insomnia, sleep, sleep medicine, functional medicine, the power of sleep, fatigue, tired, self-care

Insomnia Solution–Part Two: Treat the Root Cause

Insomnia sufferers, let’s get down to the nitty-gritty. What are the reasons for not sleeping well? And what’s actually happening when we don’t sleep? We all know it feels bad, but why is it bad and how does it lead to illness? As you can deduce from the previous discussion about what sleep does, lack of sleep has a profound effect on regulation of key aspects of our internal biology, as well as on our wellbeing. There are no positive attributes of under-sleeping.

Insomnia Basics: Common Reasons for Not Sleeping Well

  • Excesses of stress that leave us tired but wired.
  • Mood issues–such as anxiety, depression, or worry.
  • Hormone imbalances.
  • Pain and body discomfort.
  • Urinary problems.
  • Environmental problems like excess light, noise, or irritants.
  • Small children in the home.
  • Uncomfortable bedding and pillows.
  • Excessive exposure to daytime light, especially the blue light from electronics (reduces melatonin production).
  • Primary sleep problems such as sleep apnea, movement disorders (such as periodic limb movement or restless legs syndrome), narcolepsy.
  • Circadian rhythm disturbances.
  • Chronic infections, allergies, and inflammation.
  • Gastrointestinal disorders.
  • Low blood sugar.

Insomnia: What Happens When We are Sleep Deprived?

  • We lose energy due to loss of both conservation time and regulation of energy control.
  • We are exposed to a higher toxic load from oxidative stress and toxin build up in the brain.
  • We experience disruption of our circadian rhythm and the control of key aspects of our physiology by the solar cycles of light and dark.
  • We experience ramping up of our stress systems to offset the energy debt, leading to heightened fatigue, increased demand on our energy systems, anxiety, and overwhelm.
  • We become more inflamed.

The problems associated with insomnia and sleep deprivation become worse over time and snowball. More time spent awake results in loss of energy conservation, and decreased repair and restoration. It requires effort and energy expenditure, which leads to greater toxicity and need for repair and restoration. Loss of circadian rhythm control of our genetic expression (clock genes) and major hubs of our physiology, disrupts hormone signaling and important cell-to-cell communication about running the business of the body. The problems of sleep deprivation escalate, leading us straight into disaster.

Common Problems Caused by Insomnia and Sleep Deprivation

  • Fatigue.
  • Increased inflammation.
  • Increased appetite and weight gain (see below).
  • Digestive and gut motility problems.
  • Loss of function and performance in tasks.
  • Cognitive dysfunction.
  • Increased tendency toward mood problems—depression, anxiety, and irritability.
  • Increased susceptibility to accidents and mistakes.
  • Increased sensitivity to pain and discomfort.
  • Hormone imbalances
  • Multi-system dysfunction that can lead to or exacerbate any illness.

Insomnia and Sleep Deprivation Leads to Weight Gain

There is an important relationship between sleep and body weight. Not only does the timing and quality of sleep impact appetite and body weight, the timing, quantity, and quality of food intake influences sleep. Sleep deprivation and circadian rhythm disruption can lead to weight gain independent of calorie consumption. In over-weight people who are not sleeping well, it is important to correct sleep patterns first. This will release an important block to normal metabolism and achieving ideal body weight.

By correcting sleep problems without restriction of calories, most people will lose body fat. There is additional drive to gain weight in conditions of sleep deprivation that comes about by the body’s response to energy debt. It releases the control of appetite and satiation via the hormones guerlin and leptin, leading to increased appetite and over-eating in an effort to support energy production.

Likewise, the content and timing of food relative to our circadian rhythm is important for optimizing sleep. Eating after eight pm is associated with higher body weight and worse sleep. It is important to eat enough protein at each meal (see my article on optimal protein intake) because the neurochemicals that help to regulate sleep and relax the brain, such as melatonin, GABA, and serotonin, are all synthesized from amino acids, derived from the protein in our food.

