hypothyroidism causes, hypothyroidism is the smoke, hypothyroidism is a symptom, functional medicine, root cause medicine

Hypothyroidism–Part One: Just the Smoke

Hypothyroidism is just the smoke rising high above the smoldering fire that lies beneath the surface. Said another way, hypothyroidism is a symptom–it’s not a disease. It’s not the defining thing that is wrong with you. It’s just one–of many–surface-level indicators of much larger and deeper problems. Problems most likely caused by two key factors: overwhelming inflammation and unmet nutritional needs.

But that’s not how hypothyroidism is explained or treated in the conventional practice of medicine. We are lead to believe that it is the root of our fatigue and foggy heads, that a simple thyroid hormone pill will fix us, that we know all we need to know.

Wrong. Misleading. Dangerous thinking.

You may feel better on that thyroid pill. Temporarily. But if we don’t address the underlying causes of the hypothyroidism–the inflammatory-autoimmune destruction and unmet nutritional needs–there will be much bigger and difficult-to-treat problems going forward. You won’t feel nearly as good as you could feel–as you would feel–if those deeper systemic problems were corrected.

Medicine–sustainable medicine, root-cause medicine–must go upstream to find the origin of hypothyroidism, and to make the necessary corrections. You’ll feel better, and–this is huge–we’ll stop the damage caused by the persistent inflammatory-autoimmune activity and unmet nutritional needs in its tracks. We’ll put the brakes on progress of the destructive inflammation that leads to heart attack, vascular disease, dementia, cancers, and much, much more.

Thought of in this way, the hypothyroidism we diagnose now, when properly treated in a sustainable, root-cause-oriented way (think Functional Medicine), saves us from a world of hurt later on–it saves our lives.

What is Hypothyroidism?

Hypothyroidism is a condition of energy deficit that occurs when there is not enough thyroid hormone action to support optimal energy production in the body. Thyroid hormone drives metabolism–the energy needed to support the work of the cells–all cells. This is much like the thermostat in your home that controls how much your heating and air conditioning units will work to produce the temperature changes (the energy) you desire. Thyroid hormone works in concert with other hormones within the Brain-Thyroid-Adrenal-Mitochondrial axis (see below) to create and sustain vital energy.

There are several scenarios that can lead to inadequate thyroid hormone action:

  • Insufficient production of thyroid hormone (T4) within the thyroid gland due to gland destruction by inflammation and autoimmunity, radiation, or inadequate supply of nutrients involved in thyroid hormone synthesis.
  • Insufficient conversion of thyroid hormone, T4, into its biologically active form, T3. This normally occurs within all our cells and can be disrupted as a result of illness, inflammation, unmet nutritional needs, and high levels of stress.
  • Problems with hypothalamic-pituitary control of thyroid hormone production. This can occur because of trauma to the brain, severe inflammation, toxicity, unmet nutritional needs, and severe stress.
  • Thyroid hormone receptor insensitivity. This occurs when the receptors for thyroid hormone become less responsive as a result of inflammation, toxicity, or unmet nutritional needs.

The Big Energy Picture: Brain-Thyroid-Adrenal-Mitochondrial (BTAM) Axis

The thyroid is part of a larger network of organs and processes that work together to produce and sustain energy. I call this the Brain-Thyroid-Adrenal-Mitochondrial (BTAM) axis. It sounds complicated, but even this is an over-simplification–the human body is so complex! But it makes the point that many important players work in concert to provide for the energy needs of our bodies. It’s never just the thyroid–ever.

Here’s how the Brain-Thyroid-Adrenal-Mitochondrial axis work in a nutshell

  • Our brains perceive our energy needs and orchestrate communication about them via control hormones of the hypothalamus and pituitary glands.
  • The control hormones head straight to the thyroid and adrenal glands, literally changing gene expression in such a way that they either ramp up or turn down hormone production.
  • Thyroid hormones act as the cell thermostats, while adrenal hormones regulate energy fuel supplies (carbon fragments used to manufacture energy from glucose and fatty acids) and blood pressure (to deliver the fuel supply where it’s needed).
  • Finally, the mitochondria are the microscopic sub-cellular organs that literally create the chemical energy we need to support and sustain us–at everything.

