Often, when we sit in meditation, memories of the past arise- these memories may be innocent, uneventful, painful, judgmental, positive, uplifting, critical, insightful or traumatic. They may induce fear, joy, guilt, nostalgia, sadness, anger, calm, shame or other strong emotion.
Whatever arises, arises in the present. The arising of past memories is a present moment unfolding. Hidden deep in the brain is a structure called the hippocampus. The hippocampus supports memory and cognition. One type of neural signaling controls the ability to make associations, such as remembering that the neighborhood market sells farm fresh eggs. The other type is predictive and involves the ability to flexibly use memory to plan a new behavior; for example, during meditation, you remember that there are only 2 eggs left in the carton at home and you decide to stop by the market right after work before it closes at 6. The hippocampus remembers associations between time, place and what one did and allows one to predict or plan future actions based on past experiences (Cornell University, 2023).
Often, during meditation, the mind wanders. Mind wandering starts with a whisper. One to two seconds before the hippocampus whispers a memory, large parts of the brain become silent. It is possible that this happens so that other parts of the brain can better hear what the hippocampus is trying to say (Chambers, 2022). Researchers at the University of Minho in Portgual speculate that the brain acts as a resonance chamber with distant brain regions oscillating in time.
Some researchers suggest that what we experience as consciousness are fragments of memory used by our unconscious brain to help us flexibly and creatively anticipate and predict future moments and plan accordingly. Memories of the past influence a present that plans for the future. “What is completely new about this theory is that it suggests we don’t perceive the world, make decisions, or perform actions directly," explains Andrew Budson, MD, professor of neurology. "Instead, we do all these things unconsciously and then—about half a second later—consciously remember doing them.”
This theory, according to the researchers, is important because it clarifies how all of our choices and actions—which we mistakenly believe were made consciously—are actually made unconsciously. Memory, then, influences our behavior without our awareness.
This idea may not be as new as he asserts.
In the Majjhima Nikaya, a Buddhist text written sometime in the 3rd Century BCE, the author writes: "The past should not be followed after, and the future not desired. What is past is dead and gone, and the future is yet to come. Whoever gains insight into things presently arisen in the here and now is unmoved, unshaken."
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. The SYNGAP1 gene, a DNA sequence that controls memory and learning in mammals, makes proteins that regulate the strength of the synaptic connections between brain cells. SynGAP proteins are very abundant at the synapse (the. gap between brain cells). When SynGAP proteins interact with the major synaptic scaffolding protein, PSD-95, they morph into liquid droplets. This makes the synapse stronger and increases transmission between brain cells (Araki et al., 2024).
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.
This present moment is our point of power. We can reframe past experiences and rewrite new neural pathways that "liberate" us, in a sense, from regrets, remorse, and sufferings of the past. We can relax into this present moment and live more mindfully- with a lighter heart and with more gratitude, acceptance and contentment.
There is only ever this present moment. Along comes another and another. What we call "the past" are packets of limited information stored in brain cells retrieved in the present. Unique packets of proteins are sent from brain cell to brain cell. A cargo of proteins changes over time as memory is encoded.
It's also important to note that memories are not static snapshots of past experiences; they are often distorted and colored by emotion. The memory system is a confabulation system. Memories decay over time. Researchers have consistently found memory recall to be unreliable. With skill, we can exploit this vulnerability to reframe past memories that cripple or limit us.
THE SCIENCE
Memory encoding cells, or memory 'engrams,' are distributed across the brain. They are a kind of "time cell." (Umbach et al., 2020) Many 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). Note: these are simplistic and general descriptions. The brain is far more dynamic and complex.
Memories- conditioned behaviors, evaluations, assumptions, perspectives, etc.- inform the present. This essay, for example, is intelligible only to those whom have had past experiences with the English language- its vocabulary, syntax, and structure. An Indian fluent only in Urdu, for example, might see these symbols as unintelligible marks on a screen as the idiom ہاتھی کے پاؤں میں سب کا پاؤں in Urdu makes no sense to someone with no exposure to the language to draw upon. To read and understand English or Urdu, we need to access past learning from semantic memory to help us make sense of these symbols in the present.
Before experimenting with protocols, I'd like to summarize our current understanding of how memory works. By exploring the science, we can approach memories from a more detached, objective, and neutral place- with curiosity instead of dread or resistance. With this understanding, when seemingly unpleasant memories surface, we don't blend with them or take them as personally. We can begin to attend to them more skillfully here and now.
