Sleep, Circadian Rhythm, and Nervous System Reset Protocol

The Triad That Rules Everything

Sleep. Circadian rhythm. Nervous system regulation. These three are not separate health topics — they are one interlocking system. Disrupt circadian rhythm and sleep collapses. Disrupt sleep and the nervous system dysregulates. Dysregulate the nervous system and circadian rhythm cannot entrain. The triad feeds itself in both directions — a vicious cycle when broken, a virtuous cycle when aligned.

The IFM recognizes sleep as foundational — not an afterthought slotted in after supplements and labs, but the bedrock upon which every other intervention rests. You cannot heal a gut, balance a hormone, or calm an immune system in a body that does not sleep. The research is unambiguous: short sleep (under 7 hours) increases insulin resistance, suppresses immune function, elevates inflammatory cytokines, impairs cognitive function, accelerates biological aging, disrupts the microbiome, and increases all-cause mortality. Sleeping 6 hours a night for one week produces the same cognitive impairment as being legally drunk (Van Dongen 2003).

---

Circadian Biology: Every Cell Has a Clock

The circadian system is not just the sleep-wake cycle. It is a body-wide time-keeping network. Every cell in the body — liver cells, immune cells, gut epithelial cells, fat cells, muscle cells — contains clock genes (BMAL1, CLOCK, PER, CRY) that oscillate on a roughly 24-hour cycle. These peripheral clocks are synchronized by the master clock: the suprachiasmatic nucleus (SCN) in the hypothalamus.

The SCN takes its primary input from light — specifically, blue-wavelength light detected by intrinsically photosensitive retinal ganglion cells (ipRGCs) containing melanopsin. Morning light activates the SCN, which signals the pineal gland to suppress melatonin and the adrenals to release cortisol. Approximately 14-16 hours later, the SCN triggers melatonin production, initiating the sleep cascade.

When this system is disrupted — by artificial light at night, irregular schedules, shift work, jet lag, or chronic stress — the consequences cascade across every physiological system:

• Metabolic: Circadian disruption causes insulin resistance within days (Scheer 2009 — forced circadian misalignment increased glucose by 6%, decreased leptin by 17%, and reversed cortisol rhythm). Shift workers have 40% increased diabetes risk.
• Immune: NK cell activity drops. Inflammatory cytokines rise. Cancer risk increases — the WHO classified shift work as a probable carcinogen (Group 2A). Melatonin is the immune system’s circadian gatekeeper.
• Gut: The microbiome has its own circadian oscillation. Disrupted circadian rhythm alters microbial composition, increases intestinal permeability, and impairs motility.
• Mental health: Circadian disruption is both a cause and consequence of depression, bipolar disorder, and anxiety. Light therapy (10,000 lux morning light) is as effective as SSRIs for seasonal and non-seasonal depression.
• Aging: Circadian disruption accelerates biological aging through increased oxidative stress, impaired DNA repair (which occurs primarily during sleep), and shortened telomeres.

---

The Autonomic Nervous System Ladder: Polyvagal Theory for Clinicians

Stephen Porges’ Polyvagal Theory provides a framework for understanding the autonomic nervous system that goes beyond the simple “fight-or-flight vs. rest-and-digest” binary. There are three states, organized hierarchically — a ladder:

Ventral Vagal (Safe and Social) — The Green Zone

The newest evolutionary branch of the vagus nerve — the “smart vagus” — myelinated, fast, regulating heart, lungs, face, and voice. This is the state of safety, connection, and healing. When the ventral vagal system is dominant:

• Heart rate is variable (high HRV — the heart speeds up on inhale, slows on exhale, reflecting flexible autonomic regulation)
• Breathing is deep, easy, diaphragmatic
• Face is expressive, eyes are soft, voice has prosody (melody)
• Social engagement system is active — the ability to listen, connect, feel empathy
• Digestion works. Immune system functions optimally. Tissue repair proceeds. Hormones balance.

The body can only heal in the ventral vagal state. Every therapeutic intervention — every supplement, every protocol, every dietary change — works better when the nervous system is in green.

