Autoimmune Diseases
Autoimmune Diseases
There are different theories for describing autoimmune diseases.
Mainstream theory considers an auto-immune disease to be a condition where the body's immune system is active for a long time even though there is no apparent underlying infection or irritant to explain such an immune response. This theory considers the immune system to be behaving irrationally. This is the theory that your doctor will most likely tell you.
Alternative theories consider that, when your immune response is activated for a long time, there is in fact an underlying parasitic, bacterial or fungal infection that is difficult to detect. These theories consider that the immune system is behaving rationally.
Mainstream theory considers an auto-immune disease to be a condition where the body's immune system is active for a long time even though there is no apparent underlying infection or irritant to explain such an immune response. This theory considers the immune system to be behaving irrationally. This is the theory that your doctor will most likely tell you.
Alternative theories consider that, when your immune response is activated for a long time, there is in fact an underlying parasitic, bacterial or fungal infection that is difficult to detect. These theories consider that the immune system is behaving rationally.
General Treatments for Auto-immune Diseases
Prior to discussing mainstream and alternative explanations of auto-immune diseases, we list general treatments that you can implement immediately. Although academia has defined dozens of autoimmune diseases, the diseases have many common aspects and are differentiated largely by which organ or tissue the disease affects. Therefore, there are general treatments that work across a wide range of auto-immune disease.
Antiparasitic medication: Everyone has communities of parasites, in the same way they have communities of bacteria. Parasites have long been known to cause disease. One of the first steps is to eliminate parasites as a potential infection. Antiparasitic medications include drugs such as ivermectin, mebendazole, fenbendazole and praziquantel and oils such as wormwood oil, black walnut oil, clove oil and oregano oil.
Low-sugar diet: Sugar (glucose) is a primary energy source for many pathogens, including parasites, bacteria, yeast and fungi. See our medical diet.
Supplementation with thiamine: Thiamine is needed by cells for oxidative phosphorylation to create energy. Scroll down to the section on Cellular Energy Theory to understand the importance of oxidative phosphorylation. See our thiamine page.
Supplementation with vitamin D: All cells are designed to receive vitamin D to operate properly. Low vitamin D levels are associated with dozens of diseases. See our vitamin D page and vitamin D dosing guide.
Cellular Medicines’ framework for recovering from chronic (long-term) illness, pain or low energy: See our framework for recovering from chronic illness.
Antiparasitic medication: Everyone has communities of parasites, in the same way they have communities of bacteria. Parasites have long been known to cause disease. One of the first steps is to eliminate parasites as a potential infection. Antiparasitic medications include drugs such as ivermectin, mebendazole, fenbendazole and praziquantel and oils such as wormwood oil, black walnut oil, clove oil and oregano oil.
Low-sugar diet: Sugar (glucose) is a primary energy source for many pathogens, including parasites, bacteria, yeast and fungi. See our medical diet.
Supplementation with thiamine: Thiamine is needed by cells for oxidative phosphorylation to create energy. Scroll down to the section on Cellular Energy Theory to understand the importance of oxidative phosphorylation. See our thiamine page.
Supplementation with vitamin D: All cells are designed to receive vitamin D to operate properly. Low vitamin D levels are associated with dozens of diseases. See our vitamin D page and vitamin D dosing guide.
Cellular Medicines’ framework for recovering from chronic (long-term) illness, pain or low energy: See our framework for recovering from chronic illness.
Mainstream Theory
Description of Autoimmune Diseases based on Mainstream Theory
Mainstream understanding of autoimmune diseases: The body’s immune system becomes dysregulated and begins attacking the body’s own tissues instead of foreign invaders, such as parasites, yeast, viruses or bacteria.
Long-term activation: The theory is that the immune system remains activated long after the initial trigger—often an infection—has been cleared.
Incorrect identification: The immune system erroneously identifies its own healthy tissues as threats, a phenomenon referred to as molecular mimicry. The immune system mistakes normal cells for pathogens because certain molecular structures on the body's tissues resemble those of the invading microbes.
Classification: Autoimmune diseases are generally classified by the specific organ or tissue that is targeted by the immune system. For instance:
Observations: There are typically signs of immune activation, including inflammation (e.g., swelling, redness), the release of pro-inflammatory cytokines, and elevated levels of white blood cells and autoantibodies.
Mainstream understanding of autoimmune diseases: The body’s immune system becomes dysregulated and begins attacking the body’s own tissues instead of foreign invaders, such as parasites, yeast, viruses or bacteria.
Long-term activation: The theory is that the immune system remains activated long after the initial trigger—often an infection—has been cleared.
Incorrect identification: The immune system erroneously identifies its own healthy tissues as threats, a phenomenon referred to as molecular mimicry. The immune system mistakes normal cells for pathogens because certain molecular structures on the body's tissues resemble those of the invading microbes.
Classification: Autoimmune diseases are generally classified by the specific organ or tissue that is targeted by the immune system. For instance:
- Rheumatoid arthritis involves the immune system attacking the joints.
- Multiple sclerosis is characterized by the immune system attacking the myelin sheath that protects nerve fibres.
- Type 1 diabetes occurs when the immune system destroys the insulin-producing beta cells in the pancreas.
- Hashimoto’s thyroiditis involves the immune system attacking the thyroid gland.
Observations: There are typically signs of immune activation, including inflammation (e.g., swelling, redness), the release of pro-inflammatory cytokines, and elevated levels of white blood cells and autoantibodies.
