Bottom-up Healing for Trauma & Addiction: "Neurological De-Armoring" + Brainstem Relaxation
Now including various relevant lessons from trauma psychologists
When people tell me they have trauma, I generally recommend they follow my meditation/Mindset advice, including therapy, which includes somatic therapy & breathwork. To help people engage with the mindset practices, I have advised the use of my Ultimate Psychedelic protocol. But recently, I learned that there’s some more basic biological, physiological, and sociological interventions we need to implement before getting to those levels.
If you’re ready to create and adapt to a less stressful environment and take your armor off, use this protocol that I developed with Gemini, using my Heterodox Research Protocol, combined with insights I gleaned from various books on trauma psychology.
The “Biological Resilience” Protocol: v4
A Complete Guide to Bio-De-Armoring
⚠️ CRITICAL MEDICAL DISCLAIMER:
DMSO Safety: You must use 99.9% Pharmaceutical Grade DMSO. Industrial grades contain heavy metals that this solvent will drive directly into your bloodstream and brain. Ensure hands and nose are clean before handling. See my full DMSO reference here.
Electrolytes: Consult a doctor if you have kidney disease or heart conditions.
Ethnobotanicals: Iboga and Psilocybin are illegal in many jurisdictions and carry risks. Never combine Iboga with most medications (especially heart & psych meds). See full iboga guide here, and microdosing protocol here.
Behavioral Warning (The Isolation Trap): While this protocol demands starving the brain of “Phasic” Dopamine (excitement, novelty, the chase), do not isolate completely. Total social isolation spikes Cortisol, which sensitizes the brain to Glutamate and effectively locks the armor in place even without the addiction. You need “Oxytocinergic Anchoring” to lower the cortisol floor.
The Rule: Seek “Boring Love” (parallel play, reading next to someone, safe touch). Avoid “Exciting Love” (romance, high-stakes drama), as this spikes Phasic Dopamine and resets the armor.
Cognitive Warning: As you de-armor, you will feel naked and exposed. You will assume everyone can see your anxiety. Dr. Nicholas Epley, Mindwise, calls this the “Illusion of Transparency.”
The armored brain projects its own internal threat level onto neutral faces. You will think people are judging you; in reality, they are just thinking about themselves. Rule: During this protocol, do not trust your social intuition. It is calibrated to “Threat,” not “Truth.” Assume you are misreading every room until your heart rate is below 90 BPM.
Psychology is the Software; Biology is the Hardware.
Standard therapy attempts to rewrite the “code” (thoughts/behaviors) while the “motherboard” (the brain’s physical structure and chemical environment) is often overheating or damaged. The science behind this protocol focuses on four specific neuro-biological mechanisms that must be addressed before psychological tools can be effective.
The “Underpinning” Principle Dr. Bruce Perry compares treating trauma to building a house. Standard therapy attempts to “decorate” the house (changing thoughts/behaviors in the Cortex) while the foundation (the Brainstem) is crumbling. You cannot hang curtains in a collapsing house.
The Modern “Role-Self” vs. The Ancient “True-Self”
Why does the brain build this armor? Psychologist Lindsay Gibson explains that Adult children of emotionally immature parents survive by creating a “Role-Self”—a defensive personality designed to please others and manage the parent’s emotions.
But we can’t just blame our immature parents for this Role Self. It really is true what they say: “It takes a village to raise a child.” The modern large society with only one or two people caring for the children is vastly insufficient. As Dr. Bruce Perry explains, our brains evolved in hunter-gatherer bands with a ratio of 4 developmentally mature adults to 1 child. Today, our “enriched” environments offer 1 immature adult to 4 children.
We are operating on less than 1/24th of the relational density our biology requires. The “Void” you feel is real. Once you have de-armored, you cannot simply return to a lonely life. You must aggressively engineer a “High-Density” social environment (A Tribe), or the brain will eventually reach for the armor again just to survive the cold.
As we grow up, our “Role-Self” becomes calcified by Dopamine and DeltaFosB. It becomes a prison. Your addiction is often just the fuel required to keep the “Role-Self” running. This protocol dissolves the chemical glue holding that false persona together, allowing your “True-Self”—the person you were before the trauma—to finally re-emerge.