Sympathetic (Fight or Flight) — The Yellow/Orange Zone

When neuroception (the nervous system’s unconscious threat detection) senses danger — real or perceived — the sympathetic nervous system mobilizes:

• Heart rate increases, HRV drops
• Breathing becomes shallow, rapid, upper-chest
• Blood diverts from gut and reproductive organs to muscles
• Pupils dilate, muscles tense, startle response amplifies
• Mind becomes hypervigilant, scanning for threats
• Cortisol and adrenaline surge

Short-term sympathetic activation is healthy — it is how you lift heavy things, run from danger, meet deadlines. Chronic sympathetic activation is the disease state: hypertension, insulin resistance, gut shutdown (IBS, reflux, constipation), immune suppression, hormone disruption, insomnia (the “wired but tired” pattern — cortisol won’t come down at night), anxiety, panic attacks.

Dorsal Vagal (Freeze/Shutdown) — The Red Zone

The oldest vagal branch — unmyelinated, shared with reptiles. The last resort when fight and flight have failed. The body conserves energy by shutting down:

• Heart rate drops, blood pressure may drop
• Breathing becomes minimal
• Dissociation, numbness, “checking out”
• Flat affect, monotone voice, vacant eyes
• Depression, chronic fatigue, hopelessness, “playing dead”
• Fainting (vasovagal syncope is a dorsal vagal response)

Many patients with chronic fatigue, fibromyalgia, and treatment-resistant depression are locked in dorsal vagal. They are not lazy or unmotivated — their nervous system has collapsed into survival mode.

The Clinical Implication

Healing requires building capacity to return to ventral vagal and expanding the “window of tolerance” — the range of arousal (sympathetic activation) a person can handle while staying regulated. Trauma, chronic illness, childhood adversity (ACEs), and chronic stress all shrink the window of tolerance. The nervous system becomes either stuck in sympathetic (anxious, reactive, insomniac) or collapsed into dorsal (depressed, fatigued, disconnected) — or oscillating rapidly between the two.

---

Testing

DUTCH test (Dried Urine Test for Comprehensive Hormones): Four-point cortisol pattern (awakening, morning, afternoon, night) reveals the shape of the curve — not just the total. Healthy pattern: sharp rise at awakening (cortisol awakening response or CAR), peak mid-morning, gradual decline through afternoon, nadir at night. Common dysfunctional patterns: flat-low (adrenal insufficiency / late-stage HPA dysfunction), flat-high (chronic stress without recovery), inverted (high at night = insomnia), blunted CAR (depression, burnout, PTSD). DUTCH also measures melatonin (6-OH melatonin sulfate) — the first objective measure of melatonin production.

Heart Rate Variability (HRV): The time variability between heartbeats. High HRV = strong vagal tone, flexible autonomic regulation, stress resilience. Low HRV = sympathetic dominance, reduced vagal tone, poor stress resilience, increased cardiovascular mortality. Measure with: Oura Ring, WHOOP, Apple Watch, Garmin, or dedicated HRV devices (HeartMath Inner Balance). Track trends over weeks, not individual readings.

Sleep study: Polysomnography (lab-based) or home sleep test. Essential to rule out obstructive sleep apnea (OSA) — present in an estimated 80% of moderate-to-severe cases that are undiagnosed. Apnea-Hypopnea Index (AHI): above 5 events per hour is mild, above 15 is moderate, above 30 is severe. OSA causes intermittent hypoxia, sympathetic surges, systemic inflammation, endothelial dysfunction, and dramatically increases cardiovascular and neurodegenerative risk. It also makes every other health condition worse and every treatment less effective.

Neurotransmitter metabolites (OAT or DUTCH Plus): HVA (homovanillic acid — dopamine pathway), VMA (vanillylmandelic acid — norepinephrine/epinephrine pathway), 5-HIAA (5-hydroxyindoleacetic acid — serotonin pathway). These urinary metabolites reflect neurotransmitter turnover — not brain levels directly, but a clinically useful proxy.

Adrenal markers: DHEA-S (adrenal androgen — often low in chronic stress, burnout, and aging), pregnenolone (the “mother hormone” — precursor to all steroid hormones, often shunted toward cortisol production in chronic stress — the “pregnenolone steal”).

---

The Circadian Reset Protocol

Morning: Within 30 Minutes of Waking

Bright light exposure — 10-20 minutes. Sunlight is ideal (even on overcast days, outdoor light exceeds 10,000 lux). If sunlight is unavailable: 10,000 lux light therapy box at arm’s length for 20-30 minutes. This light exposure sets the cortisol peak (cortisol awakening response), suppresses residual melatonin, and begins the 14-16 hour countdown to the next melatonin onset. The timing of this light exposure is the single most powerful circadian signal available.

