Zen In the Brain

by Vered Arnon

Zen Buddhism is commonly categorized as one of the religious traditions of the world. As such, it is considered to operate solely on the more unseen dimensions of being human, what Western thinking calls “consciousness.” Zen scholars explain the workings of the mind according to a Buddhist psychological model. Understanding this model to some extent is important for comprehending the explanations offered by Zen scholars for the life-transforming changes which can occur in practitioners of Zen meditation. Indeed, there is a growing use of Zen practices within some areas of psychotherapy in North America. Anecdotal support for the therapeutic benefits of Zen practices has probably existed since the beginnings of Zen. Technological advances, however, have now enabled neuroscientists to observe – at the level of brain structures and functions – just what is happening physiologically during Zen meditation. After surveying the relevant basic Zen perspectives on the mind and a representative use of Zen practices in psychotherapy, this paper will summarize some of the current research depicting what happens in the brain during Zen practice, with a focus on how this is likely to contribute to a positive therapeutic effect. In this era of bodymind medicine and therapies, Zen meditation is a quintessential bodymind practice, both by original conception and nature and also by therapeutic effect.

A full discussion of the Buddhist model of the mind goes far beyond the scope of this paper; nevertheless, there are certain aspects of this model which are important to the Zen perspective on the therapeutic nature of meditation. The ordinary mind is considered to be unable to think clearly or to act sensibly. “The ordinary mind is obscured” (Brazier, p.87) and “Most human beings exist in a state of chronic dis-ease” (Austin, p356) are current expressions of this fundamental perspective. Zen views the human mind as ignorant and delusional, full of nonessential desires and attachments that cause sufferings. While exaggerated states result in what are viewed as psychological illnesses, from the Zen perspective, all ordinary minds are in varying states of imbalance.

A second element of the Buddhist model of the mind which needs to be considered is the theory of root relations. ”The theory of root relations states that all dukkha (mental suffering) can be traced back to three bitter roots, greed, hate and delusion, and that all wholesome states can be traced back to three sweet roots which are the opposites of the bitter ones” (Brazier, p87). Fundamentally, there are only two states of mind – closed or open (enlightened), which are derived from the relationships among the six roots. The following chart summarizes these relationships and some of their clinical manifestations (from Brazier, pp87-90):

Bitter tap root


Avidya (closed mind)


Three poisons

Bitter roots







Consequences Mild but long-lasting Severe but not long-lasting Severe and long-lasting
Manifestations Compulsiveness and reactiveness

Compulsive eating

Existential depression


Dissociation and fright


Reactive depression


Perplexity and fixed ideas


Endogenous depression



Sweet roots







Ultimate antidote

Or Sweet tap root


Vidya (open mind)


A psychotherapist who incorporates Zen practices into his therapy writes, “We all suffer from all three forms of obscuration of consciousness all the time. What we are talking about, therefore, is an imbalance or particular excess being the characteristic of a condition” (Brazier, p89).

Ordinary Zen practice and Zen-based psychotherapy share the same goal: to hasten the process of converting the bitter roots into sweet ones. The ultimate goal is the state of enlightenment (vidya), i.e., open, clear mind. In Zen, the three roots of enlightenment are not referred to by the Pali negatives (alobha, adosa and amoha), but by their more positive Sanskrit equivalents – maitri (love), karuna (compassion), and prajna (wisdom)” (Brazier, p93). As will be seen later, meditation practice is understood to facilitate the arousal of these three positive, sweet roots. From a Zen perspective, therefore, it is possible to say that meditation practice is “therapy” needed by all humans. Human beings can, of course, also learn from ordinary experience, but this learning process may take a very long time, perhaps even longer than the lifespan of the individual. What is necessary, therefore, is a way to speed up this process. Zen meditation and mindfulness practices are considered by their practitioners to hasten progress on the path to enlightenment.

The principles of Zen practice intended to harmonize the individual and correct imbalances are focussed meditation sessions and on-going mindfulness. Zen meditation refers to either zazen, a focus on the breath while maintaining a particular seated posture, or shikan-taza, a release of any focus, including that on the breath, while in the seated position. The physical particulars for engaging in this practice are strict and detailed in numerous sources (see for example, Kapleau pp29-68, and Zen Master Dogen (translation) in Tricycle, Spring 1994, pp24-33). The seated practice enables the individual to achieve a state of deep relaxation and a release of more and more distractions, both outer and inner. This focussed meditation leads to and supports mindfulness practice.

