How Does A Jnani Person Deal With The Negative Impacts of the World: Part 3/3 – Neurology


Page 1

  1. Introduction
  2. On Language, Paths and Models
  3. The Root Problem to be Addressed – Complete Ending of Negative Emotions
  4. The Root of Emotions According to Neurology
    1. Evolution of the Human Brain – The Three Brains in Us
    2. The Amygdala & Emotional Hijacking of the Brain
    3. The Amygdala: Source of Emotional Memory & Reaction
    4. The Feeling Brain vs The Thinking Brain : Amydgala vs Neo-Cortex
  5. The Solution to End Afflictive Emotions Based on Neurology
  6. The Advaita Model vs the Neurology Model

Page 2

Peter’s (Actual Freedom Trust) Solution Same as that of Advaita


In this three parts article series starting with Part 1 : How Does A Jnani Person Deal With the Negative Impacts of the World: Part 1/3 – Titiksha/Endurance, through part 2: How Does A Jnani Person Deal With the Negative Impacts of the World: Part 2/3 – Udasinata/High Indifference, I am now presenting the final part of this series. The article series is basically detailing how a Self Realized being in the path of Advaita deals with negative impacts of life. I had said in my second part of this series that I would be talking about the same issue in a scientific language to show how the ancient wisdom of Advaita can be interpreted in terms of modern neurobiological approaches that try to help man in coming out of their suffering.

In part 2 I had talked about the issue of language, paths and models. The reader is requested to please read it before proceeding further. It is certainly not an easy topic to grasp, but one should read it nonetheless. In fact, I am presuming that the reader of this article has already read the previous two articles in this series. Without it, this article will not make any sense because I am going to draw parallels between what I wrote there and what I am presenting here.

On Language, Paths and Models

Assuming you have read the section of language, paths and models in Part 2, I wish to caution the reader that what I am presenting here is just an analogous presentation of Advaitic method of self inquiry in scientific language. I am not saying that Advaita, like science, considers matter to be the ultimate reality. Unlike science, Advaita does not consider the ultimate reality to be made of discrete, self existing objects. All phenomena, according to Advaita are empty Awareness/Brahman. (They are of an indeterminate nature free from the four extremes of existence, non-existence, existence and non-existence, neither existence nor non-existence.) According to Advaita, the ultimate reality of life is free from any subject-object duality. While science considers brain to be solid matter – objectively existing reality – for Advaita, brain is empty Awareness or Brahman. While science and neurobiology reduces everything to matter with discrete parts and cause and effect relations between parts, Advaita sees no self existent parts and cause-effect relationships between them in the ultimate reality. Science, thus sees the birth, modification and death of matter, Advaita sees that all phenomena are timeless Awareness/Brahman, free from all modifications and free from all subject-object duality as their ultimate truth.

Having understood this, one may ask, how can I compare or think of relating two such disparate world-views. Well, the answer is that the ultimate reality of Advaita does not cancel the functioning of the world in any way. It just removes the ignorance of its true nature. Thus, Advaita does not negate the laws of science, it’s laws of cause and effect, and it’s efficacy in our normal life. What Advaita says is that the materialistic scientific view is not what life is from the ultimate viewpoint. For Advaita, all name-forms are nothing but superimpositions, without any inherent objective reality. There is no objective and really existent brain out there. It is just a name-form superimposed on ultimate reality – empty Awareness. So in this article I am taking the brain and the work done in the field of neurobiology, which is an objective reality for scientists, as a name-form in Advaita to show that when we do this morphing science and Advaita agree.

The Root Problem to be Addressed – Complete Ending of Negative Emotions

This three part article series has set out to address one root problem of humans – negative emotions. As all would know, the purpose of non-dual self inquiry is the ending of all suffering, which no doubt entails the ending of all negative emotions. The solution proposed by Shankara’s Vivartavada Advaita is to first gain true and direct knowledge of one’s Self as Witness and then abide to abide as Witness to root out vasanas/Prarabdha Karma/karmic defilements of past lives. In Part 1 and Part 2 of this article series I described two phases of abiding as Witness – Titiksha/Endurance and Udasinata/High Indifference. Both entailed standing as Witness equanimous to all emotions albeit with some difference in the texture and grade. Udasinata, I had said was a higher grade of Witnessing than Titiksha. For the complete implications of these two grades of Witnessing to root out all negative emotions, one has to read the articles; here, in a shorthand way I can say that Titiksha is an amoral Witnessing stance leaning more to endure all kinds of circumstances while Udasinata is a moral Witnessing stance that leans more on remaining calm and indifferent to the surge of emotions without taking any action on them.

