Arizona Center for Advanced Medicine - Martha M. Grout, MD, MD(H)
Scottsdale, Arizona    480.240.2600
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An Alphabet of Good Health in a Sick World by Martha M. Grout MD, MD(H) and Mary Budinger
An Alphabet Of Good Health
In A Sick World


Autoimmune Diseases

Most common
autoimmune diseases:

Rheumatoid arthritis, juvenile rheumatoid arthritis, lupus, scleroderma, multiple sclerosis, Hashimoto's thyroiditis, Graves disease, type 1 diabetes, Sjögren's syndrome, Crohn's disease, celiac disease, ulcerative colitis, Addison's disease, Guillain-Barre syndrome, temporal arteritis, Ménière's disease

Autoimmune diseases are the third most common category of disease in the United States after cancer and heart disease.1 Conservative estimates indicate that three-quarters of the persons with autoimmune diseases are women.2

Autoimmune disease refers to a group of more than 80 serious, chronic illnesses including diseases of the nervous, gastrointestinal, and endocrine systems as well as skin and other connective tissues, eyes, blood, and blood vessel.

Autoimmune diseases may manifest in many different places in the body, with many different diagnoses. Their common thread is that the body makes antibodies to its own tissues. The body's immune system becomes misdirected, attacking the very organs it was designed to protect.

Autoimmune diseases tend to cluster in families and in individuals – a person with one autoimmune disease is more likely to get another. This indicates that common mechanisms are at work. Studies of the prevalence of autoimmune disease in monozygotic (identical) twins show that genetic as well as environmental factors are necessary for the disease to develop.3 Also, infections play a big role in the development of autoimmune disease.

A study published in the April 1, 2007 edition of Nature Immunology concluded that allergic and inflammatory diseases may actually trigger autoimmune diseases by relaxing the controls that normally eliminate newly produced, self-reactive B cells. This is important because many autoimmune diseases are caused by self-reactive antibodies produced by such B cells.

Heavy metals, in particular mercury, are thought to be another trigger for autoimmune disease.4,5,6 Other metals are similarly implicated.7,8,9

The common thread is development of antibodies to ones own tissues.

Why would the body become “allergic” to itself?

Immunity begins at birth. Soon after giving birth, female mammals produce colostrum, which is a milk-like substance that jump-starts a newborn's immune system. Human breast milk contains large quantities of secretory IgA, lysozyme-secreting macrophages, and lymphocytes (T cells and B cells). The lymphocytes release compounds that strengthen the immune response of the infant. There is evidence that the protection given by breast milk lasts for years.10

Our lymphocytes react to all our tissues. Why, then, does the process sometimes become pathologic? Why don’t we react to our own tissues all the time?

Our immune system is designed to protect us against that which is foreign, while recognizing that which is native. If, for some reason, our own tissues become contaminated with something foreign which attaches itself to the proteins of the tissues and changes the configuration of the proteins, the body could very well become confused. The tissue is no longer exactly “me,” therefore it must be “not me.” Therefore it must be protected against. An inflammatory process begins, and we are on the road to developing autoimmune disease.

So… is the treatment answer to suppress the immune system, perhaps with steroids, so that we no longer react to our own tissues? Or attempt to kill every bacteria, virus or cancer cell that happens to come down the pike?

Mounting a war against our own bodies is probably not the best answer.

A better treatment answer is to discover what caused the abnormal response in the first place, and remove that trigger, thereby allowing the body to restore itself to health.

The first place to look is in the gut because 75 percent of the body’s immune system activity comes from the gut.

At the Arizona Center for Advanced Medicine, we identify foods and other substances (chemicals, pollens, molds) which cause gut inflammation in the individual, and work to eliminate the responsible foods from the patient’s environment. We look at the body burden of heavy metals like mercury, arsenic and lead, and make every effort to eliminate these as well, since they can be a significant cause of inflammatory response. We can provide supplements and remedies to correct the dysfunctional information systems in the body, and to heal the GI tract and improve its overall health. We show you how colonics and probiotics work to replace the damaging bacteria in the gut with ones which are actively helpful. And finally, we look at brain function, to help modify the effect of the autonomic nervous system (the stress system) on the gut. Thus, the GI tract is restored, symptoms are cleared, and health returns.

Most Americans today have weakened and impaired immune systems that are unable to function as they were designed. Experts estimate that many allergies and immune-system diseases have doubled, tripled or even quadrupled in the last few decades. Some studies indicate that more than half of the U.S. population has at least one allergy.11

Asthma, hay fever, eczema and food allergies are all "allergic diseases" caused by your immune system responding to substances that are ordinarily harmless, such as pollen or peanuts. Autoimmune diseases also result from your body's defense mechanisms malfunctioning, causing your immune system to attack parts of your body such as your nerves, pancreas or digestive tract.