Developing a clear, accurate view of the world, according to Zen, results in the realization that everything, including oneself, is complete and perfect. Actualization of this in daily life, which is the essence of mindfulness practice, is enabled by depth of concentration and clarity and accuracy of view, resulting in true harmony and peace (Kapleau, pp49-53). Mindfulness helps a person to “cast off worry and anxiety” (Kapleau, p32), and, as an on-going constant, enables a person to engage in their daily activities with heightened alertness and a sense of tranquility. Free from mental preoccupations and unhealthy behavior patterns, a mindful person is able to live in harmony with the environment (Kapleau, p33). Most people spend their lives rushing through one thing after another, without ever really noticing or paying attention, being too preoccupied with the past or the future. Mindfulness enables a practitioner to maintain the inner peace and clarity developed during seated meditation practice.

Zen meditation, in particular, zazen, has attracted the interest of a growing number of psychotherapists. This is part of a larger picture of a growing general interest in Buddhism among mental health practitioners. This interest is two-pronged, in that there is a concern with how Zen (and other Buddhist) practices can help the professional personally to become an individual who is more effective in dealing with clients, and also a concern with how these practices can be implemented in therapy and the lives of clients for a more positive and lasting outcome (Twemlow, pp1-39; Thomson, pp531-548). Zen Master Bon Soeng describes the role of Zen for the therapist as follows: “As a therapist you have to stay present and in the moment. You need to be able to get out of the way to let the process happen. I think the most important perspective which relates Zen to psychotherapy is to view the person you’re working with as the Buddha himself. That implies not sticking someone into some narrow classification, but looking to see who the person really is” (Bon Soeng at kwanumzen.com). For the client, Zen practice is an important tool for them to find out about themselves. Some therapists use a brief period of meditation at the beginning of a therapy session, as it can give a client an incredible feeling for what goes on in their minds (Bon Soeng at kwanumzen.com). What goes on in the mind during zazen, be it the mind of therapist or of client, is very similar – if not identical – to various psychotherapeutic processes. A recent writer on the subject makes this very clear when he says

Sitting zazen has something of the flavor of psychoanalysis. Some schools of Zen sit facing a wall; some sit facing outward into space. Whichever way you sit, the empty space that confronts you is more silent than the most quiet psychotherapy session, more mercilessly neutral than the strictest Freudian analyst. Inevitably, one comes up against the walls we build within ourselves. The structure of zazen, where we sit still no matter what feelings or thoughts come up, creates a safe “holding environment” in whose security repressions may loosen. Feelings, thoughts, sensations emerge, and with no one there to blame or bounce off of, our projections twist back upon themselves until our innermost desires and fears are left nakedly visible. Sitting quietly, doing nothing, we do everything we can to escape from ourselves, only to find that there is no escape (Rosenbaum, p7).

This closeness of psychotherapy and Zen (and Buddhism in general) is seen most clearly in their common goal – human liberation. In addition, both support the awakening of love, compassion and wisdom and work to reveal what blocks these elements.

There are numerous psychotherapies with some Zen basis, or at least inspiration. Many therapists have developed their own unique modalities, to which they have given a particular name. For the most part, these are therapies limited to those individual therapists. Fewer in number are those Zen-connected psychotherapies which have a widespread and established following. Hakomi Therapy involves the integrated use of mindfulness, the body, and non-violence in a psychotherapeutic setting. The Hakomi therapist looks at how body, mind, heart and spirit weave together to form the client’s experiential world (hakomiinstitute.com). Core Process Psychotherapy works with awareness and compassion in order to reveal the ways people cut themselves off from their true nature and create suffering for themselves (karuna-institute.co.uk/coreprocess.htm). Naikan Therapy is a structured method of self-reflection to help people understand themselves, their relationships and the fundamental nature of human existence. This reflection is based on three questions: What have I received from…..? What have I given to…..? What troubles and difficulties have I caused…..? (clcma.com/naikan1.htm) Dialectical Behavior Therapy, developed by Dr. Marsha Linehan, is directed towards parasuicidal patients. DBT combines techniques of cognitive-behavioral therapy with self-awareness techniques from Zen (depts.washington.edu). One of the best examples, however, to clearly illustrate the way Zen can serve as a basis for a psychotherapy is Morita Therapy.

The goal of Morita Therapy is to help clients realize their potential and live interesting, meaningful lives. The focus is on helping the client to release the maladaptive attitudes and approaches to living which are the roots of suffering. Morita therapists believe that we need to anchor ourselves in the truth of nature (including the facts of our own human nature) in order to live productive and meaningful lives. The response to nature is to be active and creative. This does not involve imposing constraints on nature, however, but rather learning to live in harmony with it. A second basic concept of Morita is that we must maintain a balance in our attention between self-preservation and self-development. This is enabled by learning to become “one with” whatever we are doing at the moment. Also important to Morita is understanding feelings (emotions) as transitory; therefore, our goals should not be based on feelings. Finally, Morita maintains that it is important to realize the “either/or” nature of much of our thinking and to see that this is not in accord with the natural world, or any part thereof, including ourselves. These concepts underlie the treatment process in Morita Therapy.

