The Right Order of Things: Peeling the Onion of Chronic Disease

In the practice of medicine, healing depends not only on doing the right things, but
doing them in the right order.

Illness is never simply one discrete process or dysfunction. It is a bundle ofthe
patient’s whole life – their genetics, early influences, environment, diet, lifestyle, habits,
travel, relationships, beliefs – and how those influences are layered and woven to create
the thing we call disease. Rooting out the original causes from the downstream effects
is the essential task of the healing process. Our job is determining how the illness is
layered or woven into your story and your biology. This helps us know where to start
first, which layer to peel away, or which knot to untangle in the web of physiologic

Doing the right thing in the wrong order will often result in failure or worsening of the
illness. Finding the one medication or surgical procedure, or the right herb, or
alternative modality, to treat a “disease” may fail, even though it is the right thing to do,
if it is done in the wrong order.

More importantly, there are often many things to do and it is difficult to choose which
to do first. But after 20 years of thinking, sorting, trying, failing, succeeding a few
things seem apparent, and here we offer them humbly to those who struggle to hold
and make sense of the infinitely variable threads of human story and disease.
Fortunately, though human biology is infinitely complex and beyond anyone’s capacity
to fully grasp, there are some principles and well-traveled routes to healing that are
straightforward and accessible for healing. In fact, I believe, this map and methodology
are our best hope. This is the map of Functional and Nutritional Wellness, or whole systems medicine.

Before You Begin

Our first task in the patient-healer partnership is to persistently seek the cause (or
causes) of the illness. Thankfully there are only a few root causes for all illness:
infections, allergens, toxins, stress (physical or psychological), and poor diet. And
genetics. That’s it, just 6 things to think about. But we must become an expert in
identifying and treating these underlying causes of disease.
The second task is to identify the 7 “ingredients” needed for optimal biologic function –

1. Real food
2. Nutrients and hormones
3. A healthy environment (water, air, light)
4. Deep relaxation, rhythm (including sleep)
5. Movement
6. Love, community
7. Meaning and purpose.

We must also become expert in assessing deficiency of these “ingredients” and helping
provide the necessary conditions for thriving.

The presence of any of the six root causes of disease, and the absence of any of the 7
essential ingredients creates imbalance in the basic biologic web like systems and
processes of the body:

1. Hormonal/Neurotransmitters
2. Immune
3. Digestive
4. Detoxification
5. Energy metabolism
6. Structural
7. Mind body

Any imbalances in any one or combination of these systems results in the manifestation
of disease, as we know it. With this map and process of thinking, the name of your
“disease” becomes increasingly meaningless.

So first we must seek the cause. When faced with multiples causes of disease – toxins,
infections, allergens, poor diet and stress which often occur together in varying patterns
and degrees, the question is what to do first, and next, and next and so on.
The trick lies in having a place to start, and understanding how to unpeel the layers of
dysfunction and in what order. Fortunately, the body knows how to heal if we remove
the impediments and provide the proper conditions in the right order. This takes time,
patience and persistence.

What is the Right Order?

These steps are listed in order of priority for peeling the onion of chronic illness. This is how we practice Functional and Nutritional Wellness and what we have found leads to the most
success in healing. Sometimes we will do multiple things at once, for example, start
hormone therapy along with immediate dietary changes and treatments to heal the gut.
Healing is a process.

And not always linear. It is more like tailoring – making adjustments each step along
the way until we get it just right.

Here are the steps we usually follow.

1.Start with food
2.Remove food allergens or sensitivities
3.Fix the gut
4.Optimize nutrient status
5.Balance hormones
6.Support energy metabolism
7.Enhance detoxification
8.Mind body balance
9.Look for hidden infections

Start with Food

Whole, real foods. As Michael Pollan writes, “Eat food. Not too much. Mostly plants.”
A refinement is what I have termed the “Nutrigenomic Index” (see Table 1). Food is by
far the most powerful clinical intervention in chronic disease. Learn to apply it, and use
it skillfully.