Some researchers suspect the rise in immune system dysfunctions may have a common explanation rooted in aspects of modern living.

First, we have undergone a revolutionary change in how we fuel our body. For tens of thousands of years, mankind ate unprocessed, truly natural food. In the last 150 years or so, our diets have changed dramatically. Our genes simply cannot adapt that quickly. The human body is not designed to run on 150 pounds per year of processed sugar, nor is it designed to run on baby formula, aspartame, pesticides, hydrogenated oils or meat from animals fed unnatural diets and hormones. Sugar for example, impairs the intestinal microflora and undermines a strong immune system.

Second, there is the "hygiene hypothesis," which suggests germ-free homes and childhood vaccinations have eliminated challenges to our immune systems so they don't learn how to defend us properly when we're young. The immune system is sort of like a muscle – use it or lose it. We eat food inoculated with antibiotics. Our children stay indoors more, play outside less. Studies suggest that children who are raised with pets, have older siblings, play with livestock on the farm, are less likely to develop allergies, probably because they are exposed to more microbes than those living in overly sterile homes. "The data are very strong," said Erika von Mutius of the Ludwig-Maximilians University in Munich. "If kids have all sorts of exposures on the farm by being in the stables a lot, close to the animals and the grasses, and drinking cow's milk from their own farm, that seems to confer protection." Researchers believe the lack of exposure to potential threats early in life leaves the immune system with fewer command-and-control cells known as regulatory T cells, making the system more likely to overreact or run wild.

Third, environmental pollution and sedentary lifestyles may play more of a role than we understand. One reason that many researchers suspect something about modern living is to blame is that the increases in allergies and auto-immune diseases show up largely in highly developed countries in Europe and North America. The illnesses have only started to rise in other The Autoimmune Epidemiccountries as they have become more developed. Donna Jackson Nakawaza, author of The Autoimmune Epidemic, implicates the bioaccumulation of toxins that pervade our home, food, and environment, as a primary cause of autoimmune diseases. What effect are plastics and other persistent organic pollutants having on human health? "Rising levels of autoimmune disease may well prove to be the next environmental disaster -- only in this case, the changes taking place degree by degree are in the interior landscapes of our bodies," Nakawaza writes. "Our immune systems may be less prepared because we're confronting fewer natural pathogens, but we're also encountering an endless barrage of artificial pathogens that are taxing our systems to the maximum."

When you look at a few of the most common autoimmune diseases, you'll see that several patterns emerge.

Let’s look at a few of the most common ones. You’ll see that several patterns emerge relative to autoimmune disease:



  • Osteoarthritis is characterized by destruction of cartilage within the joint, eventually exposing the underlying bone. The cells which produce cartilage for unknown reasons fail to maintain the balance between production and destruction of normal cartilage tissue. Compounds called proteoglycans form the cartilage itself, and these proteins are found to be deficient in cartilage from patients with osteoarthritis. Other compounds called metalloproteinases are also found in high concentration in osteoarthritic cartilage. These compounds digest proteoglycans. Metallothioneins are proteins normally present all over the body. Their functions include storing high concentrations of zinc, scavenging free radicals, protecting against cadmium toxicity. 12 These proteins are known to be neuroprotective,13 probably through their ability to scavenge free radicals.
  • Rheumatoid arthritis for most patients is a progressive disability. RA is associated with several genes, the most familiar of which is the HLA gene.14 It appears to be influenced by multiple factors, including diet15,16, inflammation, bacterial infection,17, and heavy metals. Standard allopathic treatment involves use of steroids and sometimes anti-neoplastic drugs. If anti-inflammatory therapy is initiated before joint deformities are present, it is possible to avoid the joint deformities entirely. Some patients treated with antibiotics for months have improved their arthritis symptoms.18 However, the use of long term steroids and other anti-inflammatories have led to suppressed immune system, candida overgrowth, peptic ulcers and other problems. Determination of food sensitivities and heavy metal toxicities is crucial. For many, remission has not been possible without dietary changes, particularly elimination of sugar and grains. Additionally, chronic mycoplasma infections must be investigated.
  • Spondyloarthropathies (ankylosing spondylitis is the best known of this group) involve primarily the vertebrae and the joints between the sacrum and the pelvis below the low back (SI joint). There is peripheral joint inflammation, mainly of the larger joints (knees or hips), rather then the smaller joints (hands) as typically seen in osteoarthritis. This form of arthritis is frequently associated with inflammatory bowel disease, inflammation of the eye (uveitis), and skin diseases like psoriasis. Genetics is thought to play a significant role in this form of arthritis. HLA B27 is found in 90% of patients with ankylosing spondylitis.19

A clear association has been found in some patients between arthritis and inflammatory bowel disease. Patients with increased intestinal permeability (“leaky gut”) have a higher incidence of arthritis.20 If we have abused our colons for years through an unhealthy diet, or if we have developed food sensitivities, constipation and colitis, it only makes sense to treat the colon to improve the Leaky gut.