Classical inpatient Morita Therapy consisted of four stages: absolute isolated bed rest, light work, intensive work, and preparation for daily living (morita-therapy.org/about.htm). This treatment typically takes forty days, and includes journal-keeping, interviews with the therapist, reading, group outings, and attending lectures and group meetings. This process is one of reeducation and is intended to continue once the patient leaves the hospital. The patients will practice their new attitudes and approaches toward life and continue to improve. True Morita Therapy is not available in the US, but here as well as in Japan and other countries, psychotherapies have developed which are based on Morita. These derivatives all share the basic Morita approach to living: accepting painful feelings and undesired character traits as they are and engaging with the world as a healthy person.

While Morita psychotherapy is based on principles of Zen Buddhism, it should not be equated with Zen Buddhism. Many Japanese authors have argued that Morita Therapy is based on Western medicine, but a convincing argument has been made to show that Dr. Morita developed his ideas about the formation and cure of neurosis out of Zen concepts (Rhyner, pp7-14). For example, in Rinzai Zen, a monk meditates on a koan; in Morita Therapy, the patient ponders his self-produced problem and tries to solve it. “In both cases the problem is not the problem, but the attitude of the person towards the problem. The method of solving the problem by accepting it and becoming one with it is found both in Rinzai Zen and Morita Therapy. Not rational understanding but direct personal experience is important …” (Rhyner, p13). Morita Therapy’s central concept of seeing reality as it is, rather than in terms of a constructed ideal, is clearly taken from Zen. Nevertheless, Morita is distinct from Zen practice. This is seen most clearly in the fact that Morita patients are not instructed in the basic Zen practices, such as zazen.

Up to this point, we have seen that Zen Buddhism has a particular model of the mind which is used to explain aspects of what Westerners refer to as “consciousness” as well as changes within this domain. We have also seen that Zen concepts and practices have been incorporated in a number of psychotherapies, with positive therapeutic effect. All of this discussion has so far been at the level of thought structures. That changes do occur in the lives of Zen practitioners and clients of Zen-based psychotherapies is extensively documented in the literature (almost every source consulted contains such anecdotes). Newer evidence, however, now permits us to see that changes are also occurring on the physiological level. We will look first at the physiological aspects of meditation in general. We will then consider some of the actual brain-level changes that have been observed in Zen practitioners.

Meditation can be defined in a number of ways. A more philosophical or religious definition considers meditation to be an act of spiritual contemplation. From a more psychological direction, meditation is intentional self-regulation of attention on the present moment in order to better understand the self. Many different techniques of meditation exist. One convenient way of categorizing these techniques is to divide them into mindfulness or concentrative techniques (trancenet.org/research/). In mindfulness meditation, the practitioner sits in silence and centers attention by focussing mental awareness on an object or process (i.e., the breath, a sound, a mantra, a koan, etc.). Thoughts are allowed to come and go, with the object of focus serving as an anchor to return the practitioner to the present moment. The focus is thus on a field or background perception. In concentrative meditation techniques, on the other hand, focus is held to a preselected specific object. Regardless of the technique, meditation has been found to be a state which is physiologically distinct from sleep, daydreaming, hypnosis, praying, biofeedback or what results from specific relaxation techniques.

Scientific studies of the physiological nature of the meditative state have been going on for decades. (See Austin, trancenet.org/research/, maharishi.org/tm, meditationsoflife.com, tmcork.org, ejmas.com, hanshananigan.tripod.com, ukonline.co.uk/buddhism//tinhtut6..htm, home.swipnet.se/ and pazymino.freeyellow.com/ for useful summaries of this research.) General findings are the same regardless of the technique. There is some difference in the degree of effect for certain techniques, but the similarity is so great that generalizations are permissible. Meditation has been shown to affect all body systems, most notably in the following ways: brain activity becomes more integrated and coherent; blood flow to the brain increases; respiration rate slows; heart rate slows; muscles relax; plasma cortisol (stress hormone) declines; and plasma lactate declines (tmcork.org/unique.html).

The effect of meditation on body metabolism has been the focus of many studies. Results of these studies have shown that meditation is a wakeful state accompanied by a decreased metabolism. This decreased metabolism is evidenced by a decreased breathing pattern, decreased heart rate, and decreased blood pressure. A significant decrease in the level of oxygen use and of carbon dioxide elimination by muscle tissue has also been shown. While the overall physiological response to meditation is to reduce metabolic processes, more detailed studies have shown that what is actually happening is a reduction of metabolism in some tissues with a concomitant increase in metabolism in certain other tissues. (See ejmas.com/pt/ for references to specific studies.) Specifically, these studies have shown that there is a redistribution of blood flow in meditators, with blood flow to the liver and kidneys declining, cardiac output increasing, and more blood flowing to the brain.