In this article I am going to show that recent neurology studies done by Le Doux – an American neuroscientist whose research is primarily focused on survival circuits in the human brain, including their impacts on emotions such as fear and anxiety – whose work was used by Daniel Goleman – an author and science journalist known for his theory of Emotional Intelligence – lands to the same solution of wiping out negative emotions – Witnessing. Although Daniel Goleman, working on Le Doux’s scientific studies, takes it only to the level of developing self-restraint and compassion, Peter of Actual Freedom who has developed a path on self inquiry called Actualism, uses this model for complete ending of all negative emotions by the destruction of self/ego (what Peter calls instinctual self plus psychological self). I am inspired by Peter to show how Advaita is talking of the very same thing as he is. Though I must say that I am ONLY borrowing this inspiration from Peter: I do not agree to all his denunciation of other traditional paths of self inquiry based on his misinterpretations and misreadings.

The Root of Emotions According to Neurology

Man and the higher animals, especially the primates, have some few instincts in common … similar passions, affections, and emotions, even the more complex ones, such as jealousy, suspicion, emulation, gratitude and magnanimity; they practise deceit and are revengeful; they are sometimes susceptible to ridicule, and even have a sense of humour… 

‘The Descent of Man’, published 1871 (2nd ed., 1874) by Charles Darwin; Ch. 3

The same observation was cited by Shankara as proof of man sharing the animal brain in his Brahmasutra Bhashya introduction.

That our knowledge (empirical) is no knowledge at all is further proved by the fact that we do not differ from animals in the matter of cognition. Just as a cow runs away when she sees a man with a raised stick in his hand, while she approaches one with a handful of green grass, so also do men, who possess higher intelligence, walk away from wicked persons shouting with drawn swords, while they approach those of an opposite nature. The behaviour of animals in cognition etc., is well known to be based on ignorance. Therefore, it can be inferred that man’s conduct in the matter of cognition etc., so long as they are under delusion, is also similarly based.

Brahma Sutras (Shankara Bhashya), by Swami Vireshwarananda | 1936 |

Evolution of the Human Brain – The Three Brains in Us

To better grasp the potent hold of the emotions on the thinking mind—and why feeling and reason are so readily at war—consider how the brain evolved. Human brains, with their three pounds or so of cells and neural juices, are about triple the size of those in our nearest cousins in evolution, the nonhuman primates. Over millions of years of evolution, the brain has grown from the bottom up, with its higher centres developing as elaborations of lower, more ancient parts. (The growth of the brain in the human embryo roughly retraces this evolutionary course.)

  1. Brainstem (Primitive Brain): The most primitive part of the brain, shared with all species that have more than a minimal nervous system, is the brainstem surrounding the top of the spinal cord. This root brain regulates basic life functions like breathing and the metabolism of the body’s other organs, as well as controlling stereotyped reactions and movements. This primitive brain cannot be said to think or learn; rather it is a set of preprogrammed regulators that keep the body running as it should and reacting in a way that ensures survival. This brain reigned supreme in the Age of the Reptiles: Picture a snake hissing to signal the threat of an attack.
  2. Limbic System (Emotional Brain): With the arrival of the first mammals came new, key layers of the emotional brain. These, surrounding the brainstem, look roughly like a bagel with a bite taken out at the bottom where the brainstem nestles into them. Because this part of the brain rings and borders the brainstem, it was called the “limbic” system, from “limbus,” the Latin word for “ring.” This new neural territory added emotions proper to the brain’s repertoire. When we are in the grip of craving or fury, head-over-heels in love or recoiling in dread, it is the limbic system that has us in its grip. As it evolved, the limbic system refined two powerful tools: learning and memory. These revolutionary advances allowed an animal to be much smarter in its choices for survival.
  3. Neocortex (Thinking Brain): About 100 million years ago the brain in mammals took a great growth spurt. Piled on top of the thin two-layered cortex—the regions that plan, comprehend what is sensed, coordinate movement—several new layers of brain cells were added to form the neocortex. In contrast to the ancient brain’s two-layered cortex, the neocortex offered an extraordinary intellectual edge. The Homo sapiens neocortex, so much larger than in any other species, has added all that is distinctly human. The neocortex is the seat of thought; it contains the centers that put together and comprehend what the senses perceive. It adds to a feeling what we think about it—and allows us to have feelings about ideas, art, symbols, imaginings. However, The fact that the thinking brain grew from the emotional reveals much about the relationship of thought to feeling; there was an emotional brain long before there was a rational one. Though, it would be fair enough to say that the triumphs of art, of civilization and culture, are all fruits of the neocortex.

