The Story of Enlightenment: The Neuroscience of Mindfulness Meditation

There have been many studies demonstrating the benefits of mindfulness meditation: how it can increase dopamine levels (more happiness), how it can increase the density of one’s gray matter (better memory and cognitive thinking), or how it can shrink the size of the amygdala (less stress and fear). However, to date, we have not developed a good understanding of the mechanics of how and why these changes are effected through a practice as simple as mindful observation of one’s bodily experience. This article proposes a theoretical framework that helps to explain how mindfulness meditation works. The article is prefaced with a brief summary of evolutionary biology of the nervous system and a description of the sensory system because a basic understanding of these is helpful in understanding the mechanics of mindfulness meditation.
 The Origins of the Brain
 Beginning with single-cell organisms, through billions of years of evolution, living beings have developed increasingly complex nervous structures to perceive, recognize and respond to external stimuli. At first, these processes were primarily automatic; a simple multicellular organism performed simple operations like automatically digesting food, moving closer toward a source of light or moving away from temperature extremes. These were followed by more complex organisms like simple fish and aquatic animals, which started developing rudimentary brains.

Figure 1: The nervous system and the “brain” of a simple animal

Brains helped these animals to coordinate their increasingly extensive and complex nervous systems, which learned to respond to various stimuli in different ways through conditioning, a process facilitated by the newly developed pain and pleasure response abilities. 
 Still, these organisms performed actions that were mostly only automatic responses to whatever they encountered. As time progressed, even more complex animals evolved, including amphibians and reptiles. These could perform even more complex activities like recognizing their prey, hunting, mating and communicating with each other. Still, these animals lived and survived through mostly automatic responses to their environments.

Figure 2: The Evolution of the Brain

In psychology, this type of thinking, automatic and unconscious, is often referred to as being part of brain’s System 1. On the other hand, deliberate and conscious thinking is said to be of System 2. The gradual development of System 2-type thinking allowed for more evolutionarily fit animals that could dynamically adapt to their environments, without being bound by suboptimal, habitual responses or conditioned responses that required repeated exposure and long time to develop.

Figure 3: Differences between the brain’s System 1 and System 2

We see the gradual enlargement of System 2 in mammals like mice, but an even larger development of System 2s in animals like dogs, which can communicate, hunt in packs, and make complex decisions involving multiple factors. And in animals like monkeys, the System 2 is so large and well developed that they can, for example, consciously imagine that a sharp stone could be used as a tool for hunting or that a large leaf could be used as a basket for food storage.

Figure 3: Differences between the brain’s System 1 and System 2

As for the human brain, its System 2 is so large that it allows for feats quite extraordinary in the animal kingdom.

Figure 5: Reader’s Digest, “Greatest Human Achievements”

Even for humans with their large System 2s, however, the vast majority of our reactions are of System 1 — automatic and unconscious. This is no surprise given that System 1 had hundreds of million years longer to develop in our evolutionary history. We eat, digest, walk, perceive, and recognize automatically and subconsciously. We like, dislike, get embroiled in anger, enjoy the sublimity of happiness or fall into the depths of depression automatically, often with little deliberate choice. Even very complex behavioral patterns forming our personalities, thoughts and speech simply arise automatically from our System 1s. We do not consciously decide to become angry, anxious, unconfident, sad, or depressed.
 Perception, Sensation, Reaction
 Our System 1s are very busy. Day and night, while we are awake or asleep, System 1 is constantly receiving data input through our sensory organs, processing and making sense of it, and producing reactions that lead us to perform actions. For instance, even while we are asleep, System 1 will detect an itch from a biting mosquito, and without a conscious thought lead us to swiftly kill it with a slap. If you come across some delicious food, a person you love or hate, or a situation that makes you feel happy or uncomfortable, System 1 will also automatically recognize these and generate a corresponding reaction, like joy, hunger, anger or anxiety.

If we break down the steps in the perception, sensation, reaction process, it might look like this:

Figure 6: The perception, sensation, reaction process

The scenario above is likely familiar to many of us. We can all remember a time when we saw or smelled tasty food, which stimulated a reaction in us — a desire to consume the food. In the sensation, perception, reaction process, we are most acutely and consciously aware of only the reaction the process evokes, without necessarily being consciously aware of all the neural impulses the stimulus generates. In the case of encountering a pizza, we will be very much aware of the desire the sight of pizza evokes, but will not consciously feel the myriad of neural impulses being generated all over our bodies in response to the vision and smell of the pizza. The neural impulses are dealt with primarily in the System 1 brain and only the final reaction — desire — is sent to the conscious System 2, as a nudge toward the optimal course of action.

Figure 7: Optimal course of action

In the case of listening to music as well, we similarly will most acutely only feel the reaction to the music: a like or a dislike for a song. But in fact, music fills our whole bodies with millions of neural impulses: vibrations, feelings, sensations and experiences.

Figure 8: The nervous system generates biochemical reactions all over our bodies in response to music

The System 1 automatically evaluates all of these neural impulses and decides on whether it likes or dislikes the song and sends this judgment to System 2 to decide on the optimal course of action.