Single memories are distributed and span many functionally connected brain regions (Roy et al, 2022). These memories are recalled now- in this moment. All of the words I use to craft this essay are pulled from memory and synthesized with new words like engram to create "learning." As you read and learn alongside me, for example, specific neurons are reactivated and vocabulary words like "reactivated" and "neuron" are recalled. Foundational knowledge you learned in school- e.g., phonemic awareness, letter to sound correspondences, comprehension, sentence structure, etc.- is retrieved from long term memory.
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. 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 can be deconstructed. We can build more accurate models.
MEMORY TYPES
Researchers have identified different types of memory: short term, long term, episodic, working memory, and motor memory (Cowan, 2009).
SHORT TERM
Short term memory refers to the brain's ability to hold a limited amount of easily accessible information temporarily. I introduced the word engram in paragraph 5, for example. Some readers may have already forgotten that engrams were memory encoding cells. If you research memory, however, the word "engram" is passed along and stored in long term memory.
LONG TERM
Long term memory differs from short term memory in duration and capacity.
Duration
Information in short-term storage decays with time, but long term memories stick.
Capacity
A capacity difference refers to the limit in how many items short-term storage can hold.
As an educator, to help you commit the word engram to long term memory, I might use stories, analogies, or diagrams. The diagram below, for example, is a visual representation of a memory distributed across different brain regions. It illustrates how memories are encoded, consolidated, and retrieved.
I can assign the word "engram," have you write it, ask you to repeat it, use it in a sentence, and quiz you on it later. The more you use the word "engram" and the more relevant it is, the more likely it is to stick. The word "engram" is part of a memory researcher's lexicon. Their livelihood is built atop words like these and concepts like the scientific method. These words and concepts are embedded in long term memory.
Large groups of neurons in the hippocampus fire together in rhythmic cycles, creating sequences of signals within milliseconds of each other that can encode complex information. Called "sharp wave-ripples," these "shouts" to the rest of the brain represent the near-simultaneous firing of 15% of hippocampal neurons, and are named for the shape they take when their activity is captured by electrodes and recorded on a graph. These sharp wave-ripples are the physiological mechanism used by the brain to 'decide' what to keep and what to discard (Yang et al., 2024).
EPISODIC
Episodic memory "describes our ability to weave temporally contiguous elements into rich and coherent experiences." (Umbach et al., 2020) If I asked you to describe some momentous event, you may be able to recall the episode in some detail, but not remember any of the events the previous day or the day after.
WORKING MEMORY
Working memory is used to plan and carry out actions. The word engram appears several more times in this post. If you do not add the word to your vocabulary, it may remain in working memory long enough to help you appreciate the actionable protocols below.
There are different kinds of working memory.
We rely on working memory while solving arithmetic problems without paper or to bake a cake without making the mistake of adding the same ingredient twice. Working memory acts as a bridge between perception (when we read a phone number) and action (when we dial that number). (Kwak, Curtis, 2022)
Working memory extracts only the most relevant sensory information from the environment and then sums up that information in a relatively simple code. The brain stores only the relevant information needed for the task at hand. You use working memory when you ask a friend for directions to a restaurant and then keep track of the turns and guideposts as you drive there.
MOTOR MEMORY
Motor memories are encoded differently in our brains than our memories for names or facts.
"When you're first learning to shoot a basketball, you use a very diverse set of neurons each time you throw, but as you get better, you use a more refined set that's the same every time," explains Stanford University researcher Richard Roth.
Motor memories are highly redundant. As we repeat learned skills, we are continually reinforcing the motor engrams by building new connections—refining the skill. It's what is meant by the term muscle memory—a refined, highly redundant network of motor engrams used so frequently that the associated skill seems automatic (Hwang, et al., 2022). Constant repetition is one reason for the persistence of motor memory. Memory persistence may also be affected by a skill being associated with a reward, perhaps through the neurotransmitter dopamine.
The cerebellum, associated primarily with movement, plays an important role in the storage of both positive and negative memories of emotional events. The cerebellum receives information from the cingulate gyrus – a region of the brain that is important in the perception and evaluation of feelings. And the cerebellum sends out signals to the amygdala and hippocampus, which play a central role in emotional processing and memory storage respectively. In the video below on Somatic Healing, Peter Levine guides a soldier suffering from PTSD in therapy. With assistance, the soldier gradually rewires his brain by leaning into the protective, but maladaptive, patterns the mind/body had learned.