This new addition to the neocortex brain allowed the addition of nuance to emotional life. Take love. Limbic structures generate feelings of pleasure and sexual desire—the emotions that feed sexual passion. But the addition of the neocortex and its connections to the limbic system allowed for the mother-child bond that is the basis of the family unit and the long-term commitment to childrearing that makes human development possible. (Species that have no neocortex, such as reptiles, lack maternal affection; when their young hatch, the newborns must hide to avoid being cannibalized.) In humans the protective bond between parent and child allows much of maturation to go on over the course of a long childhood—during which the brain continues to develop. But these higher centres do not govern all of emotional life; in crucial matters of the heart—and most especially in emotional emergencies—they can be said to defer to the limbic system. Because so many of the brain’s higher centres sprouted from or extended the scope of the limbic area, the emotional brain plays a crucial role in neural architecture. As the root from which the newer brain grew, the emotional areas are intertwined via myriad connecting circuits to all parts of the neocortex. This gives the emotional centres immense power to influence the functioning of the rest of the brain—including its centres for thought.

The Amygdala & Emotional Hijacking of the Brain

In humans the amygdala (from the Greek word for “almond”) is an almond-shaped cluster of interconnected structures perched above the brainstem, near the bottom of the limbic rin neocortex.

There are two amygdalas, one on each side of the brain, nestled toward the side of the head. The human amygdala is relatively large compared to that in any of our closest evolutionary cousins, the primates. The hippocampus and the amygdala were the two key parts of the primitive “nose brain” that, in evolution, gave rise to the cortex and then theTo this day these limbic structures do much or most of the brain’s learning and remembering; the amygdala is the specialist for emotional matters. If the amygdala is severed from the rest of the brain, the result is a striking inability to gauge the emotional significance of events; this condition is sometimes called “affective blindness.” LeDoux’s research explains how the amygdala can take control over what we do even as the thinking brain, the neocortex, is still coming to a decision.

In one of the most telling discoveries about emotions of the last decade, LeDoux’s work revealed how the architecture of the brain gives the amygdala a privileged position as an emotional sentinel, able to hijack the brain.

As shown in the schematic model pic above (borrowed from his research has shown that sensory signals from eye or ear travel first in the brain to the thalamus, and then—across a single synapse—to the amygdala; a second signal from the thalamus is routed to the neocortex—the thinking brain. This branching allows the amygdala to begin to respond before the neocortex, which mulls information through several levels of brain circuits before it fully perceives and finally initiates its more finely tailored response. Those feelings that take the direct route through the amygdala include our most primitive and potent.

The conventional view in neuroscience had been that the eye, ear, and other sensory organs transmit signals to the thalamus, and from there to sensory processing areas of the neocortex, where the signals are put together into objects as we perceive them. The signals are sorted for meanings so that the brain recognizes what each object is and what its presence means. From the neocortex, the old theory held, the signals are sent to the limbic brain, and from there the appropriate response radiates out through the brain and the rest of the body. That is the way it works much or most of the time—but LeDoux discovered a smaller bundle of neurons that leads directly from the thalamus to the amygdala, in addition to those going through the larger path of neurons to the cortex. This smaller and shorter pathway—something like a neural back alley—allows the amygdala to receive some direct inputs from the senses and start a response before they are fully registered by the neocortex. This discovery overthrows the notion that the amygdala must depend entirely on signals from the neocortex to formulate its emotional reactions. The amygdala can trigger an emotional response via this emergency route even as a parallel reverberating circuit begins between the amygdala and neocortex. The amygdala can have us spring to action while the slightly slower—but more fully informed—neocortex unfolds its more refined plan for reaction.