It is also important that meals be micronutrient-rich, low in sugar content, and rich in healthy fats. This allows for optimal support of the energy production needed for normal brain function. It stabilizes blood sugar and insulin levels, mitigating a potential source of arousal by hypoglycemia and inflammation (an inflamed brain does not sleep well). Intermittent fasting (no food intake—especially carbohydrates and protein—for twelve to sixteen hour blocks overnight) positively affects clock genes and improves energy production and detoxification. The available studies on fasting support its role in energy production and life extension, and I would submit that there is a positive effect on sleep. See my Liftoff Foundational Intensive Nutrition Food Plan in to dive into a food plan that helps optimize sleep.

The Gut-Brain Connection in Insomnia

The gut microbiome—the bacteria that reside within our gut and support our health—effects our sleep, and our sleep effects the microbiome. There is a deep and complex relationship that exists between our internal bugs and the rest of our bodies, including sleep. Gut microbes influence our sleep patterns through their effect on hormone balance, energy metabolism, detoxification, immune regulation, and circadian rhythm. Our sleep sufficiency influences the gut microbes via hormones, energy, food availability, and stress activation.

Having a healthy gut microbiome will improve the health of the brain, leading to better sleep.

What Constitutes Good Sleep?

  • Sleep that is sustained long enough to meet each of our unique needs.
  • Sleep that is deep enough.
  • Sleep that aligns with the solar cycle of light and dark (sleep in the dark and be awake during the day).
  • Sleep that leaves us feeling refreshed and restored.

We Must Sleep Long Enough for Our Unique Constitutions and Needs

In addition to sleeping in phase with the solar cycles, it is important that we sleep long enough for the needs of each of our unique bodies. We are all different in what those needs are—they change with age, with level of activity, and other aspects of physiological need. Newborns, as we all know, sleep most of the time—on average fourteen to seventeen hours per day. Need for sleep gradually decreases as we age. Teens require eight to ten hours on average, young adults seven to nine hours on average, and adults ages twenty-six to sixty-four need an average of seven to eight hours, with some needing as much as nine hours of sleep per night. For adults who are fatigued or suffer from chronic, complex illness, those needs are increased even further.

When we’re deprived of getting the sleep we need, a wide range of health problems can occur. The most obvious effect of insufficient sleep is tiredness—the result of physiological energy debt—and reduced effort, motivation, and performance. Over time, persistent sleep deprivation will evolve into deep fatigue, vulnerability to illness, and misery. The long-term effects of sleep deprivation include neurobehavioral disorders (such as poor attention, memory impairment, reduced cognitive function, depressed mood, and irritability), ramped-up stress physiology, hormone imbalances, increased inflammation, and impaired glucose regulation. It is linked to numerous chronic health disorders including obesity, diabetes, heart disease and stroke, cancer, arthritis, autoimmunity, and an increase in all-cause mortality. There is strong science that shows how chronic low-level sleep deprivation (chronic restriction of sleep duration to less than seven hours per night for the average person; some people require much more sleep than others, so low level sleep deprivation for them could occur with eight hours of sleep per night) is as lethal as one to three nights of total sleep loss.

We Must Sleep Deeply

The quality of our sleep is as important as the amount of time we spend in bed. This means we must pass through the structural attributes of sleep that we refer to as the sleep stages. We don’t yet understand all of the details about sleep stages and the roles they play in the restorative functions of sleep, but we do know that they are necessary. There are two main types of sleep, referred to as non-rapid eye-movement sleep (NREM) and rapid eye-movement sleep (REM).

NREM is divided into four stages: the earliest and lightest stage is stage one, continuing through stages two through four, each progressively deeper levels of sleep. Each of the sleep stages has unique brain wave patterns as well as eye and muscle movement characteristics. As we move through a full night of sleep, we cycle through both NREM stages and REM, spending most of our time in NREM sleep, and just about twenty-five percent of our time in REM. As we progress through each of the stages of NREM sleep, brain waves are slower and we become increasingly difficult to arouse.

REM cycles are typified by seemingly chaotic brain wave activity, muscle paralysis, and burst of rapid eye movement. This is the time when we dream. As we progress through the night, time spent in REM increases, and time in deep sleep decreases. Most vivid dream recall occurs when we are aroused out of this stage of sleep.

If we become unable to sustain enough time in the deeper stages of sleep, due to interruptions or conditions that are arousing—such as pain, abnormal movement, or environmental problems—the deep and necessary restorative aspects of sleep do not occur. This will be experienced as fatigue and, eventually, the impairments and illnesses listed in the previous section.

