I shared a blank map of the United States with adults on retreat. They could identify the states I pointed to and describe the weather and topography of places they had never visited and would likely never visit. They could imagine colder temperatures, pine forests, and glaciers in Alaska, for example, or volcanoes, wild hibiscus, and warm beaches in Hawaii. I then showed a blank map of the brain and pointed to different regions. No one could name a hub or region or describe their primary functions.
I pointed out the obvious. Their brains were rendering the photos of light into images and converting the sound waves into sound. Insights and understanding were arising in their brains. Their brains were coordinating other processes in that instant- regulating heart beat and body temperature, ph and electrolyte balance, metabolism, digestion, synthesizing proteins, destroying pathogens, repairing wounds, following circadian rhythms, releasing hormones neuromodulators, and neurotransmitters.
The mind, itself is an epiphenomenon of these processes. Mind colors moods, marshals thoughts, reasons, records memories, influences perceptions, directs behavior, defines who we think we are and orchestrates our very lives; it is the one thing worth attending to.
These activities are governed by highly specialized yet intricately integrated neural circuits composed of many cell types with diverse molecular, anatomical and physiological properties (Yao et al., 2023). Yet, we know so little about our own brains or minds. Even educated educators can recall meaningless trivia from memory but know little about, say, the function of memory (eg., short-term, long-term, episodic, working and motor memory), neuroplasticity and learning (e.g., formation and consolidation), or the science of attention (ie, the alerting system, the orienting system, and the executive attentional system (Posner & Petersen, 1990, 2012)).
Most of the content on this site references scientific research in an attempt to understand how this brain and body work. Learning facts is one thing, experiential learning and self-discovery is another. Both are useful for insight.
Meditation is one way to turn attention inward- to learn from experience and observation. The contemplative traditions have over 3 thousand years of records on the inner workings of mind. It's not the only way and not for everyone, but is my preferred training. Neuroscience, a relatively new field, provides empirical data that informs practice.
Here's what we know. The brain is a solid 3 pound organ that has the texture of soft tofu. The mind is its construct and has no form or weight or self. Whether what we call the self is localized or not is a subject of debate. The self itself is a construction that is influenced by the spin of sub atomic particles and the composition of macromolecules, electro-chemical signals, neurotransmitters and neuropeptides, neuronal and non-neuronal cell classes (like glia and astrocytes), subclasses, and thousands of individual cell clusters that facilitate processes which arise and pass away.
Electrically charged calcium ions flow through channels that move these signals across the brain cells. The brain uses the power of electrical voltages just as computers do to carry out various operations. In computers, electrons flow through intersections called transistors. In neurons, the signal is in the form of a wave of opening and closing channels that exchange charged particles such as sodium, chloride, and potassium. This pulse of flowing ions is called an action potential. Instead of transistors, neurons manage these messages chemically at the end of branches called dendrites. Dendrites determine the computational power of single neurons. Dendrites are the traffic lights of our nervous system. If an action potential is significant enough, it can be passed on to other nerves, which can block or pass on the message.
Voltage can be communicated in two forms: either an AND message (if x and y are triggered, the message is passed on); or an OR message (if x or y is triggered, the message is passed on). In addition to the logical AND and OR-type functions, these individual neurons could act as exclusive OR (XOR) intersections, which only permit a signal when another signal is graded in a particular fashion. How this logic squeezes into a single nerve cell and how these operations translate into higher functions remain a question.
Neurotransmitters are released. These chemical messengers pass through the synaptic cleft to a downstream nerve cell and transmit information. A protein called Asc1/CD98hc in the membrane of neurons acts as a gate that opens and closes. It acts as a specific transporter for certain key amino acids for learning and memory. The ASC1 protein is found mainly in neurons of the hippocampus and cerebral cortex in the brain. It specializes in moving two key amino acids (D-serine and glycine) into or out of the neuron for the neural connections involved in learning, memory and brain plasticity (Rullo-Tubau et al, 2024).
You can read these lines, reflect, scroll, sit, and do countless other things in this moment because of the arisings and passings of electrochemical messages. But there may be ways other than firing by which neurons could communicate, including the little-known mechanism known as the ephaptic field effect. “Ephaptic” simply means “touching.” Though not well-known, ephaptic field effects result from the electric and magnetic interactions that power our cells. Information travels much faster from ephaptic fields than from synaptic firing. A recent paper suggests that ephaptic field effects, rather than neural firing, may be the primary mechanism for consciousness and the cognition that emerges from it.
It is all so extraordinarily wondrous to this me-construct.
This me-construct is functional. It says "I" and uses possessives like "me." It has likes and dislikes, a list of accomplishments, memories, skills, and opinions. It emotes; it feels. It was assigned a name at birth- Jonathan- and a given family name- Felix. But none of the trillions of atoms that make up this frame are Jonathan and nowhere in the network of neurons or structures is there a Felix. The leptons, photons, quarks and subatomic particles that make up the atoms that make up the ions and molecules that make up the nucleotides that make up the macromolecules that make up the amino acids and proteins and organelles that make up the cells that make up the organs and bones and ligaments and systems that make up Jonathan have their own knowing.
Using advanced multimodal MRI techniques, researchers have mapped connections among the brainstem, thalamus, and cortex, forming what they call the “default ascending arousal network,” which is a proxy what what this "I" construct experiences as consciousness (Edlow et al., 2024).
I marvel at this native intelligence. DNA and RNA build proteins. A well written code guides the binding of those proteins with lipids to form membranes that wrap around all cells and cell components (Kervin et al., 2024). There is no Jonathan in this unfolding. This imagined "I" self is a useful construct all the same. Calling Jonathan an "it" or I-construct is confusing to most readers, so we follow the most superficial of conventions. My name is Jonathan, what's your name? And we take it from there.
We ask one another introductory questions or comment on this or that: "What do you do for a living?" "It's cold outside" "Did you watch last night's game?"
The brain translates thought to speech. The brain also coordinates the muscles of the tongue, lips, jaws, and throat to produce discrete units of sound- /p/, /d/, /ch/, etc- that ride on the exhalation. Whether what crosses the barrier of the teeth is wise or stupid, deep or shallow, how we speak is wondrous.
As you speak, I listen. Sound waves travel through the medium of air and enter the outer ear. These waves travel through the ear canal to the eardrum. The eardrum vibrates and sends these vibrations to three tiny bones in the middle ear: the malleus, incus, and stapes.
The bones in the middle ear amplify, or increase, the sound vibrations and send them to the cochlea, a snail-shaped structure filled with fluid, in the inner ear. Once the vibrations cause the fluid inside the cochlea to ripple, a traveling wave forms along the basilar membrane, an elastic partition that runs from the beginning to the end of the cochlea. Hair cells—sensory cells sitting on top of the basilar membrane—ride the wave. Hair cells near the wide end of the snail-shaped cochlea detect higher-pitched sounds, such as a sparrow chirping outside my window. Those closer to the center detect lower-pitched sounds, like the kick of a bass drum thumping out of the speakers of a car passing by. As the hair cells move up and down, microscopic hair-like projections (known as stereocilia) that sit on top of the hair cells bump against an overlying structure and bend, causing pore-like channels at the tips of the stereocilia to open up. When that happens, chemicals rush into the cells, creating an electrical signal. The auditory nerve carries this electrical signal to the brain. Sounds are time stamped with how much time has gone by since it entered the ear. This allows the listener to know both the order and the identity of the sounds that someone is saying to correctly figure out what words the person is saying.
The brain analyzes auditory inputs. Auditory signals are relayed to multiple regions within the brain. As signals travel "bottom-up" from the ear to the auditory centers, a "top-down" movement also occurs: the brain sends down signals to instruct the hearing faculties as to which inputs to focus on, which sounds to ignore, etc. As you speak, there may be other sounds entering the ear- a dog barking in the distance, a Carolina wren singing on the branch of a tree outside your window, an air conditioner humming, etc. The higher regions can tell whether these sounds are new or familiar, threatening or neutral, and whether they deserve attention or not.
As we listen and focus on this or that sound, the left hemisphere of the superior temporal gyrus in the auditory cortex, the frontal gyrus, superior parietal sulcus and intraparietal sulcus process the sounds. This ability to shift and control attention allows us to simultaneously attend to selective sounds and filter out the rest as noise. Both the target stream (the more important information being attended to) and competing/interfering streams are processed in the same pathway within the left hemisphere. But target streams are treated with more attention than competing streams (Evans, et al, 2015).
It is all so elegant and beautiful. Neurons in the auditory cortex alert us when something doesn't sound right- a subtle shift in tone, a response that is garbled, a non-sequitur that doesn't fit. For example, I ask you how you're doing and you say: "Broccoli" (non-sequitur) or you say "Fine!" but the tone and frown say otherwise.
The brain registers whether a sound matches or deviates from expectations. The brain is able to make precise predictions about when a sound is supposed to happen and what it should sound like. If I ask what you do for a living, I'm expecting a job description or title- nothing else. Neurons respond vigorously when what is heard violates expectations.
Then there is internal chatter. If the brain is bored, stressed or restless, the internal dialogue may arrest my attention. I may not be listening to a word you're saying.
As you speak, I see. Light falls. It reflects off objects and enters the eyes. The retina converts photons of light into electrical impulses that travel the optic nerves. The brain alchemizes these rivers of light into sight.
If the human eye were a camera, it would have over 500 megapixels. By comparison, the top digital cameras have between 102-200 megapixels. The eye processes thousands of bits of information moment by moment. The human eye is the only multi-focus lens in the world which can adjust in milliseconds. I am hardly aware of the muscles that dilate or constrict the pupils of the eye or the muscles around the eye that move the eyeballs from side to side. There are millions of receptors within the eye that detect light and color. I am aware of the empty space between me and the objects my eyes rest upon. Like a camera lens, the pupils contract and dilate, adjusting depth of field… with just a thought.
90% of the connections coming into the visual cortex carry predictions from neurons in other parts of the cortex. Only a fraction of what we "see" is raw, visual input. What we see is filtered with predictions, evaluations, memory, identification, language from other parts of the mind. In other words, we co-create what we see.
Many of the neurons that render sight are encased in the skull and have no direct access to the light of the external world. Yet they manufacture meaning and from perception comes decision and from decision comes action.
Within the brain is a "filter" that directs attention toward important external events and internal thoughts, and a "predictor" composed of pathways that anticipate rewards. These systems connect to regions that process sensory data. The predictive system is partially mediated by the the ventral striatum, a small brain region, associated brain pathways driven by the neurotransmitter dopamine. Dopamine plays an important role in predicting what will be rewarding or important and drives motivation or seeking behaviors. The salience network is part of the brain's filtering system. The salience network selectively directs our attention to important internal thoughts and external events. When the salience network is active, we can dismiss irrational thoughts and unimportant events and focus on what's real and meaningful to us- from paying attention to the car in front of us whilst driving to cutting mental elaborations whilst sitting on the meditation cushion.
The visual cortex, which primarily processes visual data, sends signals to the executive area- the prefrontal cortex- that encodes our decision to carry out certain actions, for example (Franch, et al., 2024).
What we "see" is often distorted. In a recent study published in the apex journal Nature, researchers found that visual perception at the retinal level changes to maximize personal advantage. Our cognitive biases are not just inaccurate judgments, but play an integral role in how we behave. For example, we often judge people by appearances and treat them according to our biases and calculations.
Our judgments and behavior are largely conditioned by past experiences which pull from memory. The brain has enough memory to store the entire content of the internet and is more powerful than any existing computer. But its outputs are hardly as linear or rational.
