Neural Pruning: How the Nervous System Unlearns What No Longer Serves

There is a widespread, persistent, and deeply misleading misconception that learning and improvement are exclusively about accumulating knowledge or skills, as if the brain were a large warehouse where more content automatically means more capacity and, therefore, more competence.

The more you add, the better? 

That’s not always how neurological optimization works.

In reality, the opposite is also true.

The nervous system does not grow solely by accumulation. It evolves through selection.

Selection isn’t only about what needs to be added; it’s also about what shouldn’t be kept.

When the brain identifies a neurological trait and behavior as desirable because it supports a survival strategy, it will work on making it a swift response.

It will favor and strengthen that response by either forming new neural connections or by reinforcing existing ones.

But an efficient way to prioritize this new behavior is to start neglecting and weakening the opposing tendency simultaneously.

The brain begins to strip away components of neural circuits that are no longer relevant or coherent with the organism’s current needs and direction.

This process is called synaptic pruning.

A System of Elimination

During early development, the brain creates far more synaptic connections than it will ultimately retain.

These connections form quickly, broadly, and with minimal discrimination, giving the nervous system a kind of exploratory abundance, a state of hyper-connectivity from which patterns of efficiency can later emerge.

Over time, the circuits that are consistently used are preserved and strengthened.

Those that remain unused are identified, tagged, and eventually deleted.

This selective deletion enables the brain to become more streamlined, focused, and energy-efficient.

This is not a metaphor.

It is a well-documented cellular process.

And it isn’t limited to childhood, synaptic pruning continues to occur in adulthood as well.

Microglia: The Sculptors of the Brain

The pruning mechanism is governed primarily by a class of immune cells known as microglia, which serve as the brain’s internal maintenance system.

These cells continuously monitor the synaptic landscape, detecting which connections are active and which are dormant.

Synapses that are underused become tagged with complement proteins, such as C1q and C3, molecular markers that signal the microglia to engulf and dismantle them.

This process was detailed by Stevens et al. (2007) and further validated in adult mammalian brains, where pruning continues beyond adolescence in response to lived experiences and behavioral patterns [1][2].

In other words: what you do not use, you lose. Literally. 

The consequences are structural and therefore experiential, rather than theoretical.

Less desirable behavioral responses diminish in intensity and/or frequency, and this is something you can feel, and therefore experience.

Sleep: The Time of Restructuring

This mechanism plays out most powerfully during sleep.

During deep, slow-wave sleep, the brain undergoes a remarkable series of shifts:

• Neurons shrink

• Interstitial fluid increases

• Metabolic waste, including misfolded proteins and excess neurotransmitters, is flushed out via the glymphatic system

But in parallel, the brain’s synaptic architecture is being restructured.

As proposed by the Synaptic Homeostasis Hypothesis (Tononi and Cirelli, 2003), sleep is not just a period of rest, it is a critical window during which the nervous system resets its learning potential by scaling back weak synapses and preserving the strong [3].

In practical terms, this means that what you consistently activate during waking life is not only reinforced, but also protected during sleep.

Meanwhile, what you neglect is marked for elimination.

Sleep is not passive. 

It is a nightly act of neurological triage.

And the nervous system, ever loyal to efficiency, will never keep a pattern it perceives as expendable.

The Role of Breath in Neural Clearance

What is less commonly understood, however, is that this nightly pruning process is not influenced only by what you do in high-stress conditions such as breath-holding.

It is also impacted by how you breathe in lower-intensity moments, specifically, through the practice of deep, diaphragmatic breathing.

Emerging research has shown that diaphragmatic breathing patterns can influence cerebrospinal fluid (CSF) dynamics and enhance the flow of interstitial fluid through the brain’s glymphatic system.

This flow is responsible for clearing out cellular waste, metabolic byproducts, and inflammatory proteins, precisely the conditions under which synaptic pruning becomes most efficient [4][5].