Standard allopathic treatment revolves around anti-inflammatory medication, which frequently results in intestinal side effects – heartburn, ulceration, even bowel perforation or rupture.21 In addition, physical therapy is recommended.

One study demonstrated that niacinamide, Vitamin B3, improved the global impact of osteoarthritis, improved joint flexibility, reduced inflammation, and allowed for reduction in standard anti-inflammatory medications when compared to placebo.22 The Mediterranean diet has been shown to have significant impact of the symptoms of rheumatoid arthritis,23 as does treatment with γ-linoleic acid (GLA).24

At the Arizona Center for Advanced Medicine, we use specifically calibrated diagnostic tests to uncover the root cause of the manifestation. Depending upon the individual, we may look at may test for food sensitivities (using provocation/neutralization allergy testing), as well as toxic substances like heavy metals and organic pollutants.

While we are searching for the root cause, you are still having symptoms. So what do we do about symptoms?

We will put you on an anti-inflammatory diet, and use specific medical foods which will help with your symptoms. We may use herbal anti-inflammatories which do not stop the normal “housekeeping” function of the COX enzymes (unlike medications such as Celebrex, which has been linked with heart disease). We will look at overall nutrition, and determine whether there are any blockages to nutrient absorption or synthesis. We often use acupuncture to treat both specific arthritic joints, and to treat the person overall, in order to reduce inflammation all over the body.

In the end, arthritis is a symptom of metabolism gone awry. Our job is to determine the cause and help you eliminate it, so that you can be more than just pain free – so you can be healthy.

Leaky Gut

In 10 years, it may be very common that we hear about leaky gut or LGS. Today, mainstream medicine doesn’t talk about it much, the pharmaceutical industry has no drugs for it, and it is rarely looked for. But it is likely a very common problem.

In simple terms, the lining of the intestines becomes full of holes – imagine a piece of Swiss cheese. Large spaces develop between the cells of the gut wall, and then partially digested foods, toxins, and bad bacteria pass though the small intestine into the blood stream. The body senses something foreign now in the blood, so the immune system is called in to attack it. Antibodies are formed against once harmless, innocuous foods.

When the gut is leaky, a cascade of problems ensues. The body fails to properly absorb vitamins and minerals, so the person becomes depleted. The leakage of toxins overburdens the liver so that the body is less able to handle everyday chemicals. Additionally, the body loses its ability to ward off protozoa, bacteria, viruses and fungus. Bacteria and yeasts are able to pass through the gut into the bloodstream and set up infection anywhere else in the body.

Candida, a yeast normally present in the gut in low levels, typically overgrows in this unhealthy environment and is thought to grow roots which penetrate the gut lining, creating more holes.25

Because LGS sets the stage for so much to go wrong, it is no wonder that so many illnesses can stem from it, including chemical sensitivity, fibromyalgia, escalating food allergies, arthritis inflammation, gas, bloating, abdominal pain, indigestion, alternating constipation and diarrhoea, Crohn’s Disease, periodontal disease and more.

How can LGS trigger such a wide range of problems? With LGS, just one of the things that happens is that the protective coating of the IgA family normally present in a healthy gut is disabled. IgA helps us ward off infections, so with leaky gut problems we become less resistant to viruses, bacteria, parasites and candida. These microbes are then able to invade the bloodstream and colonize almost any body tissue or organ. When this occurs in the gums, periodontal disease results. When it occurs in the synovial lining of the joints, arthritis results. And so on.

LGS is almost always associated with autoimmune disease and reversing autoimmune disease depends on healing the lining of the gastrointestinal tract.

What causes LGS? The most common factors are thought to be use of antibiotics, a diet high in sugar and other non-nutritious foods, and stress. Since those things describe so many people’s lifestyle, you can see why LGS can be so widespread.

A number of patients with LGS find dramatic improvement with colonics because it helps heal the gut.


A 36 year old woman was diagnosed at Mayo Clinic with rheumatoid arthritis. However, her blood test was not positive for the RA factor, and she found that humidity and other factors that are supposed to aggravate RA, did not bother her. She had swollen lymph nodes, night sweats, and she could barely walk because her joints were so inflammed.

"The doctors wanted to manage my disease with an array of drugs; I wanted the disease gone. I read a lot and decided my problem could be lifelong exposure to antibiotics and junk food, and the fact I had lived in Los Angeles with all that air pollution. I looked first at food because I could tell something had gone very wrong with the whole process of eating. Mayo said there was nothing I could do with diet and lifestyle, so I left Mayo.

"Food allergy tests showed I was allergic to almost everything. I got a list of about 20 'safe' foods I could eat and for 6 months, I did not deviate from the list. It was tough but I did it because avoiding foods did more to lessen the pain than the drugs.

