Triune Brain: How the Mind Rewires the Brain via Meditation/Habits

The triune brain model of the brain is no longer widely discussed. However, it provides a simple way to look at three primary brain functions, as we will see below.

Revised December 20, 2016; September 21, 2020; October 21, 2022

Triune Brain – Three Major Components of the Brain

1. Triune means “consisting of three.” The human brain, the most advanced of all animals, shows how different animals have “different levels” of consciousness.

  • The brain has three distinctive regions (see the figure below): (1) brain stem (labeled “reptilian” in the figure), (2) limbic system, (3) cerebral cortex or just cortex (labeled “neo-cortex” in the figure).
  • Details in Ref. 1. We will summarize very basic features of the “three parts” of the brain.


Reptilian Brain (Brain Stem and the Cerebellum)

2. The brain stem (reptilian brain may be a misnomer since reptiles have limbic systems) is the most primitive, and all developed animals have it. It governs automatic physiological functions such as the heart rate, respiration, digestion, etc.

  • And that is all the lowest-ranked animals can do (automatically). They are almost like fully-automated robots.
The Limbic System

3. Animals with somewhat higher intelligence have a limbic system in addition to the brain stem. But still no triune brain.

  • It coordinates sensory reception, memory, and unconscious emotional reactions. These animals with limbic systems- like snakes and lizards- react spontaneously to external influences.
  • Humans tend to do that too. In case of a threat, the limbic system instantaneously and automatically makes the “fight or flight” decision. We could say that automatic mano saṅkhārās arise via the limbic system. See “Saṅkhāra – What It Really Means.”
  • It is pretty clear from the definition of an Arahant that even this instantaneous response can be entirely tamed by cultivating wisdom (paññā), i.e., by following the eightfold path. An Arahant’s mind would not attach to any ārammaṇa.
The Cerebral Cortex (Neocortex)

4. The cerebral cortex (learning brain; neo-cortex in the figure) is the most advanced part of the brain. It can make “rational decisions” by contemplation but is time delayed. Therefore, it is called the “thinking brain.”

  • The cortex is responsible for language capability, logic, reasoning, learning, and critical thinking, the good stuff.  All primates have it, but of course, humans have the largest.
  • In other words, we generate vaci and kaya saṅkhāra with the help of the neocortex.
  • In contrast, even higher animals like apes and elephants have limited capabilities. However, they are not “robots,” as clearly illustrated by this elephant: 


5. All our sensory inputs are processed in the neocortex before they are sent to the hadaya vatthu, or the “seat of the mind” in the gandhabba close to our physical heart. 

  • Since it takes time for our brains to analyze the “incoming data,” typically, there is about a 100th of a second delay between incoming sense inputs and our mind generating thoughts about that sensory input.
  • The brain can handle only one sensory input at a time. This means it can handle only about 100 sense inputs in a second. So, even though our minds generate an initial response quickly, the follow-up “thoughts” are delayed due to this “processing delay” in the brain.
  • This process is discussed in detail in “Citta and Cetasika – How Viññāṇa (Consciousness) Arises.”
  • That pre-processing is minimal even in “higher animals” with small cortexes, like dogs and apes. This is why humans are unique. We have a large cortex that slows the response time and helps us “analyze the situation” rationally.
Ways to Improve Brain Functionality

6. Neural pathways in the brain are strengthened by:

  • Repeated application (meditation included). Repeated activity forms both good and bad habits, as we discussed in several posts, and is the key to molding the character (gati); see “The Law of Attraction, Habits, Character (Gati), and Cravings (Āsavas),” and other related posts.
  • Good foods and regular exercise increase the production of Dopamine and other “good” chemicals.
  • Exercise and meditate! It will keep you healthy and alert; see”‘Spark’ by John Ratey” for information on the value of a good exercise program.
Brain Plasticity

7. Until about the late 1980s, there was wide belief that one had to live with the brain that one was born with. But since then, the ability of the brain to change (neuroplasticity of the brain) has been demonstrated, and studies on the effects of meditation on the brain have become an active research field.

  • Of course, 2500 years ago, the Buddha said that the mind is the precursor to everything. The mind does not arise from the brain. It controls all body parts, including the brain.  See “Brain and the Gandhabba.”
  • The key is that insight meditation should DRASTICALLY change neural wiring. However, there have not been any brain scans of someone who has cultivated the “correct versions” of Satipaṭṭhāna and Ānapānasati meditation.
  • Other posts at the site describe this “re-wiring” of the cortex that leads to a change in our gati. See, for example, “9. Key to Ānapānasati – How to Change Habits and Character (Gati).”
Effects of Meditation on the Brain

8. As shown in the references below, there is compelling scientific evidence that even mundane versions of meditation improve both the cortex AND the limbic system.

  • Those studies show that basic Samatha meditation helps, but Mettā Bhāvanā (compassion meditation) is particularly effective.
  • It must be noted that Tibetan Samatha (breath meditation) or Mettā Bhāvanā (mundane version) are anariya versions. For the Ariya versions, see “6. Anäpänasati Bhävanä (Introduction)” and “5. Ariya Mettā Bhāvanā (Loving Kindness Meditation)“. I am sure that a brain scan of Ariya (Noble person) will yield more revealing results.
  • For example, meditation also affects breathing patterns (thus, the brain stem). Therefore, meditation affects overall brain function. An Arahant can stop breathing for up to 7 days in Nirodha Samapatthi. It will be extremely interesting to see a brain scan of an Arahant.
The malleability of the Neocortex and the Limbic System

9. The following case illustrates the complex role played by the brain. A developed left brain (of the neo-cortex) indicates compassion for others and enhanced happiness for oneself, and a larger right side indicates an aggressive character.

  • Here is the link to a video showing the results of brain scans of an advanced meditator who had done loving-kindness meditation for an extended time compared to 150 non-meditators.

  • The discussion on the brain scan data is from about 17:00 to about 18:20 minutes if you don’t want to watch the full video. 
  • We must also remember that Tibetan loving-kindness meditation is an anariya version of the Mettā Bhāvanā. See “5. Ariya Metta Bhāvana (Loving Kindness Meditation).”
Humans Have Control Over Their Lives

10. Furthermore, we are not programmed by our genes, environment, or even our past kamma. However, all of those can affect our destiny. The most powerful is our mind. In other words, citta niyama dominates kamma niyama.

  • The saying goes, “You can do anything you put your mind to.” This is the factual basis of free will.

11. Even though scientists are making some progress regarding the mind, the brain is not the mind, just as the physical eye is not the cakkhu pasada rupa; see “Manomaya Kaya (Gandhabba) and the Physical Body” and other related posts. Yet it is essential to keep the physical eye (and other physical sense faculties) and the brain in good condition for the whole body and the mind to work correctly.

  • Finally, the triune brain model is no longer widely discussed. However, it provides a simple way to look at three primary functions of the brain.

Next, “How Habits are Formed and Broken – A Scientific View“, …………………


1. Wikipedia article on Triune Brain. More details in “The Triune Brain” by P. D. MacLean (1990).

2. “The emotional life of your brain” by Richard Davidson (2012).

3. “You are the Placebo – Making Your Mind Matter,” by Joe Dispenza (2014).

 You can open the following documents by clicking on them:

4. Effects of meditation on Amygdala-G. Desbordes et al., – 2012

5. Psychological effects of meditation-P. Sedlmeir et al., -2012

6.  How does mindful meditation work-B. K. Holzel et al., – 2011

7. Alterations in Mindful Meditation-R. J. Davidson et al., -2003

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