All memories arise now, in this present moment, and there is only ever this present moment. We pull from memory NOW to make sense of the present moment and to predict what follows. If I ask you your name, I'm waiting for your mouth to return a sound by which you can be identified and known. If I asked for your name, I would expect a response like "Mark" or "Sally." If you said "Kenji" or "Juanita" the brain would translate those less familiar sounds and save them into the name category. If I ask: "What is your name?" I wouldn't expect "Peanut butter and jelly sandwich on rye" or "The square root of 420,489." The brain would return a prediction error response. If your answer was not what I was expecting, this might trigger laughter... or threat. I may think you're interesting... or crazy. Whether I think you're funny or insane would depend on context. Comedians and pick-up artists alike violate norms and expectations to provoke laughter or interest. They use language, nuance, timing, and affect with a degree of skill, social intelligence and confidence.
As we get to know one another, we might speak of past accomplishments or experiences: "Oh, you lived in Hawaii? What part? I was surfing in Honolulu last summer."
What we call "the past" are packets of limited information stored in brain cells retrieved in the present. Memory encoding cells, or memory 'engrams,' are distributed across the brain. They are a kind of "time cell." (Umbach et al., 2020). Specialized brain cells stamp and temporally track time. Temporally periodic cells (TPCs) exhibit unique periodic behavior across time scales, potentially providing metrics for both time and space in the brain.
Many time cells are stored in the hippocampal and amygdala regions, as well as thalamic, cortical, midbrain and brainstem structures. The hippocampus plays a major role in learning and memory. The amygdala colors memories with emotion- affectively influencing memories. The thalamus processes and routes memories to the cortex. And the cortex creates meaning from memory. Memory storage in the brain may also reside in the lipid bilayer of neuronal membranes (Katsaras et al., 2023).
Memories are not static snapshots of past experiences; they are often distorted and colored by emotion. Memories decay over time.
As we talk, our brains are evaluating, judging, making predictions. As our lips move, the brain is deciding "Do I like this person?" "Do I trust this person?" "Am I interested in holding this conversation?"
The brain is a collection of functional modules (Bertolero, 2015), a connectome of neural networks that help us process data from sense organs (sight, sound, touch, smell, taste), sense detectors/receptors (temperature, pain, pressure, contraction, etc). I may have a visceral reaction to what you say or how you say it.
The adult brain contains an estimated 86 billion neurons and another 80 billion non-neuronal structures including glia, a class of brain cells that provide structural support, nutrients and insulation to neurons while also regulating how they send signals. Scientists have identified over 3,300 different brain cell types: mirror neurons, Purkinje cells, granule cells, von Economo neurons, stellate cells, fast spiking interneurons, Golgi cells, pyramidal cells, retinal ganglion cells, and parvalbumin-expressing GABAergic interneurons to name just a few (Masland, 2004).
A single neuron is very small—only 10 to 100 micrometers—and when it fires, its action potential (the spike in electrical activity) only lasts about two milliseconds. Each of 86 billion neurons has its own electrical firing pattern. Groups of neurons with similar patterns generate oscillations of electrical activity, or brain waves, which can have different frequencies. There are six brain layers with distinct patterns of electrical activity. In the topmost layers, neuronal activity is dominated by rapid oscillations known as gamma waves. In the deeper layers, slower oscillations called alpha and beta waves predominate (Mendoza-Halliday et al., 2024). All six layers of the neocortex contribute to the processing of sensory information (Huang et al., 2023).
Layer 1 is packed with long branches of apical neurons which play a key role in perception. Neurons in the deepest layer- layer 6b, appear to influence the sleep-wakefulness cycle by connecting to and supporting activity in the thalamocortical system. This system has a strong effect on cortical state and is associated with wakefulness, sleep, cognition, attention, and perception. The higher order thalamocortical system is one of the most important systems in the brain. Its axons communicate with neurons throughout the cortex, as well as the deepest regions (Zolnick et al., 2023) .
The brain generates electrical activity to represent 'reality.' During that process of neural representation, the brain encodes sensory information and thoughts into models.
Our moods are influenced by neural representation. Changes of neural representations and brain states impact mood fluctuations over time. These representations are constructs and can be deconstructed.
We experience this complex orchestration of information flows as thinking. The prefrontal cortex acts as a 'simulator,' mentally testing out possibilities using a cognitive map stored in the hippocampus (Jensen, Hennequin & Mattar, 2024). The brain processes all of this complexity in milliseconds as thought. Our thoughts and moods are influenced by neural representation. These thoughts form part of the super-complex we call ego, the little self.
Interestingly, even if the brain is compromised, it can create an identity- a self. In 2007, a 44 year old French man was diagnosed with hydrocephalus- 90% of the man's skull was full of liquid; only a thin layer of brain tissue remained. The few neurons he did have were still able to generate a theory about themselves. The man was conscious of his actions. He was a father of 2 and worked for the government. Cognitive psychologist Axel Cleeremans explained: “He was living a normal life. He has a family. He works. His IQ was tested at the time of his complaint. This came out to be 84, which is slightly below the normal range."
The seeming "I" self that types sits in wonder of it all- in a blissful state beyond joy- even as it types and thinks and turns attention back in on itself to marvel and celebrate this precious moment of being. This seeming self I often called the little self has been a good custodian of the life it was gifted and, in deep gratitude to the Mystery that gave it, continues its investigations and exploration with a deep reverence and child-like wonder that was never lost.
The little self organized itself to study and understand that from which it derives its light and sustenance. It reads research with the same humility and hunger of a rabbi, priest, or imam reading from a Holy Book and seeks to understand the workings of the Holy One conjured by mind. The Holy Temple is this body, this light, this life; the Holy Book is this brain, this mind. Religion is a short-hand way of worshipping this intelligence and an attempt to make sense of the complexity that is me.
So let us turn to chapter 1, verse 1: "In the beginning..."
In the beginning was a single fertilized egg. Within this single cell are 46 chromosomes, 23 from the father and 23 from the mother. This single cell has its own intelligence, its own knowing. Within it is a blueprint. It self-generates. Every cell has an identical set of instructions- 3.2 million letters from your mother and 3.2 from your father. These letters make up our genome and DNA.
There are about 63,000 genes in the human genome, all composed of DNA. 43,000 are transcribed to non-protein-coding RNAs (ncRNAs) that serve a variety of regulatory functions. The genome also codes for about 20,000 protein types, the building blocks of life. Antibodies, enzymes, structural collagen, hormones, transport ATP, and contractile monocytes are types of proteins.
The Nr5a2 protein regulates zygotic genome activation in 2-cell embryos. Nr5a2 is required for progression beyond the 2-cell stage (Tachibana, et al, 2022). Kdm1a plays a role in preserving the identities of cells once they've been differentiated and assigned a role (del Blanco et al., 2024).
Different cell types emerge from a single genome. Organizer cells instruct the fates and morphogenesis of surrounding cells, steering their development into specific tissues and organs (Arias and Steventon, 2018). Each cell contains about 40 million proteins that perform all the tasks the cell needs to function and replicate. The PLK-1 protein, for example, regulates cell division (Barbieri, et al, 2022). Specific proteins must be concentrated in specific amounts, at specific times, and at specific locations. Such a delicate distribution requires extreme precision and intelligence.
Another protein, called Cachd1, plays a crucial role in establishing the distinct neural wiring and functions on each side of the brain. The left and right hemispheres of the human brain have functional differences that influence neural connections and cognitive processes like language. Cachd1 may influence this asymmetry (Powell et al., 2024).
From one microscopic speck grows 206 bones made of calcium, 32 teeth of enamel and cementum, high elastin fibers and collagen bundles to make up the cartilage of the ear and nose. The single cell goes on to produce gases like carbon dioxide and nitric oxide, liquids like tears and saliva and solids like bone and ligaments. That single cell goes on to make 21.5 square feet (2m/sq) of skin that senses and repels and protects, 8 yards (7.5m) of intestines, lungs, one slightly smaller than the other to accommodate a heart. It grows you in your mother's womb and knows when to stop growing.
The brain is a masterpiece of this Intelligence. An embryonic neural tube mushrooms into a brain with more than 80 billion interconnected neurons. Epiregulin, a growth factor, promotes the division and expansion of stem cells in the developing brain. While still in utero, neurons in the developing central nervous system and brain congregate in layers, or neighborhoods, fitting into an alignment that will dictate their function. Adhesion molecules grab onto neurons which are pulled into a specific layer or neighborhood and are "zippered" into place (Sengupta et al, 2021). The developing fetal brain grows, on average, about 250,000 nerve cells per minute. In order to move, brain cells exert pushing and pulling forces on their surroundings. During brain development, growth cones at the tip of advancing axons pull themselves and their axons. Axons can also push their way through the tissue. Mechanical forces that lead to cortical folding (Pillai & Franze, 2023).
All of this knowing and more complexity that scientists are only beginning to understand is contained in that one single cell.
From the very first weeks of life, countless connections are forged between neurons as tracks are laid down in a rail network. Signals will travel along this neural infrastructure. These connections gradually shape the final architecture of the brain, known as the connectome. Our ability to perform complex cognitive tasks rests on its structure (Dichio et al., 2024).
A fully mature brain processes millions of bits of information per second and has a memory capacity of 2.5 petabytes. A “petabyte” is equivalent to a million gigabytes, or about 4.7 billion books of memory. Yet it consumes the same amount of energy as a 12 watt lightbulb. The brain devotes between 40-50% of a cell's effort to an individual task.
The remaining effort is dedicated to scalable teamwork. Cells work together to build larger, coordinated networks, creating an organization with each fractal-like scale mirroring those above and below. This fractal hierarchy optimizes information flow across the brain, allowing it to adapt to change (Munn et al., 2024). This may be a fundamental design principle as this same organizational structure is also found in fruit flies, nematodes, zebrafish, mice and monkeys.
Not only do brains use just a few watts of power, they need very little data to succeed. Artificial intelligence, by contrast, currently uses multiple kilowatts of power and needs billions of parameters to "learn" and generate results.
Even seemingly simple tasks are wondrously complex. As I type, for example, the press of the press of the keys sends ripples of activity across neurons spanning the entire brain (Swann, et al, 2023). Even neurons and regions previously not thought to be movement related are active. The wrist pitches and yaws. The delicate muscles of the hand contract and extend. My fingers press the keys that will print out the letters that will make the words that I’ll string into paragraphs to express the wonder that is in my heart. The brain orchestrates these movements. It initiates a plan before initiating and executing a movement, tracking it through completion. Interestingly, brain signals predictive of movement are also active. The brain perceives and selects a course of action and anticipates where a future body-orientation once the arc of a movement is complete (Shioiri, 2023). The intention to type and the typing itself run along two different pathways. My brain has woven strings of thoughts together to form words that make paragraphs, and, step-wise, the thoughts precede the movements of the fingers. My fingers cannot type at the speed of thought, and thought, itself, is slower than the speed of intention. The speed of thought ranges from 500 milliseconds to 3.3 seconds. Less than 200 milliseconds is the domain of intention. I type about 1.1 words per second. Intention drives thoughts; thoughts drive action.
Like intention, the sensory system, too, processes data faster than thought. The beautiful brains at Caltech quantified the speed of human thought: a rate of 10 bits per second. However, our bodies' sensory systems gather data about our environments at a rate of a billion bits per second, which is 100 million times faster than our thought processes (Meister & Zheng, 2024).