The Significance of Waking Up Feeling Refreshed and Restored

Feeling refreshed and restored is the best indicator that we are receiving sufficient high quality sleep. We don’t need fancy tests for this. The body can be trusted to let us know. If you are uncertain, or have difficulty reading the signals of your body, observe yourself carefully: Are you as alert and awake as you like to be? Is your effort and performance of tasks where you want them to be? Are others expressing concern about your performance? Are you yawning, irritable, restless, having headaches, or falling asleep at inappropriate times during the day? Are you having to awaken to an alarm in the morning? Do you depend on caffeinated drinks, stimulants, or sugar to get through the day?

If you answered, “yes” to any of these questions, you may not be getting enough sleep or there is a problem with the quality of the sleep you do get. I’ve had clients who spend ample time in bed, feel they are sleeping, but we discover problems that interfere with their ability to stay in the necessary deep stages of sleep.

Insomnia Solutions: Restoration of Healthy Sleep

Our deepest restoration and healing occurs while we sleep. It doesn’t come easily for everyone. And we tend to sell ourselves short here, slipping into patterns of trading sleep and restoration for continued effort in our waking lives.

There are health conditions that can make sleep difficult. Pain, excessive stress, menopausal symptoms, urinary tract problems, obstructive sleep apnea, limb movement disorders, and metabolic problems caused by thyroid or adrenal dysfunction, to name just a few, are common causes of chronic sleep disturbance. In addition, any condition that causes an excess of inflammation will lead to an inflamed brain and can disrupt sleep.

It is important to work with your trusted health practitioner to get these problems solved. You may need lab tests to check your thyroid and adrenal function, iron levels, nutrient levels, and indicators of inflammation. You may need to have a sleep study done at a professional sleep lab where they monitor the quality of your sleep, in addition to oxygen levels, movements that may lead to arousals from sleep, quality of your breathing, and in some cases, brain wave activity. I do sleep studies routinely in my clients who have persistent fatigue without an obvious cause after a thorough evaluation or if they had symptoms suggestive of a complex sleep disorder. This has led to many diagnoses of periodic limb movement (PLM) or apnea that had previously gone undetected or suspected—even by the patient and their families. PLM leads to arousals out of the deeper stages of sleep, decreasing the restorative aspects of sleep. Apnea leads to oxygen deprivation as well as frequent arousals, diminishing sleep quality.

For most of us sleep disturbance is a lifestyle issue—one we can readily correct with the right knowledge about its impact and the intention to improve this deeply valuable and necessary part of our lives.

Reverse Insomnia: The Practice of Cultivating Deep Sleep

Good sleep is a practice like all the others you are learning about in this book. It is easy to sacrifice this vital restorative time in favor of the competing obligations and activities of the day. Or to lose our ability to be peaceful enough for deep sleep because of stress and worry. We must practice good sleep—setting aside ample time and creating the optimal conditions—as part of our daily self-care regimen.

Make Sleep One of Your Core Self-Care Habits

  • Consider sleep to be as vital to your health as good food, movement, and all other aspects of your life that you make a priority.
  • Plan a regular bedtime that makes sense for your life and stick to it. The brain likes habitual behavior and will get into the groove with time.
  • Plan for enough sleep. Stay in bed long enough to meet your needs. This will be different for everyone. The average number of hours adults need for optimal sleep is eight to eight and a half hours, but there are many exceptions to this. Our bodies will always let us know. If you experience tiredness or lack of restoration after a night of sleep, you are not getting enough. If you are recovering from an illness, you need more sleep than usual.