Neurological De-Armoring is underpinning (not redecorating). This protocol acts as a metabolic solvent—an HDAC inhibitor—that softens the neural concrete of the brainstem by modulating Glutamate and introducing Ketones (BHB). We are digging underneath the house to pour a new foundation so that, eventually, the psychological “software” updates upstairs will actually install.
The Anti-Breakthrough (Micro-Dosing) As Dr. Perry explains, we need to temporarily abandon the therapy ideal of the “hour-long breakthrough.” A sensitized, armored nervous system cannot metabolize sixty minutes of trauma processing; that is a flood, not a fix. Dr. Perry’s data indicates the “therapeutic window” for a dysregulated brain is often only seconds long.
Your goal is Micro-Dosing Safety: 30 seconds of regulated breathing, twenty times a day. We are not running a marathon; we are doing physical therapy for a broken nervous system. Frequency beats intensity.
Part 1: THE SCIENCE (Why We Do This)
Before applying the tools, you must understand the specific “Hardware Failures” that occur during trauma, withdrawal, or chronic stress.
A. The Metabolic Red Line
We often assume we can “think” our way out of a trigger, but data proves that anatomy overrides intellect. Dr. Perry identifies a “Metabolic Red Line” for the traumatized brain: when the resting heart rate is elevated or heart-rate-variability reduced (a state of “Fear”), the brain physically shunts blood flow away from the Cortex (Logic/Reason) and down to the Brainstem (Survival).
In this state, functional IQ drops substantially. More importantly, this state floods the Nucleus Accumbens with the exact cocktail of catecholamines that transcribes new DeltaFosB proteins (the “armor”). The Takeaway: If you attempt to process trauma while living above this red line, you are not de-armoring; you are actively re-enforcing the armor.
B. The “Overheating” CPU: Glutamate Excitotoxicity
The Problem: Glutamate is the brain’s primary excitatory neurotransmitter. In states of stress, the brain floods with Glutamate. This is the “voltage spike”—the engine is redlining.
The Metabolic Red Line: We often assume we can ‘think’ our way out of trauma, but Dr. Bruce Perry’s data proves that anatomy overrides intellect. When trauma survivors become highly dysregulated, prefrontal cortical functioning often decreases while survival-oriented neural systems become more dominant. In this state, learning and memory processes may favor reinforcement of existing fear networks rather than integration of traumatic material. For this reason many trauma therapies emphasize staying within a manageable "window of tolerance" rather than overwhelming activation. You can often tell when you’re dysregulated by noticing if your heart is beating faster or if your heart-rate variability declines. DeltaFosB may be the master switch, but the research isn’t settled.
The Mechanism: Excess Glutamate over-activates NMDA receptors, acting like a key stuck in the “On” position. This causes “excitotoxicity”—literally vibrating cells to death. Subjectively, this feels like anxiety, rage, or an “itchy brain.”
The Signal Dial (GluD Receptors): Beyond the "voltage spike" of NMDA, Johns Hopkins researchers have recently discovered the brain uses GluD receptors as a master volume knob. While NMDA is the spark, GluD manages the baseline "hum" of the synapse. In an armored state, this dial is often jammed in the "High" position (Cerebellar Ataxia/Hyper-vigilance) or "Low" (Apathy/Schizotypy).
D-serine may support therapeutic memory updating through NMDA-dependent learning mechanisms, while also engaging GluD receptors that regulate synaptic activity/tone. The specific drug form studied is D-cycloserine. which has evidence as an exposure-therapy augmenter because it can facilitate NMDA-dependent consolidation of extinction learning. It does not erase fear directly; it appears to strengthen whatever learning occurs during or after the exposure session. This is why session quality matters: if the exposure produces corrective learning and ends with reduced fear or mastery, DCS (and possibly D-serine also) may help consolidate that new memory; if the exposure is overwhelming or ends badly, it may consolidate the wrong association.
The Fix (”Lock, Stock, and Barrel”):
The Vacuum (NAC): Clears the flood by exchanging glutamate for cystine.