During focused, slow breathing, especially through the diaphragm, changes in intrathoracic pressure create mild pulsations in venous return and influence craniospinal fluid dynamics.

A 2022 study using real-time MRI showed that voluntary breathing rhythms significantly modulate the velocity of CSF flow, amplifying the clearance mechanisms within the glymphatic pathways [4].

These findings suggest that conscious breath practices do not merely relax the nervous system, they may actively assist in the structural reset process that takes place during sleep.

In other words: the quality of your sleep and breathing supports the positive results from your quality practice. 

The Antidote Principle

Within BreathHoldWork®, this principle states that it is not enough to merely inhibit or suppress an unwanted response to stress, such as impatience, tension, or panic.

Suppression alone does nothing to build the alternative.

The nervous system cannot install a new pattern unless it is experienced.

And it cannot uninstall an old one unless it is no longer reinforced.

To stop reinforcing an old pattern, you must strengthen a new one.

If, during breath-holding, your default response is to panic, and your strategy is to attempt to resist the panic, then you are still activating the same circuitry, even if only to fight it.

In that case, the synapse survives. The circuit persists. You are feeding it, even as you struggle against it.

But if, instead, you consciously shift into an alternative response, if you embody patience, or deliberately inhabit calm, even while your physiology is under stress, then you begin to fire a different circuit entirely.

You are not merely overriding the old pattern.

You are building the new one.

And by refusing to activate the former, you are marking it for removal.

The Practice That Rewrites You

This is how neural sovereignty is trained: not through suppression or theoretical understanding, but through substitution, experience, and repetition.

You must choose the new pattern and do the new pattern.

You must live it under pressure, again and again, until it begins to install itself into the architecture of your nervous system.

And then, during sleep, the pruning process does the rest.

It retains the structure you rehearsed.

It dismantles what you no longer need.

This is not “self-help.”

This is biology.

You are a biological system.

The question is: how do you choose to operate and alter yourself?

It is no different from how the body reshapes itself under progressive resistance.

Use builds. Neglect dismantles. 

There is no middle ground.

So, when you catch yourself rehearsing emotional chaos, defensive thinking, shallow breathing, or overreactive habits, understand that you are not just expressing a pattern.

You are reinforcing it.

And when you instead take the deliberate action to shift, rewire, and re-pattern, especially under stress, you are not just fighting for a better outcome.

You are retraining your nervous system to be something else.

Then, when you sleep, the synapses you activated are reinforced.

The ones you ignored are diminished.

And you wake up not just rested, but changed.

This is why mindful repetition matters.

This is why stillness under pressure matters. 

This is why what you practice, not just what you wish, becomes who you are.

When you start mastering your inner experience is when you start becoming who you've chosen to be.

Erwan Le Corre

Founder of BreathHoldWork®

References

[1] Stevens, B., et al. (2007). The classical complement cascade mediates CNS synapse elimination. Cell, 131(6), 1164–1178. https://doi.org/10.1016/j.cell.2007.10.036

[2] Schafer, D. P., et al. (2013). Microglia sculpt postnatal neural circuits in an activity and complement-dependent manner. Neuron, 74(4), 691–705. https://doi.org/10.1016/j.neuron.2012.03.026

[3] Tononi, G., & Cirelli, C. (2003). Sleep and synaptic homeostasis: a hypothesis. Brain Research Bulletin, 62(2), 143–150. https://doi.org/10.1016/j.brainresbull.2003.09.004

[4] Fultz, N. E., et al. (2022). Breathing modulates cerebrospinal fluid flow in humans. Scientific Reports, 12(1), 13699. https://www.nature.com/articles/s41598-022-15034-8

[5] Zareen, N., et al. (2017). The influence of breathing on the central nervous system. Journal of Neurophysiology, 119(5), 1459–1475. https://www.researchgate.net/publication/325511727_The_Influence_of_Breathing_on_the_Central_Nervous_System