I can sense the smoothness of the keys through my fingertips. Lots of nerve endings there. In one square inch of hand, we have nine feet of blood vessels, 600 pain sensors, 9000 nerve endings, 36 heat sensors and 75 pressure sensors.
The hands are wondrous. A disproportionate share of the brain’s motor cortex is dedicated to the muscles of the hand. With our hands, we draw, build, push, paint, pull, wipe, cook, carry, catch, throw, tear, fold, grab, brush… scroll down.
As I reach for a cup of tea, the brain calculates. It sees where the cup is. The brain then has to process this information internally to coordinate the activity of the muscles and perform the movement. I program robots, but the brain simply coordinates the x, y, and z axeses of the joints, calculates the tensile strength needed to raise the cup of tea, coordinates the lips, and stops the breath while I ingest and swallow.
Control over the simple mechanics of walking or running is also complex. The mesencephalic locomotor region (MLR) of the brain sends signals to neurons in the spinal cord, which send inhibitory or excitatory impulses to motor neurons governing muscles in the leg: Stop. Go. Stop. Go. Each signal is a spike of electrical activity generated by the sets of neurons firing.
When goals are introduced, such as when a soccer player wants to run to an exact spot on the field or a running back wants to stop and pivot to intercept a catch, the brain translates a goal (stop running) into a precisely timed signal that tells the mesencephalic locomotor region to hit the brakes?
The brain performs a bit of calculus, allowing a player to anticipate and predict. If I know the derivative, the rate of change of velocity, then I can predict what my velocity will be at the next step. If I know I have to stop, I can plan for it and make it happen.
Yet, it all seems so effortless- walking, running, catching a ball. How do millions of neurons perform such complex tasks (neural activity, behavior, inputs/outputs) so effortlessly?
Paying attention to these blessings is a gift we give ourselves.
This genius is native to each of us. It is indifferent to whatever illusions you have about your intelligence or worth. Indeed, your very intelligence is a gift of that Intelligence which predates it. Before the brain conjured its first thought, there was Intelligence. Before we were assigned a name, a nationality, or an ethnicity, there was Intelligence.
The brain is made up of the telencephalon (also known as the cerebral hemispheres), diencephalon (which gives rise to anterior forebrain structures), mesencephalon (also known as midbrain) and rhombencephalon (also known as hindbrain). The telencephalon consists of five major brain structures: isocortex, hippocampal formation, olfactory areas, cortical subplate and cerebral nuclei. The first four brain structures—isocortex, hippocampal formation, olfactory areas and cortical subplate—make up the cerebral cortex. The diencephalon consists of the thalamus, hypothalamus, posterior portion of the pituitary gland, and the pineal gland. The telencephalon and diencephalon are also collectively referred to as the forebrain. The hindbrain is divided into pons, the medulla and the cerebellum.
The structure and function of this or that brain hub- the amygdala, the cerebellum, the anterior mid-cingulate cortex, etc- depend on the distribution and arrangement of neurons. The distribution of neuron densities influences network connectivity. While the statistical distributions of neuron densities are largely unknown, they appear to follow a distinct mathematical pattern called lognormal distribution. A lognormal distribution is a natural result of processes that multiply. The way the brain is structured could be the byproduct of development in utero and evolution and adaptation to the environment (Morales-Gregorio, van Meegen & van Albada, 2023).
Within each of these major brain structures, there are multiple regions and subregions, each comprising many cell types. Pyramidal neurons, for example, pass low levels details (e.g. line, color, shape, contrast, etc.) along to larger neurons which are passed along to larger neurons. The brain layers the data (auditory, visual, tactile, etc) with more abstract and compressed packets of information (e.g. a valence: good or bad; perceived threat level; reward probabilities, etc). As information is passed along from lower to higher centers of the brain, there is more convergence- a process neuroscientist Lisa Feldman-Barrett likens to "summaries of summaries of summaries."
These briefs are sent to the executive office of the brain for evaluation, interpretation and response. Each "voice" may have originated in a different region of the brain, following its own path until it arrives in conscious awareness.
These interactions are dynamic. Whether paying attention or mind wandering, walking or lying down, playing an instrument or fading out the din of traffic, brains switch states depending on the task. Neurons gate and calibrate information flows throughout the brain. Interestingly, the data seem to suggest that some decisions may have already been rendered before arriving at the executive's desk. The body may pre-empt conscious choice. Visceral and physiological changes (e.g. blood pressure, heart rate, breath) precede rational thought and influence choices. The brain is predictive and filters these packets with memory. "Last time we experienced this (sensation), this is what happened next."
Signals may be processed this way or that (e.g. my voice or the content of my speech may trigger frustration, boredom, or other emotion in you, but bring joy to another). Each neural pattern triggers different physiological states which express as emotion.
Many emotions have biochemical substrates and unique functional brain connectivity patterns. Different brain regions are involved in processing different emotions (Fang, Liu, 2022). Whatever decision we ultimately make, signals will be routed this way or that; connections will become more robust or weaker. Indeed, the mind operates more like a "we" than an "I." It's as if there were sub-minds rather than one unified "I." Although the brain is an integrated organ, "I contain multitudes," as the poet Walt Whitman wrote.
At the experiential level, we may experience these sub-minds as parts. One part, for example, may trigger a donut craving. Pulses of dopaminergic neurons may travel from the ventral tegmental area and project to different parts of the brain causing feelings of craving. The man thinks, "I want a donut." But he's on day 5 of a no-sugar challenge. Another part resists. The infralimbic cortex sends a “no-go” signal. Subtle structural changes in the prefrontal cortex may induce inhibitory control. The man thinks, "I want a donut, but I want to quit my addiction to sugar even more."
Interestingly, dopamine pulse fluctuations have been detected in three different striatal subregions. One area involves motor control. Dopamine fluctuates frequently, and the response to a reward-predictive cue is strong only if it predicts reward delivery within a fraction of a second. A second striatal area processes rewards within tens of seconds, and a third about hundreds of seconds. Researchers think there may be a continuous gradient of reward prediction time scales, involving parallel circuits within the brain, such that the brain may judge an immediate gratification with some regret minutes or hours later.
The different striatal subregions could explain previously reported experimental observations recording different dopamine signals. In addition, the existence of different reward prediction time scales could underpin some of the complex and apparently incoherent behaviors we perform (Mohebi et al., 2024).
The posterior parietal cortex is an integrative hub. The posterior parietal cortex receives and processes sense data to help animals make decisions. Connections between groups of neurons may help sculpt decisions made by one "part" by shutting down neural pathways offering alternative options (Kuan et al., 2024). Excitatory neurons activate other brain cells. Inhibitory neurons suppress other brain cells. Specific sets of excitatory neurons fire when we decide on one decision; these neurons activate a set of inhibitory neurons that curbed activity in neurons that might trigger a different course of action.
We can over-ride, re-route and/or strengthen signals- for better or for worse. The good is one thing and the pleasant is another. You’ll find this truth in ancient texts… and in scientific lectures.
“The good and the pleasurable are two different things," wrote the author of the Katha Upanishad in the 5th century, BCE. "They motivate a person to pursue two different goals. The one who embraces the good meets with auspiciousness. But the one who embraces pleasure is lost.”
Understanding how the brain seeks to balance pleasure and pain is vital to our well-being. Pain and pleasure are processed in the same area of the brain. The ability to recognize and respond to potential rewards or punishments depends in part on a part of the brain called the ventral pallidum. The balance between signals that either inhibit or excite neurons in the ventral pallidum appears critical in controlling motivation.
The neuromodulator dopamine modulates our subjective experiences of pleasure and pain. Dopamine amplifies the activity of brain circuits associated with pursuing goals, motivation & reward. When dopamine levels rise above baseline, we experience pleasure. When they fall below baseline levels, we experience them subjectively as pain. Pleasure often gives way to pain, and pain to pleasure.
Dopamine does not act alone. A brain protein found in astrocytes called vesicular nucleotide transporter (Vnut) appears to play an essential for regulating mood and motivation. When Vnut was removed from brain cells in mice, they displayed higher anxiety, depression-like behavior, and decreased motivation. This effect was linked to reduced dopamine (Huang et al., 2024).
Like dopamine, the neurotransmitter GABA (gamma-Aminobutyric acid) also seems to play a role in reward seeking. Neurons that use the neurotransmitter glutamate to excite brain circuits appear essential for avoiding punishment. Both dopamine, GABA, and glutamate respond when we're presented with the potential for both punishment and reward: high blood sugar (punishment) vs a donut (reward).
Inhibition may offset the constant stimulation we seek, resetting the pleasure-pain balance. We strengthen the neural networks that promote inhibition and non-reactivity- the stop-brain. This is a path to self-mastery, and it gives us some degree of control over our dopamine schedules, such that when it is time to pursue a goal- we can throttle the go-brain... but stop when we need to stop. This is self-discipline.
It is misguided to think the pursuit of pleasure and the avoidance of pain will bring happiness. I have found the opposite to be true: pain and discomfort and struggle can be the path to peace and joy and strength, while the pursuit of pleasure often leads to numbness, dissatisfaction, distraction, and dissipation. This is ancient wisdom. The 13th century Persian poet wrote:
"Be warned, intoxicated lover. You are unaware that you are on the edge of the roof. Disaster may come suddenly. You may not see the edge, but the Spirit does, and fears that your unawareness signals the start of your descent. All sudden shocks, calamities, and deaths occur on the roof of enjoyment."
There is a Zen quote that says: "The search for happiness is one of the chief sources of unhappiness."
The man with the donut craving will experience conflict. There will be multiple voices vying for attention. Attention creates reality. "What we focus on expands," author Wayne Dyer wrote. Each of these seeming selves, or voices, has its own identity (in a sense), priorities and direction.
There is far more information in our environment than the brain can fully process. The attention system is like a flashlight. Attention allows us to select, filter, and direct our brain’s computational resources to a smaller subset of the information.
Attention wanders. Attention is not steady. Attention filters and distorts. Attention is regulated by emotions and habits. Sleep, exercise, and diet affect attention, memory, mood, cognition, well-being.
The brain is not an island unto itself. Our gut has its own nervous system, sometimes called the enteric brain. The entire digestive tract is lined by a vast network of millions of neurons and glial cells called the enteric nervous system. It has over 100 million neurons and 35 neurotransmitters. It contains as many nerve cells as your spinal cord.
Our bodies are also home to trillions of bacteria. They outnumber our own cells 10 to 1. They’re spread across the digestive system. Most live in the intestines and colon, commonly called the gut. This community of gut bacteria is called the microbiome. The gut microbiome not only regulates digestion, vitamin supplementation and metabolism, but affects brain function, neural development, immune function, pain perception, and mental health. Gut microbes communicate with the brain using three primary channels: the nervous system, the immune system, and the endocrine system.
The foods we eat affect the milieu of our gut flora. This microbiome plays a vital role in both our physical and mental well-being. 95% of the information received in the gut goes to the brain; it’s not the other way around. What we eat, in other words, affects our concentration, energy levels, and moods for better or for worse.
The microbes in our guts produce neurotransmitters identical to those that our brains use to communicate from one cell to another and to their host. The neurotransmitters include dopamine and serotonin, two of the most important chemicals involved in regulating mood, attention, and behavior. Too much or too little of these neuromodulators can quickly alter your mood for better or worse.
Gut microbes communicate with the brain through several routes, for example, by producing metabolites, such as short-chain fatty acids and peptidoglycans, neurotransmitters, such as gamma-aminobutyric acid and histamine, and compounds that modulate the immune system.