"Then I decided to add colonics to the effort. The first session itself wasn't surprising. But when it was over and I was getting dressed, I suddenly realized I had no pain in my joints. Incredible! Even 85 milligrams of prednisone had never done that. In about an hour, the pain came back, but that dramatic experience told me that what people say about the toxic body burden was a big part of my problem and I could solve it by cleaning out on all levels. I did about 75 colonics in the next three years. I learned to eat fresh, organic, nutrient-dense, whole foods. I bought 'green' non-toxic products before they were fashionable. And as I read more and understood more about health, I came to see that RA was not the proper diagnosis; Leaky Gut was. I have no symptoms now. My mainstays for supplements are enzymes, vitamin C, and marine phytoplankton. For maintenance, I still do several colonics and coffee infusions each year."

Multiple Sclerosis

Multiple sclerosis typically begins in early adulthood. The National MS Society estimates that about 400,000 people have the disease. MS affects twice as many women as men, and 80% of patients have the relapsing/remitting type of disease. This type is initially responsive to steroids, but less responsive as time goes on. For 20% of MS patients, the disease is a relentless progression, equally distributed between men and women.26

The disease occurs because the myelin (or insulating) sheaths of the nerve cells is destroyed, thereby markedly diminishing the speed at which nerve impulses can be transmitted along the nerve. Diagnosis is made mostly by symptoms of nerve dysfunction (numbness, weakness, paralysis of eye muscles), and by watching the progression of disease in the brain with MRI scans.

The prevalence of MS is highest in northern Europe, southern Australia and middle America, suggesting some environmental influence. MS is thought to stem from a complex combination of environmental, genetic, and autoimmune factors.

Vitamin D deficiency has been proposed as a causative factor, because MS seems to be more common in people who live farther from the equator.27 In 2006, researchers from Britain's Keele University reported that excessive exposure to aluminum may be associated with multiple sclerosis; they found that MS patients tended to have extremely high urinary excretion of aluminum, particularly among patients who have the relapsing-remitting form of MS.28 The association of MS with the Epstein-Barr virus suggests a virus may play a role in at least some individuals.29 Many MS patients believe vaccinations contributed to the rise in MS.

Genetic factors also play a part. The incidence of MS is 6 times higher among identical twins.30 The HLA-DR2 genetic variation is also associated with higher incidence of MS.31

Lupus (Systemic Lupus Erythematosus, SLE)

Lupus is an autoimmune disease which affects more women than men, generally starting in 30’s or 40’s.

Systemic lupus is potentially debilitating and sometimes fatal. The body’s immune system typically attacks the skin, joints, blood vessels, heart, lungs, liver, kidney, and nervous system. The progression of SLE is unpredictable, with periods of illness called flares alternating with periods of remission.

Its symptoms vary so widely it often mimics or is mistaken for other illnesses. Also, the symptoms come and go unpredictably.

The American Rheumatism Association has a list of 11 criteria for the diagnosis of lupus – at least four of them must be present to make the diagnosis. Criteria include:

Malar Rash 

Red “butterfly” rash over cheeks and the bridge of the nose 

Discoid rash 

Red, scaly rash on the face, scalp, ears, arms or chest 


Unusual reaction to the sun 

Oral ulcers 

Small sores on the moist lining of the nose or mouth 


Pain in the joints of the hands, arms, shoulders, feet, legs, hips, or jaws which may move from joint to joint and be accompanied by heat, redness and swelling 


Pleurisy - chest pain or abnormal sounds heard by physician 
Inflammation of the lining of the heart. Documented by ECG or heard by physician 

Renal (kidney) 

Excessive protein and/or cellular casts in the urine 


Seizures and/or psychosis 

Hematologic (blood) 

Disorder which can include a decrease in the number of red and white blood cells or platelets 


Positive anti-DNA test 

Antinuclear antibody (ANA) 

Antinuclear antibody (ANA) Positive 

The presence of large amounts of serum antibodies to double-stranded DNA is specific for systemic lupus erythematosus.32

Lupus can affect almost any organ system in the body. Classically, there is skin involvement, with the “lupus butterfly” shaped rash across the nose and checks. Often there is severe reaction to exposure to sunlight (in the UVA and UVB frequencies, but not in the UVC frequencies).33

In one study, 88% of patients who subsequently developed lupus had measurable antibodies up to 10 years before they became symptomatic.34 Antibodies against cell nuclei are commonly present, but also antibodies against the phospholipids which make up the cell membrane.

Treatment for lupus is often very similar to treatment for rheumatoid arthritis.

Chronic fatigue syndrome

Chronic fatigue (immune deficiency) syndrome, CFIDS, is a clinically defined condition characterized by debilitating fatigue, persistent for over 6 months, with associated muscle pains, tender lymph nodes, joint pains, low grade fevers, and problems with focus and memory.