This ‘quick and dirty processing pathway’ results not only in a direct automatic bodily response to either an actual or a perceived danger, but because the amygdala also has a direct connection to the neo-cortex – it causes us to emotionally experience the feeling of fear – i.e. we feel the feeling of fear a split-second later than the bodily reaction. Not only is the primitive brain’s response ‘quick and dirty’, it is also very powerful in that it primes the whole body for action – which is precisely why instinctual reactions and the resulting instinctual passions are ultimately so hard to keep in control.

Now, these are things we all know well from personal experience as well as from observation of others, but it is fascinating that scientific investigation of the ‘hardware’ of the human brain is now providing the biological evidence of how what is known as ‘human nature’ operates. That the Amygdala is quicker than cognitive awareness is easily experienced in driving a car and very suddenly encountering a dangerous situation. The foot is on the brake before we are consciously aware there has been any danger. With the awareness of danger comes an emotional response induced by the Amygdala along the stronger pathway to the brain. Even when the danger has ceased it can take a while to calm down – the pathway back to the Amygdala being ‘considerably weaker’.

The Amygdala: Source of Emotional Memory & Reaction

The amygdala can house memories and response repertoires that we enact without quite realizing why we do so because the shortcut from thalamus to amygdala completely bypasses the neocortex. This bypass seems to allow the amygdala to be a repository for emotional impressions and memories that we have never known about in full awareness.

Not only that, the amygdala seems to imprint in memory most moments of emotional arousal with an added degree of strength—that’s why we are more likely, for example, to remember where we went on a first date, or what we were doing when we heard terrible news. The more intense the amygdala arousal, the stronger the imprint; the experiences that scare or thrill us the most in life are among our most indelible memories. This means that, in effect, the brain has two memory systems, one for ordinary facts and one for emotionally charged ones. A special system for emotional memories makes excellent sense in evolution, of course, ensuring that animals would have particularly vivid memories of what threatens or pleases them. But emotional memories can be faulty guides to the present.

As the repository for emotional memory, the amygdala scans experience, comparing what is happening now with what happened in the past. Its method of comparison is associative: when one key element of a present situation is similar to the past, it can call it a “match”—which is why this circuit is sloppy: it acts before there is full confirmation. It frantically commands that we react to the present in ways that were imprinted long ago, with thoughts, emotions, reactions learned in response to events perhaps only dimly similar, but close enough to alarm the amygdala. The emergency route from eye or ear to thalamus to amygdala is crucial: it saves time in an emergency, when an instantaneous response is required. But this circuit from thalamus to amygdala carries only a small portion of sensory messages, with the majority taking the main route up to the neocortex. So what registers in the amygdala via this express route is, at best, rough and then it responds with a rapid “turn on” emotion.

LeDoux calls it “precognitive emotion,” a reaction based on neural bits and pieces of sensory information that have not been fully sorted out and integrated into a recognizable object. Small wonder we can have so little insight into the murk of our more explosive emotions, especially while they still hold us in thrall. The amygdala can react in a delirium of rage or fear before the cortex knows what is going on because such raw emotion is triggered independent of, and prior to, thought.

These investigations also substantiate the fact that no matter what degree of control is exercised by the neo-cortex in terms of morals, ethics, good intentions, etc., when ‘push comes to shove’ we revert to type – and reverting to type means animal-instinctual. This is clearly verified by the being ‘overcome’ by rage, fear or sadness and being unable to stop it.

The Feeling Brain vs The Thinking Brain : Amydgala vs Neo-Cortex

While the amygdala is at work in priming an anxious, impulsive reaction, another part of the emotional brain allows for a more fitting, corrective response which are the prefrontal lobes of the neocortex just behind the forehead. This neocortical area of the brain brings a more analytic or appropriate response to our emotional impulses, modulating the amygdala and other limbic areas.