WHY ARE SOME MEMORIES RECALLED AS EITHER "GOOD" OR "BAD"
ENCODING "GOOD" MEMORIES
The neurotransmitter dopamine is linked with motivation, learning and memory (Clos, 2018). Encoding and consolidating memories requires the stimulation of dopamine receptors as part of a brain loop that orchestrates the formation of new memories (Cohen et al., 2010; Lisman, 2005). Dopamine enhances feelings or reward, motivation, and seeking behaviors. If an experience is encoded as pleasurable, the brain orients to seek out more of it. The route the brain takes may be negative and maladaptive or positive and adaptive- whether it's the calm that comes after smoking a cigarette or the calm following an hour of meditation, the bliss that comes from snorting cocaine or the bliss that arises naturally when one feels connected to life, the satisfaction that comes from sporting a luxury car or the satisfaction that a craftsman feels comes from doing a job well. Like a mouse pressing a lever for a bite of cheese, once the brain finds a source to pleasure, it encodes the path to it and motivates the being to seek more of the same.
ENCODING BAD MEMORIES
Under stress, the brain releases norepinephrine. Norepinephrine helps the brain focus on perceived threats. The pupils dilate, and the visual field narrows. Brain cells that process visual data have a specific "receptive field," meaning they activate in response to stimuli that appear in a particular zone of a person's visual field. I focus on the perceived threat to the exclusion of all else. This data gets encoded.
Threats trigger the physiological response we interpret as fear. Fear heightens brain activity. Brain cells form more synaptic connections. There is more mitochondrial activity (Liu et al., 2022). Mitochondria provide cells energy for cellular activity, and, at the neuronal level, help cells regulate calcium- the molecule that triggers the release of neurotransmitters. Norepinephrine is a neurotransmitter that also causes a bursting pattern of electrical impulses in a brain structure called the basolateral amygdala. The amygdala plays a critical role in the formation of both positive and negative memories (Beyeler, 2016). Norepinephrine activates a biochemical signaling pathway. A single brain molecule called neurotensin released in the basolateral amygdala may influence whether the brain links positive or negative emotions to certain memories (Tye et al., 2022). Neurotensin assigns information a valence- "good" or "bad." It's the molecular equivalent of a thumbs-up/thumbs-down switch. The basolateral amygdala encodes the value of a memory and routes it to the nucleus accumbens, the central amygdala, or the ventral hippocampus depending on its valence. Depending on how a signal is routed will determine whether it is perceived as good or bad, positive or negative, rewarding or aversive. When neurons in the basolateral amygdala assign a memory a positive valence, that information- excited by reward predictive cues- is projected to the nucleus accumbens. When neurons in the basolateral amygdala assign a memory a negative valence, that information -excited by aversion predictive cues- is projected to the central amygdala. Projection from the basolateral amygdala to the ventral hippocampus drives behaviors of innate negative valence (Beyeler, 2016). More specifically, NAcBLA neurons receive inputs from the basolateral amygdala and project to VTAGABA (VTA, ventral tegmental area) neurons and LHGlu (LH, lateral hypothalamus) neurons to control reward-seeking behavior. NAcPVT input neurons receive PVT inputs, and project to LHGABA neurons to promote aversion (Zhou, et al., 2022).
Behaviorally, we tend to seek out the good, the pleasurable, the rewarding, and resist or reject the bad, the unpleasant, the aversive. Experientially, if you were mauled by a dog as a child, you may find the company of dogs very stressful and unpleasant. Conversely, if you had a loving bond with dogs, your memories may be pleasant.
How a molecule decides whether an experience should be encoded as good or bad is not understood. Likely, it is evolutionary. We evolved to take negative emotions seriously- which explains why past negative experiences and traumas are harder to shake off. If I was mauled by a dog as a child, for example, the experience may wire the brain to overgeneralize that all dogs are threatening to protect the self. Although the perception is distorted, the brain assumes the worst to keep us safe. It's evolutionary advantageous to remember dangerous events so as to avoid being hurt again in the future. This can be maladaptive, however, if fear becomes paralyzing (e.g. I isolate myself and stay home for fear of encountering dogs on the street).
Traumatic memories can rewire the brain. Researchers found that fear conditioning led to learning-specific changes in neuronal-network activity in the dorsal part of the medial prefrontal cortex (Nagai, 2023). The dorsal part of the medial prefrontal cortex (dmPFC) is critical for the retrieval of associative fear memory. The dmPFC shows specific neural activation and synchrony during fear-memory retrieval and evoked fear responses, such as freezing and heart rate deceleration.
Prolonged stress alters the structure and function of neurons in the amygdala, a brain region essential for emotional regulation and a critical mediator of both the stress response and fear learning. Neurons in the amygdala connect to the prefrontal cortex (involved in cognitive control), the nucleus accumbens (helps translate motivation to action), and the hippocampus, which plays a significant role in memory and learning. Under chronic stress, neurons connected to the hippocampus are drastically altered, while those linked to the prefrontal cortex and the nucleus accumbens remain unchanged. In one study, researchers found that glucocorticoid receptors (stress hormones) appeared to significantly increase the intensity of expression only for neurons projecting into the hippocampus (Zhang, et al., 2022).