The Lock (Zinc/Magnesium): Physically blocks the receptor channel to stop the voltage.
The Repair (Leucine/L-Serine): L-Serine acts as a precursor to D-Serine to recalibrate the GluD 'Volume Dial' to enhance therapeutic sessions that end with low fear/high mastery (although conversion to D-serine is inefficient, which is why some people use D-serine itself which has higher risk/benefit). Leucine facilitates structural repair while simultaneously tuning synaptic gain to reduce the 'itchy brain' sensation
C. The “Hardened” Circuit: Dynorphin & DeltaFosB
The Problem: To protect itself from the Glutamate storm, the brain eventually releases Dynorphin, a chemical blanket that suppresses dopamine. This creates the “Void”—a state of apathy, grayness, and an inability to feel pleasure.
Why Standard Meds Failed You If you have tried SSRIs (antidepressants) and failed, you are not crazy. Ipser & Stein 2012 study showed that Prozac had zero effect on male combat veterans with calcified PTSD. And the side effects are well-known, including anhedonia, zombification, and sexual dysfunction.
Why don’t these drugs work on calcified PTSD? Because standard serotonin drugs treat the “software” (mood), but they cannot penetrate the “hardware” (the structural changes in the amygdala caused by severe trauma). This protocol uses Ketones and HDAC Inhibitors to remodel the physical structure of the brain that resists standard medication.
The Hardening: Chronic cycles lead to the accumulation of DeltaFosB, a protein switch that permanently alters gene expression to cement the trauma circuitry (Vialou, et al, 2010).
The Fix (The Unlock): You cannot “wait” for this to pass. We use “System Reformats” (Shrooms/Iboga) to stimulate GDNF, which physically rewires the brain around these hardened loops.
D. The “Lagging” System: Toxicity & Hypometabolism (The Fog)
The Problem: “Brain Fog” is often a fuel crisis. Trauma causes cerebral insulin resistance—your neurons are swimming in glucose (sugar) but cannot burn it. The engine is flooded.
The Fix: If the brain cannot burn sugar, we switch fuels. We use PQQ to boost ATP, and Ketones, which bypass the broken glucose pathways and enter the mitochondria directly. This turns the lights back on immediately. We alternate hot and cold showers to boost p131 and heat shock proteins and reduce inflammation.
E. The “Save Button”: Memory Reconsolidation
The Problem: Every time you have a flashback, your brain attempts to “save” the memory again, often reinforcing the emotional trauma loop.
The Fix (”The Jammer”): Memories require visual processing power to be restored. If you occupy the Visual-Spatial Working Memory (e.g., playing Tetris) during the critical window after a flashback, the brain fails to “save” the visual details. The memory is restored, but the emotional “sting” is permanently reduced.
Instead of Tetris (which requires app/phone), you can use the “Color-Path Connect” method. This is more effective than simple counting because it forces your brain to map 3D space, which directly competes with the visual “saving” of a traumatic memory.
How to play:
Pick a color (e.g., Blue).
Trace a Path: Find every blue object in the room and mentally draw a line connecting them from left to right.
Add Complexity: Now, mentally “rotate” those objects in your mind or imagine them changing into a different shape (e.g., “That blue chair is now a blue cube”).
The Goal: You must do this for 10–20 minutes immediately after a trigger to “jam” the memory reconsolidation.
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Part 2: Reducing Anxiety & Depression
Lower the Cortisol Floor (Phosphatidylserine)
Before ketones, before D-Serine, address cortisol directly — because cortisol is what sensitizes the brain to Glutamate and locks the armor in place (see the Isolation Trap above). The single most useful nutrient I’ve found for this is Phosphatidylserine (PS), a phospholipid that blunts the HPA-axis cortisol response to stress.
Who it’s for: People running high or reactive cortisol — the “wired and tired,” can’t-downshift, waking-at-3-a.m. type. This includes many people with slow COMT (the Val158Met variant that clears catecholamines slowly, so stress hormones linger and you stay on high alert). One friend, Scott, with exactly this profile got more out of PS than anything else in this protocol. Be honest about the evidence, though: the cortisol-lowering effect is best documented in chronically stressed people; the slow-COMT angle is mechanism plus my own observation, not a controlled finding.