Meditation has a profound impact on the autonomic nervous system. Researchers have long known that skin resistance to electrical current decreases at times of anxiety and stress and increases during relaxation. Many studies have shown very large increases in skin resistance in meditators. Using skin response indicators, some studies have shown that meditators recover more quickly from stress and show more stability in their responses to stress than do non-meditators. These patterns of response to stress (i.e., those of meditators) are those which have been associated with good mental health. In addition, meditation has been shown to involve decreased limbic arousal in the brain. The hypothalamus, which is part of the limbic system, controls the autonomic nervous system (see below for fuller discussion).

Studies of the effect of meditation upon the endocrine system were undertaken to see if blood levels of stress-related chemicals decreased during meditation. A pattern was discovered in which blood levels of certain of these indicators – lactate, cortisol and epinephrine – do indeed decrease during meditation. In fact, the levels of these chemicals tend to remain significantly lower for some time after meditation as well. In addition, some studies have found that during meditation there are certain unique patterns of blood hormone levels and blood flow to various organs including the brain (see ejmas.com/pt/ for references to some of the most important of these studies). Increased levels of gamma aminobutyric acid (GABA), melatonin, and dehydroepiandrosterone sulfate (DHEA-S) have been shown. These three substances have all been shown to have a stress-reducing effect on the brain. Other studies have shown that the physical effects of meditation continue after the meditation session. For example, some individuals control their hypertension solely by meditation, without medication.

The central nervous system is brought to a heightened level of sensitivity by meditation. This apparently enhances neural conduction, resulting in the improved motor performance skills reported by meditators. Most studies of brain activity during meditation have used the electroencephalograph to measure brain wave electrical activity. Meditators show a slowing and synchronizing of brain waves, with a predominance of alpha waves. The more experienced the meditator, the greater the slowing; some show the emergence of theta waves. “Apparently, an alpha wave pattern is most conducive to creativity and to the assimilation of new concepts, while the theta response seems to be a stage at which the mind is capable of deep insights and intuition” (Shin at ejmas.com/pt/). One study correlated brain waves with breathing patterns during meditation and found that deep (diaphragm) breathing (as favored in Zen practices) was more correlated with alpha waves than was shallow (chest) breathing. A number of studies now seem to indicate that meditation inhibits the usually dominant left hemisphere of the cerebral cortex (i.e., verbal, linear, analytic functions), and shifts activity to the right hemisphere, enhancing spatial, nonverbal, holistic, receptive functions. Other studies of a similar nature show that meditators seem to have a greater flexibility for shifting between the hemispheres, showing a greater level of integration.

In the area of psychology and meditation, until the very recent advances in the study of “the molecules of emotion,” studies have been primarily limited to outcome observations. In general, these studies showed that meditation promotes psychological health. Practitioners have reported subjective experiences of vast changes in their perceptions of self and the world. They have also reported very positive mood changes, increased confidence, a sense of self-control, greater empathy, improved cognition and concentration, reduced stress, and enhanced perceptual sensitivity.

The physiology of meditation is now an enormous research area. One of the most significant contributions to our knowledge in this area is the lengthy and detailed 1998 monograph, Zen and the Brain, by James H. Austin, who is a medical doctor, neurologist, and Zen practitioner. The following section of this paper will summarize some of this current research and its connections to Zen practice, as described by Dr. Austin.

The thesis of Zen and the Brain is that “awakening, enlightenment, occurs only because the human brain undergoes substantial changes” (pxix). Throughout this book Austin explores the relationships between prior meditation and these changes in the brain. The first part of the book considers the nature of Zen. Part two looks at the basic physiology of meditation. The next three sections consider various states of consciousness and where they arise in the brain. The last section discusses some of the social consequences of ongoing enlightenment. What follows is not a review of this book, but rather a selective summary of those discussions which support the purpose of this paper – i.e., to show supporting evidence for the bodymind nature and therapeutic value of Zen meditation practice.

When considering the physiological nature of meditation, Austin acknowledges the changes described in the previous section of this paper (pp78ff). He believes, however, that these are only secondary physiological changes in the body and the brain, which occur during “low arousal meditative states.” Studying these changes has sidetracked researchers from what should be their focus: “those primary processes in the central nervous system which underlie alternate states themselves” (p83).

