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Sitting at the Intersection of Neuroscience and Mindfulness

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Exploring the effects of meditation on the brain

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As a student of both meditation and neuroscience, I’ve been present for the convergence of the two areas in my life, and I’ve noticed how both awareness of how the brain works (through studying neuroscience) and awareness of how my brain works (through practicing meditation) has helped me tremendously to understand my mind, appreciate the way it operates, and use it to my advantage.

About a year ago I began meditating every day to help relieve stress and anxiety and was amazed at the benefits it brought with not only stress relief, but with awareness and focus, relationships, appreciation, emotional strength and control, and so many other aspects of my life as well. Around the same time, I opted to take introductory neuroscience classes to fulfill a part of my engineering degree. I’ve always been interested in how the brain works, and it was only natural for me to try to connect the dots between what I was learning in the classroom and the benefits I saw from meditation. I was curious…what is it about meditation that helps us to feel more calm, aware, and let go of our destructive thought patterns and internal chatter? This article explores my ideas and understanding of the mind and my hypothesis of how meditation and neuroscience are tied together, and also reviews some scientific research on the topic.

What many people think of when I tell them I frequently do meditation. Source.


When mentioning meditation to friends, it can be fun for them (and me) to joke about sitting cross legged on the floor saying ‘om’, and I’ll often get a sarcastic inquisition about how my chakras are doing. As much as I like to picture myself looking like a glowing ball of rainbow energy while I meditate, and it is often fun to play around with those ideas, I also realize how completely not silly meditation is, and how rooted it is in science. The brain is plastic and ever-changing and meditation helps it to change for the better.

The Neuroscience Side

A Very Brief, Oversimplified Introduction to How the Brain Works

Your brain is made up of billions of neurons that need to communicate with each other and other parts of your body in order to act like a cohesive system and accomplish tasks like movement, speaking, feeling, seeing, hearing, problem solving, and anything else you can think of that makes you you. Each neuron has three main parts:

  1. The cell body- the part that contains the nucleus
  2. The axon- the part that sends out messages to other neurons
  3. The dendrites- the part that receives messages from other neurons

The place where the axon and dendrites ‘talk’ to each other is called a synapse. The way that they ‘talk’ to each other is by sending electrical pulses called action potentials. An action potential propagates positive charge down the axon quickly until it reaches the axon terminal, where it triggers a series of events that result in the release of a chemical substance called a neurotransmitter into the synapse, and onto the dendrites of another neuron. This next neuron reacts to the neurotransmitter by opening ion channels through which charged sodium and potassium ions can flow. If the flow of charges makes the cell positive enough, it will trigger an action potential of its own that can repeat the process and continue communicating with other neurons. Each neuron receives inputs from many other neurons and sums up all of its inputs to decide whether it should propagate its own action potential and continue the line of communication.

It may not seem like much when each neuron can only ‘choose’ to send out an action potential or not based on the sum of its inputs, but with hundreds of trillions of synaptic connections, the brain can create circuits with unfathomable complexity. We have synaptic connections to all the senses around our bodies and connections to our muscles that are all wired together in a miraculous way so that we can take in and react to the world around us.

What Is Learning?

Most synaptic connections are not static and permanent, they can be strengthened or weakened so that some inputs have more influence on the neurons they ‘talk’ to than others. This strengthening/weakening of synapses is, at the lowest level, how we learn and remember things. The phenomenon of strengthening synapses due to high rates of activity at that synapse is called long term potentiation (LTP).

When a synapse recieves a strong amount of input due to many action potentials occurring in quick succession, an abundance of the neurotransmitter substance is released in the synapse. When this happens, in addition to the usual channels that open the cell to sodium and potassium flow, another type of channel is opened that allows the flow of calcium into the cell.

The resemblance is uncanny. Source.

As my neuroscience professor likes to say, “calcium is the Vince Young of ions, when it gets into a cell, all hell breaks loose, just like when Vince Young got onto the football field.” (Can you guess what school I go to?) The large amount of calcium triggers a series of events that ultimately result in more sodium/potassium ion channels being placed at the synapse and more permeability of the channels to sodium/potassium ions, allowing for more positive charge to enter the cell at a time. In other words, the next time even a small amount of neurotransmitter is released onto the synapse, the cell can much more easily react and become positive and therefore generate an action potential of its own. These effects persist from hours to weeks, and can even persist for months or longer if LTP occurs multiple times in a row. Once LTP occurs, it becomes easier for it to occur again (due to the ease of positive charge flow from the new and improved sodium/potassium channels). In other words, the rich synapses just keep getting richer.