Hypothyroidism: a Systemic Problem

Most hypothyroidism in the United States is the result of an inflammatory-autoimmune process. This drives damage to the thyroid gland and disruption of multiple nodes of the BTAM energy system. This destructive inflammation leads to decreased thyroid hormone production and action, and dysfunction of other aspects of energy production within the BTAM axis.

The inflammatory-autoimmune problem is usually compounded by unmet nutritional needs. These are deficiencies of the vital nutrients necessary for thyroid hormone production and support of thyroid gland health. They contribute to persistent stresses to the entire BTAM energy system.

What happens when we treat hypothyroidism with just a thyroid hormone pill?

Standard treatment for hypothyroidism by conventional American medicine is to provide thyroid hormone replacement, which is vital for restoration of the thermostat function of the BTAM energy system. Treating hypothyroidism with just a hormone pill, however, does not address the inflammatory-autoimmune process or nutritional deficiencies that are part of the cause, and that lead to system-wide problems.

Understandably, it’s the symptoms of our under-active thyroid gland that grab our immediate attention–the sluggishness, fuzzy-head, depression, or poor energy. We seize the opportunity for a fast solution to how we feel (who wouldn’t?) and the promise of getting our lives back.

The thyroid hormone pill props us up but does not address the myriad other problems downstream from the root causes–the inflammation and unmet needs–that likewise make us miserable (think headaches, achy joints, irritable bowel, brain fog). And it doesn’t support the other key players in our energy system.

What Gets Missed

Thyroid hormone will drive the work of your cells. If your cells are already over burdened and struggling in the face of an unmet need, you will simply be adding fuel to the fire.

If, for instance, your adrenal hormone levels are inadequate to meet the demands for fuel or blood pressure support, additional thyroid hormone will ask your cells for what they cannot deliver. This will over stimulate your cells, and exacerbate nutrient deficiencies and cellular stress.

Likewise, if there are suboptimal levels of nutrients necessary to support the thyroid gland and other aspects of the BTAM energy system, ramping up the thermostat (increasing thyroid hormone) without addressing the supply of those nutrients, exacerbates the unmet needs. This will lead to worse and varied problems related to the functions of those nutrients–all players in diverse aspects of our biology.

If there are gut-related problems driving a systemic inflammatory-autoimmune process that damages your thyroid, simply taking a thyroid pill doesn’t address that. It completely fails to explore and create solutions for the myriad forms of tissue damage taking place concurrently–also as a result of the gut-derived inflammation and toxicity. These other points of damage may yet to manifest themselves in symptoms that you can feel. Vascular disease, dementia, and cancers, depending on your genetics, may take many more years to become apparent–perhaps when it’s too late. We can put a stop to these now.

After the Hypothyroidism Diagnosis: Follow the Smoke to the Fire

Enlist some help on this–you’ll need a Functional Medicine doc, trained in clinical systems biology thinking, or one of the many excellent self-help books available on the subject.

Once hypothyroidism has been diagnosed: We now see the smoke. You’ve felt it for months, maybe years. Now, where’s the fire? What is causing the inflammatory autoimmune problem? What nutrients are deficient? What do you need to do to heal?

By all means, accept the prescription for thyroid hormone. But never do this without simultaneously addressing inflammation, nutritional needs, and other existing  challenges to your energy.

How to Diagnose Hypothyroid-Autoimmune Syndrome

We’ll pick up this discussion in part two of this series: Hypothyroidism–Part Two: How to Diagnose Hypothyroid-Autoimmune Syndrome. Stay tuned for next week’s article… We’ll dive into the details of what you can do now to reverse the inflammatory-autoimmune distruction that causes the majority of hypothyroidism in the United States. And I’ll give you step-by-step instructions for correcting the unmet nutritional needs that exacerbate thyroid dysfunction and help propagate inflammation.


Karyn Shanks, MD. Hypothyroidism–Part Two: How to Diagnose Hypothyroid-Autoimmune Syndrome. 2017.

Amy Myers, MD. The Autoimmune Solution: Prevent and Reverse the Full Spectrum of Inflammatory Symptoms and Diseases. Paperback, 2017.

Izabella Wentz, PharmD. Hashimoto’s Thyroiditis: Lifestyle Interventions for Finding and Treating the Root Cause. 2013.

Karyn Shanks, MD. Energy Recovery 101: Root Cause Solutions for Healing Your Adrenals, Part One. 2016.

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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