Dose: 300–600 mg/day, taken earlier in the day. Below ~300 mg the cortisol effect is unreliable; above ~800 mg adds nothing.
Food instead of capsules: One of the few supplements you can actually eat your way to. Atlantic mackerel (~480 mg/100g) and herring (~360 mg) are richest; tuna is lower (~194 mg). A 200g mackerel fillet ≈ 960 mg PS — above clinical doses. (Don’t lean on tuna daily — mercury.)
⚠️ The catch, again: PS is only for genuinely high cortisol — and there are two ways to find out you guessed wrong. PS works by blunting cortisol. If yours isn’t actually elevated, lowering it pushes you down the other side of the curve, where the symptoms look almost identical to high cortisol. Watch for either signal:
Flat / numb / no drive — you’ve over-suppressed. Classic too-little-cortisol.
More wired, not less — racing thoughts, 3 a.m. waking, irritability, vivid or stressful dreams. Counterintuitive but real: when cortisol drops too far, the body leans on adrenaline to hold up blood pressure and alertness, and you feel more stressed, not less.
Either one means PS is the wrong tool for you right now. Don’t raise the dose to push through — stop. If you want to know before you start, a 4-point salivary cortisol test tells you whether you’re actually high. (A minority also report low blood pressure, water-weight gain, or restless legs — all consistent with cortisol going too low.)
The rule of thumb if you can’t test: Wired, tired, can’t switch off, 3 a.m. waking → probably high, PS is worth a trial. Numb, low-drive, flat → probably not high; PS will likely make it worse. Skip it or test first.
Fixing ATP Signaling if Cortisol Isn’t High
Recent neuroscience (Tian-Ming Gao, et al, 2025) has shown in male mice that anxiety and depression are a result of reduced hippocampal ATP signaling. Calabrese, et al (2024) have shown in one study that’s part of much broader research that ketones and reduced carbohydrate intake are highly effective for anxiety, depression, and other mental illnesses. To address both issues, you can trial a morning dose of 20mg of PQQ and ketones.
KETONE DECISION: You must choose your fuel strategy. This determines your electrolyte protocol.
Strategy A: The “Crisis Mode” (BHB, Beta-hydroxybutyrate Salts)
Method: You eat a standard low-sugar diet but drink Ketones (BHB Salts) to clear the fog.
Strategy B: The “Resilience Mode” (Keto Diet)
Method: You restrict carbs (<20g/day) to force your liver to produce Ketones.
Fat: EAT FAT TO SATIETY. This is your new energy source. Do not rely on lean protein alone (chicken breast), or your body will convert the protein to sugar (Gluconeogenesis), keeping you out of ketosis.
To avoid side effects, refer to the Keto Adaptation Guide.
Part 3: THE SHIELD (Flu-Proofing & Voltage Control)
Goal: Stabilize voltage to prevent the “Biological Crash” (Headaches/Panic).
1. Electrolytes (Choose Your Path)
If on Quick Fix, Strategy A (BHB Salts / Standard Diet):
Sodium: Standard intake. DO NOT load extra salt (Risk of High Blood Pressure).
Potassium:
Goal: Install the “Brake Pads” for your nervous system.
Mechanism: Potassium Channels (KCNQ).
The Science: Your neurons have “brakes” called KCNQ channels that stop them from firing uncontrollably. These brakes run on Potassium ions. If you are low on potassium (common in high stress), your brakes fail. You can push the pedal (breathe), but the car won’t stop.
The Mandate: You must hit 4,700 mg of Potassium daily.
The Source: Food Only. (Supplements are dangerous and limited to 99mg).
The Menu (The “Shield” Foods):
Potato (Baked with skin): ~925 mg (The King of Potassium).
Beet Greens (Cooked): ~1,300 mg per cup.
Salmon: ~1,000 mg per filet.
Avocado: ~700-900 mg.
Coconut Water: ~600 mg per cup.