Figure 9: Optimal course of action

However, automatic System 1 reactions do not always lead us toward optima.

The automatic reactions generated by System 1 are hard to control. It can be hard to not feel upset about serious verbal abuse, to stop feeling anxious, or to resist the urge to overeat. And what is more, every reaction we generate is saved in our memories to be remembered and learned as a conditioned response that will alter our personalities: likes and dislikes, wishes and hatreds, or ambitions and aversions. Subject to our System 1s, we will react to circumstances in non-optimal ways and become tense bundles of conditioned responses that can breed stress, unhappiness and dissatisfaction.

Taking Rein of System 1
 Building Bridges
 There is a way, however, to take greater control of our unruly System 1s. Unlike in other animals, our System 2 brains are large enough to be capable of changing the habit patterns of our subconscious System 1s. We can train our System 1s using our System 2s to become less reactive, calmer, and happier and that is what, in essence, what one does through the practice of mindfulness meditation.
 As a prerequisite to training the System 1 with System 2, one needs to establish a greater connection between the two brains so that the two brains can communicate better. Therefore, in the initial stages of meditation, one starts by building this connection by consciously observing one’s breath — a practice that is remarkable in that it engages the brain right in the figurative intersection of the unconscious System 1 and conscious System 2. Respiration is an activity that is both subconscious — we breathe without consciously thinking about it — but also one that we can be easily made consciously aware of and that we can deliberately control to a certain degree.
 As one observes their breath, and the conscious connection between the two brains strengthens, System 2 awakens to the busy life of System 1 — it becomes consciously aware of all the different neural impulses, sensations, feelings, and experiences that System 1 is constantly subconsciously reacting to. One becomes consciously aware of how music produces sensations and feelings all over our bodies and how unwanted events produce sensations or experiences of literal coldness or heat. And whereas before meditating, one might have thought that they were reacting to external stimuli — a “good” person, a “bad” person, a “beautiful” woman, a “terrible” event — as one meditates and comes in touch with their System 1, it becomes abundantly clear that what we react to is, in fact, not the external stimuli themselves, but only the feelings and sensations our nervous systems generate on our bodies after perceiving the stimuli. We do not react to objects, people or events. In truth, we only react to the feelings and sensations they evoke in our minds and on our bodies, explaining why different people will react differently to different songs, people and events: every person’s brain and nervous system is unique; perceiving, processing and reacting to things in different ways.

Figure 10: During meditation, one becomes consciously aware of the bodily sensations the System 1 brain is constantly and subconsciously reacting to.

As Training a Dog
 Once our System 1s and 2s are better connected, the training can begin. Because the core evolution of System 1 predates language development or deliberate reasoning, it cannot be trained through explicit instructions or logical reasoning. Instead, as is the case for all other animals, System 1 learns primarily through its own lived experience, and if one wants to change its habit patterns, one has to train it as one trains any other animal, like training a dog through conditioned responses.

Figure 11: Like in a dog, the System 1 brain can be trained to respond (or to not respond) to different stimuli.

Ordinarily, System 1 is constantly perceiving, generating neural impulses and sensations on our bodies and reacting to them automatically. It constantly nudges us to seek more of something or less of something, to cling to or to hate, to be dissatisfied or endlessly ambitious and greedy. When one meditates, however, there is another option besides reactivity — pure perception and objective and non-judgmental observation.
 In a meditation retreat, one is required to not communicate with others and to avoid contact with the world outside the confines of the retreat. In effect, this eliminates all the regular external stimuli our brains are constantly reacting to, and when starved of outside external stimuli, things that are inside of us start coming up: past memories and experiences, pleasant and unpleasant; desires, wishes, regrets and ambitions, mental complexes, and deep-seated repressions.
 With a well-connected System 1 and 2, one also consciously experiences how, along with these recollections, there also arise on our bodies the corresponding neural impulses, biochemical reactions and sensations. Unpleasant memories might bring back with them unpleasant feelings of coldness and tremor-like sensations, while pleasant recollections might bring back feelings of warmth and pleasant vibrations.

Figure 12: When remembering the past or pondering on the future, the corresponding neural impulses, biochemical reactions and sensations arise on our bodies.

In our ordinary lives, these recollections would have also led to automatic reactions in our System 1s. While meditating, however, we can observe them without reacting or passing judgment, training our System 1s to fully embrace the reality of the experience as it is.
 The brain is very much like a muscle — it becomes better at whatever it does and becomes worse at whatever it does not do. By playing chess, one becomes better at it, and if one does not practice mental math, one becomes worse at it. Similarly, if instead of reacting to a feeling or a sensation, one simply observes it without reaction or judgment, embracing the experience as it is, the brain becomes better at calmly weathering that feeling and sensation, learning to become better at perceiving reality as it truly is, and lessens its reactive tendency in regard to that experience. 
 As one keeps on meditating, different feelings and sensations arise, and if meditating correctly, gradually reduces one’s reactivity to each and every one of them. In time, there will come a stage when one trains their brain to be able to maintain equanimity and calmness whatever it is that life may bring on.

