Activating Mindfulness: A Neuroscience Framework

Activating Mindfulness: A Neuroscience Framework

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Understanding Mindfulness: A Neuroscience Framework


How does the concept of mindfulness relate to our physical health? The word “mindfulness” conjures the thoughts in many of us of gurus in the practice of meditation, therapeutic breathing, and yoga poses. Many may have given it some thought, tried these practices, and did not find them sustainable for the average human. However, mindfulness may be understood in a more simplified way with neuroscience:  mindfulness simply is…


Mindfulness and The Heart-Brain Axis

Let us start with biology and explain how intimately connected the neurologic and cardiovascular systems are. Although they develop from different tissues in the embryo (the ectoderm, as does the skin and dentition, for the nervous system; the mesoderm for the cardiovascular system), they developed alongside one another. The main way both systems connect are via the autonomic nervous system, which includes the parasympathetic and sympathetic outflow tracts. This concept has been described as the heart-brain axis.

Extreme examples of the heart-brain axis illustrate the association.  Conditions that occur in the brain may affect the heart, and vice versa. Those who have a heart problem known as atrial fibrillation may develop emboli, or blood clots, that get lodged in the cerebrovascular system, resulting in the brain tissue injury of a stroke.   When there is a profound stress state, such as mediated by the heart, emotional, or structural brain trauma (e.g. traumatic brain injury or brain hemorrhage), heart conditions referred to as neurogenic stress cardiomyopathy and Takotsubo cardiomyopathy may occur.  Takotsubo is sometimes referred to as “broken heart syndrome,” because it can be seen with grieving.  Stroke patients can also develop cardiac injury or arrhythmias (rhythm problems), even without prior heart disease. Heart dysfunction may even be a cause of death in stroke sufferers.  Finally, both brain or heart injuries can cause depression, anxiety, and post-traumatic stress disorder (Chen, 2017).

Beginning in utero, the autonomic nervous system (ANS) begins to be shaped, influenced by factors in the development of the embryo, such as maternal health, stress, and nutrition. These may even be determinants on how this system develops through childhood and the foundation of neuropsychiatric disorders (Mulkey, 2018).

  • The ANS associates with the limbic system in the brain, the center of rewards, emotions, and behaviors. The two divisions of the ANS innervate various organs and evoke a physiological response:  the sympathetic is responsible for “fight or flight” and the parasympathetic is responsible for “rest and digest.”

The limbic system consists of the amygdala, thalamus, fornix, hippocampus, hypothalamus, and cingulate gyrus.  The amygdala is primarily a processor of memory associations, learning, mood, and rewards systems. it is telling to think that the amygdala, a center where prediction of a future reward influences behavior (i.e. the dopaminergic pathway), is also the place that links the brain with physiological responses and emotional circuitry.

Fear triggers a physiologic response of fight or flight, which includes dilated pupils, bronchodilation (opening of airways), and increases in blood pressure and heart rate.

The neuronal system in the brain is activated through neurotransmitters, which lead to intracellular mechanisms that complete a signal.  Each neurotransmitter type activates a specific pathway to achieve a response.  The sympathetic pathway is regulated by neurotransmitters epinephrine and norepinephrine and the hormone cortisol. The brain calculates an experience or expectation of a stressor through memory heuristics, or short-cuts and trigger this pathway. It may be a real threat or a perceived threat, but perceptions are not always accurate.

The parasympathetic branch of the ANS is primarily mediated by the vagus nerve; the limbic centers are the dorsal motor nucleus of the vagus (DMV) and the nucleus ambiguous (NA).

The brain is largely a fluid-structure, and as with many other responses, the two systems work in concert, regulating the extent of the response of one or the other.  The activation of one pathway can lead to changes in both sympathetic and parasympathetic tone. In this way, the brain acts like a muscle, that can increase its neuronal units and connectivity with ongoing use of one pathway. This is the basis of the concept of Hebbs’s theory, or neuroplasticity.  “If it fires, it wires.” (Fox, 2016). It also supports the concept, sometimes referring to muscles,  “use it or lose it.”

The brain may change from chronic stress and fear: the amygdala volume increases, while the other limbic structures such as the hippocampus (responsible for memory and positional sense) and prefrontal cortex decrease in volume. Impaired vagal tone is associated with increased anxiety, depression, or post-traumatic stress disorder (PTSD). Imagine that the amygdala, a center that processes signals promoting fight or flight responses, enhances with stress, leading to more sensitivity. Greater amydalae volume has been found in people with long-term clinical depression. Essentially, the brain grows or adjusts based on the states we are in; someone who is chronically depressed becomes better at being depressed. This can make it especially challenging to change behavioral pathways.


Mindfulness vs Mindlessness 

The terms mindfulness and mindlessness relate to the state of the brain when it is experiencing the present world around it. The mind can either respond vegetatively, i.e. pro-growth, with connectivity and creativity, or quiescently, i.e. pro-survival, with protection and reaction. The brain uses heuristics to forecast the world around it, essentially projecting a reality.  These short-cuts are wired from prior experiences.

Unfortunately, they can mistakenly interpret direct significance, harm, or threat, and cloud the experience of reality. The mindlessness response is born from the “fight or flight” reaction governed by the amygdala and sympathetic nervous system. The mindfulness response results from slowing down the processing and becoming aware of them. It is governed by the pre-frontal cortex and activation of the parasympathetic nervous system. What we consider to be positive or negative qualities is the result of neurotransmitter signals. Have a look at the words in the following and think about examples of both groups in your life. Remember a time in your life where you acted out reflexively, when you felt threatened or unsafe.