Chronic fatigue is estimated to affect almost 1% of the population, and is not limited to white Caucasian middle aged females, as previously thought, but is found in all age groups, races, and economic strata.35 About twice as many women as men are affected.

It is not a condition which fits neatly into the allopathic model of illness. Diagnosis is made by ruling out all other “treatable” causes of fatigue. There are no definitive diagnostic tests. Patients suffering from chronic fatigue are often diagnosed with depression or other neuro-psychiatric labels.

Diagnostic criteria, as defined by the International Chronic Fatigue Syndrome Work Group,36 are as follows:

  • clinically evaluated, unexplained, persistent or relapsing chronic fatigue that is of new or definite onset [has not been lifelong]; is not the result of ongoing exertion; is not substantially alleviated by rest; and results in substantial reduction in previous levels of occupational, educational, social, or personal activities; and
  • the concurrent occurrence of four or more of the following symptoms, all of which must have persisted or recurred during 6 or more consecutive months of illness and must not have predated the fatigue:
    • self-reported impairment in short-term memory or concentration severe enough to cause substantial reduction in previous levels of occupational, educational, social, or personal activities;
    • sore throat;
    • tender cervical or axillary lymph nodes;
    • muscle pain,
    • multi-joint pain without joint swelling or redness;
    • headaches of a new type, pattern, or severity;
    • unrefreshing sleep; and
    • postexertional malaise lasting more than 24 hours

By these criteria, chronic fatigue syndrome could very well be a disease of mitochondria – the tiny organelles inside cells which are responsible for energy production. There is some evidence for this. One study showed abnormal mitochondrial function in a subgroup of patients with abnormal lactate responses to exercise (production of lactic acid occurs when there is insufficient energy to fully utilize all the glucose presented to the cell).37

Chronic viral infection is another possible causative factor.38 Some commonly performed tests are those for chronic viral infection (Ebstein-Barr virus, for example), Candida albicans, and immunologic function including cell population analysis. None of these tests is specific for CFIDS, but they may indicate contributing causes.

Patients with chronic fatigue syndrome have significantly decreased ability to exercise.39 Decreased production of neurotransmitters in the central nervous system may also be a factor.40

Excessive body burden of heavy metals is another possibility. Heavy metals can cause significant loss of function of enzymes which promote the cell’s biochemical reactions, experienced in the body as fatigue.

There is some thought that chronic fatigue is almost always a result of simple toxicity or nutritional imbalance, perhaps early metabolic syndrome, from years of eating the typical non-nutritious American diet of processed foods and sugars.41

Author Mary Nash Stoddard has proposed that aspartame poisoning may give rise to a number of health problems including chronic fatigue and Fibromyalgia.

Once the diagnosis is established, allopathic medicine has little to offer in the way of treatment. Common wisdom states that most patients will take over 18 months to recover, although some will remain debilitated for the rest of their lives.

There is no need to suffer from chronic fatigue syndrome. First, one needs to understand that mitochondrial dysfunction results in the generation of free radicals and reactive oxygen species (ROS). Both can irreversibly damage DNA, and even cause cell death.42,43,44 Therefore, taking antioxidants like CoQ-10, glutathione, Vitamin C, Vitamin E and other similar substances can go a long way toward improving mitochondrial function and relieving the symptoms of chronic fatigue.45,46 These are sometimes best administered in IV form.

Second, we know mitochondrial function is significantly disturbed by heavy metals.47 Workup for excessive body burden of heavy metals is very appropriate in the chronic fatigue patient.

Third, intolerance to gluten (wheat, barley, rye and a few other grains) and other food items can result in neurologic symptoms like extreme fatigue without any intestinal symptoms at all. Therefore investigation of gluten intolerance and other food sensitivities should be part of the initial work-up. Food intolerance has been shown to increase inflammatory mediators in the body48 and to erroneously activate the immune system.49

Food intolerance may be determined in any one of several ways. The classic elimination diet works well for those who can tolerate its rigors.50 For those less tolerant, keeping a food and symptom diary may prove very helpful.51 There are many other ways of diagnosing this condition, including direct provocation tests, blood tests, and the classic intradermal injections.

Food intolerance has also been shown to be related to several other dysfunctions commonly associated with chronic fatigue syndrome: asthma or respiratory distress,52 inflammatory bowel disease,53 and irritable bowel syndrome (IBS).54

At the Arizona Center for Advanced Medicine we make every effort to diagnose the dysfunction on the metabolic level, and to eliminate any source of toxicity to the body, so that full function and health may become a reality.

Inflammatory bowel disease (IBD)

Crohn’s disease and ulcerative colitis are collectively known as inflammatory bowel diseases (IBD). They are chronic relapsing disorders of the bowel that cause abdominal pain, diarrhea and intestinal bleeding. They can lead to weight loss, and in extreme cases may even progress to cancer of the bowel. They may affect more than 1 million Americans.55

The official cause of IBD is unknown.