Gut bacteria produce neurochemicals that the brain uses to regulate physiological and mental processes which affect learning, memory, mood, and by extension behavior. 90 percent of the neurotransmitter serotonin, for example, is produced in the gut. Serotonin, sometimes called the calm molecule, influences both mood and gastrointestinal activity. When serotonin levels are elevated, we feel a sense of contentment and calm. Serotonin inhibits the amygdala, which plays a role in threat detection. The serotonin secreted in the raphe nuclei of the brain modulates mood. But how well it performs in the brain is impacted by what happens in the gut.
Researchers at Brigham and Women's Hospital linked bacteria in our gut to positive emotions like happiness and hopefulness as well as improved emotional regulation (Kubzansky, et al., 2023). People who reported greater contentment had lower levels of Firmicutes bacterium CAG 94 and Ruminococcaceae bacterium D16. By contrast, those who reported more distressing emotional episodes had more of these bacteria.
The gut microbiome appears to play a role in temperature regulation. Temperature gives us important information about the body's inflammatory and metabolic state. It also plays a key role in the stress response.
The term “stress,” originally introduced by Selye (1956), refers to a challenge or stimulus, psychological or physical in nature, that threatens (or that is perceived to threaten) the self. A stressor is anything that triggers a physiological response: increased heart rate, rapid breathing, muscle tension, etc. Stressors can be “real” (e.g. a fire in your kitchen), or "imagined" (e.g the frown on your bosses face as you deliver your presentation). The intensity of our reaction to a stressor is highly individual and situationally dependent (Dewe, 1993; Peters et al., 1998). One person may be terrified of a hognose snake, for example, a herpetologist who studies them may be fascinated by the same snake. Storylines, implicit or explicit neurocognitive appraisals, coping strategies, social support, and past experiences are variables that affect the physiological stress response in any given situation (Anshel et al., 1997; Anderson et al., 2002; Barbenko et al., 2015; Ambeskovic et al., 2017).
How the body responds to a stressor occurs largely outside conscious awareness. (Le Doux and Pine, 2016; Ginty et al., 2017). In response to a stressor, the brain coordinates a response. The sympathetic branch of the autonomic nervous system is activated. The autonomous nervous system is divided into sympathetic and parasympathetic branches (Thayer and Sternberg, 2006). Although the relationship between the sympathetic and parasympathetic system is complex and should not be thought of as a binary (either/or), it is generally accepted that during a stress response, the sympathetic nervous system is activated and the parasympathetic system, responsible for calming and stabilizing the body, is dialed down (Thayer and Sternberg, 2006). The degree of a sympathetic nervous system response is thought to be determined by one’s perception of how threatening the stimulus is, even if the perception is not within conscious awareness (Kalisch et al., 2015; LeDoux and Pine, 2016). Further, the physiological responses during stress can be enhanced or diminished by psychological factors, such as perceived control over the situation (McEwen, 2008).
Although neuroscience is a relatively new science and more is unknown about the brain and consciousness than is known- we know enough to make sensible decisions. Sleep, exercise, diet, supportive social connections, and mindfulness practices are generally good for the brain. The happiness, equanimity, and fulfillment we seek are the by-products of a healthy brain.
The brain wires for habit. Habits promote efficiency. We don't have to think to walk for example. By contrast, goal-directed behavior (like learning to meditate or learning to play an instrument), is characterized by active deliberation and exacts higher computational costs (Daw et al., 2005). Automaticity allows the brain to free up attentional and decision-making resources. However, automaticity can also be detrimental and lead to bad habits, compulsions, and addictions.
The brain writes sub-routines and algorithms it uses to map the outside world. Special brain cells create systems that help us track where we are in a sequence of actions. Some researchers liken it to a music box playing different tones, where our brain cells can execute different action sequences (El-Gaby et al., 2024).
If we don't like the music, we can configure the music box to play any sequence of tones. Similarly, if we don't like the outputs, we can learn to rewrite the code. The brain can reorganize itself. The brain's ability to do this is called neuroplasticity. The brain's of young children are very plastic; they learn easily. Connections become more stable in adults because glue-like glia hold neurons in place. Adults learn differently than children. For adults, it’s not so much about adding or deleting connections, but tuning the strength of synapses.
It takes time for connections to build strong signal strength and for familiar and strong ones to weaken until they are extinguished. The speed of habit formation or extinction differs- from a few weeks to months or years- depending on the habit and other factors (Camerer, 2023). There are over 80 billion neurons. Each is connected to thousands of other neurons. The sum is over 100 trillion connections. That's a lot of possibilities which we see reflected in the diversity of cultures, languages, genres of music and dance, and lifestyles.
Right motivation is the first step on the path to change. We have to really want to understand, to learn, to change, to grow, to evolve (however you wish to phrase it). Jonathan Felix really wants to understand what this mystery is all about. It starts with intention.
Intention is not enough, however. We need resolve- the persistence and tenacity to see our intentions through. What we call willpower or tenacity has a biological substrate. Evidence suggests a central role for the anterior mid-cingulate cortex in subserving tenacity. The anterior mid-cingulate cortex acts as a structural and functional hub connecting multiple brain regions that render the experience we call persistence, or will power, or tenacity (Barrett et al., 2020). The anterior mid-cingulate cortex also receives and integrates a wide range of signals from other brain regions to predict energy requirements that are needed for attention allocation, to encode new information, execute physical movement, and facilitate goal attainment (Barrett, Touroutoglou, 2020). It influences and is influenced by rest, memory, emotion, mindset, interoception, etc. Together, they regulate the amount of effort directed toward any potential behavior. What we call tenacity will influence performance particularly wherever there is challenge. Intentionally doing things that suck every day strengthens these networks and structures.
Exercise, eating right, and meditation suck. We do it anyway!
The best time to meditate or exercise is when I don't want to. This resistance trains the anterior mid-cingulate cortex. I build persistence and resolve and do those things I know to do.
Perseveration is another behavior with a neural substrate researchers are just beginning to understand. Perseveration, is associated with neurological and psychiatric disorders including autism, obsessive-compulsive disorder, Huntington's disease and Tourette syndrome. A distinct group of astrocytes located deep in the central region of the brain, known as the central striatum, regulate communications between neurons. Astrocytes play a key role in supplying energy to neurons during high-demand activities by rapidly activating their own glucose stores and metabolism (Gourine et al., 2024). Unlike other astrocytes, however, this group of astrocytes express the gene Crym, which encodes for the protein known as μ-crystallin. By reducing expression of Crym in astrocytes of the central striatum, researchers uncovered mechanisms related to a specific behavior called perseveration. That is, too little of the gene Crym, and the brain locks in to OCD like behavior (Ollivier et al., 2024).
Two structures in the brain have been implicated in taking or inhibiting action: the prelimbic cortex (PL) and infralimbic cortex (IL) (Amaya and Smith, 2018). Inhibition is like an off switch.
The prelimbic cortex mediates a “go” signal. An electrical charge passes messages from neuron to neuron.
The infralimbic cortex sends a “no-go” signal (Moorman et al., 2015; Gourley and Taylor, 2016). Neurons stop firing. How these regions aid in initiating or inhibiting actions in the service of avoiding aversive outcomes or obtaining rewarding ones is complex. The infralimbic cortex facilitates active avoidance and suppresses inappropriate actions in aversive contexts. By contrast, contextual valence, or the subjective value we assign something, plays a critical role in how the prelimbic cortex is recruited in initiating or suppressing actions, which may relate to the degree of cognitive control required to flexibly negotiate response or motivational conflicts and override strong habits (Capuzzo & Floresco, 2020). In other words, you have to want something badly enough to override lethargy, sloth, indifference, complacency, habit, etc.
It is very important to train these systems intentionally! The objective here is to execute a go signal for those things we've decided to do and send no-go signals to inhibit or suppress behaviors we don't want.
Intention and tenacity are not enough, however. We need discipline. And regimentation can aid you in that.
Habits are automatic. They can be healthy (e.g. dental hygiene) or unhealthy (e.g. munching on cookies to self-soothe). The brain wires for habit. Habits promote efficiency. Automaticity allows the brain to free up attentional and decision-making resources. So, with intention, tenacity, and wisdom we start with discipline to regiment our day. Once we lock in the right daily disciplines, automaticity follows. The good (e.g. physical and mental health) are by-products of that. Neglect discipline, by contrast, and suffering comes. The pain comes seemingly unbidden and unwelcomed, but, it, too, is a consequence of in-action or the wrong actions.
"Failure is subtle," Jim Rohn rightly observed. If we fell severely ill after eating one donut or were diagnosed with cirrhosis after drinking a pint of whiskey or suffered a broken heart after complaining or experienced poverty after subscribing to cable, we would quickly change. But we don't get severely ill after eating one donut; we are not diagnosed with cirrhosis after drinking a pint of whiskey; we aren't heart-broken after complaining to our spouse; we aren't filing for bankruptcy after subscribing to cable. Just as small, intentional, daily disciplines build good health, wealth, and relationships, so are bad habits gradually shaped, and once formed are devilishly hard to break. The more we reinforce any habit, whether good or bad, the more robust the connections.
Brain Care
Sleep is one of the most impactful habits that affects brain health for better or for worse. Each cell in our bodies contains a built in timer, or series of clock genes (PER, BMAL, CLOCK, etc) that regulate cell function. These processes are entrained, or fixed, to light cycles. Each cell has its own circadian rhythm. There are subsidiary clocks in other brain regions and peripheral clocks throughout the body. A number of processes throughout the entire gastrointestinal tract and liver, for example, appear to be under circadian control- such as nutrient uptake, processing, and detoxification (Reinke, 2016). The intestinal microbiome is regulated by circadian rhythms, which can significantly impact immune function and metabolism (Voigt et al, 2016). The heart, too, has its own rhythms which affect output, workload, and energy supply-to-demand ratios (Young, 2006). The brain's ability to clear Amyloid-Beta 42, a protein closely linked to Alzheimer's disease, is tied to the circadian cycle (Clark et al, 2022).
When our rhythms are entrained, or fixed to diurnal cycles of night and day, our cells function optimally. When they are disrupted, our hormonal schedules become dysregulated, our mood suffers, our health is compromised. We increase the risk of cancer, obesity, heart disease, anxiety-disorders and depression, Type II diabetes, and the kind of neurodegeneration typical of dementia and Alzheimer's disease.
Mood and attention are dependent on sleep. After a good night's sleep, it's as if stores of these neurotransmitters were replenished. We wake up feeling alert and motivated. By contrast, when we do not sleep well night after night, we wake up with brain fog and begin to feel unmotivated. Over time, this dampens our mood causing chemical imbalances. Anxiety, depression and lack of sleep are strongly correlated.
A good night's sleep helps with memory and learning. Sleep restores the brain’s computational power. Neuroplasticity, which refers to the brain's capacity to form and reorganize synaptic connections, especially in response to learning or experience, occurs during sleep. Knowledge and memory are consolidated after a good night's sleep. The brain regions also synchronize to create motor memory. Sleep is like the Save function in an application, but sleep is also essential before learning. It primes the brain to absorb new information. There's a 40% decrement in memory consolidation without sleep.
The brain produces bursts of rapid, rhythmic brain wave activity called sleep spindles. They are thought to be a feature of memory consolidation—when your brain gathers, processes, transfers, and filters new memories you acquired the previous day (Andrillon et al., 2011).
