The Human Operating Manual

The Circadian Rabbit Hole

The Circadian Rabbit Hole

To be explored…

Topics listed below are ideas that are yet to be summarized. 


Lucid dreaming. As fun as it may be, I find it hard to believe that training your brain to have greater executive function and control during a period of rest is conducive towards a well-rested sleep. At a guess, I would assume you’re probably limiting your creative problem-solving abilities by not allowing your brain to explore information without your top-down control. Unless you have night terrors and are desperate to establish some form of autonomy over your dreams, it’s probably best to leave avoid lucid dreaming.  

Sleep deprivation and anxiety:

Sleep deprived teens sugar intake increase:

Sleep deprivation and immune system suppression:

Poor sleep and amyloid-b build up:

Glymphatic system:

Flip flop switch that integrates the brain areas that represent stress, light, eating, adenosine build up, etc.

Advice for night shift workers.

UVB and UVA exposure representing expected sun exposure evolutionary response. Without feedback of such an ingrained cue, positive feedback loops are executed. 

REM sleep and the connection with warm blooded animals. Divergent evolution between mammals and birds. 

Sleep’s connection with consciousness.

Metabolic clearance and the lack of placing a heavy demand on the system -> lower energy availability -> muscle and brain atrophy to compensate.

Sleep and learning.

Huberman Lab


Rapid Eye Movement Sleep

Before initiating REM, the brain stem sends a message to alpha motor neurons, that control voluntary skeletal muscles, to induce paralysis.

During REM sleep we go through periods where heart rate and blood pressure fluctuate (autonomic storms). This is when vaginal lubrication and erections may happen.

It’s thought that eyeballs are left inactive for too long there may be oxygenation issues. Which might be why we have rapid eye movement. 

Eye movements are not just side to side. The connection between the pons and the thalamus are involved in generating movements. Waves of activity from the brainstem, to the thalamus, up to the cortex is facilitating the eye movements.

Serotonin is absent during REM. This is why you don’t want to have 5-HTP supplements before going to bed. It may stay in your system during SWS and instead of transitioning into REM during the first cycle, you may wake up. 

NE is absent. We are paralyzed so don’t need it.

Growth hormone is more REM sleep dependent.

When you learn spatial information, the same brain activity often gets replayed during sleep (similar areas and order firing).

Emotions, Mental Health & Longevity

There are no psychiatric disorders where sleep is normal. REM sleep is the strongest predictor of longevity. Every 5% reduction in REM sleep led to a 13% increase in mortality.


Not enough REM sleep is a cause. Can use NSDR if waking too early.

Sleep to Delete (Spatial & Emotional)

Replay of spatial information during REM sleep. Helps to remember spatial mapping of a new area. Forms a relationship with certain algorithms, themes, and locations. Piecing together relevance of things to each other.

Deprived, things get distorted and people can hallucinate.

Without REM sleep we can start to incorrectly link things. REM can eliminate meanings that don’t matter.

Without adequate REM sleep we can react badly to events that don’t matter due to too much connectivity. Emotional stability is about the elimination of connections.

Paralysis & Hallucinations

Experienced dreaming as a hallucination. No epinephrine around and no desire to move as a consequence. Released in the brain.

We can experience replays of things in the absence of fear and anxiety. Meaning we can emotionally deescalate memories that were emotionally charged. Unlearning of emotional events.

There’s a good chance that nightmares occur during SWS. Not having Epinephrine during REM sleep makes it unlikely nightmares will happen during REM. Bound to be instances though.

It could be that the moment you wake up epinephrine is available and it is released then.

Sleeping While Awake

The panic of waking may be associated with the dream.

Some people have atonia while waking and are terrified. Can also be hallucinating. Alien abductions are very similar to the atonia and paralysis.

Could be the invasion of sleep state into the waking state.

Marijuana can increase atonia experiences. Don’t know why.


Set a queue. A statement you make in dreams. Doing it before sleeping so you can remember in sleep and tether to reality.

If you don’t like lucid dreaming, wake up at the end of an ultradian cycle.

Food, Supps, and Exercise

Using Exercise & Food to Set Your Clock

Don’t eat too close to bedtime. Usually ceasing eating 2-4 hours before bed time is okay. 

Food intake timing, exercise, drugs, etc., can affect circadian timing. Light viewed by melanopsin cells are way more effective than exercise or food timing though.