Researchers do not fully understand how past negative memories can be reframed as rewarding or positive. But it has been done. Therapists, psychologists, psychiatrists, and contemplatives have found strategies that work... for some people some of the time.
Therapeutic Interventions
One of the most effective interventions for trauma and anxiety related disorders aimed at reducing pathological fear are exposure-based therapies like extinction therapy (Milad, 2014). People are gradually exposed to stressors (eg. systematic desensitization) until their fear of the stressor abates (at least enough to allow us more freedom from incapacitating fear). For example, If I suffer acrophobia, the fear of heights, I might start by standing a few rungs up on a ladder- not high enough to trigger panic, but just enough to experience and lean into mild stress: the subtle palpitations, changes in breath, perspiration, etc. With time, I'm exposed to greater heights until I learn to manage my physiological response. Cognitive behavioral therapy is another approach. It is top-down. That is, we use reason and logic to temper strong emotions and disarm our cognitive distortions. A third intervention is hypnotherapy. A therapist may use relaxation and guided imagery to help a person with acrophobia face and unlearn the fear response. Virtual reality is also a promising tool for facing our fears. Scientists are working with veterans to treat post traumatic stress disorder using VR combined with a technique called prolonged exposure therapy. A fifth intervention is Somatic Experiencing. Somatic refers to the body. We go into the body, feel the sensations- the palpitations, the nausea, the rapid, shallow breathing and help the body return to a rested and natural state. In the following video, Peter Levine, helps treat a Marine suffering from Post Traumatic Stress. The soldier's transformation is dramatic and speaks to the power of the body's ability to self-correct.
Meditation Techniques: An Analogy
During a break from researching and writing this, I sat at the piano and played two notes (an E and a G). If I played a root note of C, I created a major C chord. If I played the B note, I created an E minor chord. One sounded happy, one sounded sad. Memory engrams are a lot like notes. We can root them and give them color and context. In a sense, we can learn to reharmonize the past to create something beautiful in the present. We compose the soundtrack of our moment to moment experience.
Memories degrade or decay with time. They are mutable, changeable. Suppose, during recall, I root a memory to gratitude. This is a choice. While I may not be grateful for the suffering that came from an experience, I might be grateful for the learning that came from that suffering. Or I can root a memory to another value like compassion or empathy. If I suffered from an experience, I can stand in solidarity with others who are experiencing a similar misfortune and work to alleviate their suffering. With practice, I can reharmonize memories. I can select how they express.
There are visualization techniques that help us generate those qualities. We imagine some past suffering. Then we imagine someone else relieving us of that suffering. We hold the feeling. Then we imagine someone else in the same predicament, and we imagine ourselves rendering aid. Again, we hold on to the feeling.
Ours is a predictive brain. By visualizing and generating feelings in this way, we train the brain to respond more thoughtfully to the suffering of others. We are creating responsive maps for the brain to follow and are using aversive past experiences for good.
Visualization is a top down strategy. We use imagination, reason, and other faculties of mind to reframe past experiences. Interoceptive awareness is a bottom up strategy. We go directly into the body and listen as it expresses whatever arises as it arises. Somatic Experiencing, the therapeutic technique featured in the video above, builds off of interoception.
Deep, controlled breathing, often used in mindfulness practices, can improve working memory capacity, the kind of memory we use to hold and manipulate information over short periods. The rhythm of our breathing creates electrical activity in the brain, enhancing emotional judgment and memory recall, with this effect being most pronounced during inhalation through the nose. The amygdala and hippocampus, brain areas linked to emotion and memory, are significantly affected by the rhythm of breathing, suggesting that the act of breathing can modulate the functions of these regions (Zelano et al., 2016; Kee et al., 2012; Arshamian, 2018).
Another technique is to simply let go and remain with present moment awareness. The past is an illusion rendered by the mind NOW. Time cells fire NOW. Appreciating this, I can let go of past conditioning and memories as they arise.
I am sitting at my desk in my office NOW. But I can retrieve a Caribbean beach from memory. I can see, feel, and sense details... but these are just illusions appearing in the mind's eye NOW. There are no gulls, no waves, no surf only this present moment- this laptop, this desk, this breath, a barking dog, the hum of traffic, the clacking of keys as I type, and THAT which enables the senses to hear and see and sense and from which thoughts and memories emerge. But what we call memories are arisings, patterns of neuronal activity, movements of mind.