Sleep restores balance between order and chaos. During sleep, the glymphatic system clears out toxins and metabolic waste from the brain. It takes 7 to 8 hours for the glymphatic system to flush out metabolic waste. The glymphatic system is like an irrigation system. In conjunction with lymphatic vessels within the brain, noxious toxins are drained into thin tubes-which allows for the circulation and removal of brain waste fluid. That fluid exits the brain and drains into channels in the outer tissue layer that surrounds it (Mehta et al., 2022).
Waste removal is a critical function for preventing diseases.
Waste fluid moves from the brain into the body much like how sewage leaves our homes. Once the ‘drain pipes’ leave the brain's housing, it connects up with the sewer system within the body.
Arachnoid cuff exit (ACE) points, are a “cuff” of cells surrounds blood vessels as they pass through the brain’s protective arachnoid barrier into the dura mater. The dura mater is the outermost and toughest layer among the three layers of membranes called the meninges that surround and protect the brain and spinal cord. This membrane is composed of dense, fibrous connective tissue (Smyth, 2024).
These ACE points act as conduits, allowing the transfer of waste fluids, immune cells, and other molecules between the brain and the dura. In the brain, clogs at ACE points may prevent waste from leaving. Toxins, like sewage, collect in the brain. When this happens, immune cells trigger brain inflammation. But it is not only drains that get clogged, the whole system becomes dysregulated.
Heart health affects sleep and sleep affects heart health. Pulsations of the cerebral arteries help to drive the clearance of toxic brain byproducts in the perivascular spaces with each heartbeat. However, high blood pressure over the long term stiffens arteries, impairing function and the ability to clear toxins. This disruption of blood flow and brain fluid underlies many neurodevelopmental disorders.
Lifestyle choices such as sleep position, alcohol & caffeine intake, exercise, omega-3 consumption, diet, meditation, intermittent fasting and chronic stress also modulate glymphatic clearance for better or for worse.
Side sleeping improves glymphatic clearance compared to either supine (on the back) or prone (front-lying) positions. Alcohol impairs sleep. Ingesting caffeine late in the day (for most people) affects the quality and quantity of sleep. Pharmacologically, caffeine is an adenosine-receptor antagonist (Nehlig, 2004). Adenosine is a hormone that regulates sleep and sleep induction (Huang, 2011). Caffeine blunts adenosine, which explains why it is harder for most people to fall asleep after ingesting caffeine.
Many hormones that regulate hunger and appetite are replenished after a good night's sleep. Sleep upregulates the satiety hormone, leptin, and downregulates the appetite-stimulating hormone, ghrelin. Sleep deprivation affects energy homeostasis and has been associated with perturbed blood levels of peptide hormones. Hunger and appetite increase after a poor night's sleep. Not only do we eat more, we crave the kinds of nutrient-poor, sugary foods that compromise sleep, which leads to more stress on the body and mind which leads to more bingeing which leads to weight gain, increasing our risk of stress and illness which further compromises sleep, mood, and affect. Like this, we can easily fall into a negative feedback loop.
Chronic sleep deprivation can negatively affect immune cells which leads to inflammation and cardiovascular diseases . Losing even an hour and a half of sleep a night potentially increases these risks according to a 2022 study published by researchers at the School of Medicine at Mount Sinai.
Daylight Savings Time (DST) is like a global controlled experiment, asserts sleep researcher Matthew Walker. During the spring, when we lose an hour of sleep, a 24% increase in heart attacks follows that day. In the autumn, when we get an extra hour of sleep, we see a 21% reduction in heart attacks (Gurm, 2018). We see similar patterns in car accidents and suicide rates. Fatal car accidents, attributed to sleep deprivation and circadian misalignment, spike by 6% after DST (Vetter, 2020). Sleep disruptions during the Spring transition are also associated with a 6.25 percent increase in suicide (Osbourne-Christensen, 2022).
Men who sleep five hours or less per night have smaller testicles than those who sleep seven hours or more. Men who sleep five hours or less per night will have a level of testosterone equal to that of men ten years older. Lack of sleep ages a man by a decade. The number of people who can get by on 6 hours of sleep or less without any impairment rounded to a whole number and expressed as a percentage of the population is ZERO, according to Matthew Walker.
Sleep deprivation compromises our immune systems. Natural killer cells (NK) identify pathogens and foreign invaders- such as viruses, bacteria- and destroy them. Reducing sleep to 4 hours is associated with a whopping 70% decrease in NK activity. That is a compromised state of immune deficiency which puts us at risk for acute illnesses like the cold or flu and, over the long term, more serious threats like prostate, bowl, and breast cancer.
Chronic Sleep Restriction (CSR) is defined as sleep durations that are more than four hours but less than seven hours a night. CSR can lead to a range of brain deficits, including impaired attention and learning, and is associated with increased risk of neuropsychiatric disorders and other conditions.
Growing evidence has demonstrated that CSR is linked to a low-grade inflammation, as reflected by increased inflammatory plasma cytokines and by the presence of other markers of inflammation in the brain, such as activation of microglia cells.
Heightened pain sensitivity can result from chronic sleep disruption (CSD)- a condition researchers call CSD-induced hyperalgesia. N-arachidonoyl dopamine (NADA), a type of neurotransmitter called an endocannabinoid, helps manage neuroinflammatory diseases or pain. After a poor night's sleep levels of NADA drop in an area of the brain called the thalamic reticular nucleus. Activity of the cannabinoid receptor 1, also involved in controlling pain perception, decreased as well after sleep was disrupted (Ding, et al., 2023).
Insufficient sleep can lead to the accumulation of intracellular reactive oxygen species (ROS) and/or reactive nitrogen species (RNS), resulting in an unbalance between the oxidant and antioxidant systems of the body. Excessive ROS and RNS levels can cause cellular damage and increased risk of disease.
The very fabric of our lives- our genes and DNA- begin to unravel when sleep is chronically compromised. One study found that after one week of insufficient sleep (6 hours versus 8 hours), 711 genes were up- or down-regulated (Dijk, 2013). Those genes that were down-regulated or switched off were associated with the immune system. Those genes that were up-regulated or switched on were associated with inflammation, tumors, and cardiovascular disease. "Sleep," asserts according to Matthew Walker, "is a non-negotiable biological necessity."
Again, this partially explains why, in some cases, therapy and prescription drugs will not move the dial on brain health- unless we address the fundamentals.
Meditation is a way to rewire the brain. This presupposes you want to train it. The mind is powerful. In Zen, training the mind is likened to training an ox (which is this site's logo). In Tibet, it is likened to training an elephant.
In America, we can liken it to training a wild bronco or a dog.
In the 9 stages of training the mind, we move from distractibility to equanimity. In the beginning stages, it is common for the mind to wander. Meditation at this stage is like bronc riding for ten minutes. The meditator attempts to hold on to the object of focus for eight to ten seconds as the mind bucks. We get tossed, dust ourselves off and get back on.
This analogy is not foreign to the West. Likening the horse to the mind appears in Ancient Greek philosophy. In the Phaedrus, Plato presents the allegory of the charioteer. The soul is described as having three components: a charioteer (Reason), and two winged steeds: one white (spiritedness, the irascible element, boldness) and one black (the appetitive element, concupiscence, desire). The goal is to train the horses and ascend to divine heights.
With practice, we can rewire the brain to maintain effortless attention on an object of focus for hours without interruption. In Pointing Out the Great Way, by Dan Brown and The Mind Illuminated by John Yates, salient characteristics of each stage and milestones are outlined.
1. Beginner: Distractions, dullness of mind and other hindrances are common.
2. Beginner: The practitioner has established a daily practice and can maintain attention on the meditation object for about a minute.
3. Beginner: Practitioners can maintain attention on the object of focus for about 10 minutes. Distractions may push the object to the periphery, but a practitioner is able to detect mind wandering quickly and reorient attention.
Milestone: Uninterrupted continuity of attention marks the first stage of development of skilled concentration. The meditator is no longer a novice, prone to mind-wandering and falling asleep.
4. Skilled: Practitioner can maintain attention for an hour or more without losing her mental hold on the object of meditation.
5. Skilled: Develops continuous awareness to make corrections before subtle distractions become gross. Gross distractions no longer push the breath into the background. Breath sensations don’t fade.
6. Skilled: Subtle mental dullness or laxity is no longer a great difficulty, but now the practitioner is prone to subtle excitements which arise at the periphery of meditative attention.
Milestone: Sustained single-pointed attention to the meditation object.
7. Adept: Attention no longer alternates. Attention is stable. Although the practitioner may still experience subtle excitement or dullness, they are rare and s/he can easily recognize and pacify them.
Milestone: Effortless stability of attention, also known as mental pliancy.
8. Adept: In this stage the practitioner can reach high levels of concentration with only a slight effort and without being interrupted by subtle laxity or excitement during the entire meditation session.
9. Adept: The meditator now effortlessly reaches absorbed concentration and can maintain it for about four hours without any single interruption.
Milestone: Stability of attention and mindful awareness are fully developed, accompanied by meditative joy, tranquility and equanimity, qualities which persist between meditation sessions
At each stage, we set our intentions and let the intention do the work. We can only act in the present moment. A goal implies a future, imagined state. The intention orients the mind to the present such that, with clear focus, we can incrementally, moment by moment, walk toward the goal. Over time, results become more consistent and the qualities cultivated- such as patience and determination, become more persistent. We reach each milestone.
When addressing some audiences, I liken meditation to training a puppy. First, we must have the desire and commit the time to training our minds.
Stage 1: Establish a daily meditation practice. Committing to a daily practice is a way to develop cognitive and attentional control. But establishing a daily practice is not easy. Several qualities of mind must be rooted and dominant, among them are: 1. resolve, 2. discipline, 3. commitment, 4. time management, 5. faith. In stage 1, the trainer commits to working with his puppy-mind daily. Benefits come relatively quickly. A 2023 study found improvements in attention, memory, mood, and emotional regulation after 8 weeks of meditation for just 13 minutes per day.
Stage 2: Appreciate the ‘aha moment that recognizes mind wandering. Intend to engage with the breath as fully as possible. Shorten the periods of mind-wandering and extend the periods of sustained attention. At this stage of trainer, we train our puppy-mind to sit and reward it with a dopamine snack. Celebrating those aha moments is key! The usual reverie's are interrupted; we acknowledge these small victories.
Stage 3: Invoke introspective awareness to make corrections before you notice distractions or dullness. Engage with the breath as fully as possible without losing peripheral awareness. Here, we're training the puppy-mind to heel. When it wanders or leads, as it inevitably will, we give it a gentle tug and, with time, train it to heel.
Skilled
Stage 4: Remain vigilant. Introspective awareness becomes continuous. Notice and immediately correct strong dullness & gross distraction. Observe the process of how mental events arise without cognitive elaboration. At this stage, we train the puppy-mind to "drop it!" That is, to drop mental elaborations, narratives, storylines, attachments to self.
Stage 5: Notice and immediately correct for subtle dullness. At this stage, we train the puppy mind to watch and remain alert.
Stage 6: Establish a clearly defined scope of attention, and completely ignore subtle distractions. At this stage, the puppy-mind is no longer distracted by squirrelly thoughts.
Adept (Note: I have not yet attained the stage of an adept. These stages are usually reserved for monks and nuns who've sat multiple, multi-year retreats. Caveat: Many teachers in stage 1 or 2 pretend to have arrived).