Early investigators hoped that they could see what is happening in the central nervous system during meditation by studying brain waves; the consensus from these earlier studies was summarized above. Austin, however, points out some crucial limitations to the use of brain waves in concluding anything about the meditative state. Alpha wave activity is found to vary considerably from person to person during normal states. Just looking at alpha waves on an EEG tells nothing about the form or content of the person’s mental state. More alpha activity occurs during “thinking”, especially nonvisual thinking. Persistent attention facilitates alpha, so that if a person is told to pay attention to what they are seeing, more alpha is produced than if they were just viewing something. Alpha disappears when thinking becomes difficult or the person attends to some brief external signal. Alpha also shows regional differences within the brain and is affected by whether or not the person’s eyes are open. All this leads Austin to conclude “…many inferences about meditation based on whether alpha is present or absent have not been substantiated” (p85). Theta activity, while not as conspicuous in the EEG of normal awake persons, likewise can vary significantly between individuals (pp85-86). Due to the considerable amount of variation in EEGs, between people as well as within one individual, and considering that meditation is not a single static episode but a series of dynamic changes, Austin finds most EEG studies of meditation open to criticism (p88).

Some generalizations can, however, still be made about what happens with brain waves during meditation. Early in meditation there will be increased alpha activity, followed by an increase in theta, with some fast beta sometimes superimposed on the slower waves. The focus of attention in early meditation accounts for the increase in alpha. Apparently, emotional arousal can generate faster alpha frequencies. Very important for meditation is brain wave coherence (i.e., how many of the EEG peaks and valleys from different electrodes are in synchrony). Some studies have shown that meditation leads to periods of coherence. Austin notes that “The strong and sustained alpha coherence which can occur during meditation distinguishes it from the way non-meditating subjects lose EEG coherence when they start to drop off into normal sleep” (p89). EEG studies have shown that theta predominates during zazen, but alpha activity will still also be occurring in parts of the brain (p89). In deep meditative states, a fast beta wave activity can be superimposed over the slower waves; even faster gamma activity has been recorded. Interestingly, one study has shown that persons in this deep meditative state can still be alert enough to send signals out to other persons, without this affecting the meditator’s EEG (pp90-91). Studies have shown that many meditators go in and out of sleep cycles of varying lengths. More experienced meditators may be able to enter and remain stable in a state that is between sleep and wakefulness (p91). Regarding what this evidence for sleep indicates about the nature of the meditative state, Austin says that meditative training “…is teaching the person how to reach – and hold on to – one of several abilities to attend. Even so, the most highly trained meditators will still slip up occasionally and drift off into sleep” (p92). EEG studies have also been used to support conclusions about brain lateralization during meditation. Austin cites a review of these studies which concludes “…that meditation does not shift the way the brain processes information from a mode that is primarily “linear” and left-hemisphere into an approach that is more “holistic” and right-hemisphere” (p92).

Breathing is a central focus in zazen, and Austin devotes a chapter to its discussion, explaining that the breath “gives us a sensitive, reliable index of how our emotional life influences the rhythmic workings of our brain stem” (p93). The brain stem is where the chemical signals for oxygen and carbon dioxide in the bloodstream control our breathing. Experienced meditators can greatly slow their respirations, reduce the volume of air breathed, lengthen their exhalations and increase abdominal breathing. All of these factors are correlated with increased relaxation. Austin suggests a brain-level explanation: “whenever we breathe more quietly and prolong the phase of expiration, we are probably quieting the firing activity of many nerve cells, both in the medulla and above” (p95). Some recent research has shown that the times when meditators say that thoughts have dropped out of their consciousness correlate with times of apnea (no breathing). These episodes last on average from 19 to 31 seconds, with the longer durations happening with more experienced meditators. Austin hypothesizes that this is linked not just to lessening activity in the brain stem, but also to physiological changes taking place within the deep, central parts of the brain (pp96-97).

Some researchers have suggested that the meditative state could be just a result of sensorimotor deprivation. It is true that the body position in zazen does create both sensory and motor deprivation. After a period of time, individuals in zazen retreats and subjects in sensorimotor deprivation experiments all are impelled towards probing topics related to the universal search for existential meaning. Both groups also report the arousal of various kinds of visual phenomena. Despite these similarities, sensorimotor deprivation does not produce the positive, life-changing effects which can be seen in some meditators.

Just how life changes experienced by meditators are brought about is the most important question we can ask about the nature of meditation. Austin answers this question by saying that these behavior changes occur when there is a reconfiguration of the flow of impulses throughout a sufficient number of networks in the brain (p154). After a review of basic brain anatomy (knowledge of which will be assumed in this paper), Austin goes on to describe how the brain works as a set of coordinated networks which synthesize higher functions. We should no longer think of the brain as a fixed map, but rather think of brain cells as parts of a “dynamic meganetwork.” All parts of the brain are thus interconnected. Some of the circuitry is less flexible, such as our life support systems, whereas other circuitry, such as that which reflects how we were brought up, is more flexible.

