How Functional Medicine Can Reverse Your Autoimmune Disease

Any historian of the evolution of medicine understands the inextricable marriage between the pharmaceutical industry and the conventional medical establishment. Business magnate and philanthropist, John D. Rockefeller, funded the earliest American medical schools on the condition that synthetic, petroleum-based drugs from which his businesses would profit be the cornerstone of disease treatment.

He also hired Abraham Flexner to submit his famous early twentieth century report to Congress, which made illegal the practice of medicine by 'itinerant healers' such as hydropaths, chiropractors, naturopaths, and herbalists. This produced a climate of warring practitioners and fostered "sectarian antagonism," "internecine hatreds," and "mutual hostility" in the medical profession, and led to the concerted dissemination of propaganda dismissing their healing modalities as "quackery" (McKeown, 1979).

The American Medical Association sponsored a massive smear campaign such that natural medicine practitioners were marginalized and barred from inclusion in orthodox medical societies, forbidden from formal licensure, and stripped of prestige and legitimacy. For instance, "A committee of the AMA recommended that the Massachusetts Medical Society, which continued to harbor homeopaths among its members, lose representation until it purged itself of heretics" (McKeown, 1979). Thus ushered in the era of chemotherapy and synthetic pharmaceutical drugs, the magic bullet solution to all of humanity's ills. As a consequence, here we stand today, in the largest chronic disease epidemic in human history, where only one third of medical doctors receive a single course in nutrition during their professional training (Adams et al., 2006). Among that third who receive nutrition instruction, the average time spent learning nutrition-related material is a mere 23.9 hours (Adams et al., 2006).

Thus, if you are seeking advice on therapeutic nutrition and holistic lifestyle interventions from your conventional physician, you're barking up the wrong tree.

The American Heart Association estimates that 1 in 20 Americans will develop coronary heart disease, whereas the National Center for Health Statistics predicts that 1 in 14 will develop cancer at some time in their life. In contrast, a whopping 1 in 12 Americans (and 1 in 9 women) will develop an autoimmune disorder.

In addition, the American Autoimmune and Related Diseases Association (AARDA) states that autoimmune diseases collectively affect 50 million Americans, while cancer affects less than one fifth this number, at 9 million, and heart disease less than half this number, at 22 million (AARDA, 2017).

In fact, the AARDA states that 50 million represents an underestimate, since this approximation is only based on data from 24 autoimmune diseases (AARDA, 2017). Researchers have identified 80 to 100 autoimmune diseases and suspect that an additional 40 conditions have an autoimmune origin (AARDA, 2017). Further, the AARDA has used epidemiological studies and patient group data to demonstrate that approximately 1 in 5 Americans (63 million people) are affected by autoimmune disease (AARDA, 2017). Despite its growing epidemic proportions (see graph reproduced from Bach et al., 2002, which resembles trends observed in an outbreak of infectious disease), autoimmune diseases receive less than ten times the researching funding that cancer does.

Growing Epidemic of Autoimmune Disease

Even worse, the AARDA highlights that it takes most autoimmune patients up to 4.6 years and 5 doctors before receiving a proper diagnosis, with over 45% of patients being labeled as hypochondriacs or malingerers in the early stages of their disease (AARDA, 2017). Given the historically patriarchal nature of the medical establishment, this is no surprise, since autoimmune disease disproportionately affect women at a rate of 3:1 (although for Hashimoto's thyroiditis, the most common autoimmune disorder, some research suggests the ratio of women to men may be as high as 30:1).

Ratio of Women to Men Afflicted by Various Autoimmune Diseases

Because allopathic medicine is black-or-white, failing to recognize a spectrum from health to disease with gradations of deviation from the norm, the symptoms of people with sub-acute autoimmune manifestations are often dismissed as psychosomatic in origin.

For instance, hypothalamic-pituitary-adrenal axis dysfunction, colloquially known as "adrenal fatigue," is not acknowledged by conventional providers, although it often presents with adrenal cortex antibodies, which have a 70% positive predictive value that the patient will progress to Addison's in a 10 year period (Betterle et al., 1997). Instead, only the two extremes of adrenal failure—Cushing’s and Addison’s disease—are perceived with legitimacy.

As another example, take Hashimoto’s thyroiditis. Rather than optimal levels of bio-available, metabolically active, free thyroid hormone (free T3), conventional medicine relies on a pituitary hormone (TSH, or thyroid stimulating hormone), the antiquated marker for thyroid function. Moreover, TSH reference ranges are extremely lax, as they were established based on a sick population, so a symptomatic patient remains untreated longer and their condition continues to deteriorate.