Stage 7: We approach the threshold of effortlessness. Purposely relaxing effort from time to time will let us know when effort and vigilance are no longer necessary. We surrender the need for control.
Stage 8: Meditative joy arises. The intensity can perturb the mind, becoming a distraction and object of craving.
Stage 9: Profound tranquility and equanimity persists even between sessions.
4 Locations
No one embarks on a journey without knowing the final destination. Stage 9 is not the terminus. The mind simply ceases to be an obstacle and impediment. Experiences of bliss, connectedness and peace become more persistent.
I came across an interesting study years ago by Dr. Jeffrey Martin on persistent non-symbolic experiences. It provides one of the clearer descriptions on the topography of inner landscapes.
Martin conducted an international study on persistent non-symbolic experience (PNSE), more commonly known as: enlightenment, nonduality, the peace that passeth understanding, unitive experience, and hundreds of other terms. The term persistent denotes a consistent, ongoing experience versus a transient one- however powerful, mystical or ecstatic. His research resulted in a classification system for these types of experiences. It also led to the discovery that these were psychological states that were not inherently spiritual, religious, or limited to any given culture or population.
Instead of levels or stages, Martin proposed 4 locations. Locations are clusters of experience that emerged from the data.
He wrote:
Location 1 participants experienced a dramatic reduction in or seeming loss of an individualized sense of self. Their minds seemed much quieter because of a reduction in the quantity and/or emotional strength of self-related thoughts, but there were still some emotionally charged thoughts that could pull them back into more active thought streams. They experienced a range of positive and negative emotions, but these emotions were much more transient and did not have the power over them that they once did. Conditioning could still trigger thought streams and stronger emotions, but even these passed in a matter of seconds. The overall change in their thoughts and emotions left them with a deep sense of peace and beingness. This beingness felt more real than anything previously experienced and made the external world and their former experience of an individualized sense of self seem less real by comparison. This deep peace could be suppressed by external psychological triggers, but would recover once the stimulus was removed. Their sense of self seemed larger and to expand beyond the physical body. There was a new sense of connectedness between what was formerly perceived as the internal and external worlds.
Location 2 participants experienced an increased loss of self-related thoughts as well as a continued reduction in the ability of the thoughts that did remain to draw them in, when compared to Location 1. As they progressed through this location the range of emotions they experienced became increasingly positive. Participants in Location 2 were more likely to feel that there was a correct decision or path to take when presented with choices. Participants who progressed to this location from the previous one reported an increased sense of well-being.
By Location 3, participants had shed their negative emotions, and now experienced one dominant emotion. This single emotion felt like a mixture of various positive emotions such as impersonal/universal compassion, joy, and love. Parts of negative emotions, which one participant called proto-emotions, were sometimes still felt but did not form into full emotions. The single remaining positive emotion was a constant experience and companion for Location 3 participants. The remaining traces of self-referential thought had continued to fall away. In Location 3, participants’ experience of inner peace and beingness continued to deepen. So too had their feelings of connectedness and union/unity. Participants at Location 3 often saw the world as unable to be any other way than it already is in the moment. While all participants expressed this to some degree it seemed to have grown very deep roots by this point. These participants generally did not place importance on choosing the correct decision or path like Location 2 participants.
Location 4. All remaining vestiges of self-related thoughts are gone by this point, as are experiences of emotion. Feelings of deep interconnectedness and union with God, an all pervasive consciousness, and so forth also disappeared. These participants reported having no sense of agency or any ability to make a decision. It felt as if life was simply unfolding and they were watching the process happen. Severe memory deficits were common in these participants, including the inability to recall scheduled events that were not regular and ongoing. Participants who progressed to this location from one or more previous ones reported the highest level of well-being. Often this amazed them as they did not imagine anything could have been better than Location 3.
Commonalities
Virtually all of the participants discussed a pronounced shift in the nature and quantity of thoughts. The nature and degree of the change related to a participant’s location on the continuum. On the early part of the continuum, nearly all participants reported a significant reduction in, or even complete absence of, thoughts. Around 5% reported that their thoughts actually increased. Those who reported thoughts, including increased thoughts, stated that they were far less influenced by them. Participants reported that for the most part thoughts just came and went, and were generally either devoid of or contained greatly reduced emotional content. Almost immediately it became clear that participants were not referring to the disappearance of all thoughts. They remained fully able to use thought for problem solving and living what appeared outwardly to be a ‘normal’ life. The reduction seemed limited to self related thoughts.
There do not appear to be negative cognitive consequences to this reduction in thought.
When asked, none said they wanted their self-referential thoughts to return to previous levels or to have the emotional charge returned to them. Participants generally reported that their problem solving abilities, mental capacity, and mental capability in general had increased because it was not being crowded out or influenced by the missing thoughts. They would often express the notion that thinking was now a much more finely tuned tool that had taken its appropriate place within their psychological architecture.
The amount of self-related thoughts as well as the percentage with emotional content
continued to decrease as participants moved along the continuum. During the earlier parts of the continuum participants could still be ‘grabbed’ by thoughts and have their mind pulled into thought sequences similar to what other research has shown in mind wandering (Smallwood & Schooler, 2006). They reported noticing this process occurring relatively rapidly and stated that this noticing led back to the experience of reduced thoughts. This ‘grabbing’ process also reduced as participants moved along the continuum. At the farthest extreme, participants reported no self-referential thoughts at all.
With PNSE, in a matter of seconds (reported as 2 to 90 depending on the severity of the incident involved, and usually on the extreme low end of the range if not life-threatening) their emotional state would return to a baseline of high wellbeing, and they were no longer reactive or bothered by the incident. They stated that prior to PNSE they would have remained upset much longer in similar situations. Commenting on the difference, they typically speculated that the lack of an individualized sense of self seemed to affect whether or not, and how long, they held onto the perceived injuries from these events.
All participants reported a significant increase in their experience of and focus on what was happening in the present moment along with a dramatic reduction in thoughts about the past and future.
As they moved deeper into the continuum, participants were increasingly able to control their reactivity to external events. As this progression continued this active control faded and became increasingly less necessary. Participants reported simply having fewer and fewer internal experiences arise in reaction to external events.
It's important to note that being further along in the continuum does not necessarily mean better. At a particular stage in life, location 1 may be preferable to 3 for some. A business man, for example, might perform better at Location 1 than 4. At Location 4 feelings of deep interconnectedness and union with God may pervade consciousness. But having no sense of agency or any ability to make a decision can be detrimental if he has stakeholders to address, meetings to schedule, products to deliver, or staff to manage. Severe memory deficits were common for participants in Location 4. This would not be helpful to a parent of 3 children who had conferences or games to attend, investments to make, or a mortgage to pay. As much as I might like to retire to a monastery, I must abide at Location 1 for a while. I have reports to complete, board meetings to attend, grants to write, children to raise, a property to maintain, groceries to buy, meals to cook, and an elderly mother to care for- among other worldly concerns. That said, even an abbot at a monastery or head at a nunnery must attend to the mundane- scheduling, discipline, cleaning, maintenance, etc. and cannot abide in Location 4 without things falling apart. At many monasteries, therefore, leadership is often shared to give senior members the opportunity to go on solitary retreat and abide in Location 3 or 4 for a time.
At this stage, I am where I'm supposed to be.
How do we move from stage to stage or location to location?
There are many different techniques and well-trodden paths. There is nothing mystical about training. Meditation is to mind as exercise is to body. Meditation is defined as a family of complex emotional and attentional regulatory strategies developed for various ends (Lutz, Slagter, Dunne & Davidson, 2008). While there are other definitions, this one is the broadest, encompassing the others.
Just as exercises can be classified as aerobic or anaerobic, meditation techniques can be grouped by type: focused attention, open monitoring, body scanning, generative, and analytical. These meditations have different effects. Just as different exercises contribute to overall health and challenge the body in different ways, the type of meditation technique one chooses drives different cognitive-control states.
We often begin with some compelling end in mind: to reduce stress/anxiety, for self-discovery, pain management, enlightenment; to cultivate more empathy, to improve focus and concentration, to enhance creativity, to optimize performance, to be more present, to manage strong emotions, to improve sleep, for mental health, to delay or prevent age-related cognitive decline, or to enhance one's sense of well-being. The motivation has to be strong enough to get the brain to cooperate and commit.
As we grow, our reasons may change. Stress relief, for example, is a low level desire, but sufficient to get us to commit and sit. Once we learn how the sympathetic nervous system works and can leverage it skillfully, we may set new goals, as we do in exercise. After following through on our commitment to walk a mile every day, for example, we may increase the intensity as our conditioning improves and walk 10% farther or faster, with a load or on an incline. Similarly, as new connections are strengthened and the brain improves in, say, concentration, we may increase the duration or quality of the attentional hold or develop a broader awareness.
In focused attention meditation, the practitioner focuses on a particular object (e.g. breath), word/s, images, sensations, external objects (e.g. candle flame) or phenomena (e.g. sound). Anything else that attracts attention is actively ignored. Attention is constantly redirected back to the object of focus. Mental repetition of a word or phrase, anapana (breath focus), shambhala (focus on exhalation), and zazen (focus on sitting & posture) are some examples of focused attention techniques.
Most focused meditation techniques work the mind in the same way. Practitioners cycle through 5 intervals which involve neural networks that connect different nodes (or parts) of the brain:
1. Sustained attention (Executive network)
Attention is single-pointedly focused on an object (the object of focus could be the breath, a word, a thought, an image, a sound, a sensation).
Active nodes: right parietal cortex, right frontal cortex, thalamus
2. Mind wandering (Default Mode Network)
For beginners, mind wandering is common; it is the default state. Intermediate and experienced meditators may also experience distractions. Depending on their level of training, they can quickly detect and reorient their focus. Adepts can maintain high levels of concentration without interruption and with little effort. Adepts demonstrate decreased default mode network activity and connectivity.
Active nodes: posterior cingulate cortex, posterior lateral parietal/temporal cortices, cingulate cortex, parahippocampal gyrus
3. Awareness of mind wandering (Salience Network)
This is the moment a practitioner realizes attention has wandered. This is the most important of the 5 intervals. This is the "Aha!" Moment. It's when we "wake up".
Active nodes: cingulate cortex, anterior insula
4. Letting go (Executive function) This is a critical choice point. The experienced practitioner lets go of the distraction.
Active nodes: basal ganglia, lateral ventral cortex and the anterior cingulate cortex (ACC)
5. Re-orienting (Executive function)
The practitioner redirects attention to the object of focus.
Active nodes: superior colliculus and frontal eye fields, temporal parietal junction and the superior parietal cortex
Understanding the intervals of the attention cycle allows us to train properly. When we become aware that the mind has wandered, for example, we know this is just an interval, we cut mental elaborations and reorient attention. Beginners, by contrast, return to default. They question, they judge, they doubt, they evaluate their performance. Rather than reducing cortical noise, they agitate their minds with more thoughts. Instead of simply cutting and letting go as per instructions, they cling to mental elaborations and become enmeshed in them, blending with them, identifying with them.
When attention is focused and sustained on the breath, I know by inference that those regions associated with executive control are active. I cannot see the posterior cingulate cortex lighting up when my mind wanders any more than I can see the anaerobic breakdown of glucose in my body after an intense set, but I can feel the effects. In meditation, when the mind is easily distracted and attention is flighty, I can infer that the posterior cingulate cortex is active as this node is associated with mind wandering. I am not unnerved by it anymore than I would be if I felt breathless after sprinting. Understanding is there.