Understanding how brain arousal takes place is important for understanding what happens in the brain during meditation. Arousal is a complicated process, in which many mechanisms blend to enter into it and also issue from it (p158). Research has shown that the midbrain reticular formation is a crucial region, capable of generating arousal, alertness and desynchronized EEG activity. In animal studies, deactivation of much of the midbrain reticular nerve cells results in a being which, when engaged in one activity, will not display normal orienting responses to outside stimuli (p161). This has very interesting implications for Zen. The midbrain is not the only area involved in arousal. Considerable research has now shown that several hierarchical brain levels are involved in an intricate interplay. Arousal and activation relays ascend from the brain stem to the hypothalamus, then on to the thalamus, cortex, limbic system – and back down again. The level of arousal will be increased when more of certain chemicals – norepinephrine, dopamine, various amino acids – are released into the midbrain (p164). Another chemical which has a pivotal role in determining the nature of consciousness is the neurotransmitter acetylcholine. The ACH systems in the central nervous system operate in multiple ways: the activation may be very brief or sustained and can occur at all levels from medulla up to cortex (p169).

It has long been known that the limbic system deep within the brain is central for emotions. We now also know that it has connections throughout the brain. The functions of the limbic system are summarized as “mating, memory, mood, motivation, fear, fighting, food””(p170). Linked within this system is the cingulate gyrus. Together, these parts of the system help us to focus our attention and to attach it to things that are in our external environment. The relevance of meditation is seen in Austin’s comment: “So, whatever process cuts down on the flow of nerve impulses throughout this network on one side of the brain could dissolve the way a person melds affect and higher functions. And the result could lead the subject to “devalue” emotionally – and so to depersonalize – events which are taking place in the opposite half of space” (p174). As Austin acknowledges, the effect of meditation in this regard is still mostly at the level of hypothesis.

Many studies have shown that people change when they are feeling happy, self-confident and comfortable in the world (pp350-351). Moreover, these positive feelings seem to spread out and become linked to “1. Being helpful; 2. Avoiding being unhelpful; 3. A more ready access to positive material in memory; 4. Rapid screening and efficient decision making” (p351). Studies of the limbic system and cingulate gyrus show us part of how Zen can promote major lasting attitudinal changes. Certain limbic pathways extend into the frontal lobes and affect these areas by their positive or negative characteristics. In addition, when the cingulate gyrus is stimulated, it can activate the prefrontal cortex (p352). Cutting down the flow of nerve impulses through this region can free a person from addictions; Zen meditation has been shown to decrease the flow of impulses in this area of the brain. By affecting the limbic system, therefore, meditation can promote a “positive atmosphere” within the practitioner.

The amygdala is the source of our fear of death. The medial amygdala contributes to our general survival skills. This area affects our behavior before any “high-minded thought” from the cortex can affect us. This explains why having the “right thinking” will not banish deep fear or rage. The amygdala, however, has many receptors for opioids and antianxiety chemicals and so can also be involved in the quieting of fears. Research has shown that breathing in results in the discharge of many amygdala nerve cells, but exhaling results in the firing of only half as many. In Austin’s words: “Not only does meditation affect breathing; breathing can go on to influence meditative experience. More specifically, expiration quiets down the firing of the central amygdala” (p178). The amygdala is not the sole controller of fear or aggression. It is a node in a network of circuits that mobilize our entire body in a fear response. Changes which help to stop the firing of amygdala cells as well as eliminate other contributing arousal factors within the whole network may account for those times in meditation when a person loses all fear (p179).

The hippocampus is a very small part of our brain which receives preprocessed messages from all areas of the cortex. Once the hippocampus has been “primed” by messages from a particular pathway, its subsequent responses will be greatly enhanced. This is called long-term potentiation. Research has shown that the most effective rate at which to deliver potentiating stimuli is theta frequency. The transmission will remain increased as long as three weeks after the initial potentiating stimulus. The hippocampus is of interest to Zen because alternate states of consciousness have been postulated to be due to particular changes taking place in certain hippocampal cells. Austin evaluates this hypothesis (pp182-189). The hypothesis specifically states that enlightenment is due to a blockade at a particular synapse. Austin shows that if this were so, the flash of enlightenment would blot out both immediate ongoing and recent past memories. In brief enlightenment states, however, neither loss occurs. What does happen is the following: earlier maladaptive associations drop out; fresh ongoing perceptions are registered; present moment impressions are preserved indelibly; the impact and clarity of the peak moment are retained; and change happening during the peak moment can be accessed later (pp187-188).

The hypothalamus is located at the base of the brain and has two primary types of functions: it performs local duties and also acts as a bridge. It integrates and participates in our instinctual drives. “Zen sponsors a systematic unlearning in human beings” (p190), and the hypothalamus seems to play a central role in this when it receives certain negative feedback messages from higher centers and these are used to dampen more reflexive behavioral responses. The lateral hypothalamus is a nodal region active in our development of polarized responses. These visceral positive or negative responses end up attached to our ideas of good/bad, right/wrong, etc. Zen affects these connections. Since it is the intent of Zen to change behavior, the brain will have to be modified in at least three sets of ways: “(1) the way it perceives stimuli; (2) the way it responds to stimuli at basic visceromotor levels, and (3) the way its many other layered systems reinforce the interactions between the first two” (p191). All of these are in part controlled by the learning/unlearning functions of the hypothalamus.