The proper testing for Hashimoto’s, which includes thyroid peroxidase (TPO) and thyroglobulin (TG) antibodies, is not routinely performed, and subclinical hypothyroidism is not recognized as warranting treatment. TPO antibodies are ignored if TSH is in range, despite the fact that TPO has a positive predictive value of 92% for developing Hashimoto's within 7 to 10 years (Kita, Goulis, & Avramides, 2002).

When I was diagnosed with Hashimoto’s thyroiditis, my endocrinologist told me we had to wait until my thyroid had been completely “killed off” before they could administer exogenous thyroid, despite the fact that prophylactic thyroid hormone replacement has been demonstrated to produce significant decreases in TSH, TPO, TG, and a significant increase in free T4, decrease thyroid volume (shrink goiters), as well as “stop the progression or even manifestation of the disease” (Aksoy et al., 2005; Padberg, Heller, Usadel, & Schum-Drager, 2001, p. 249).

Part of the reason for this is the reductionism and compartmentalization that predominates in the biomedical paradigm, whereby physicians are silos into their respective compartments. Despite the identical underlying pathophysiology in ALL autoimmune diseases (loss of self-tolerance, breach of gut barrier integrity, dysfunction of self-regulatory mechanisms), conventional mechanisms fails to identify autoimmunity under one all-encompassing umbrella.

Instead, if you have vitiligo or psoriasis, you see a dermatologist. If you have Hashimoto’s thyroiditis or Addison’s disease, an endocrinologist manages your care. If you have lupus or Sjogren’s syndrome, you are referred to a rheumatologist. If you have celiac disease or Crohn’s, a gastroenterologist orchestrates your treatment. For patients with multiple autoimmune disorders, like myself, our diseases are treated as separate clinical entities when they in fact represent the same underlying mechanism.

Similarly, conventional medicine does not offer any early recognition, such as predictive auto-antibody screens, or preventative holistic measures to delay autoimmune development in genetically susceptible patients, instead relying exclusively on full-blown disease manifestation for diagnosis.

For instance, instead of investigating the HLA genotype and performing comprehensive gluten sensitivity testing, conventional providers do not diagnose celiac disease unless there has been complete endoscopy-confirmed Marsh grade 3 villous atrophy, which is accompanied by massive tissue destruction and micronutrient depletion. They do not recognize the mild gradations of histological atrophy that precede Marsh grade 3 as celiac disease. Sadly, insurance networks and health maintenance organizations interfere with a physician’s autonomous decision-making regarding early screenings, and specialized genomic and predictive auto-antibody testing is often cost prohibitive due to lack of insurance coverage. This is where functional medicine comes in. Institute for Functional Medicine (IFM) certified functional medicine practitioners are the consummate generalists, addressing the root causes behind the etiology of all autoimmune diseases—stealth and occult infections, dysbiosis, mitochondrial dysfunction, food sensitivities, toxicity, blood sugar dysregulation, latent inflammation, micronutrient deficiencies, methylation imbalances, hypothalamic-pituitary-adrenal axis dysregulation, and hormonal aberrations (Fasano, 2012; Bigazzi, 1997; Bach, 2002; Vojdani, 2014; Seaman, 2002; Cutolo, 2008).

In juxtaposition, the edifice of Western medicine takes a surface-level approach and plays a game of wack-a-mole, designing chemical bullets to selectively target isolated biochemical pathways, which inevitably leads to the emergence of new symptoms as the finely orchestrated molecular symphony is disturbed. This is akin to chopping off one of Medusa’s heads--another rears its angry face.

Rather than the gentle modulation of the immune system with botanicals, nutraceuticals, mind-body therapies, and dietary interventions, a strategy employed by integrative medical practitioners, the magic bullets of conventional medicine are designed to indiscriminately tone down the functioning of the immune system using steroids, biologics, and immunosuppressants in cases of autoimmunity, which can generate disastrous side effects such as cancer and infection.

Lastly, instead of addressing the underlying, upstream immune imbalance, and targeting root causes of dysfunction such as intestinal permeability, dietary irritants, latent infections, and toxin exposure, from a medical anthropology perspective, conventional medicine allocates the blame squarely on the patient, branding the autoimmune disorder as genetic, which conveys the sense that the condition is permanent and immutable.

This stands in stark contrast to functional medicine. While functional medicine offers bio-individualized dietary and lifestyle strategies that allow patients to reclaim autonomy in their health management, conventional medicine peddles only synthetic pharmaceuticals upon which patients become dependent, creating lifetime users but no permanent recovery. From a medical anthropology lens, this practice also reinforces the hierarchy wherein the practitioner is superior to the patient and represents the guardian of sacred body of knowledge and cures. It likewise conveys the message that there is nothing lifestyle-oriented that the patient can do in the way of self-care, prevention, and disease reversal---which could not be further from the truth.

