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

Revised December 20, 2016

Human brain, which is the most advanced for all animals, shows how different animals have “different levels” of consciousness. It has three distinctive regions (see the figure below): (1) brain stem (labelled “reptilian” in the figure), (2) limbic system, (3) cerebral cortex or just cortex (labelled “neo-cortex” in the figure).


1. The brain stem (lizard or reptilian brain) 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 lowest-ranked animals can do (automatically). They are almost like fully-automated robots.

2. The limbic system (sometimes called the midbrain) is the emotional command center; that evolved in the next “intellectual phase” in animals with somewhat higher intelligence.

  • It coordinates sensory reception, memory, and unconscious emotional reactions. These animals with limbic system — like snakes and lizards — just react spontaneously to external influences.
  • Humans tend to do that too. In case of a threat, the “fight or flight” decision is made instantaneously by the limbic system. Very loosely, we could say that automatic mano sankhara arise via the limbic system; see the “Living Dhamma” section.
  • It is quite clear from the definition of an Arahant that even this instantaneous response can be completely tamed by meditation.

3. 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 it 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 the humans have the largest.
  • The cortex is involved in generating vaci and kaya sankhara that arise with a time delay. By controlling our vaci and kaya sankhara, we have the ability to change our gathi. This is the “modern scientific rationale” behind the basis of Buddha Dhamma; see the “Living Dhamma” section.

4. All our sense inputs are processed in the cortex before they are sent to the hadaya vatthu or the “seat of the mind” that is located in the gandhabbaya close to our physical heart. 

  • Since it takes time for our brains to analyze the “incoming data”, normally there is about 100th of a second time delay between incoming sense inputs and our mind generating thoughts about that sense input.
  • The brain can handle only one sense 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.
  • I will discuss this in more detail (and it has been discussed in bits and pieces in the posts on the gandhabbaya, but the key point is that our actions and thoughts are “slowed down” by this pre-processing in the cortex.
  • That pre-processing is minimal in even in “higher animals” with small cortexes, like dogs and apes. This is why humans are unique. We have a large cortex that not only slows down the response time, but also helps us “analyze the situation” rationally.

5. One aspect of the role has been illustrated in the following case. A developed left brain (of the neo-cortex) indicates compassion for others and enhanced happiness for oneself, and a relatively larger right side indicates 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 a long period of 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 keep in mind that Tibetan loving kindness meditation is an anariya version of the metta bhavana; see below.

6. Until about late 1980’s there was wide belief that one had just 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 has become an active research field.

  • Of course, 2500 years ago the Buddha said that mind is the precursor to everything, and that any body part (including the brain) is controlled by the mind. The mind does not arise from the brain; the mind controls the brain.
  • The key is that insight meditation should DRASTICALLY change neural wirings; no studies have been done on the brain of someone who has cultivated the “correct versions” of satipattana and anapanasati meditation.
  • There are other posts at the site which describe this “re-wiring” of the cortex that leads to change in our gathi.

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

  • Those studies show that basic samatha meditation helps, but metta Bhavana (compassion meditation) is particularly effective.
  • It must be noted that Tibetan samatha (breath meditation) or metta bhavana (mundane version) are anariya versions. For the Ariya versions, see, “6. Anäpänasati Bhävanä (Introduction)” and “5. Ariya Metta Bhavana (Loving Kindness Meditation)“. I am quite positive that brain scan of an Ariya (Noble person) will yield more interesting results.
  • For example, we also know that meditation affects breathing patterns (thus the brain stem). so the overall brain function is affected by meditation. 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.

8. 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 in molding the character (gathi); see, “The Law of Attraction –  Habits, Character (Gathi), Cravings (Asavas)“, and other related posts.
  • Dopamine (and other good chemical) production is enhanced by omega 3 and other good foods, and exercise, including interval running.
  • 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.

9. Furthermore, it is clear that we are not programmed by our genes, environment, or even our past kamma, even though all these can affect our destiny. The most powerful is our mind, i.e., citta niyama can even dominate kamma niyama.

  • As the saying goes, “you can do anything that you put your mind to”. This is the true basis of free will.

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

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


“The Truine Brain”, by P. D. MacLean (1990).

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

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

 You can open the following documents by clicking on them:

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

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

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

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

Print Friendly

Leave a Reply

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