Ordinarily the prefrontal areas govern our emotional reactions from the start. The largest projection of sensory information from the thalamus, remember, goes not to the amygdala, but to the neocortex and its many centres for taking in and making sense of what is being perceived. If in the process an emotional response is called for, the prefrontal lobes dictate it, working hand-in-hand with the amygdala and other circuits in the emotional brain. This progression, which allows for discernment in emotional response, is the standard arrangement, with the significant exception of emotional emergencies. When an emotion triggers, within moments the prefrontal lobes perform what amounts to a risk/benefit ratio of myriad possible reactions, and bet that one of them is best. For animals, it is, when to attack, when to run. And for we humans . . . when to attack, when to run—and also, when to placate, persuade, seek sympathy, stonewall, provoke guilt, whine, put on a facade of bravado, be contemptuous—and so on, through the whole repertoire of emotional wiles.

The neocortical response is slower in brain time than the hijack mechanism because it involves more circuitry. It can also be more judicious and considered, since more thought precedes feeling. When we register a loss and become sad, or feel happy after a triumph, or mull over something someone has said or done and then get hurt or angry, the neocortex is at work. Thus, emotional hijackings involve two dynamics: triggering of the amygdala and a failure to activate the neocortical processes that usually keep the emotional response in balance. At these moments the rational mind is swamped by the emotional. One way the prefrontal cortex acts as an efficient manager of emotion—weighing reactions before acting—is by dampening the signals for activation sent out by the amygdala and other limbic centres—something like a parent who stops an impulsive child from grabbing and tells the child to ask properly (or wait) for what it wants instead. Thus:

If the amygdala often acts as an emergency trigger, the left prefrontal lobe [neocortex] appears to be part of the brain’s “off switch” for disturbing emotion: the amygdala proposes, the prefrontal lobe disposes. These prefrontal-limbic connections are crucial in mental life far beyond fine-tuning emotion; they are essential for navigating us through the decisions that matter most in life.

Daniel Goleman, Emotional Intelligence

Thus, the above discussion on neurobiology makes it glaringly obvious that, no matter how ‘good’ or well intentioned ‘I’ am, it is factually impossible to be free of malice and sorrow unless I am free of the instinctual animal programming in its entirety.

The Solution to End Afflictive Emotions Based on Neurology

Working on the above neurology model, Daniel Goleman suggests the concept of Emotional Intelligence. He says:

The emotions, then, matter for rationality. In the dance of feeling and thought the emotional faculty guides our moment-to-moment decisions, working hand-in-hand with the rational mind, enabling—or disabling—thought itself. Likewise, the thinking brain plays an executive role in our emotions—except in those moments when emotions surge out of control and the emotional brain runs rampant.

In a sense we have two brains, two minds—and two different kinds of intelligence: rational and emotional. How we do in life is determined by both—it is not just IQ, but emotional intelligence that matters. Indeed, intellect cannot work at its best without emotional intelligence. Ordinarily the complementarity of limbic system and neocortex, amygdala and prefrontal lobes, means each is a full partner in mental life. When these partners interact well, emotional intelligence rises—as does intellectual ability.

This turns the old understanding of the tension between reason and feeling on its head: it is not that we want to do away with emotion and put reason in its place, as Erasmus had it, but instead find the intelligent balance of the two. The old paradigm held an ideal of reason freed of the pull of emotion. The new paradigm urges us to harmonize head and heart. To do that well in our lives means we must first understand more exactly what it means to use emotion intelligently.

Daniel Goleman, Emotional Intelligence

On the other hand Peter of Actual Freedom uses this model not just to balance thought and emotion but for complete destruction of self. According to him, the complete way to end afflictive emotions is to weaken this ‘signalling‘ from the amygdala to the frontal cortex to such an extent that eventually the ‘signalling’ ceases altogether. With the cessation of this ‘signalling’, the chemical flows from the amygdala, comes the extinction of the instinctual ‘self’ – one’ very, ‘being’, the associated instinctual passions. One can live without any identity whatsoever, be it societal or instinctual. The first step is societal – stepping out of society – one’s social identity is left behind, there is no illusionary person in the ‘executive suite’, no ‘little man inside the head pulling the levers’. I have written about it in my article What is psychological becoming and how it causes suffering? The second step is instinctual, one’s instinctual being is left behind, the ‘signalling’ from the amygdala ceased completely. And the solution he provides to end this link between the amygdala and the neocortex and thus to end the self is

Neither repressing nor expressing, neither denying nor transcending, neither rejecting nor accepting, but actively observing and developing an understanding of these emotional signals and how they cause malice and sorrow in your life.