The Strategy: Eat 2 large potatoes and 2 cups of greens every single day. This saturates your cells, lowering your “resting voltage” so you become physically harder to trigger.
If on Deep Fix, Strategy B (Keto Diet): See my Keto Adaptation Guide for electrolytes.
2. The Glutamate Shield (Anxiety):
Sulforaphane from 1 cup of broccoli sprouts (which also contain the myrosinase needed).
Function: It acts as a “Guardian of the Proteasome,” preventing the premature degradation of the cleanup machinery you are working so hard to build. Sulforaphane is also a potent Nrf2 activator; if you are in a “Glutamate Storm,” it helps clear oxidative stress.
NAC: 1.8g – 2.4g (divided doses). Mops up glutamate.
Agmatine Sulfate: 1g/day. Stabilizes NMDA receptors.
Magnesium Glycinate: 400mg (Night). The “Plug” for the anxiety channel.
The Dynorphin Bridge (Apathy):
Cordyceps mushrooms / Uridine: Upregulates Dopamine receptors without burning them out.
3. The “Nuclear Option” (Ethnobotanical)
The Stack: Microdose Iboga Nasal Spray (Bypasses digestion, quicker effect). Read my iboga microdosing guide to keep safe. While shrooms are often better for a functional mood brightener effect, iboga is its own kind of therapist that shows you what you need to see in a non-threatening way.
Female Iboga: For “Numbness/Fog” (Anima).
Male Iboga: For “Helplessness/Relapse” (Animus).
Shrooms: Hillbilly or Mazatapec strains are some of the best (0.1g - 0.2g).
Part 4: THE JAMMER (Acute Symptom Management)
Instructions: When the symptom wave hits, identify the Type and apply the Fix.
Scenario A: The “Glutamate Storm”
Symptoms: Anxiety, Rage, “Itchy” Brain, Racing Thoughts, Flashbacks.
Mechanism: The brain is firing too hot. You need to cool the system and jam the reconsolidation.
The Perry-Sequence (Rhythmic First, Visual Second)
Anatomy overrides intellect. If your heart rate is elevated or heart-rate-variability (HRV) reduced significantly, your “Reasoning Brain” is offline.
Step 1: Rhythmic Regulation (Brainstem): Perform 5 minutes of rhythmic, repetitive sensory input—walking, drumming on your thighs, or rhythmic “Therapeutic Sighing”.
Step 2: Check Your Baseline: Once your heart rate is within normal range, you cerebral cortex is receptive. Phosphatidylserine (PS, see Part 2) is a daily baseline agent that lowers how often and how hard these storms hit; it's not an in-the-moment tool.
Step 3: Apply the Jammer: Now use Tetris or the “Color-Path Connect” game to overwrite the visual memory
Advanced tactic: The D-Isomer Memory Re-consolidator. While L-Serine provides the building blocks for myelin, taking D-Serine (700mg–1400mg) on an empty stomach 45 minutes before a de-armoring session acts as a “memory (re)consolidator” which can cement the benefits of therapies like EMDR which aim to rewire the affective tone of memories.
D-serine has shown efficacy in studies where it was used to augment exposure therapy for treating a variety of conditions such as social anxiety, PTSD, and fear of public speaking. The idea is that it facilitates the consolidation of the newly formed memory of how the anticipated negative consequences of the exposure to what you fear didn't actually happen. Some studies ssuggested that d-serine is more effective at this when the practice exposure to what you fear ends on a positive note as opposed to a negative one. Again, all d-serine is doing is making it easier to consolidate the memory of the experience into a long-term memory.
Use L-Serine for daily maintenance and background hardware support.
Use D-Serine for acute sessions where you need to “force” memory reconsolidation. Best price from LifeLab. You should take it 45 minutes or so after taking PQQ & Ketones so that your brain is fueled when the GluD dial is turned down.
Warning: Direct D-Serine carries a higher renal (kidney) load than L-Serine. Do not exceed 30mg/kg and ensure high water intake. This risk is compounded by the higher renal load caused by a keto diet or high protein intake.
Scenario B: The “Fog”
Symptoms: Confusion, Disassociation, Low Energy, “Lagging.”