A visualization of the lasting effects of long term potentiation. Notice the enhanced response of the action potential to a weak pulse (C — right side) that persists after a strong test pulse (B) induced LTP. Source.

Associative Learning

One of the coolest parts of LTP is that if a synapse is stimulated strongly, and a neighboring synapse is also stimulated at the same time, even very weakly, the reactions of both synapses are strengthened as if they were both firing very strongly. The key idea here is that they must both be firing at the same time. Paraphrasing Hebb’s postulate, “cells that fire together wire together.” For example, if a mouse’s foot is shocked at the same time a buzzer plays, the mouse will learn to associate the sound of the buzzer with pain, and will become afraid of the sound, as Sadegh Nabavi et al. demonstrated in Engineering a Memory With LTD and LTP.

Can You Unlearn Something?

The process of synaptic strengthening can be reversed, synapses can be weakened. The flip side of LTP is LTD or long term depression at the synapse. LTD occurs when a very small amount of calcium is let into the cell due to low frequency stimulation. Since LTP works by adding ion channels to a synapse and making them more permeable to ions, LTD removes ion channels from the synapse and de-phosphorylates them to make them less permeable to ions. This way, the next time neurotransmitter is released onto this synapse, the cell is less likely to let in positive current and therefore less likely to trigger an action potential than before.


The goal of mindfulness meditation is to be aware of the present moment without judgement or resistance to what is going on externally or internally within our own bodies and minds. My experience with meditation has been doing guided sessions through an app called Headspace, which I would highly recommend to anyone looking to start their own meditation journey.

For about ten minutes each morning, I sit with the intent to be present with the exercise, which can range from focus on the breath to a visualization of light, warm, and spacious energy within the body. Naturally, thoughts and emotions will pop up in the mind, and although many people new to meditation try to resist these thoughts and chase them away, over time it becomes clear that it is that very resistance that is inhibiting the benefits of the exercise and many parts of everyday life. In learning to let go of the resistance, to simply let thoughts, feelings, and emotions come and go, and gently bringing the focus back to the exercise, we learn to let go of resistance to our own thoughts and emotions in every day life. All we have to do is learn to accept the mind, body and environment as they are.

My Hypothesis on How Meditation Affects the Brain

Because the brain is mutable, we have the ability to ‘unlearn’ our patterns of thought that are undesirable.The bottom line is that the brain is plastic and changing, and by training the mind through meditation, we are able to make sure it is changing in a positive way. The first step in changing our thought patterns is to let go of the negative ones that we’ve already built up.

Throughout our lives, we learn patterns of resistance in our thinking. If you look for it, it’s everywhere, and it’s pretty ironic. We resist anxiety and worry with thoughts of anxiety and worry — “oh no, it’s happening again, I don’t want to feel anxious. Why am I so anxious? There must be a reason.” We feel sad about feeling sad. We get angry that we are getting angry. We resist people we don’t like, situations we don’t like, and there are many negative emotions involved — frustration, anxiety, sadness, feelings of hurt, and instead of simply recognizing that there is something present that we don’t like and accepting it, we try to fix it. We get stuck resonating over the same parts of the mind, not realizing that in fixating so much on that negative space, we end up giving it power over ourselves. Our minds go into overdrive trying to think our way out of our own thoughts.

These emotional thoughts and the resistance to them cause certain neuronal circuits to fire intensely as we go over and over the same thoughts, thinking with a force strengthened by emotion. As these neurons continuously fire action potentials, the synapses become strengthened by LTP, engraining these emotional thoughts into our heads and making it easier to slip into the same thought pattern again and again in the future. The same thing also happens with positive emotions. Any strong experience of ours that we think intensely about literally shapes our brain and our synaptic connections.