Table 1: Nutrigenomic Index

Plant based diet: a whole, unprocessed predominately plant based diet provides the
highest Nutrigenomic Index based on the following properties:

• Low Glycemic Load – the overall balance of the meal
• Proper Fatty Acid Composition – high level of healthy omega-3 fats vs. omega-6
fats, low in saturated fats and no trans fats.4
• High Phytonutrient Density – high level of phytonutrients and antioxidants
• Healthy Protein – lean, healthy predominately plant based proteins, or pastureraised animal products
• High Micronutrient Density – contains high amounts of vitamins and minerals
• Low Allergenic Burden – low in foods that are highly allergenic (gluten, dairy and
others based on personalized prescription)
• Low Toxic Burden – minimizes toxic burden of food, e.g. no/low added hormones,
pesticides, antibiotics or any other artificial additives
• Healthy PH Balance – provides proper balance between acidity and alkalinity
• Healthy Salt-Potassium Ratio – low in salt and high in potassium
• High Fiber Content – high in fiber to help slow the insulin response and optimize
digestive health

Remove Food Allergens or Sensitivities

Delayed food sensitivities are among the most potent triggers for chronic symptoms
and an inflamed immune system. A trial of a comprehensive elimination diet for 2-3
weeks with systematic food reintroduction is a powerful therapeutic and diagnostic
tool. The closer you follow this, the faster you will know how much food is playing a
role in your illness. Sometimes we just recommend elimination of the most common
triggers of symptoms – gluten and dairy, and sometimes we recommend a more
comprehensive program based on a comprehensive elimination diet.

After introducing a whole foods, low glycemic load (low sugar/flour), phytonutrient
dense diet, food elimination/reintroduction is the least expensive and most powerful
diagnostic and therapeutic tool available. Gluten elimination is one of the most
powerful treatment methods for chronic illness of many types.

Fix the Gut

Health starts in the gut. The digestive tract has an independent nervous system, and
contains 60% of our immune system. We will assess your gut through history and
appropriate diagnostic tests (for gluten sensitivities, inflammation in the gut, unwanted
bugs like parasites or yeast). And then we will aggressively treat the causes of gut
dysfunction, including leaky gut, delayed food allergies, small intestinal bacterial
overgrowth (SIBO), yeast overgrowth, parasites, and worms.

We may use herbs, antibiotic, anti-fungal, anti-parasitic, and anti-worm medications or
botanicals to eradicate the triggers of intestinal dysfunction. Repair and healing of the
gut requires use of digestive enzymes, pre-biotics (food for healthy bacteria), probiotics
(healthy bacteria), and nutrients needed for repair of your gut lining including zinc,
omega 3 fats, GLA, glutamine and anti-inflammatory botanicals such as quercetin and

Optimize Nutrient Status

Nutrient deficiencies affect up to 92% of Americans. Vitamins and minerals are
necessary for every biochemical reaction in your body. Without adequate amounts for
optimal health your biochemistry gets stuck and you get sick. However the most
clinically relevant and effective nutrient therapies are few.
The most common are magnesium (think anything that is tight, irritable or crampy –
muscles, bowels, lungs, moods), zinc (for immune function), vitamin D (for anyone
who lives in the upper northern and lower southern hemispheres not on
supplementation), methylation (B6, folic acid, B12) necessary for detoxification,
cognitive function and DNA repair among hundreds of other essential biologic
functions, and omega 3 fatty acids (EPA and DHA) the stuff of which we are (or are
supposed to be) made. Depending on testing, other deficiencies may be found and
Balance Hormones
Hormonal and neurotransmitter dysfunction is rampant because of dietary influences
on hormones (sugar and refined flour), endocrine disruptors or xenobiotics
(petrochemicals and heavy metals) and chronic stress.
The delicate balance of hormones is essential for health and understanding the factors
that cause disruption and restore balance of hormones is essential. Of the dozens of
hormones, four categories are the most important for treatment of chronic disease:
insulin resistance, the stress response and adrenal insufficiency, thyroid dysfunction
and sex hormone dysfunction. Diet, exercise, stress management, bio-identical
hormone replacement, nutrient support and herbal therapies are among the most
effective tools we use, along with complementary or alternative therapies including
acupuncture and Traditional Chinese medicine.