Movement — Even a 10-minute walk outside (combining light and movement) anchors circadian rhythm powerfully. Exercise in the morning enhances cortisol’s natural peak (which is healthy and necessary) and improves nighttime melatonin production.

Cold water on the face — A brief cold stimulus activates the vagus nerve (the dive reflex) and promotes alertness through norepinephrine release. A cold shower (30-60 seconds to finish) accomplishes the same.

Daytime

Consistent meal timing — Food is a circadian zeitgeber (time-giver). The liver, gut, and pancreas have their own clocks synchronized by meal timing. Eating at random times creates internal circadian desynchrony — different organs on different time zones. Regular meal times (within the same 1-hour window each day) support circadian alignment.

Outdoor light — Get outside during the day. Bright daytime light strengthens the circadian signal, improves mood, and enhances nighttime sleep quality. Even 30-60 minutes of outdoor time during work hours makes a measurable difference.

Exercise before 4 PM — Vigorous exercise too close to bedtime raises core temperature and cortisol, delaying sleep onset. Morning or early afternoon exercise is optimal for circadian support.

Caffeine cutoff at noon to 2 PM — Caffeine’s half-life is 5-7 hours in most people. But it is significantly prolonged in: oral contraceptive users (up to 10 hours), pregnancy (up to 15 hours), liver disease, and CYP1A2 slow metabolizers (genetic — approximately 50% of the population). A 2 PM coffee can still have 50% of its caffeine active at 9 PM. For many patients, caffeine cutoff at noon is non-negotiable for sleep quality.

Evening: 2-3 Hours Before Bed

Dim lights — Below 10 lux is ideal (candlelight, salt lamps, amber-tinted bulbs). Standard indoor lighting (100-300 lux) is bright enough to suppress melatonin production by 50% or more. The key wavelength is blue light (460-480 nm) — but even standard warm white light at sufficient intensity suppresses melatonin.

Blue-light blocking glasses — Amber or red-tinted lenses that filter blue and green wavelengths. Brands like TrueDark (yellow-tinted for daytime computer use, red-tinted for evening) and Ra Optics provide validated blue-light filtration. Put them on 2-3 hours before bed if you must use screens in the evening.

Screen reduction — No screens is ideal. If screens are necessary: Night Shift mode, f.lux software (on computers), dark mode on all devices, and blue-blocking glasses. The combination of light suppression plus the cognitive stimulation of screen content makes screens a double threat to sleep.

Light dinner — Eating a heavy meal close to bed raises core body temperature, activates the sympathetic nervous system for digestion, and disrupts sleep architecture. Finish eating 2-3 hours before bed. If evening hunger is an issue, a small snack with tryptophan (turkey, pumpkin seeds, tart cherry juice) and complex carbs (which facilitate tryptophan transport across the BBB) can actually promote sleep.

Warm bath or shower — 90 minutes before bed. Paradoxically, warming the skin surface causes vasodilation and rapid core body temperature drop afterward — and it is the drop in core temperature that triggers melatonin production and sleep onset. A warm bath raises core temperature by approximately 1 degree; the subsequent rapid cooling is a powerful sleep signal.

Wind-down practices — Magnesium supplement, herbal tea (chamomile, passionflower, lemon balm), gentle stretching, yoga nidra (non-sleep deep rest), journaling, gratitude practice, prayer or meditation.

Sleep Environment

Pitch dark — Blackout curtains or a high-quality sleep mask. Tape over any LED lights (chargers, smoke detectors, electronics). Even dim light through closed eyelids suppresses melatonin and disrupts sleep architecture (Obayashi 2014 — nighttime light exposure in the bedroom was associated with increased depression, obesity, and dyslipidemia in a large Japanese cohort).

Cool temperature — 65-68 degrees Fahrenheit (18-20 degrees Celsius). Core body temperature must drop 2-3 degrees for sleep onset and maintenance. A warm room prevents this drop. This is one of the simplest and most effective sleep interventions.

Quiet — White noise or pink noise machine if environmental noise is an issue (pink noise may enhance deep sleep — Ngo 2013). Earplugs for sensitive sleepers.

No electronics in the bedroom — The bedroom is for sleep and intimacy. Phones, tablets, laptops, and televisions emit light and create psychological association with stimulation and work. Charge the phone in another room. Use an analog alarm clock.