Peter at

I totally agree with Peter on this solution. What I don’t agree to, is, he thinks that all traditional paths missed this solution, and he is the first one to have found it. It is indeed very surprising that he thinks so, because every non-dual path, including the teacher he had followed in his own spiritual journey – J Krishnamurti – had taught the same solution: total ending of psychological memory/consciousness. In fact, what he proposes above is exactly what I described as Udasinata/High Indifference in my previous article. I shall quickly show how Advaita is talking about the same solution.

The Advaita Model vs the Neurology Model

Advaita has a very simple five sheaths model comprising a human being based on pure observation. We can map the brain parts of the neurobiology model with the sheaths of Advaita in the following way:

  • Amygdala = Manomaya Kosha/Mind Sheath
  • Neocortex = Vignanamaya Kosha/Intellect sheath
  • Emotional Memory = Anandamaya Kosha/ Causal Body containing vasanas/karmic imprints/emotional memory

Once this is done, we can now see what Peter has proposed as a solution is exactly what is proposed by Advaita. For this I am resorting to quotes from a very revered Advaita text called Vivekachudamani. The solution in Advaita is to “dissolve” the subtle body – manonasha and vasankshaya – which means to dissolve manomaya kosha by ending the vasanas/emotional memory: exactly similar to what Peter says, to weaken this ‘signalling’ from the amygdala to the frontal cortex to such an extent that eventually the ‘signalling’ ceases altogether. With the cessation of this ‘signalling’, the chemical flows from the amygdala, comes the extinction of the instinctual ‘self’ – one’ very, ‘being’, the associated instinctual passions. The work is done in two stages

  1. Arrive at Witness stage through Self knowledge
  2. Abide as Witness to see through all vasanas – Titiksha & Udasinata stages (As Peter says, Neither repressing nor expressing, neither denying nor transcending, neither rejecting nor accepting, but actively observing and developing an understanding of these emotional signals and how they cause malice and sorrow in your life.)

Following are the quotes from Vivekachudmani:

Verse 267. Even after the Truth has been realized, there remains that strong, beginningless, obstinate impression that one is the agent and experiencer, which is the cause of one’s transmigration. It has to be carefully removed by living in a state of constant identification with the Supreme Self. Sages call that Liberation which is the attenuation of Vāsanās (impressions) here and now.

Verse 269. Realizing thy own Inmost Self, the Witness of the intellect and its modifications, and constantly revolving the positive thought, “I am That”, conquer this identification with the non-Self.

Verse 276. Being ever fixed on his own Self [Witness], the mind of the meditator ends. Then there is complete cessation of vasanas. So negate entirely your superimpositions.

299. So long as one has any relation to this wicked ego, there should not be the least talk about Liberation, which is unique.

Verse 300. Freed from the clutches of egoism, as the moon from the eclipse, man attains to his real nature, and becomes pure, infinite, ever blissful and self-luminous. 

I don’t need to elaborate anything on these verses, they are self-explanatory. They go on to show exactly what Peter of Actual Freedom claims as his enlightenment [despite his misgivings and wrong interpretations about traditional paths]. Ultimately, one can see how that there is a great match between Advaita and neurobiology if we take the neurobiological model as a language and conceptual model. In the next section I shall show examine Peter’s model and show how it too exactly maps with Advaita. Please click link below for next page…

2 thoughts on “How Does A Jnani Person Deal With The Negative Impacts of the World: Part 3/3 – Neurology

  1. Sir does Peter say something about deep sleep? In the neurology model does he say deep sleep is recorded in the brain too? Consciousness? (Or am I asking an irrelevant question).


    1. I have not read much of Peter, to be able t comment on his views on deep sleep. As far as I see, he just uses the Neurology as a model for his self inquiry. What do you mean by sleep is recorded in the brain?

      At any rate, whatever studies you do of the brain, you can only do as a scientist in the waking state on another subject who is sleeping. So nothing invalidates the claim of Advaita that there is no universe in the sleep state.


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