 Prepare Your Body for Sleep

  • Follow one of the Liftoff food plans depending on your needs. A diet rich in nutrition that comes from plants, healthy proteins, low sugar content fruits, and good fats leads to a healthier brain and body that can sleep deeply and restoratively at night. Eat lightly at night, not within two hours of going to bed, and fast for twelve to fourteen hours over-night from the time of your last meal. Avoid all commercial animal products, which are high in palmitic acid, a known pro-inflammatory fat. Don’t rush eating.
  • Use probiotics and prebiotics to optimize the microbiome.
  • Start each day with something hot to drink, like pure water, tea, or bone broth (coffee if allowed on your food plan). This wakes up the gut and signals the body that a new day is beginning. Rest a bit while consuming rather than leaping right out of bed and into action. The process of waking up is the most stressful event of the day. This is a good time to meditate, write in your journal, or review affirmations that set a positive tone to the start of your day.
  • Boost your natural light exposure during the day. Spend some time outdoors or near windows. An hour of sunlight at noon every day is best when possible. Allow darkness to set in at the normal time.
  • Avoid excesses of light and electronics for a couple of hours before bedtime. This allows for your brain’s circadian rhythm to get in sync, releasing melatonin to calm your nervous system, preparing for deep sleep. Use blue light filters on your electronic screens and read on devices with a black background.
  • Stay well hydrated throughout the day. Drink ample fluids—a minimum of two quarts per day for most people. However, avoid drinking too close to bedtime or your full bladder may awaken you during the night. Hold off on fluids for at least two hours before going to sleep.
  • Move and exercise your body every day. Intense exercise early in the day helps with deeper sleep. Avoid it late in the day as the increase in stress hormones can interfere with falling to sleep.
  • Limit caffeine use to early-mid morning. Caffeine helps over-ride the perception of tiredness from sleep deprivation by its effect on adenosine receptors. It delays the secretion for melatonin from the pineal gland. Some people should use no caffeine at all as the effect on their stress mechanisms can interfere with rest and sleep many hours later.
  • Avoid excesses of alcohol, which can impair sleep. Some folks are very sensitive to this effect and should avoid it all together.

Prepare Your Mind for Sleep

  • Start the process of letting go of the concerns of your day at least two to three hours before laying your head on your pillow. Turn down lights, turn off electronics (banish the TV and computer from your bedroom!). Decrease noise and begin to move into more restful phase of your day.
  • Unload your worries or “to do” list onto your peripheral brain (write them down or enter them into your electronic device). This will allow you to rest rather than worry about what needs to be done tomorrow.
  • Allow yourself to relax at night. This is especially beneficial for those stressful days when your mind is not quite ready to settle down. This practice could be as simple as reading an enjoyable book before bed, doing a calming meditation, a guided meditation, quiet prayer, listening to soothing music, or other settling, calming activity. Some meditations are energizing and may not be conducive to letting go into a deep sleep—trust your body to tell you what works best for you.
  • Meditate during the day. Daytime meditation, practiced in the morning or as late as early evening, balance the stress and nervous systems, making sleep more available to us at the end of the day. Meditation increases the production of melatonin from the pineal gland and creates a biochemical milieu that favors deep sleep.
  • If you have a hard time getting your mind to quiet down at bedtime, use affirmations about deep sleep that activate the power of your intentions:
  • I let go, rest my mind and sleep deeply.
  • Thank you for the perfect sleep and restoration.
  • I am safe and comfortable in my bed.

 Create an Environment that Nurtures Good Sleep

  • Create a pitch dark, quiet, and comfortable environment for sleep. Cover all mirrors or lights of any kind. Use black out shades in your bedroom or wear a soft eye mask when you sleep. One photon of light can interfere with melatonin production and sleep. Reduce extraneous noise and consider wearing soft earplugs if needed.
  • Assess your bedding—are your mattress, pillows, and covers perfectly comfortable? Are you warm or cool enough?
  • Bedtime readers, be careful with electronic formats as they can emit a lot of brain-stimulating light. Reduce the light output by blackening the background and reduce the whitening of the words. It is also good to use blue light filters on all electronic devices throughout the day.
  • Work to reduce the clutter in your bedroom. Piles of laundry, books, or work-related materials stress us–even if we aren’t aware of it–and can get in the way of the deep letting-go we need to sleep well.