Evidence shows that change in the deep structures of the brain, especially the hypothalamus, is key to the behavioral transformation sought by Zen. Changes in the hypothalamus will cause shifts in behavior that are major and enduring. The hypothalamus region integrates basic brain mechanisms necessary for species preservation (p336). The hypothalamus is central to the function of the endocrine system. Hormones produced in the endocrine glands exert their influence on the hypothalamus, resulting in aggressive, gentle or balanced traits. To regulate its response to these hormones, the hypothalamus regulates their production with biogenic amines.

Biogenic amines exert a powerful influence over the whole cerebral cortex because of the huge network of terminals spread out from each cell. One of the three major amines is seratonin, high levels of which inhibit the release of certain endocrine hormones (p195). Low levels of seratonin correlate with depression. Indeed, stress responses begin in the hypothalamus and are characterized by dramatic, unstable fluctuations of seratonin levels (p206). Since Zen meditation raises the seratonin levels in the brain, it can have positive effects on both mood and behavior, and has even been shown to significantly decrease the capacity to develop addictions.

In addition to seratonin, the neurotransmitter l-glutamic acid plays an important role in how meditation affects the brain. Also known as glutamate, this neurotransmitter is released in the brain during meditation, affecting all brain systems. Glutamate is a fast-acting, powerful amino acid that causes heightened consciousness (p654). Excesses of it can kill brain cells. Through selective stimulation of glutamate-producing nerve cells, it is possible to dismantle conditioned pathways that have been learned and etched into the brain. Zen meditation calms and clears the action of brain cells, and in the absence of synaptic clutter, specific cells can be targeted, and specific pathways that were not penetrable during normal brain activity become penetrable and can be dismantled (pp653-659).

A more detailed look at the amygdala at this point can help us to better understand one circumstance of how learning/unlearning can take place. Impulses from visual stimuli travel down to the amygdala where emotion biases the visual associations. Circuits are formed between visual cells and the amygdala by memories, and these networks create distinctions between notions of priority, gain, loss, and so on, which motivate preference, desire, and repulsion. Affective connotations are infused into the neutral stimuli (pp247-249). The more distinctions one has, the more conditioned emotional responses one develops, the more overload there is in the frontal, temporal, and limbic circuits of the brain (p250). The brain literally becomes cluttered and entangled with complex pathways. The amygdala comes to instant conclusions about survival or the reinforcement value of incoming signals, and then relays these affectively biased signals to other circuits. This orchestrated response creates and reinforces pathways (p179). These pathways are an acquired, conditioned way in which the brain perceives and responds to stimuli. This is where the formulation of what is perceived as “wrong” and what is perceived as “right” takes place. Zen practice helps to reduce the chemical impulses which cause us to instinctually focus on our own cravings and desires, by selectively targeting the pathways that the amygdala uses to trigger conditioned emotional responses and dismantling them. In all of this, it is the influence of glutamate on the amygdala which is the primary influence for the way the brain perceives and responds to stimuli. The amygdala has extensive entangled connections to the hypothalamus, so affecting the amygdala also affects the hypothalamus. And since all these connections then go throughout the brain, including the cortex, we can see how glutamate’s role in dismantling pathways can affect both behavior and attitudes.

The deconditioning resulting from Zen meditation’s influence on conditioned behavioral patterns enables a person to act instinctually in a humane, compassionate way (p334). The reduction of selfish impulses (resulting from dismantling pathways surrounding the amygdala) results in a resurgence of compassionate impulses which have been seen to be instinctual in infants. As the brain is conditioned, these instinctual impulses are suppressed by the entanglement of connections and pathways. When the pathways are broken and the amygdala no longer triggers the conditioned emotional responses, people become more altruistic, concerned about others and helpful towards others (pp645-653). Moreover, aside from the direct effect of dismantling conditioned pathways, delayed effects of the surge in glutamate transmission caused by Zen meditation have been shown to improve memory and task performance (p659).

This summary of salient points from Austin’s lengthy monograph brings together Zen concepts and neuroscientific observations. From this discussion we are able to begin to see how Zen works in the brain to elicit a positive therapeutic effect. And we can begin to understand to some extent just what must be taking place in psychotherapeutic clients to make the Zen-based psychotherapies described above now so popular.

