The Three-Legged Stool: The Autoimmune Answer

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The Three-Legged Stool: Autoimmunity occurs when the body’s immune system attacks itself, and despite the rise in autoimmune conditions, there is no single solution to cure the symptoms.

Autoimmunity is the label given to a cluster of unexplained symptoms, including eczema, celiac disease, type 1 and 2 diabetes, Hashimoto’s, leaky gut, lupus, and IBS. Today we explore a concept known as the three-legged stool to tackle autoimmunity from a functional medicine perspective.

The Three-Legged Stool: What is the Immune System?

The immune system is an extensive network of cells and proteins that defends the body against infection. The immune system keeps a record of every foreign invader (called antigens) it has ever attacked so that it can recognize and destroy the microbe faster if it enters the body again 1.

Key players of the immune system include white blood cells, antibodies, the complement system, the lymphatic system, the spleen, the thymus, and the bone marrow. Although these are the parts of the body that actively fight infection, the whole body always plays a role, less directly.

What is Autoimmune Disease?

Autoimmune disease is diagnosed when the body’s immune system attacks healthy cells. In reality, this “disease” is not a proper diagnosis and is simply the blanket term given to an illness to which the root cause is not understood 2.

Some examples of autoimmune diseases include: 2-3

  • Rheumatoid arthritis
  • Lupus
  • Celiac disease
  • Sjögren’s syndrome
  • Multiple sclerosis (MS)
  • Type 1 diabetes
  • Inflammatory bowel disease (IBD)
  • Guillain-Barre syndrome
  • Psoriasis
  • Grave’s disease
  • Hashimoto’s thyroiditis

The Three-Legged Stool: Common Autoimmune Symptoms

You may be reading so far and think that “this article is not for me… I don’t have an autoimmune disease.” Still, the reality is that autoimmunity can’t be specifically tested for, and the long list of diseases that fall under the category of autoimmunity are not proper diagnoses.

Suppose you know something is out of whack with your body. In that case, the collection of symptoms you’re experiencing may be autoimmunity, even if they don’t fall under one of the classic labeled types.

Common symptoms of autoimmunity include: 4-5

  • Headaches
  • Anxiety
  • Brain fog
  • Dry mouth
  • Swollen glands
  • Attention-deficit problems
  • Body rashes
  • Acne
  • Eczema
  • Psoriasis
  • Rosacea
  • Dermatitis
  • Allergies
  • Asthma
  • Frequent colds
  • Underactive or overactive thyroid problems, including Hashimoto’s disease or Graves disease
  • Fatigue or hyperactivity
  • Feeling “wired and tired.”
  • Weight gain or loss
  • A general feeling of unease
  • Muscle pain and weakness
  • Stiffness and pain, including rheumatoid arthritis or fibromyalgia symptoms
  • Exhaustion
  • Digestive tract upset including irritable bowel disease (IBS) or Crohn’s disease
  • Abdominal pain
  • Stomach cramping
  • Gas
  • Bloated stomach
  • Diarrhea
  • Constipation

Autoimmunity is not that helpful of a diagnosis because it is not uncovering a root cause. It is simply the collection of unexplained symptoms that cause the body to attack itself 5. Often, we dismiss such a type of diagnosis by suggesting that it’s a normal reaction to life.

Terms like “mommy brain,” “that time of the month,” or simply “getting old” dismiss the very real symptoms that are diminishing your quality of life. Before ignoring your symptoms merely because they are common, best understand how the three-legged stool analogy may bring you back to thriving.

The Three-Legged Stool: The Autoimmune Answer

People are getting sick and not getting well; what is going on? The three-legged stool analogy addresses the “why” behind the explosion of autoimmune diagnoses we have coming out of the West.

Although humans generally want there to be one answer to their question, the reality is that autoimmune illness is complex. Western medicine has primed our brains to seek one pill, one shot, or one operation to ‘fix’ the problem, but as we can see by the booming and unsolved autoimmune diagnosis, this one problem one solution mindset just does not work.

The concept itself is straightforward: for a stool to function, all three legs have to be present. Take one (or more) away, and the chair falls. Like a stool, your body has three main pillars that must be supported for you to experience good health, they are:

  1. Stressors (Physical, Chemical, and Emotional)
  2. Gut/ Microbiome
  3. DNA


Stress comes in three forms: chemical, emotional, and physical. Every drop of stress builds up in the body until the metaphorical bucket begins to overflow 6-8. This overflow s why some people hit a wall out of “nowhere”: your stress bucket has been accumulating for years. So the final event that tipped the scale might not have seemed like anything major, but in fact, it’s the cumulative effect of stress over a lifetime.

Chemical stressors are found everywhere in our modern environments. They include toxins found in 6-10

  • Food (GMOs, pesticides, herbicides, processed foods)
  • Mercury in amalgam fillings
  • Heavy metal toxicity (industrial exposure, air or water pollution, foods, medicines, improperly coated food containers, or lead-based paints)
  • Black mold found in homes, schools, stores, and office buildings
  • Tap water toxins (including chlorine and fluoride)
  • Conventional body care products (including SLS, parabens, and fragrances)

Physical stressors are also common-place in modern life. They include:

  • Too little or too much exercise
  • Stagnancy (sitting or standing in one position all day long)
  • Unaddressed biomechanical imbalances
  • Wearing conventional shoes (too narrow, or with a heel)

Emotional stressors are perhaps the least acknowledged form of stress because they are perceived stress. Perceived stress from negative emotions has just a real impact on stress hormones in the body. Although all emotions are healthy and normal, emotional stress is when stress becomes chronic and a looping feeling, without any resolution. These emotions include: 11

  • Grief
  • Sadness
  • Anger
  • Frustration
  • Anxiety
  • Depression

Gut/ Microbiome

Dysbiosis in any of the body’s microbiomes (like the gut, oral, and skin) is associated with chronic inflammation in the body 12. The gut is significant when it comes to autoimmunity since it plays such a large role in regulating the immune system 13. Changes in the gut microbiome (too much, too little, or an imbalance of the “good” to “bad” bacteria) can cause immune dysregulation, which can lead to autoimmune disorders 14.