Clean air — A HEPA air purifier reduces particulate matter, allergens, and VOCs. Air quality directly impacts respiratory function and sleep quality. A bedroom plant (snake plant, pothos) adds a biological element but HEPA is the more powerful intervention.

Consistency

Same bedtime and wake time 7 days a week, within a 30-minute window. “Social jet lag” — sleeping 2 hours later on weekends — creates measurable metabolic disruption equivalent to crossing time zones. One study showed that each hour of social jet lag was associated with an 11% increase in cardiovascular disease risk (Wong 2015).

---

Vagal Tone and Nervous System Regulation Toolkit

These are not relaxation techniques — they are nervous system exercises. They build vagal tone the way weightlifting builds muscle: through regular, deliberate practice.

Breath work — The fastest vagal tonic available. The vagus nerve is the only cranial nerve you can voluntarily activate through breathing. Key patterns:

• 4-7-8 breathing (inhale 4, hold 7, exhale 8) — Andrew Weil’s technique, powerful parasympathetic activator
• Box breathing (inhale 4, hold 4, exhale 4, hold 4) — used by Navy SEALs for stress regulation
• Coherent breathing (5 breaths per minute — inhale 6, exhale 6) — synchronizes heart rhythm, breathing, and blood pressure oscillation into “coherence”
• Extended exhale — any pattern where the exhale is longer than the inhale stimulates the vagus via respiratory sinus arrhythmia (the heart naturally slows on exhale through vagal activation)

Cold exposure — Cold water on the face activates the mammalian dive reflex — an immediate vagal response that slows heart rate by 10-25% and shifts the nervous system toward parasympathetic dominance. Cold showers (30-60 seconds of cold to end a warm shower) build cold tolerance and vagal tone over time. Cold plunge (2-5 minutes at 50-60 degrees Fahrenheit) produces a large norepinephrine release followed by vagal rebound — the sense of calm and clarity after cold exposure is the vagal rebound.

Humming, chanting, and singing — The vagus nerve passes through the larynx and pharynx. Vibrating these structures directly stimulates the vagus. “Om” chanting has been shown to increase vagal tone and deactivate the amygdala (Kalyani 2011). Group singing produces the largest effect — heartbeats synchronize in choirs (Vickhoff 2013).

Vigorous gargling — Same mechanism. Gargle with water vigorously enough to activate the muscles of the soft palate and pharynx. Do it for 30-60 seconds, 2-3 times daily. Simple, free, surprisingly effective.

HeartMath Inner Balance — A biofeedback device that measures HRV through an ear sensor and guides users toward “coherence” — a measurable state where heart rhythm, breathing, and blood pressure oscillate in phase. Clinical studies show: reduced cortisol, reduced blood pressure, improved immune function (increased sIgA), reduced anxiety and depression scores. 10-15 minutes daily practice.

Meditation and prayer — Activates the ventral vagal state. Loving-kindness meditation (metta) is particularly effective for vagal tone — Kok 2013 showed loving-kindness meditation increased vagal tone and positive emotions in a reciprocal upward spiral. Even 10 minutes daily produces measurable vagal tone changes within 8 weeks.

Social co-regulation — Nervous systems are not isolated — they attune to each other. A calm, regulated person can co-regulate a dysregulated person through their presence, voice, and eye contact. Safe, attuned relationships are the most powerful vagal tonic that exists. This is why isolation is so destructive to health and why “prescribing” community, group activities, and therapeutic relationships is legitimate medicine.

Somatic experiencing (Peter Levine) — A body-based trauma therapy that works directly with the autonomic nervous system. When trauma occurs, the fight/flight/freeze response gets “stuck” — the survival energy is never discharged. Somatic experiencing gently helps the body complete the defensive responses that were interrupted, releasing the stored sympathetic or dorsal vagal charge. Essential for patients with complex trauma, PTSD, or chronic nervous system dysregulation that does not respond to supplements and lifestyle alone.

EMDR (Eye Movement Desensitization and Reprocessing) — Bilateral stimulation (eye movements, tapping, or auditory alternation) appears to facilitate reprocessing of traumatic memories, reducing their autonomic charge. Extensive evidence base for PTSD. Can produce rapid shifts in nervous system regulation around specific traumatic memories.

Neurofeedback — Real-time EEG monitoring that trains specific brain wave patterns. Can directly address insomnia patterns, anxiety-dominant brain signatures, and trauma-related dysregulation. Requires a trained practitioner and specialized equipment.