Mindfulness vs. Mindlessness

•         Peaceful/Calm/Still •         Tolerant

•         Seeking to understand

•         Relaxed

•         Forgiving

•         Directive/Assertive

•         Restoring/Creative

•         Patient

•         Angry •         Frustrated/Intolerant

•         Offended/Hurt

•         Stressed

•         Begrudging

•         Aversive/Passive

•         Draining/Destructive

•         Impatient


Atrophy, Quiescence, and Growth States of the Brain

There are three phases of the brain: atrophy, quiescence, and growth. Visualize a plant when it receives all the right ingredients, including sunlight, soil ph, nutrients, and water, it will take the step to growth outwardly, resources permitted. It will reach a more quiescent period, when the demand for water, etc is not being met. During this phase, cellular metabolism decreases to a bare minimum, enough to preserve the cells, but not enough to grow further.  After a period of a less ideal environment, such as during colder weather, less sunlight, or a dry season, life cannot persist; parts of the plant are allowed to atrophy to preserve global function.

Likewise, the same occurs within our brains. In many ways, the quiescent phase (static or dormant) is the way the brain reacts in a stressed environment.  It maintains its usual pathways, does not step outside this zone of comfort to learn a new skill or take a chance.  It follows the pathway of least resistance.

When the brain is nourished (and body), providing it rest, exercise, healthy air for oxygen, and healthy food, a chance for growth, learning, creativity exists. It takes positioning yourself toward an area of interest, a hobby, or a new social, or physical opportunity. Growth forges new circuits in the brain; the prior behavioral cycles dampen down, as new circuits are formed.


Is good character, resilience, growth possible after Trauma?

Neurotransmitters, neurohormones, peptide ligands, and hormones provoke changes that occur in our brains and bodies. Is it possible that attributes considered positive, such as courage, patience, compassion, come from an interaction of neurotransmitters that have led to certain behavioral pathways? Most certainly. For instance, perhaps one’s response to dopamine, which leads to craving and movement toward a stimulus may be the difference between impatience and patience.

Some people may have a negative experience, yet overcome it and be stronger after it.  Others may experience a negative pressure and resort to harmful, maladaptive behaviors. Resilience is a pathway that can be developed. It is characterized by a response toward growth and maintenance even after a challenge that perturbs or leads to trauma.


Summary of Mindfulness for Life: The Heart-Brain Axis

  1. The brain interacts with what is taken in by our senses and influences our reality experience.  The reality gets projected out.  All people have different realities, based on memory affecting interpretation.
  2. Just like a visual illusion, our brains can misinterpret sounds, tastes, smells, touches and even words. A sensitivity of this possibility opens dialogue.
  3. The two controlling mechanisms of the internal organisms are the sympathetic and parasympathetic systems. They are triggered by the brain and are actuated by hormones which induce a response to the internal organism, amounting to “high alert” vs “relax.”
  4. The driving force of our thoughts and decisions relate to moving toward pleasure or reduced pain and moving away from pain or reduced pleasure. Occasionally, these lines can get crossed – and we move toward pain and away from pleasure.


Mindfulness Strategies 

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  1. Any movement of the body or practice with the senses in a directed, positive way can be used to restore the body into a more relaxed state. Examples include massage (touch), aromatherapy (smell), music (auditory), art (visual-auditory-kinesthetic), other hobbies, and movement exercises (Tai chi, yoga, exercise, walking/jogging).


  1. For daily brain conditioning: Meditation, adequate sleep and breathing techniques can be used to tone down the sympathetic signaling.


  1. In the heat of the moment: After sensing “high alert” in the interpretation of words or actions, consider pausing the initial response.  Understand an action or statement comes from another person who themselves has had experiences that effectively influenced their communication or actions. Techniques that slow the sudden response, such as breathing, asking questions or staying calm, can help you break free of narrative tangles and escalation that shut off reasoning.  Consider these “mindfulness instances.”


Mindfulness Key Elements

  1. Neurons that “fire together, wire together.” (Hebb’s theory)

The more you get into the practice of forming new behaviors, the more likely they will become the routine thoughts. Even simply developing a concept in your mind of an intended behavior change can get you on the start to making it happen. After the behavior has been executed several times, it becomes the preferred pathway for the brain.


  1. Life is experienced from the inside-out. (Perception is our reality)

We feel and then we think.  Be aware of the motivations that affect your decisions and slow down the stage of acting on the thought processes to ensure that the response is not just a reflex of an emotional heuristic.


  1. Reflex thoughts or “gut instincts” can narrow our brain’s “eye” for protection but can limit our understanding of reality and lead to injury – to self and others. (Pattern thinking)


We have biases that can limit our objective interpretability and trap us into cyclical reactive behavior. It is often a very simple concept, such as feeling loved and fear of being abandoned. Remember that your brain started to become more efficient even before you were able to speak.  Learn what yours might be.


  1. Small changes begin with the understanding of altered judgement based on bias, including the fears that guide our decisions away or toward things. The brain has a method to preserve its efficiency.  Growth can be a painful experience.  The brain may hold you back from this, favoring the prior patterns even if they are not as healthy. Creative generativity develops after breaking away from instinctual behavioral cycles and leads to freedom in the moment.



Mindfulness does not need to be a cerebral concept: It can be physical too. Photo by meo on


Here is a Conference on Mindfulness




Fox K, Stryker M.  Integrating Hebbian and homeostatic plasticity: introduction.  Philos Trans R Soc Lond B Biol Sci. 2017 Mar 5; 372.

Mulkey S, du Plessis AJ. Autonomic nervous system development and its impact on neuropsychiatric outcome. Pediatric Research. 85, 120-126(2019).

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