Zen explanations of what is happening in the person as a result of meditation and mindfulness practice are phrased in terms of changing bitter roots into sweet roots. Actually, as has been illustrated by this paper, this is but a metaphoric rendering of what neuroscientists are now beginning to be able to observe at the cellular level in the brain. Observing brain-level events, however, does not provide some final, reductionist answer to the most basic human questions of the nature of existence and consciousness. If we wish, however, to exercise our mental capacities in the pursuit of these vital issues, then perhaps Zen meditation practice has very much to offer in the support of our efforts. As Austin has said “…in the final analysis, Zen training means brain training” (p11). But then, as Austin has so amply shown, in the process of the Zen training our previous issues and questions will most likely just dissolve into the greater wonder of simply being.  


 Monographs and Journal Articles

Austin, James H. Zen and the Brain: Toward an Understanding of Meditation and Consciousness. MIT Press, 1998.

 Brazier, David. Zen Therapy: Transcending the Sorrows of the Human Mind. John Wiley & Sons, Inc., 1995.

 Butler, Katy. “On the Borderline: How a Zen-friendly psychologist revolutionized the treatment of patients once thought hopeless.” Tricycle Spring 2002: 47-49, 98-106.

 Dogen, Zen Master. “The Principles of Zazen.” Tricycle Spring 1994: 24-33.

 Epstein, Mark. Thoughts without a Thinker: Psychotherapy from a Buddhist Perspective. Basic Books, 1995.

 Halpern, George J. The Security Circuit: A Proposed Construct for the Central Nervous System. EBSCO Publishing, 2000. (full text available online at ehostvgw4.epnet.com) 

 Kapleau, Roshi Philip. The Three Pillars of Zen. Anchor Books, 1980.

 Magid, Barry. Ordinary Mind: Exploring the Common Ground of Zen and Psychotherapy. Wisdom Publications, 2002.

 Rhyner, Bruno. “Morita Psychotherapy and Zen Buddhism: A Comparison of Theoretical Concepts.” Psychologia 31 (1988): 7-14.

Rosenbaum, Robert. Zen and the Heart of Psychotherapy. Brunner/Mazel, 1999.

 Thomson, Roger F. “Zazen and Psychotherapeutic Process,” American Journal of Psychotherapy 54 (2000): 531-548.

 Twemlow, Stuart W. “Training Psychotherapists in Attributes of “Mind” from Zen and Psychoanalytic Perspectives: Part I: Core Principles, Emptiness, Impermanence, And Paradox. Part II: Attention, Here and Now, Nonattachment, and Compassion,” American Journal of Psychotherapy 55 (2001): 1-39.

Internet Sources

buddhanet.net/crazy.htm (Patrick Kearney, “Still Crazy after all these Years: Why Meditation isn’t Psychotherapy”)

buddhanet.net/medpsych.htm (Greg Bogart, “Meditation and Psychotherapy: A Review of the Literature”)

clcma.com/morita1.htm (“Morita”)

clcma.com/naikan1.htm (“Naikan”)

depts.washington.edu/psychweb/Newsletter/Fall2001/suicide.html (“Suicide: The Complicated Search for an Agreed On and Effective Preventive Treatment”)

ejmas.com/pt/ptart_shin_0400.htm (Dr. Jooyoung Julia Shin, “The Physiology of Meditation”)

hakomiinstitute.com/ (“About Hakomi”)

hanshananigan.tripod.com/meditation.html (Scott McDonald, “Physiological Aspects of Meditation”)

home.swipnet.se/tmdoctors/eng/tmunique.htm (Jaan Suurkula, “Transcendental Meditation – neurophysiological transformation by way of a unique fourth state of consciousness”)

karuna-institute.co.uk/coreprocess.htm (“Core Process Psychotherapy”)

kwanumzen.com/primarypoint/v18n1-2000-winter-BSZM-PsychotherapyAndZen.html(Zen Master Bon Soeng, “Psychotherapy and Zen”)

maharishi.org/tm/research/summary.html (David Orme-Johnson, “Summary of Scientific Research on The TRANSCENDENTAL MEDITATION* and TM-SIDHI* Programs”)

meditationsoflife.com/ (“The Physiology of Meditation”)

meditationtherapy.com/ (domain for zenbodymind.com, medicalmeditation.com and zazentherapy.com)


morita-therapy.org/about.htm (“About Morita Therapy”)

pazymino.freeyellow.com/KiMeditation.html (Guillermo Paz-y-Mino, “Ki Meditation: Good for the Mind, Good for the Body”)

tmcork.org/unique.html (“A Unique State of Rest”)

trancenet.org/research/2000perezdealbeniz.shtml (Alberto Perez-De-Albeniz and Jeremy Holmes, “Meditation: concepts, effects and uses in therapy,” International Journal of Psychotherapy, Mar2000, Vol. 5 Issue 1, pp49-59)

web.ukonline.co.uk/buddhism/tinhtut6.htm (Dr. Tin Htut, “The Effects of Meditation on the Body”)

Leave a Reply

Your email address will not be published. Required fields are marked *