Mechanism: Hypometabolism (Low Fuel) or Toxicity (Static).
Scenario C: The “Void”
Symptoms: Numbness, Boredom, “I want to Relapse.”
Mechanism: The Dynorphin block is active. You feel “dead.” You need to force a spark.
We will utilize the science of hot and cold showers as a vascular pump, and plant medicine as needed:
Hot (3 Minutes): As hot as you can safely handle. This relaxes muscles and induces mild hyperthermia, signaling the body to start producing repair proteins (HSPs/PI31).
The Metabolic Red Line: If your resting heart rate is elevated or HRV reduced, do NOT use high heat yet. Heat mimics exercise and will raise your heart rate further, which can re-enforce your “armor”. Stick to lukewarm-to-cold until your baseline heart rate is below 90 BPM.
Cold (1 Minute): Turn it to max cold. This provides the acute stress spike needed to activate the transport motors (p38 MAPK).
Repeat: Do this 3 times. Always end on cold.
Fun with fungi: If the showers aren’t enough, you can microdose Hillbilly or Mazatapec (balanced, happy, spiritual) shroom strains (100-300mg daily). This stimulates 5-HT2A receptors to bypass the “numb” receptors.
Activate the “Inner Father”: If you are lacking discipline, try a male iboga nasal spray micro-dose. 1 spray (equal to about 150mg of bark) in the morning, as it lasts 12 hours. Make sure to check all the dangerous iboga drug interactions. Full iboga guide here.
Part 5: THE TIMELINE (The 8-Week Path)
Weeks 1–2: The Glutamate Storm (Anxiety Phase)
Protocol:
Self-care: Hot & cold showers, alternating, ending on cold. No hot showers if heart rate elevated or heart-rate-variability reduced.
Supplement daily: Phosphatidylserine 300–600mg, earlier in the day (lowers the cortisol floor — see Part 2 for who it's for and how to know it's working) + 1 cup broccoli sprouts + Magnesium Glycinate (400mg) + NAC (2.4g) + Agmatine (1g). If PS leaves you flat OR more wired, you're not a high-cortisol responder — drop it.
Fuel: Start with BHB Salts (Strategy A) to manage initial fog.
Rescue: “The Fire” + Chantress Seba or other music + The Repair Stack (Zn/Leu/Ser) + Tetris/Color Path for acute attacks.
Weeks 3–5: The Dynorphin Void (Depression Phase)
State: The anxiety stops, but the world turns gray/boring.
Protocol: Taper off Phosphatidylserine here. This phase is low-drive and gray by design — you do not want to keep blunting cortisol in an already-flattened system, or you'll deepen the numbness. PS was for the anxiety phase; the Void phase needs the opposite. (If you never felt the wired/high-cortisol state in Weeks 1–2, you probably shouldn't have been on PS at all.)
Hot & cold showers, alternating, ending on cold). No hot showers if heart rate elevated or heart-rate-variability reduced. Reduce or stop phosphatidylserine here — you don't want to suppress an already-flattened system. Micro-dose Male Iboga (if heart is ok).
Transition: Consider moving to Strategy B (Keto Diet) for long-term repair (Autophagy) now that the acute storm has passed.
Rescue:
If Foggy: Inhale DMSO + Drink BHB.
If Numb: Micro-dose Male Iboga and/or Hillybilly/Mazatapec shrooms.
Week 8+: The Baseline
State: DeltaFosB degraded. Hardware reset complete.
Maintenance: Cycle off NAC. Maintain metabolic flexibility (Low Carb/Seasonally Keto).
The Aftermath: The Relational Vacuum
As the armor decays, you will experience a frightening but beautiful side effect: Interoception. Van der Kolk describes this as the ability to “feel” your own body again. For years, you have likely been numb—living in your head to avoid the pain in your chest.
As the dopamine armor fades, you will feel your heart beat. You will feel your gut churn. You will feel the wind on your skin. Do not mistake this sensitivity for anxiety. It is not a symptom of sickness; it is the symptom of coming back to life. Welcome it.
Why shrooms, there are other kind of médecine