IBD patients have an inflamed and swollen intestine. Crohn's disease usually causes ulcers (open sores) along the length of the small and large intestines. Ulcerative colitis usually causes ulcers in the lower part of the large intestine, often starting at the rectum. With IBS, there is no significant structural bowel damage. This is a “functional” state of GI irritability.

The inflammation may further progress to irritation of the gut, when it is called colitis. There is still no significant structural damage at this stage.

It may progress to ulceration of the mucosal lining of the gut, at which point the disease is called ulcerative colitis.

inflammation in the gutWith further inflammation, the inflammatory response spreads throughout the wall of the gut, and is creation of lumps, or granulomas, in response to activation of immune cells within the gut wall. Now we see actual tissue damage and scarring, and the dysfunction is called Crohn’s disease. In the accompanying Xray of the large bowel in a patient with Crohn’s Disease (NEJM May 26, 2005), the arrow points to an area of extensive scarring and narrowing of the large bowel in this patient.

If the inflammation is discovered and treated early enough, it is possible to prevent progression to bowel damage, thus avoiding a great deal of pain, and the need for surgery.

There are experimental pharmaceutical treatments available, but the most promising one, which disables antibodies that trigger IBD, also disables the host defenses against latent JC virus, which is retained within the body, but not currently active, in 80% of people.56 Activation of this latent virus is associated with increased incidence of GI cancers, which seems like a somewhat risky course of action.

It is pretty clear that genetics have something to do with who is susceptible to inflammatory bowel disease. IBS is more prevalent in descendants of Ashkenazi Jews, it does appear in family clusters, and identical twins (single egg that splits) also have a much higher incidence as compared with fraternal twins (two eggs).

It is theorized that inflammatory bowel diseases are triggered by an abnormal reaction to bacteria which normally exist in the GI tract.57,58 Recently researchers found an association between IBD and an abnormal receptor for a protein called IL-23. Both Crohn’s and ulcerative colitis patients have this abnormal receptor, which is associated with the increased susceptibility to the inflammation characteristic of IBD. Other associations have been discovered to other chromosomal abnormalities.59

Micronutrients influence the integrity and function of the mucosal immune system,60 although we may not see clear cause-and-effect relationships. Zinc deficiency, for instance, affects the production of cytokines. The autonomic nervous system has a marked effect on the immune system, suggesting that people with high sympathetic nervous tone can be significantly susceptible to inflammatory bowel changes.61,62

Conventional treatment involves giving anti-inflammatory medication to suppress the inflammation in the gut. This is a good idea, in the acute condition, because suppression of the inflammation relieves the symptoms. However in the long term, if the underlying cause is not identified, the inflammation will return.

What is at the root of IBD? Chronic inflammation of the GI tract typically stems from food sensitivity and/or abnormal bacterial flora as a result of using antibiotics.

Interaction between nutrients and the immune system is unique within the GI tract, since nutrients provide continual stimulus for development of the immune system. Gut-associated lymphoid tissue (GALT) is the largest immune organ in the body, and naturally needs a good supply of all the nutrients. When the GALT is well supplied, the immune system can make many “soldiers” to fight off bad germs, viruses, etc. Use of antibiotics over the years denigrates the integrity of the GALT and allows abnormal bacterial flora to populate the gut.

Food tolerance is established when the infant first consumes something other than breast milk. Activation of T cells at weaning causes a transient localized inflammatory response, resulting (usually) in tolerance to the foods ingested. When too many grains and sugars are fed too early, the stage can be set for food sensitivities and intolerances.



Vitamin D deficiency has been strongly linked to autoimmune disease.63 Nearly every auto-immune patient tested will be found to be very deficient in this nutrient.

According to a large study of 187,563 women,64 those who took vitamin D supplements via multivitamins were 40 percent less likely to develop multiple sclerosis (MS) than women who did not take supplements. The study questioned if MS can be caused by lack of sunlight, since the body cannot not make its own vitamin D in the absence of sunlight, and only makes Vitamin D in the sunlight if there is nothing blocking the ultraviolet rays from the skin. Going out with sunscreen applied to the skin does nothing for our Vitamin D levels except lower them.

In animal studies, vitamin D has been shown to suppress the autoimmune response in rats with a disorder very similar to MS.

How vitamin D affects cell activity is key. Vitamin D status affects chemicals that modulate the immune system called cytokines. Vitamin D keeps cells in check. When the body has too little D, cell activity can go haywire, become overly active or multiply too quickly. It is well-known that in higher latitudes where there is less sun exposure, there is a higher risk for MS. Higher sun exposure during childhood and early adolescence are associated with a decreased risk of multiple sclerosis.65

While many advertisements warn us about the use of sunscreen and the dangers of sunlight in promoting the development of melanoma, it is very clear that the number of cases of MS is nearly zero near the equator and increases with latitude in both hemispheres. The increased sunlight near the equator allows the body to produce more vitamin D, and appears to reduce the incidence of MS, skin cancer, and the like. There is growing evidence that skin cancer occurs in people woefully deficient in vitamin D and omega-3 oils.