With this understanding, I can observe quietly the chatter of a busy mind. The Observer remains clear-eyed even when the mind is cloudy. This is metaphorical.
Low-frequency fluctuations may play a key role in regulating higher cognition such as sustained attention. These fluctuations are periodic. With skill, the longer I sit, the more observant I become.
In a recent study, researchers found that when a subject's focus level changed, different regions of the brain synchronized and desynchronized, in particular the fronto-parietal control network and default mode network. The fronto-parietal control network is engaged when a person is trying to stay on task, whereas the default mode network is correlated with internally-oriented thoughts (which a participant might be having when less focused).
When a meditator is out-of-the-zone, these two networks synchronize, and are in phase in the low frequency Conversely, when one is in the zone, these networks desynchronize.
As with exercise, form is key. The squat is a great exercise for building core, quad, and leg strength. Performed improperly, however, the exercise can lead to injury. Focused meditation is like this. Practiced properly, the technique is great for stabilizing the mind as squats are excellent for stabilizing the core. How we deal with mind wandering (form), depends on technique. Cutting ruthlessly, acknowledging, touching lightly with non-judgmental awareness, and labeling are some strategies to correct a vagrant mind. But performed improperly, a beginner can fall deeper into rumination, self-criticism, and self-doubt.
Just as a body builder pushes muscles to failure, a meditator can experience a vigilance decrement, or attentional fatigue. The longer a person spends on a task, regardless of whether the task is difficult or easy, the more the mind starts to wander (Zanesco, 2024). As a runner trains to improve endurance, a meditator can improve their concentration, as well as the length and quality of the hold.
Open Monitoring
While focused attention is best for encouraging convergent thinking, open monitoring encourages the kind of divergent thinking associated with creativity.
In open monitoring, a practitioner observes whatever thought, emotion, sensation or phenomenon that arises as it arises without attachment, without focusing or fixating on it, without trying to change it in any way (Brewer et al., 2011); attention is flexible and unrestricted. Non-directive meditation, some labeling techniques, Acem, and dzongchen are examples of this type of meditation.
Open monitoring meditation techniques are practiced with a relaxed, but broad focus of awareness that allows spontaneously occurring thoughts, images, sensations, memories, and emotions to arise and pass away freely, without any expectation that mind wandering should abate.
Even though “effortful selection” or “grasping” of an object as primary focus is gradually replaced by “effortless sustaining of awareness without explicit selection,” the core activity of the practice is to sustain attention with the shifting flow of experiences, sometimes detecting emotional tone as a background feature (Lutz et al., 2008).
Focused/Open Hybrids
As there are aerobic/anaerobic exercises like high intensity interval training or tabata, there are focused/open hybrids. Transcendental Meditation (TM) and Conscious Mental Rest (CMR) are examples.
In CMR, focus is on the position of the eyes in their resting state. The frontal eye fields are active during the reorienting phase of the attention cycle. I suspect this is one reason a focus on eye placement is emphasized in this and other techniques. In TM, a relaxed focus of attention is established by effortless, mental repetition of a short sequence of syllables or non-semantic meditation sound like "da," "vo," or "eng" (Benson et al., 1975; Carrington et al., 1980; Ospina et al., 2007; Davanger et al., 2010; Travis and Shear, 2010). In both CMR and TM, whenever the meditator becomes aware that the focus of attention has wandered, attention is gently redirected to repetition of the meditation sound or the placement of the eyes in their resting state. There is no judgment. Nor is there vigilance as in focused attention techniques, as this implies effort. Attention is not directed toward observing the spontaneous flow of experiences like in open monitoring meditation (Lutz et al., 2008b). Consequently, techniques such as TM or CMR comprise a distinct style of meditation (Cahn and Polich, 2006; Ellingsen and Holen, 2008; Travis and Shear, 2010).
As mind wandering is permitted, brain patterns and activity register differently in EEG tests. TM is characterized by theta and alpha activation. The DMN is active. Focused Attention is characterized by gamma EEG and DMN deactivation (Travis, 2017).
Implication: if the mind is too busy or too dull to sustain focused attention- which requires effortful attention- TM, CMR, or similar technique might be the best practice for that session.
There are additional benefits to this class of meditation and TM specifically. In one study, significant increases in 5-HIAA (5-hydroxyindoleacetic acid) were detected in the urine of practitioners. 5-HIAA is the by-product when the body metabolizes the "feel good" neuromodulator serotonin. Elevated levels of 5-HIAA suggest the systemic presence of serotonin in the body- which translates as calm, rest, relaxation. A decrease in catecholamines (a stress hormone) is also present ( M. Bujatti, 1976).
Body Scanning
Body scans, yoga nidra, vipassana/insight, and somatic experiencing are examples of this technique. These techniques are excellent for developing equanimity and resilience, for cultivating interoception (awareness of the mind/body connection), and for reducing cognitive and emotional reactivity. These techniques are useful for those struggling with addictions, for managing strong emotions, for pain management, or simply as a technique for dealing with the vicissitudes of life.
Interoception is the sense that answers the question: "How am I feeling?" in any given moment. It is one of our lesser known senses. Interoception is the perception of bodily sensations- the tingling, throbbing, heat, coldness, pulsing, swelling, tickling, perspiration, contraction, expansion, numbness, or pain you may feel even now as you read this.
Interoceptive awareness brings these processes to conscious awareness (Cameron, 2001). The ability to consciously monitor and feel certain physiological states (such as thirst and hunger), detect potential tissue damage or pain is essential for species survival- any species' survival. This neural circuitry is ancient and predates us.
In today's modern world, the ability to identify, access, understand, and respond skillfully to the body's signals helps us meet life's challenges and stressors (Craig, 2015). Interoceptive awareness can be trained. Simply check in: what are you experiencing in your face and head now? In your neck and shoulders? In your arms and hands? In your chest and abdomen? Back? Hips? Thighs? Legs? Feet? We are not using imagination. We are simply observing. This is a useful skill to develop in a world that manufactures so much unnecessary stress. It can be trained.
A 2016 study found that engaging in meditation over an extended period led to structural alterations in the brain's "white matter," responsible for transmitting sensory (interoceptive) information.
In another study, fMRI were used to assess the thickness of the brains of twenty Westerners who had experience with insight meditation. It was determined that their brains were thicker in regions of the brain involved with somatosensory, auditory, visual and interoceptive processing.
Brown University scientists proposed that practitioners gained enhanced control over sensory cortical alpha rhythms that helped regulate how the brain processed and filtered sensations, including pain, and memories such as depressive cognitions.
In another study, meditators learned not only to control what specific body sensations they paid attention to, but also how to regulate attention so that it did not become biased toward negative physical sensations such as chronic pain.
The findings suggest that these techniques evoke a brain state of enhanced perceptual clarity and decreased automated reactivity, which can be useful for those struggling with addictions, under stress, or in the throes of a strong emotion.
Stress induces muscle fatigue. Muscle sympathetic nerve activity is a key mechanism for maintaining tension during physiological stress. At the cellular level, motor neurons discharge bursts of action potentials to keep muscles primed to fight, flee, or freeze. You can feel this in the body. Your brain forms behavioral responses. At the most basic level, you may feel a sensation- like muscle tension. How the brain interprets this sensation may lead to an evaluation. That evaluation leads to a behavioral response.
In meditation, we interrupt this process, by simply observing and not reacting to whatever sensations arise. You realize, from your own experience, how the brain reacts to conditioned neural patterns in response to stress. These patterns inform your ANS and create habitual responses. By simply sitting, you "see" how these conditioned patterns unfold and how the tension keeps creeping in. We keep relaxing into whatever arises, intentionally leaning in, relaxing, letting go of tension.
This is experiential learning at a subtle level. At the molecular level, a thought can trigger an action potential in motor neurons which triggers depolarisation and calcium ion release. The myosin heads form a cross-bridge with the actin filaments within the muscles. The myosin heads move the actin filaments the way an oar propels a row boat. Actin filaments are anchored to Z lines. The dragging of actin pulls the Z lines closer together, shortening the sarcomere (the muscle fibers) and causing contraction.
As I keep relaxing the body, I imagine a more subtle body that slows these signals and neural patterns. I imagine relaxing at the molecular level and visualize calcium ions being reabsorbed as the muscles relax. The body gives me constant feedback. I know whether the firing rate has increased or decreased by observing. Am I relaxed fully and completely? With practice, I get better at this and can fall into a relaxed state deeper and faster. Once the body is fully relaxed, I can relax the mind. Once the mind is relaxed, I can focus. Once focused, I can maintain single-pointed attention on the breath or other object of focus and keep attention narrow or open.
Generative
Generative styles of meditation include metta, loving-kindness, training on compassion, empathy or perspective-taking, visualizations, and contemplative practices. Practitioners seek to cultivate desirable qualities like compassion, forgiveness, or kindness through imagery, visualization, and imagination. Through these practices, we change how we relate to ourselves and others. These techniques often use imagination to evoke certain affective responses which we can then apply to real-world situations. If we are practicing compassion, for example, we might visualize ourselves helping others. We cultivate the feeling associated with it. We create simulations for the mind. When we see someone in distress, the response of the trained meditator will bend toward empathy, compassion, or altruism- not because they are nice people, but because they've trained themselves to respond with humanity to the suffering of others. Our brains are predictive. We've simulated how we would respond to suffering. When the situation arises, we can summon empathy, compassion, or altruism to help relieve the suffering of others. This generosity of spirit and goodwill is rewarded with oxytocin, serotonin, and dopamine. We feel good when we help others.
Analytical
Analytical techniques are of two types. The first recruit reason to uproot unwholesome thoughts. Reflecting on the deleterious effects of anger is an example of this practice. The second type of practice overwhelms the logical or thinking mind by giving it a puzzle or self-paradoxical riddle that taxes and overloads it. The Zen koan is an example. "The point of the koan," writes Gary McGee, "is to exhaust the analytic and egoic mind in order to reveal the more intuitive no-mind. They are not about arriving at an answer, but to see for ourselves that our intellections can never provide us with a completely satisfying answer. Some might even claim that koans are anti-intellectual. But they are neither anti-intellectual nor intellectual. They simply point out that reality itself cannot be 'caught.'"
“When both hands are clapped a sound is produced; listen to the sound of one hand clapping.”
Self-inquiry is another variant of the analytical style. The mind is given the task of self inquiry. "Who am I?" is the query used to investigate the nature of the mind. As the thinking mind derives its light from that which cannot be conceptualized, the imagined self comes undone. Awareness beyond thought remains.
Attending to the fundamentals is just the beginning of our work. We'll have a better go at dealing with our stuff when we are well rested, well fed, physically fit, mindful, and intentional.
Then comes the examination and deconstruction.
Researchers have identified a region of the brain called the "gestalt cortex" which appears to play a role in the co-construction of identity (Lieberman, 2022). Parts of the brain responsible for processing vision, sound, and touch interface with a structure called the temporoparietal junction, which is part of the gestalt cortex. The temporoparietal junction helps people integrate and create meaning from the world they see.
Perceptions, biases, memories, and assumptions influence our thoughts. Few investigate them, however. Most assume our senses to be undistorted and our thoughts to be true and an accurate representation of reality. Researchers call this phenomenon "naive realism."
In computer science, the acronym GIGO stands for garbage in garbage out. The quality of the input determines the quality of the output. In other words, the quality of data coming out is only as good as what went in. Teachers, parents, clerics, professors, scholars, journalists, pundits, influencers, experts, and others with the best of intentions influence what and how we think. A child receives these inputs on faith. As we mature, grow in experience, and learn, we have the opportunity to investigate, deconstruct, and reflect on what we've learned. In some cases, we must unlearn what we've learned. This is our work.