The old paradigm of disease often blamed genetics for our illnesses. Whatever runs in the family was understood to be inevitable when that simply is not the case. The newer branch of epigenetic science understands that although genes are present, they act as a loaded gun. Having a gene that predisposes you to cancer, diabetes, or Alzheimer’s makes it more likely to develop a disease but does not actually pull the trigger 15.

What pulls the trigger is lifestyle choices 15—particularly the two legs of the stool mentioned above: stress and gut/ microbiome. When stress or the gut microbiome is out of balance, this can trigger a genetic trait to turn on.

With all the incredible genetic testing available, we can get very informed about the pre-dispositions that our DNA holds, but it’s important not to let that scare you. The awareness of these pre-dispositions can cause more mental stress than benefit.

Rather than assuming an APOE-e4 gene (for example) will pretty much guarantee you develop Alzheimer’s, or that the BRCA1 or 2 genes will give you breast cancer 16— better to use this information as a reminder—your healthy lifestyle choices are more important than ever.

Getting Your Life Back: A Multi-Therapeutic Approach to Autoimmune Disease

You can understand autoimmunity as the perfect storm of stressors, as generally all three of these stool legs have been lost by the time you have an autoimmune diagnosis.

By understanding the source of the imbalance, we can then tackle autoimmunity with a multi-therapeutic approach to support or re-build these pillars (legs of the stool) so that you can get your life back. Knowing the cause also gives us the solution.

One of the most common missing links while addressing autoimmune disease healing is the chemical or toxic stressors on the body. Although the concept of detox is well known to most, an appropriate approach is not. Quick fixes, store-bought detox teas, or foot baths fail to safely and effectively target the cellular source of toxins.

The 5R Approach

The 5R approach to detox targets toxicity all the way upstream to the source: the cell. Cellular detox is not a quick fix, and although many symptoms can and often do alleviate within the first few months, it’s essential to stick with the protocols for much longer to undo years of toxic build-up.

The 5R approach entails:

  1. Removing the Source
  2. Regenerating the Cell Membrane
  3. Restoring Cellular Energy
  4. Reducing Inflammation
  5. Reestablishing Methylation

If you are dealing with chronic issues of autoimmunity, the best way to navigate a 5R healing approach is under the care of a functional medicine practitioner. This is why thousands of doctors across America are trained in this method to support a safe and effective journey out of chronic illness and back to health. You can connect with a practitioner by calling (800) 833-2941.

Ancient Healing Techniques

Alongside the 5R approach to safe and effective detoxification, ancient healing techniques are used to harness the power of hormesis. Hormetic stress generates hormesis, a positive adaptation in the body. This strengthens the bodily systems to be more flexible and resilient against changes in the environment 17.

Some examples of hormetic stressors include:

  • Dietary adaptation (some ketogenic low carb days, some high carb days, some fasting days)
  • Intermittent fasting (periods of feeding and periods of fasting, within a 24-hour cycle)
  • Feast/ famine cycling (periods of extended fasting)
  • Hot/ cold therapy
  • Exercise (some explosive training days, some slow heavy training days, some recovery days)

It’s important to understand that although hormetic stress is “good” stress, it is still stress. If you are dealing with debilitating autoimmune symptoms, hormetic stressors need to be introduced very gently.

Some ways to ease into hormetic stressors:

  • Dietary adaptation would involve more high carb days, as you slowly become more metabolically flexible, you can introduce more low carb and fasting days.
  • Intermittent fasting could hover around 12 hours of feeding and 12 hours of fasting per day. This fasting can increase slowly with time, as the body can handle it.
  • Longer fasting periods can be introduced once metabolic flexibility is increased through dietary adaptation and intermittent fasting and under the care of a practitioner.
  • Instead of taking an ice bath right off the bat, you can take a quick cold shower at the end of a hot shower. You can even start off by simply doing a cold face plunge in a big bowl with a few ice cubes.
  • Exercise for shorter periods regularly, and increase intensity over time. For someone who is very sick, stick to relaxing forms of movement like gentle walks or yoga, knowing that as the body heals, you will introduce more intense forms of exercise.


Autoimmune diseases are on the rise, and diagnoses include various illnesses where the immune system attacks itself. However, the diagnosis itself to autoimmunity does not address the root cause because the diagnosis is based on symptoms. One way to understand, and therefore start to heal from, autoimmunity is the three-legged stool analogy.

Stress, the gut/ microbiome, and DNA form the three legs of the stool, and autoimmunity becomes an issue when one or more (but generally all three) are off. The perfect storm that creates autoimmunity can countered with a multi-therapeutic approach that uses the 5R method for detox and ancestral healing techniques.

Medical Disclaimer: This article is based upon the opinions of Dr. Daniel Pompa. The information on this website is not intended to replace a one-on-one relationship with a qualified health care professional and is not intended as medical advice. It is intended as a sharing of knowledge and information from the research and experience of Dr. Pompa and his associates. This article has been medically reviewed by Dr. Charles Penick, MD for accuracy of the information provided, but Dr. Pompa encourages you to make your own health care decisions based upon your research and in partnership with a qualified health care professional.


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