Vaccines by their very design suppress the immune system. Additionally, vaccines often contain mercury and aluminum, both of which are not only immuno-suppressive but also neurotoxic. Mercury actually causes changes in the lymphocyte activity and decreases lymphocyte viability.66

Vaccines deplete our body of vital immune-enhancing nutrients, like vitamin C, vitamin A and zinc.67 Nutrients like these boost the immune system, and feed white blood cells and macrophages which become the immune system “soldiers.”

The conventional medical wisdom states that we experience a small dip in our immune system after a vaccination, and in return receive life-time immunity to one disease. Renowned vaccine expert and author Sherri Tenpenny has said no, that we experience a total immune system depression (our only defense against all known disease - including millions of pathogens) for a temporary immunity against one disease, usually an innocuous childhood disease. As author Eustace Mullins put it, "We are trading mumps and measles for cancer and AIDS."68

Vaccines by-pass the digestive system. Since the vaccines are injected directly into our subcutaneous tissues, they are able to clog the lymphatic system with large protein molecules which have not been adequately broken down. These large vaccine-associated proteins act as circulating immune complexes (CICs) which can trigger allergies.

One hundred years ago, children received 1 vaccine (smallpox). Forty years ago, children typically received 5 vaccines (diphtheria, pertussis, tetanus, polio, and smallpox) and as many as 8 shots by 2 years of age. Today, children receive 11 vaccines routinely and as many as 20 shots by 2 years of age.69 Up until the year 2000 most childhood vaccines were preserved with thimerosal, a form of mercury used as a preservative. This substance was banned in the year 2000, but thimerosal-containing vaccines continued to be used until the supplies were exhausted, about 2002.

Despite the controversy about the safety or efficacy of vaccines, ever-growing number of individuals are suffering adverse, auto-immune reactions to vaccinations.


Soy products, including soy-based baby formulas, contain a plant estrogen called genistein which is a hormone-like compound that appears to impair immune function.

The Proceedings of the National Academy of Sciences reported in 2002 that when the plant estrogen genistein found in soy was injected in mice, levels of several immune cells dropped and the thymus, a gland where immune cells mature, shrank.70

Additionally, processing of soy milk makes it often very high in aluminum.71


A root canal procedure leaves a tooth without a blood supply to its interior. Circulating antibodies cannot reach the bacteria in residence inside that tooth. As author Dr. George Meinig explains, root canal fillings can become a lifetime bacteria “factory” which sows the seeds of disease throughout the body.72

Dr. Weston A. Price documented how entrenched dental bacterial can contribute to heart and circulatory diseases, as well as autoimmune diseases of the joints, the brain and nervous system.73

A strong immune system will control the germs that escape from teeth into other areas of the body. But this holding action may tie up so many of the immune system’s “soldiers” that when it comes time to fight off the flu, for example, there may not be enough immune system lymphocytes (white blood cells) remaining in action to ward off the virus.



Sugar can cause many problems with the gastrointestinal tract including: an acidic digestive tract, indigestion, malabsorption in patients with functional bowel disease, increased risk of Crohn's disease, and ulcerative colitis. Sugar feeds cancer cells and has been connected with the development of cancer of the breast, ovaries, prostate, rectum, pancreas, biliary tract, lung, gallbladder and stomach. Sugar can interfere with the absorption of protein.


Fatty acids are essential for the proper development of the human brain during gestation and the first two years of life. The Omega-3 essential fatty acid linoleic acid, and its derivative, DHA (docosahexaenoic acid), is so essential to a child's development that if a mother and infant are deficient in it, the child's nervous system and immune system may never fully develop. This can cause a lifetime of unexplained emotional, learning, and immune system disorders. Look at the ingredients listed on labels of the powdered baby formulas commonly available in grocery stores. You’ll see they are generally are made with processed oils which contain high levels of detrimental trans fatty acids. And note the widespread use of high fructose corn syrup.