There are many analytical techniques we can use to examine and deconstruct conditioned thought patterns. What follows is not exhaustive. We can label/identify distortions (see the list of the most common distortions and fallacies here). We can simply cut or ignore them. We can let go of the storylines and simply sit and investigate the sensations and our real-time experience. We can question arising thoughts (demanding specificity or evidence). Byron Katie asks these questions when cognitive distortions arise: "Is it true? How do I know it's true? How do I react, what happens, when I believe the thought? Where would I be/How would I feel without this thought?" Another strategy is to identify the need behind the distortion. If, for example, I fail at a project and overgeneralize ("I'm a failure") and catastrophize ("I'll never succeed"), I can go deeper into the feeling (disappointment) and need (competence, to contribute). I may find other ways to satisfy this need (e.g. through volunteer service). Reattribution is another strategy. If a close friend or someone dear to you berated themselves, what would you say to them? Befriend yourself and direct that empathy inside. Semantics can also be used to dissect a cognitive distortion. "I'm a failure" and "I haven't succeeded yet" are two very different ways of seeing the same setback. The former can be characterized as low-performance self-talk, the latter suggests persistence. "I'll never succeed" and "This approach didn't work. Let me try another" yield different results both in affect/attitude and outcome (quitting vs persisting). The language we use to frame our perceptions matters at the neuronal level.
If I am experiencing strong emotions, I usually practice counting (to activate the ACC and executive seat of the brain), a body scan (to sit with the sensations associated with the emotion, focusing on equanimity or non-reactivity), repetition (using a word or phrase to condition the mind), or an analytical style of meditation if I detect cognitive distortions, fallacies in logic, or habitual patterns of thinking.
I also attend to fundamentals. If I'm rested, for example, my focus is better. Acetylcholine, a neuromodulator, is secreted when a practitioner pays attention to something specific (e.g. the flow of the out breath, the touch of the in breath at the ring of the nostrils, etc.). Attention acts as a spotlight. With heightened alertness, cognitive processes become more flexible and efficient. We can rewire implicit memory, improve neuropatterning, and change biochemistry, or as a therapist might say, overcome traumas, phobias, cognitive distortions, or other hindrances.
When we exercise, the body releases endorphins. When we meditate properly, we improve our ability to control our internal reward schedules. The feel-good neuromodulators- dopamine, serotonin, and oxytocin- enhance or suppress brain activity, energy, and motivation. Just as a runner can train both type 1 and type 2 muscle fibers through endurance or strength training, a meditator can improve their sense of well-being.
Dopamine plays a role in how we experience pleasure. When we set goals, the dopamine system is primed to look for milestones. Dopamine is not only released as a reward but also in anticipation of rewards. When we take small, actionable steps toward a goal, dopamine is released. Epinephrine is often released with dopamine. If both are present, we feel excitement; if dopamine is absent, we may feel agitation and stress. The body secretes adrenaline and cortisol.
As a meditator, I set goals. My goals are not lofty. I do not seek enlightenment or even calm. I seek consistency and isolate my goals. Committing to 10-20 minutes of daily practice from 6-6:20 AM, for example, is specific, measurable, attainable, realistic, and time-based- achieving nirvana is not. Training the salience network- those 'aha' moments- by keeping the mind focused on the exhalation for 5 sets at 2 minute intervals is specific, measurable, achievable, realistic, and time-based- excising fear is not. Meditating in an ice bath and down-regulating the stress response for 3 minutes to train the vascular system and anterior mid-cingulate cortex (it really sucks!) is specific, measurable, actionable, realistic, time-bound, and engaging (as far as results); a vapid one-liner like "Relax, Calm down" does nothing. Each time I sit to meditate, I cue the reward system. I am working toward a goal. I am affirming my resolve. I am amplifying the positive effects.
If, however, I have the expectation that I should be calm, that my mind should be empty or focused, that my thoughts should be still, and I do not achieve this, I get a prediction error. The brain signals the habenula to down-regulate dopamine. I feel disappointed.
Conversely, if I have no expectations and just sit to train non-reactivity or simply observe the mind and I experience pleasantness, a dopamine pulse may indicate that we have found ourselves feeling better we expected, and so our prior estimates of reward need to be updated.
The pursuit of a goal primes the reward system. When I set the intention to meditate daily, the doing is the reward. I make the conscious effort, during preliminaries, to affirm my effort. After meditation, I set my intentions for the day. That I have already achieved one goal- to meditate- reinforces self-efficacy. It's self-encouraging. I reward the effort, the process and keep my reward system primed as I begin the day.
The serotonin system is also recruited in meditation. It is sometimes referred to as the Here and Now reward system. It promotes quiescence and calm. When serotonin is secreted, we are soothed, content, grateful. When I evoke the relaxation response or practice gratitude, pulses of serotonin are released. When I practice compassion or loving kindness meditation, oxytocin is released. Oxytocin supports bonding.
With practice, I can go deeper. This realization motivates me to prioritize my training and get after it every day. I'm as obsessed with training the mind as athletes are with training their bodies. But without standardized tools, measurements, or performance markers I can use to gage, say, a concentrative hold, it is harder to improve or to identify a more advanced practitioner from whom I can learn.
For contemplatives, humility is a desired trait. Meditators, moreover, tend toward compassion and cooperation, not competition. I don't pretend to be as evolved. I want to know how my concentration measures up against that of a Tibetan lama who has just completed a 3 year meditation retreat. I want to be inspired. I want to continue learning and growing from true masters.
But it is difficult to determine who's who. Unlike exercise, a meditator cannot measure results the way an athlete can. A simple mirror, scale, tape measure or stop watch can provide an athlete in training with needed feedback. A bodybuilder with a tape measure can record hypertrophy, a sprinter can track speed with a stop watch, a middle aged woman who wants to complete a marathon can record her weekly mileage. But, we cannot measure the volume of the anterior mid-cingulate cortex by looking in the mirror; we cannot measure cortisol levels by standing on a scale. It must be inferred.
Tools are emerging to see what cannot be seen and to measure states that were hitherto inaccessible to science- like volume, blood flow, or hsCRP levels, but these are not items we can readily find at your local fitness retailer- scales, yes; functional near red spectroscopy headsets, not yet.
But the tools exist and the research is emerging. In one study, researchers attempted to map 4 distinct mind states to their neural substrates as measured by electroencephalogram (EEG). EEG data were collected from 30 advanced meditators. Alpha, beta, and gamma frequencies were analyzed. The results revealed that compared to baseline, density across frequencies significantly decreased upon meditation onset- that is, the electrical activity that researchers could measure was dialed down in regions associated with self-referential thoughts and executive-control. At the experiential level, the mind gets quiet; the practitioner reports a feeling of Oneness or non-duality, yet the mind remains awake and aware. During meditation, gamma increased significantly, within the anterior cingulate cortex, precuneus, and superior parietal lobule, whereas beta-band activity increased within the insula. "These findings suggest a dissociation between brain regions regulating self-referential vs. executive-control processing, during non-dual, compassionate states, characterized by brilliantly awake awareness, free from conceptual thought and 'doing'." (Schoenberg et al., 2018). In simpler terms, what scientists were able to measure may approximate what the mystics call 'enlightenment.' Much more research would need to be done, however, before we had a working definition for such an elusive state.
Recently, researchers at Harvard used an ultra high field 7T MRI to map an adept meditator’s brain activity during jhana, a form of advanced meditation. Brain activity during jhana showed correlations with attention and qualities crucial for well-being.
Spectral analyses of the EEG data provide evidence for the ability of experienced meditators to voluntarily modulate their state of consciousness (Chowdhury et., al, 2023).
While many of us wear smart watches or fitness trackers, we do not have 32 channel EEGs at home or wear continuous glucose monitors to track levels in real time. So, we must infer progress based on experience. Science helps. There are biomarkers, for example, that one can request from a primary care physician when they go for their annual physical to measure, say, inflammation which, by inference, can mean stress. (e.g. hsCRP, white blood cell count, eosinophil, monocyte, neutrophil and basophil counts, etc). But most of this data is not in real-time... nor is it affordable for most.
Most meditators monitor their experience moment by moment to get inferential data to measure progress (Note: setting goals and expectations can be a slippery slope for intermediate practitioners, but not for beginners who should set them or for adepts who learned when to let go).
There are simple questions we can ask ourselves to self-monitor: are my muscles tense? Is my breathing irregular? Is the mind agitated? Over time, we may see improvements (assuming our practice is tracked and our methodology is as scientific and objective as possible). We may spend a lot of time simply noting (there are specific techniques to do this): the breath is shallow or the breath is deep; the breath is coming in or going out; the muscles in the forehead are contracted or I'm experiencing subtle vibrations throughout the body; attention is open or narrow; the mind is agitated or still; there are movements of mind in the distance or the mind is grasping at thought.
We do the best we can with what we have- and awareness, reason, observation and attention make excellent tools. I approach meditation with the spirit of kaizen, a word of Japanese origin that connotes continuous improvement. The results will take care of themselves.
Hard it is to train the mind, which goes where it likes and does what it wants. But a trained mind brings health and happiness. The wise can direct their thoughts, subtle and elusive, wherever they choose: a trained mind brings health and happiness. -Dhammapada
My respect for the brain, the mind, and the little self is deep. The mind is like a well-trained elephant. I direct it to exercise, it moves. I direct it to study multiple languages, me obedece. I desire to learn multiple instruments, it learns the chords and notes. I want to learn to cook, the brain follows the recipes step by step. I want to learn a skill or trade, it mobilizes the resources to craft something beautiful. I draft a 5 year plan and it identifies the necessary steps, executes, and delivers. I order it to refrain from sweets, alcohol, diversions, temptations, or intoxicants, and it abstains.
That said, there is no terminus or happy ending- just more moments of happiness, equanimity, acceptance, curiosity, gratitude. The title of Jack Kornfield's book says it all: After the Ecstasy, the Laundry. No matter how "enlightened," most of us still have children to raise, mortgages to pay, jobs to do, grass to cut, or dishes to wash. Profound experiences do not inoculate us from the vicissitudes of life. Indeed, we often experience what St. John of the Cross called Dark Nights of the Soul- sadness, confusion, dissolution, disgust, and other strong emotions. Past traumas and inner demons arise to torment and challenge us as Satan appeared to Jesus in the wilderness. He retreated to the mountains to find solitude, not to be tormented, but that's when he was tested. For many of us, our tests come when we think we have arrived. These are not retrogressions, but progress that often confuses those on the path. Without a map, however, discouragement may arise. This is when we go all in.
Many who reside in Locations 3 or 4 have had to navigate all of life's misfortunes and setbacks and struggles. We are betrayed, disappointed, grow old, experience loss and disillusionment, get sick, and eventually pass away. No one escapes alive.
Brain training simply gives us more tools and the skill to use those tools to craft a more meaningful and beautiful life with what is here and now. The What-Is also crafts something beautiful out of this clay, this flame, this breath, this moment.
The content on this site is my effort to make sense of the brain's workings and this construction we call the self. We examine causes and conditions, provide frameworks that may be useful, and apply evidence-based protocols to cultivate greater physical, emotional, and cognitive well-being.
May we all know real peace and equanimity in this lifetime regardless of circumstances. May we grow in wisdom and insight.
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