 Use Safe Sleep Aids to Support Your Sleep

  • Work with herbs that can calm the brain and assist with sleep: chamomile, lemon balm, valerian, kava, skullcap, passionflower. These come in combination formulas that are safe and affordable. Note that there are some people who experience paradoxical alertness when using valerian.
  • Try safe nutritional supplements that relax the brain: GABA, 5-HTP, l-theanine, magnesium glycinate, glycine.
  • Melatonin can help re-establish the internal circadian rhythm that helps regulate sleep. It can be especially helpful for time zone changes, shift workers, sleep changes associated with aging, and inflammation. Start with 1-3 mg taken in the evening, an hour or two prior to bedtime.
  • For those who are exhausted from too much stress, but too wired to sleep, adrenal support may be helpful. Phosphatidyl serine is an excellent neutralizer of the stimulating effects of cortisol on the brain. Work with a trusted health care provider who is knowledgeable about such treatments.
  • Therapeutic modalities such as massage, acupuncture, energy medicine, or hypnotherapy can be very helpful for sleep.

Manage Complex Sleep Disorders

  • Find help for relieving pain and discomfort. This can be a challenge for a multitude of problems. Seek professional advice.
  • Your sleep may be particularly challenged by pain, menopausal symptoms, or other distressing symptoms. Work with a trusted health practitioner on these problems.
  • You may have restless legs or sleep apnea. Your current symptoms may make this obvious. A sleep study and work with your doctor will help sort this out.
  • Some people need sleep medication as a ‘bridge,’ allowing them to sleep as part of their recovery plan, while the other aspects of their illness are being addressed. The need to correct sleep problems with the use of medications must be balanced with their addictive potential and habit forming nature.
  • Remember: there is always a solution. Mobilize your health support team. Get a new opinion. Don’t despair or give up!

Create Your Personal Sleep Restoration Plan

  • Do you wake up feeling restored and refreshed in the morning? If yes, keep doing what you are doing! If no, there’s work to be done.
  • Do you depend on the alarm to wake you up in the morning? This may be a clue that you are not getting enough sleep.
  • Do you have trouble falling to sleep?
  • Do you wake up in the night and have trouble falling back to sleep?
  • Do you wake up early—before you are ready—and find it hard to get back to sleep?
  • Are there any interfering factors to your getting a good night of sleep?

Work through the strategies for sleeping well listed above. Make a list of those factors that may be interfering with you getting a good night of sleep. Diligently work toward resolution. If you need to go to bed earlier to get more sleep, don’t do it all at once. Gradually go to bed earlier, perhaps in fifteen-minute increments every couple of weeks, until you are humming along.

If you find yourself unable to get the sleep you need on your own, if it becomes overwhelming in any way, or if you have health conditions that are interfering with your ability to rest and stay in a deep sleep, seek advice from your trusted health practitioner. If you have already done that and are still having problems, I highly suggest you find someone in your community who practices Functional Medicine—they can look at your sleep difficulties in the context of your whole health and life story. They’ll provide you with root-cause solutions rather than quick fixes that simply suppress symptoms. Look for someone who is certified by the Institute for Functional Medicine. Ask around—word-of-mouth recommendations are best, in spite of someone’s qualifications.

Consider the following questions about your personal sleep strategy:

My Personal Sleep Goals are:

The Things I Need to Work On to Improve My Sleep Are:

What one thing can I change about my sleep habits today?

(hint: start there)


Karyn Shanks MD. Insomnia Solution–Part One: The Power of Deep Sleep. 2017

Leonard A. Wisneski, The Scientific Basis of Integrative Medicine, 2009.

Max Hirshkowitz, PhD, et al. National Sleep Foundation’s sleep time duration recommendations: methodology and results summary. Sleep Health, March 2015: Volume 1, Issue 1, Pages 40-43: read here

Xaquin Castro Dopico, et al. Widespread seasonal gene expression reveals annual differences in human immunity and physiology. Nature Communications 6, article number: 7000. 12 May 2015:  read here

Sleep Disorders and Sleep Deprivation: An Unmet Public Health Problem. Institute of Medicine (US) Committee on Sleep Medicine and Research; Colten HR, Altevogt, BM, editors. Washington (DC): National Academies Press (US), 2006: read here

Mindy Engle-Friedman. The effects of sleep loss on capacity and effort. Sleep Science. Volume 7, Issue 4, December 2014, pages 213-224: read here

Karyn Shanks MD


Karyn Shanks, MD, is a physician who lives and practices in Iowa City. Her work is inspired by the revolutionary science of Functional Medicine, body-mind wisdom, and the transformational journeys of thousands of clients over her twenty-eight year career. She believes that the bones of healing are in what we do for ourselves.

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