The adult population witnessed a decline in the use of nutrient dense coconut oil. Some 50 years ago, manufacturers of hydrogenated vegetable oils began to compete aggressively for market share. It was said that coconut oil was a saturated fat, and saturated fats were bad. Food processors stopped using coconut oil. In its place, processed oils and “fake” foods like margarine were introduced into the food chain. Humankind had never before eaten these foods, with their highly saturated and trans configurations. The shelf life of the new fangled fats was superb, so they proliferated. However, we also began to see a concurrent rise in heart disease, diabetes, and other chronic illnesses. Unrefined coconut oil feeds the thyroid gland, promotes weight loss, and contains lauric acid, the same compound that is in breast milk to give babies immunity.74

By modifying natural fats, we have altered the basic building blocks of the human brain, weakening the brain’s architecture. And, like unstable buildings that come apart in an earthquake or storm, poorly structured human brains are failing to cope with the mounting stress of modern life


Gluten is thought to be one trigger for autoimmune disease.75 Indeed gluten sensitivity may be a major trigger for autoimmune disease.76 Researchers have found an association between gluten enteropathy and/or celiac disease and thyroiditis,77,78 Alzheimer’s brain tissue,79 diabetes,80 and autoimmune disease in general.81


Conventionally grown food often comes with chemical residues. The Environmental Protection Agency (EPA) considers 60 percent of herbicides, 90 percent of fungicides, and 30 percent of insecticides to be carcinogenic. Pesticides can have many negative influences on health, including immune system suppression, disruption of the endocrine system, nervous system disorders, and carcinogenicity.

Studies show that organic produce has more vitamins and minerals, especially Vitamin C, than conventional produce.82

The impact of genetically modified food on human health has not been extensively studied. Once again, humankind is being served altered foods never before eaten. There is a growing concern that GMO foods are injurious to health. Food crops are increasingly modified to include viruses and other unnatural elements like insecticide resistance, which could certainly impact those who eat the crops.


The Standard American Diet tends to kill off good gut flora. We need bacteria in the gut to digest food and extract nutrients. But the good bacteria may be starved by processed foods. Before the convenience era with its refrigerators, “lacto-fermentation” was used to preserve food. Additionally, lacto-fermentation adds a whole army of beneficial micro-organisms to food, making them easier to digest and increasing the healthy flora in the gut. Convenience dictated pasteurization and processing of milk and foods; in return however, many beneficial enzymes and nutrients are killed. There is some popular understanding of this loss today, as demonstrated by television commercials advertising yogurt with “friendly probiotics.”

Sally Fallon, an expert on fermented foods and author of Nourishing Traditions, suggests that, “by abandoning the ancient practice of lacto-fermentation, and insisting on a diet in which everything has been pasteurized, we have compromised the health of our intestinal flora and made ourselves vulnerable to legions of pathogenic microorganisims."83


Stress can seriously impact health. Researchers evaluated several hundred studies on stress and concluded that the kind of stress that most negatively compromises the immune system is chronic stress .84 Stress is thought to be a very significant trigger for chronic illness. Some patients and doctors have discerned that there is nearly always a stressful event that triggers the outbreak of rheumatoid arthritis, lupus or scleroderma.


We have now learned that children who frequently use antibacterial soaps are not exposed to common bacteria that may protect them from allergies and asthma. Indeed, exposure to bacteria and viruses acts as a natural vaccine to boost the ability of the immune system to fend off invaders. Farmers used to eat carrots and other vegetables right out of the field during the day as a snack. They might wipe off the dirt on their pants, but wash and scrub the vegetables? No. They got a small dose of dirt with its population of good microorganisms. The immune system is a bit like a muscle – use it or lose it. People who are confined to a wheelchair develop severe muscle atrophy within a very short time. So too does the immune system atrophy if it does not receive the kind of small challenges nature designed for it.


Several themes run through this discussion of auto-immune diseases.

  • Auto-immune diseases seem to develop in people who have experienced an on-going lack of nutrients in their diet.
  • Auto-immune diseases seem to be associated with environmental toxicity.
  • The susceptible individual has very likely experienced significant and prolonged chronic stress.
  • The immune system in the susceptible individual may have been fighting on more than one front – for example dealing with a root canal infection as well as multiple amalgam (mercury) fillings, and does not have enough activity left to overcome a serious infection or inflammatory state.
  • The body starts to experience chronic inflammation and eventually breaks down; genetics will determine where the weakness occurs, and therefore the timing and location of the breakdown.
  • Steroids and other drugs may suppress the inflammatory symptoms for a time, but do not have the capacity to heal. In fact, they certainly contribute to overall suppression of the immune system.

Reversing autoimmune disease is a process of education and medical assistance regarding:

  • Identification of foods which cause an allergic reaction.
  • Identification of molds, pollen and other airborne allergens.
  • Identification and elimination of heavy metals.
  • Identification of malfunctioning information systems within the body and use of supplements and energetic medicine to re-establish healthy function.
  • Learning how to eat a nutrient dense diet.
  • Learning how to heal the GI tract and promote good intestinal flora. Colonics work really well for this.
  • Reduction of stress.
This article is particularly lengthy, and yet we barely touched on many things. Much of what is presented here is not found in the daily mainstream press. If you read it all, congratulations! Chances are excellent you have the dedication to work with us to restore your natural, healthy state.

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