The intergeniculate leaflet regulates clock input by non-photic influence. Use this and light timing to change circadian rhythm.

Higher body temperature windows – where performance is improved and injury risk is reduced – are 30 minutes after waking (correlates with cortisol release), 3 hours after waking (body temp high), and the afternoon (11 hours after waking).

If you regularly workout in the morning, your body will anticipate it and wake up early. Intensity of exercise might be too high if one wakes up feeling unrested even though they are still sleeping plenty.

Drugs & Supplements

Most compounds will have an effect on our biology in some way. This doesn’t mean it is useful. Anything will make your sleep behavior change somehow. Anything that changes epinephrine or dopamine. Don’t push back on the neuromodulator system.

Magnesium: can have positive effects by increasing GABA (inhibition neurotransmitter). Magnesium threonate is associated with increasing transporters that bring more into cells to feel sleepier. Increases depth of sleep. Threonate is more bioavailable, shuttled preferentially to the brain and activates GABA pathway – turns off areas of the forebrain. Can be neuroprotective. Malate preferentially for muscle relaxation. Citrates main effect is as a laxative. He has 300-400mg, 30-60 minutes before sleep.

Theanine: It gets put in energy drinks to take off jitters. Energy drinks also have taurine which turned his whites (sclera) red. Microvascular damage from his taurine in his energy drinks. Activates certain GABA pathways. 100-300mg can have a calming effect. 30-60 minutes before bedtime (same timing as magnesium).

Apigenin: Increases some of the enzymes that are associated with GABA metabolism. A derivative of chamomile. Passionflower also does. Designed to increase sleepiness (hypnotic). They work on chloride channels and cells become less active when more chloride (negatively charged) hyperpolarizes neurons. Shutting off/inhibiting thinking. Also, may suppress conversion of androgens to estrogens (not necessarily a good thing as we all need healthy levels of estrogen). 50mg of apigenin. Can make dreams very vivid so be careful. 

Valerian has no real evidence. 5/7 RCT – no benefits.

Tart cherries reduced the amount of time spent awake at night. One had an 84-minute increase. The compound in tart cherry rather than the cherry itself.

Kiwifruits touted to have benefits. Decreased time to fall asleep and stayed asleep longer in a study. Skin and all. An animal model had a similar result. You could block the effects with a GABA blocking agent.

Only use supplements once you’ve done everything else first. You can’t cover up bad behavior with supplementation. 

Serotonin: Slippery Slope

You can change the absorption of natural tryptophan by taking the supplements. Serotonin also has specific timing during sleep so you don’t want to mess with that. You don’t want serotonin during REM sleep because it gets shut off, as well as acetylcholine getting ramped up. Low serotonin is associated with SWS, so getting REM early on with supplements may result in waking up after a few hours.

5-HTP (serotonin) and L-tryptophan (precursor) are not great. Sleep is dreadful and messes up the sleep cycles. Some people are fine with supplementation, so maybe it depends on diet, genetics, and lifestyle.


Dopamine mechanism (alerting), adenosine receptor antagonist (accumulates in the brain and is a metabolic byproduct of energy combustion). A1 and A2 receptors. Adenosine turns off wake systems and promotes sleep centers.

Caffeine crash (half-life 4-6 hours). Liver enzyme – cytochrome P450 enzymes dictate the metabolism of it.

People may not be able to fall asleep, or alternatively, stay asleep. Depth of deep sleep may be affected too. Quality of sleep decreases, plus the receptor change may lead to more caffeine consumption to get the same effect.

Taking caffeine too early can result in a mid-morning crash. Delay until at least 2 hours after waking. Otherwise, you’ll suppress your body’s own natural adenosine regulation in the morning.


Sedative, not a sleep aid. Sedates the cortex rather than initiate sleep. You just lose consciousness. Sleep is also fragmented, waking up often. Blocks REM sleep, which reduces emotional “self-therapy.” Emotional sensitivity increases. Things that increase serotonin and GABA are going to disrupt patterns.

Even a single glass of wine with dinner has an effect of less REM sleep.

REM sleep deprivation during consuming alcohol had a 50% drop in GH release. Testosterone gets reduced acutely.

Better to have a drink earlier to decrease the number of byproducts by the time you go to sleep.


Disrupts sleep. CBD is non-psychoactive. THC can speed up sleep time but it is not natural. THC blocks REM sleep. Sleep rebound occurs when alcohol or weed is no longer taken. There can be a dependency tolerance if you’re using it for sleep. Leading to insomnia and anxiety withdrawal.