In contrast, functional medicine encourages an egalitarian, therapeutic partnership in which the patient is an active participant engaged in pro-active, pre-emptive health-promoting strategies to both prevent and reverse autoimmunity.

As illustrated, autoimmune patients are incredibly underserved within the symptom-suppressive, pill-for-every-ill paradigm that epitomizes allopathic medicine. This is illustrative of a larger phenomenon---that conventional medicine excels at acute, emergency, and catastrophic care, but fails when it comes to treatment of chronic illness. Instead of going for the emanating branches on the tree, which represent only the visible expression of disease, or the tip-of-the-iceberg so to speak, functional medicine goes for the trunk, resolving impairments in assimilation, energy, defense and repair, communication, transport, and structural integrity (See image below, reproduced with permission from the Institute for Functional Medicine at

If you fail to address these underlying core clinical imbalances, you are only putting a synthetic symptom-suppressive pharmaceutical band-aid on the problem, and additional autoimmune diseases are likely to develop. Because autoimmune disorders share a common underlying mechanism, it becomes a domino cascade where one begets another, leading to the coexistence of many autoimmune diseases (polyendocrine syndrome, polyglandular autoimmune syndrome, or what I have, multiple autoimmune syndrome).

Moreover, as functional medicine providers we dig deeper, uncovering the antecedents (predisposing factors like genetic inheritance), triggers (instigating events like trauma or infection), and mediators (perpetuating factors like stress or diet) that set the stage for autoimmune disease.

As articulated by Dr. Shilpa Saxena of the Institute for Functional Medicine, "The antecedents set the stage, the triggers start the show, and the mediators are the characters in the play".

Functional medicine likewise addresses critical inputs such as sleep and relaxation, exercise and movement, nutrition, stress, and relationships, all of which represent the inextricably intertwined and entangled roots of the tree, from which health is cultivated. From which vitality grows.


Adams et al. (2006). Status of Nutrition Education in Medical Schools. American Journal of Clinical Nutrition, 83(4), 941S–944S.

Aksoy, D.Y., Kerimoglu, U., Okur, H., Canpinar, H., Karaagaoglu, E., Yetgin, S.,…Gedik, O. (2005). Effects of prophylactic thyroid hormone replacement in euthyroid Hashimoto's thyroiditis. Journal of Endocrinology, 52(3), 337-343.

American Autoimmune and Related Diseases Association .(2017). Autoimmune Statistics: Autoimmune Disease Fact Sheet. Retrieved from

Bach, J.F. (2002). The effect of infections on susceptibility to autoimmune and allergic diseases. New England Journal of Medicine, 347(12), 911-920.

Betterle, C., Volpato, M., Rees-Smith, B., Furmaniak, J., Chen, S., Zanchetta. R.,…Presotto, F. (1997). Adrenal cortex and steroid 21-hydroxylase autoantibodies in children with organ-specific autoimmune diseases. Journal of Clinical Endocrinology & Metabolism, 82, 939–942.

Bigazzi, P. E. (1997). Autoimmunity caused by xenobiotics. Toxicology, 119(1), 1-21.

Cutolo, M. (2008). Vitamin D and autoimmune rheumatic diseases. Rheumatology, 48(3) 210-212.

Fasano, A. (2012). Leaky gut and autoimmune disease. Clinical Reviews in Allergy and Immunology, 42(1), 71-78.

Kita, M., Goulis, D.G., & Avramides, A. (2002). Post-partum thyroiditis in a Mediterranean population: a prospective study of a large cohort of thyroid antibody positive women at the time of delivery. Journal of Endocrinology Investigations, 25, 513–519.

Padberg, S., Heller, K., Usadel, K.H., & Schumm-Drager, P.M. (2001). One-year prophylactic treatment of euthyroid Hashimoto's thyroiditis patients with levothyroxine: is there a benefit? Thyroid, 11(3), 249-255.

Seaman, D.R. (2002). The diet-induced pro-inflammatory state: A cause of chronic pain and other degenerative disease. Journal of Manipulative and Physiological Therapeutics, 25(3), 168-179.

Thomas McKeown, "The Medical Connection" from The Modern Rise of Population, Academic Press, 1979.

Vojdani, A. (2014). A potential link between environmental triggers and autoimmunity. Autoimmune Diseases, 1-18. doi:10.1155/2014/437231

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