intellectual ability, concentration, and coordination. Eventually we may hallucinate, associated with feelings of boredom, anxiety, irritability, paranoia etc. [In mediation this is the rise of normally unconscious material after practice of sense withdrawal]. It is important to note that while stress may lead to disease, it actually does in only some people. Others get sick without much objective stress, while some with a great deal remain healthy. It is more how one reacts to stress than the stress itself which is important.[HB]

Atmospheric Ions

Concentrations of negative or positive ions in the air affect our brain chemistry. Negative ions increase serotonin, which brings a more positive mood, while positive ions adversely affect our mood, energy level, and health. Closed buildings, air pollution, and hot winds produce a balance of positive ions, while water falls and the ocean produce negative ones. In rats, those raised in a negative ion environment developed larger cortices. [HB]

See also these articles notes.

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Page Created, March, 1998.
Last updated January 19, 2001.
© Alan McAllister

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