Support Energy Metabolism

The end result of many nutritional, toxic, allergic, infectious and dietary insults is injury
to the mitochondria, (our body’s energy factories), unchecked oxidative stress and the
loss of energy and ultimately cell death.
This has led to epidemics of obesity, diabetes, fatigue, developmental and
neurodegenerative disorders, and accelerated aging. We assess mitochondrial
dysfunction using organic acid analysis, and support and protect mitochondrial
function through the use of phospholipids, essential fatty acids, acetyl-L-carnitine,
coenzyme Q10, D-ribose, magnesium/potassium aspartate, arginine, resveratrol, alpha
lipoic acid, NADH, riboflavin, niacin, n-acetyl-cysteine (NAC). This is often an
important step in supporting health and recovery from chronic illness.

Enhance Detoxification

Detoxification is one of the most important and metabolically demanding functions of
our physiology, and one that health professionals learn little about. Just ask anyone
with renal or liver failure or chronic constipation. The toxic burden of 2.9 billion
pounds of petrochemical toxins and 6 million pounds of mercury unloaded into our
environment every year has put an undue stress on our capacity for detoxification.
Identifying heavy metal toxicity particularly mercury and lead through provocation
challenge testing is an important part of diagnosing and treating chronic disease.
We always test for heavy metals at the first visit, but do not usually treat this until 3-6
months after our first visit after we have normalized your digestion, immune function,
hormones and nutritional status as much as possible. Then we can safely begin the
detoxification and chelation of heavy metals.

We support your body’s own detoxification enzymes through phytonutrients, amino
acids, vitamins and minerals. However, mobilizing toxins must be done after all other
aspects of our biologic systems have been optimized and pathways for detoxification
are working full speed.

Mind Body Balance

Finding meaning and connection in the context of your illness and within the tapestry of your life, relationships and beliefs is indeed, an essential pillar of the healing process.
We support you to develop skills in self-care and nourishment and stress management,
such as exercise, yoga, meditation, or other ways to balance your mind and body. These
are actually both the first and the last step in healing. Learning to deeply relax, let go of
worry, and build trust in life and the healing process, is a necessary ingredient for
becoming well.

Look for Hidden Infections

If we find you don’t respond fully to treatment of the basic systems outlined so far, or if
you have an elevated high sensitivity C-reactive protein, testing for hidden infections
often identifies unsuspected triggers: viruses, atypical bacteria, tick-borne illness, and
dental infections (root canals). If there are no bugs inside, we must think mold in the
home or workplace, particularly black mold or Stachybotrys.

The Right Order of Things

Despite the exceedingly complex world of systems biology and medicine, the way into
the web of dysfunction and healing is actually quite simple and effective for most
patients with chronic disease. The puzzle of chronic illness is not so difficult if we start
with food, address food allergens, fix the gut, optimize nutrient status, balance
hormones, support energy metabolism, enhance detoxification, teach self-care and
nourishment of mind and soul, and if we get stuck dig around for hidden bugs. Slowly
progressing along this road into the web of chronic disease works for most patients,
most of the time. It is based on a clear framework for understanding the impediments
for optimal function, and the necessary conditions for thriving, and an understanding of
the essential physiologic systems that are at the root of the more than 12,000 different
“diseases” that, indeed, are only the effects of these causes. Keeping in mind the right
order of things will get us from effect to cause, from illness to health.
Thank you for your trust in partnering with us on your healing journey.

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