CBD levels are no way near what they claim to have on the labels. Although, not as detrimental as THC. Low dose, CBD is wake promoting. Above 25mg leads to more sedation. Can create hypothermic effects, anxiolytic, can alter the signaling of adenosine. The weight of adenosine has a stronger pressure. These three effects are not quite proven to be useful enough yet.

Neuroplasticity & Food/Chemicals

If you eat on a tight schedule you will start to anticipate the meal times. Peptide signals like hypocretin orexin signal to the hypothalamus to make you awake, alert, and hungry. You can do the same with waking and exercise.

Improve learning and memory by cuing with a certain smell during learning and then using that smell during sleep. Or using a tone. You could also use a quiet metronome.


Temp lowest around 4am and creeps up to around 6pm. It can get anchored by entrainment with exercise, light, etc.

Your Temperature Minimum

Temperature being the effector is how you can make all the different cell types sync up. Can be determined by taking the last week of wake-up times and averaging them, then a few hours before that time will be your temperature minimum.

Expose your eyes to bright light 4 hours after the temp min to shift the circadian clock earlier. If you view the light 4-6 hours before your temp min you will delay your wake-up time and sleep time.

Sleepiness during the day, unless around the temperature peak, is a sign of insomnia. Fatigue is different.

Temperature and Exercise

In preparation for travel, wake up progressively earlier/later and eat, exercise, get light exposure an hour after your expected temp min time for the new destination.

Morning Chills

If your temperature clocks start to split from the central clock mechanism, you may get cold. Temperature and day length are linked. Temperature has an effect on the metabolism too.

The SCN secretes a peptide that goes to the cells and it also synchronizes the temperature under which those cells exist. The temperature is essentially the effector of the clock.

In an ice bath you have a rebound of thermogenesis, which can reset your clock. As temp increases you are shifting your day. Cold can trigger melatonin release, but if you have an early ice bath you will have a rapid rise in body temp which phase advances your clock, so you wake up earlier the next day. Can change by about half an hour.

Using cold exposure to raise stress threshold can be useful by resisting the shiver response. However, if you are using cold exposure for fat loss you really want to actually shiver as muscles release succinate, which travels through the bloodstream and activates brown adipose tissue (BAT). Mostly in the scapula and back of neck. These brown fat cells generate heat and thermogenesis, increasing the metabolism.

Try to maintain a state of calm for stress inoculation, or shiver for fat loss. Morning daily cold exposure for earlier phase shift and later for melatonin release (temp drop).

Temperature is the effector and light is the trigger. Eating can change the temperature and has the hypocretin orexin response too.

The precursor to serotonin and melatonin is tryptophan. Tyrosine is the precursor for dopamine and epinephrine. Food can influence neuromodulators to an extent. Red meats are rich in tyrosine. Lends themselves to increased dopamine and epinephrine. Fasting states are associated with more alertness and fed states with more serotonin and relaxation. Food rich in tryptophan are white meats and carbohydrates.

Low carb = wakefulness. Higher carb = sleepy. Unless working out hard. Then have carbs.

Eating For Heating

Eating induced thermogenesis is greatest with amino acid rich foods.

Volume of food will affect wakefulness too. Sensory fibers in the gut will send a message to the nodose ganglia in the brain stem, which is involved in the production of many neuromodulators.

Sex, Orgasm, Masturbation, Oxytocin, Relationships

You can be wired and tired, which prevents sleep initiation.

Sex that results in orgasm, as well as masturbation, can be used as a sleep tool. Oxytocin for pair bonding and hormonal benefits that are sleep promoting.

Reproductive hormones are affected by sleep and disrupted with deprivation. For every one hour of sleep a woman gets, the more interested they are to have sex with their partner. Sleep deprivation correlate with relationship conflict. Less empathy.

Sexual activity increases testosterone in both genders, as long as the relationship is a healthy one.


Write down when you get sunlight and for how long.

Write down meals and timing.

Exercise type and time.

When you feel cold or hot.

When you meditate, nap, or do NSDR.

Measuring REM / SWS

Rings, bands, and watches can be useful. Can subjectively measure to see if well rested. Regular sleep is more important than total sleep for the sake of learning.

For every hour of variation there was a 17% reduction in performance.

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