---

Supplement Support

For Sleep

Magnesium glycinate or bisglycinate — 300-600 mg elemental magnesium at bedtime. Glycine itself has sleep-promoting properties (enhances NREM sleep — Bannai 2012), and magnesium activates GABA receptors, reduces cortisol, and relaxes muscle tension. The single most important sleep supplement for most patients.

L-theanine — 200-400 mg at bedtime. An amino acid from green tea that increases alpha brain waves (relaxed alertness), enhances GABA, and reduces anxiety without sedation. Promotes sleep onset without next-day grogginess.

Glycine — 3 grams before bed. Lowers core body temperature (facilitating sleep onset), improves subjective sleep quality, and reduces next-day fatigue (Inagawa 2006, Bannai 2012).

Melatonin — 0.3-5 mg 30-60 minutes before bed. Start with the lowest effective dose — 0.3-0.5 mg often works as well as higher doses for sleep onset (physiological dosing). Higher doses (3-5 mg) are used for circadian rhythm disorders, jet lag, and their antioxidant/neuroprotective effects. Extended-release formulations help with sleep maintenance (middle-of-the-night waking).

Apigenin — 50 mg at bedtime. A flavonoid from chamomile that binds GABA-A benzodiazepine receptors — producing a mild anxiolytic and sedative effect without the risks of pharmaceutical benzodiazepines.

Phosphatidylserine — 100-200 mg at bedtime. Blunts the cortisol response — particularly useful for patients with elevated evening cortisol (the “wired but tired” pattern). By reducing cortisol, it facilitates the natural cortisol nadir needed for sleep.

For Nervous System Support

Ashwagandha (Withania somnifera) — 600 mg per day (KSM-66 or Sensoril extracts are the most studied). Reduces cortisol by 23-30% in clinical trials (Chandrasekhar 2012). GABAergic activity. Improves sleep quality, reduces anxiety, supports thyroid function. Take in the evening or split AM/PM.

Holy basil (Ocimum sanctum / Tulsi) — 500 mg twice daily. An Ayurvedic adaptogen that modulates cortisol, reduces anxiety, and supports cognitive function. Gentle, well-tolerated, good in tea form.

Rhodiola rosea — 200-400 mg in the morning (energizing — do not take at night). An adaptogen that improves stress resilience, reduces fatigue, and enhances cognitive function under stress. Particularly effective for burnout and adrenal fatigue patterns. SHR-5 extract is the most studied.

GABA — 500-750 mg at bedtime or during acute anxiety. The primary inhibitory neurotransmitter. Whether supplemental GABA crosses the BBB is debated — but clinical studies show anxiolytic effects (Abdou 2006), possibly through peripheral GABA receptors, enteric nervous system effects, or limited BBB crossing in states of barrier permeability.

L-theanine — 200 mg as needed for daytime anxiety (non-sedating) or at bedtime for sleep. Versatile, safe, no dependency risk.

Reishi mushroom — 1-2 grams in the evening. Triterpenes have calming, anxiolytic properties. Traditionally used as the “mushroom of spiritual potency” for its effects on the shen (spirit/mind) in Chinese medicine.

Lemon balm (Melissa officinalis) — 300-600 mg. GABAergic, anxiolytic, and mildly sedative. Particularly effective for anxiety-predominant insomnia. Also has antiviral properties against HSV.

Passionflower (Passiflora incarnata) — 500 mg at bedtime. GABA-A receptor modulation. A clinical trial showed passionflower extract comparable to oxazepam (a benzodiazepine) for generalized anxiety, with fewer side effects (Akhondzadeh 2001).

---

The Integration

Sleep, circadian rhythm, and nervous system regulation are not three separate health goals — they are one goal viewed from three angles. Align the circadian rhythm and sleep improves. Improve sleep and the nervous system gains capacity to regulate. Regulate the nervous system and circadian rhythm entrains more easily.

Start with light. Morning sunlight, evening dimness. This costs nothing and changes everything. Add consistent timing — meals, sleep, wake. Layer in vagal toning practices — breathing, cold, community. Support with nutrients — magnesium, adaptogens, melatonin if needed. Address the structural barriers — sleep apnea, trauma, chronic pain.

The body was designed to sleep deeply, rise alert, and navigate stress with flexibility. When it cannot, something is interfering. Find the interference. Remove it. The rhythm returns.