Loving Kindness and Boundless Empathy

In the closing part of a mindfulness meditation session, one practices a different type of meditation — meditation of loving kindness. Also taking advantage of the brain’s plasticity — the fact that the brain, just like a muscle, becomes better at whatever it practices — during a meditation of loving kindness, one practices feeling and experiencing compassion, love and peacefulness toward all living beings through one’s whole body. Gradually, the parts of the brain responsible for empathy grow in size, and as a result, one becomes more understanding of and closer to others, feeling universal joy and compassion toward all living beings.

Two Lessons Learned Through Meditation
 A human being can learn and understand a concept to different degrees. Some things we only grasp intellectually, gaining a superficial understanding of how they work, while others we truly internalize, understanding them to the core, and when we do so, the lessons alter our worldviews and habit patterns. 
 Most things we learn about in school, read or hear about, we learn only superficially, on the intellectual level. We may understand the concept in our System 2s, from a logical perspective, but the understanding does not get passed on to our System 1s, where the lesson could get fully internalized. To truly understand something until it alters the behavior patterns in one’s System 1, one has to learn through experience. 
 There are two important lessons one is constantly teaching their System 1 through direct experience every moment they meditate. 
 First, one truly learns to perceive and accept things as they really are. It might seem trivial and easy to understand with our System 2s that we should perceive things as they really are. Indeed, most people believe that how they view the world is how the world really is. In fact, however, our System 1s abound with countless reality distortion mechanisms — biases, stereotypes, preconceived notions and simplified mental models — that are very hard to escape.

For instance, when one hates another person or a group of people, they are only reacting to the simplified mental image or model that they have built in their mind of the other party. If one truly and fully understands others, one discovers that there is, in fact, nothing to induce hatred: To understand all is to forgive all. When this lesson is truly internalized and understood by System 1, it is an immensely freeing experience.
 When one perceives things as they really are, many things will also start to seem possible, within reach. Oftentimes, the reason we cannot accomplish our goals is that our goals are unrealistic or that we place artificial mental barriers and limits on what we can or cannot do. By being able to have realistic goals and by taking full advantage of all of one’s potential, one can accomplish the great. Becoming in complete synchrony with reality is an invaluable skill to anyone that is seeking to better their own circumstance in this world.
 Second, one learns that nothing is permanent and that everything is in flux. This might also seem like a trivial lesson. It is indeed very easy to understand intellectually, in our System 2s, that things always change, that any physical structure will fall apart and that all living beings will come to pass away. However, while meditating, one is constantly teaching their System 1 brain, through direct experience, the impermanence of all experience by observation of the arising and passing away of all sensory experiences on our bodies. And if one truly understands, in one’s System 1, that nothing lasts forever and that everything is temporary, that is one of the most profound insights one can gain about life and the world.

Figure 13: Through meditation, one teaches one’s System 1 brain the wisdom of understanding universal impermanence.

If one truly understands that everything is temporary, one does not get embroiled in the highs and lows of life, but instead lives gracefully through all, come what may be. One enjoys the pleasant more because one appreciates its fleetingness and uniqueness, and one endures the difficult better because one understands its temporariness. One does their best to take the most advantage of their time because one realizes how short human life is and cares deeply for others because one realizes how temporary and unique each and every human being is.

Figure 14: Meditation helps one appreciate the uniqueness and temporariness of the people in our lives.


Figure 15: Enlightenment

Meditation teaches one the ability to remain equanimous, unperturbed, and happy in any situation. It teaches us to feel boundless compassion and universal love toward all living beings. And it also teaches us to perceive reality as it is, and gives us the profound wisdom of understanding universal impermanence. One who is able to cultivate all these qualities will have truly escaped all worldly suffering and achieved Nirvanic Peace, a stage in meditation practice called Enlightenment.
 “May all beings be well and safe, may they be at ease.
 Whatever living beings there may be, whether moving or standing still, without exception, whether large, great, middling, or small, whether tiny or substantial,
 Whether seen or unseen, whether living near or far,
 Born or unborn; may all beings be happy.
 Let none deceive or despise another anywhere. Let none wish harm to another, in anger or in hate.”

Learning to Meditate

There are many ways to learn to meditate. For new learners, it can be very useful to first attend a meditation retreat to learn and get established in the technique thoroughly. Many meditation retreats are available and as long as the core practice is based on mindfulness and equanimous observation of one’s lived experience, the results should be beneficial at any retreat.

This article is based on the author’s experience with Vipassana meditation at retreats available through These retreats are held at hundreds of meditation centers around the world, and are offered on a donation basis, free of charge.

Image Credits:

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Figure 5: Reader’s Digest, “Greatest Human Achievements”

Figure 6: Adapted from

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Figure 14: Associação Portuguesa de Famílias Numerosas

Figure 15: Source: Meditation.html