Unlearning Our Circuits

During meditation, we learn to break these existing thought patterns. We learn to see the thoughts and emotions from a distance and not engage with them. The way I have grown to envision the process occurring in my brain is that during meditation, when a thought or feeling pops up and we recognize it, accept it, and gently return our attention back to the exercise, we don’t take the usual bait of spiraling down into the same thought patterns. We are calm and aware, and our brain has space to breathe. It is my hypothesis that meditation stimulates those neuronal circuits in a low frequency way, giving way to LTD so the brain can alter its plasticity and weaken the synapses. It allows us to have a fresher start, to rid the mind of our past resistances and experience each moment with a present, spacious mind. At the same time, we are strengthening other parts of the mind with LTP as we repeatedly practice awareness in a non-judgemental way.

In many of the meditation exercises I have done, we are first asked to take the brain to a place where we might usually experience resistance. For example, I once did a mediation series on strengthening relationships with others. The exercise began with envisioning a person towards whom you experience resistance. Then, a calming, warming visualization exercise is done, which allows the mind to rest in that space which is usually crowded with resistance towards that person. This calming exercise is what I believe to be the low frequency stimulation that induces LTD to undo our previous tensions and negative experiences when thinking of that person.

Scientific Studies on Mindfulness Meditation

The conjectures about LTD and LTP happening in certain areas of the brain during meditation, are simply a reflection of what makes sense with my own experiences and my state of knowledge about these neuro-phenomenons. However, the idea that the brain is plastic and ever-changing implies so much about the way it operates that even if some of the exact mechanics of LTP and LTD are not activated by meditation specifically, there is evidence that the brain is indeed physically changed, even if by a different mechanism.

Some research has been done on the effects of mindfulness meditation on an individual’s behavior and health, as well as their brain’s structure and functionality. In The Neuroscience of Mindfulness Meditation, Tang et al. review multiple studies on the subject, some that used neuroimaging to show how the brain changes when a person starts to practice meditation. One such study found:

Eight brain regions were found to be consistently altered in meditators: the frontopolar cortex, which the authors suggest might be related to enhanced meta-awareness following meditation practice; the sensory cortices and insula, areas that have been related to body awareness; the hippocampus, a region that has been related to memory processes; the anterior cingulate cortex (ACC), mid-cingulate cortex and orbitofrontal cortex, areas known to be related to self and emotion regulation; and the superior longitudinal fasciculus and corpus callosum, areas involved in intra- and inter-hemispherical communication.

Brain regions involved in the components of mindfulness meditation including attention control, emotional regulation, and self-awareness. Source: The Neuroscience of Mindfulness Meditation

When looking into studies on the effects of meditation on emotional regulation:

These studies have reported various positive effects of mindfulness meditation on emotional processing, such as a reduction in emotional interference by unpleasant stimuli (source), decreased physiological reactivity and facilitated return to emotional baseline after response to a stressor film (source), and decreased self-reported difficulties in emotion regulation (source).

There are many studies that reflect the effects of meditation on the brain, both physical and functional, and it is clear that it does have effects, although the exact underlying mechanisms are not completely clear. Some have hypothesized that more controlled reactions to emotions due to meditation stems from a strengthening of synapses in the “prefrontal cognitive control mechanisms,” therefore weakening activity in regions such as the amygdala which usually react to emotions like fear. What’s important is that something happens during meditation that changes the structure of the brain. It changes the way we think and experience life.


The bottom line is that the brain is plastic. Meditation affects the brain’s functionality, structure, and thought patterns. If you take away anything from this article, let it be that the rich synapses only get richer — stop strengthening your negative synapses and start strengthening ones that will improve your life. It can be tempting to indulge in negative emotions, to let them take over… in a strange twisted way, some people crave emotions like sadness, anger or stress. However, each time you indulge in these negative thoughts, you are (literally) strengthening their power over you. On the flip side, letting go of these resistances and undesirable thoughts and feelings makes it easier to let go of them in the future. As Aristotle once said, “we are what we repeatedly do.” We think what we repeatedly think, so repeatedly think of goodness. Meditation is a great jumping off point to take control of your mind and lead a happier, calmer, and more aware life.

To reiterate, this post was in no way meant to be a formal scientific study, more so a reflection of what I’ve learned in both fields, how I make sense of everything I’ve learned, and my hypothesis of how the two fields are twined together. There are surely levels of the story which I have not learned yet (you mean I didn’t conquer the entire field of neuroscience during my one semester in Introduction to Neural Systems I?!?), and I am very open to discussions on this topic and corrections/more complex explanations from those with more expertise in either of these areas.

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