Treatments based on Mainstream Theory
Prescription drugs for suppressing the immune system: Immunosuppressive drugs, such as corticosteroids or disease-modifying antirheumatic drugs (DMARDs), are commonly used to suppress the immune response. Immunosuppressants understandably increase the risk of infections and have long-term side effects, such as increased susceptibility to cancer or organ damage.
Prescription drugs for suppressing inflammation: Anti-inflammatory drugs reduce the inflammation that arises from the immune response.
Prescription drugs for replacing chemicals naturally produced in the body: In cases that the affected organ or tissue is no longer functioning properly—such as the insulin-producing cells in type 1 diabetes or the thyroid in Hashimoto’s thyroiditis—replacements for the lost function can be provided. For example, insulin injections are taken by people with type 1 diabetes, while synthetic thyroid hormones are given to individuals with Hashimoto’s thyroiditis.
Prescription drugs for suppressing the immune system: Immunosuppressive drugs, such as corticosteroids or disease-modifying antirheumatic drugs (DMARDs), are commonly used to suppress the immune response. Immunosuppressants understandably increase the risk of infections and have long-term side effects, such as increased susceptibility to cancer or organ damage.
Prescription drugs for suppressing inflammation: Anti-inflammatory drugs reduce the inflammation that arises from the immune response.
Prescription drugs for replacing chemicals naturally produced in the body: In cases that the affected organ or tissue is no longer functioning properly—such as the insulin-producing cells in type 1 diabetes or the thyroid in Hashimoto’s thyroiditis—replacements for the lost function can be provided. For example, insulin injections are taken by people with type 1 diabetes, while synthetic thyroid hormones are given to individuals with Hashimoto’s thyroiditis.
Chronic-infection Theory
Description of Autoimmune Diseases based on Chronic-infection Theory
Chronic-infection understanding of autoimmune diseases: An intuitive explanation for a prolonged immune response is that there is in fact a chronic low-grade infection that, although difficult to detect, requires a continual response from the immune system.
Rational immune system: In this explanation, the immune system is behaving rationally, as it is continually fighting a real threat rather than a non-existent threat or mistaking the body's tissues for foreign invaders.
Long-term collateral damage: However, because the immune system always does collateral damage to tissues when activated—even if fighting an infection for a short time—organs and tissues are damaged by both the infection and the long-term response of the immune system.
Chronic-infection understanding of autoimmune diseases: An intuitive explanation for a prolonged immune response is that there is in fact a chronic low-grade infection that, although difficult to detect, requires a continual response from the immune system.
Rational immune system: In this explanation, the immune system is behaving rationally, as it is continually fighting a real threat rather than a non-existent threat or mistaking the body's tissues for foreign invaders.
Long-term collateral damage: However, because the immune system always does collateral damage to tissues when activated—even if fighting an infection for a short time—organs and tissues are damaged by both the infection and the long-term response of the immune system.
Treatments based on Chronic-infection Theory
Treating the underlying infection: The obvious treatment is to kill the underlying long-term infection. This is not straight-forward, because chronic infections are notoriously hard to diagnose, locate and treat.
Challenges in diagnosing infections: It is challenging to determine the specific infection. The body contains parasites, bacteria, viruses and fungi such as yeast. These microorganisms exist in an ecosystem, where they support, infect and compete with one another. You might be infected with parasites that are producing waste that yeasts are thriving on, with the yeasts in turn supporting a bacterial infection.
Challenges in treating bacteria: Bacteria form biofilms for protection, go dormant to reduce the effect of treatments, and mutate and share resistance genes to survive treatment. They particularly benefit from creating biofilms in joints, where there is nutrient-rich synovial fluid and less immune activity because of less blood flow.
Challenges in treating yeast: Yeasts evade treatments by switching into more invasive and resistant forms, hiding in biofilms and deep tissue, and developing resistance.
Challenges in treating viruses: Viruses hide and go latent when under attack.
Challenges in treating parasites: Parasites actively move within organs and between body tissues, with some migrating to safer organs, such as the eyes and brain, where it is harder to treat them. Moreover, parasites form protective cysts.
Treating the underlying infection: The obvious treatment is to kill the underlying long-term infection. This is not straight-forward, because chronic infections are notoriously hard to diagnose, locate and treat.
Challenges in diagnosing infections: It is challenging to determine the specific infection. The body contains parasites, bacteria, viruses and fungi such as yeast. These microorganisms exist in an ecosystem, where they support, infect and compete with one another. You might be infected with parasites that are producing waste that yeasts are thriving on, with the yeasts in turn supporting a bacterial infection.
Challenges in treating bacteria: Bacteria form biofilms for protection, go dormant to reduce the effect of treatments, and mutate and share resistance genes to survive treatment. They particularly benefit from creating biofilms in joints, where there is nutrient-rich synovial fluid and less immune activity because of less blood flow.
Challenges in treating yeast: Yeasts evade treatments by switching into more invasive and resistant forms, hiding in biofilms and deep tissue, and developing resistance.
Challenges in treating viruses: Viruses hide and go latent when under attack.
Challenges in treating parasites: Parasites actively move within organs and between body tissues, with some migrating to safer organs, such as the eyes and brain, where it is harder to treat them. Moreover, parasites form protective cysts.
Orthomolecular Theory
Description of Autoimmune Diseases based on Orthomolecular Theory
Orthomolecular understanding of autoimmune diseases: The dysfunction of organs is not due to a misguided immune response targeting healthy tissue but rather a lack of nutrients required for normal organ function.
Cause of nutritional deficiencies: Underlying infections feed off nutrients in the body. The immune system subsequently uses up energy and nutrients in fighting the infections.
Orthomolecular understanding of autoimmune diseases: The dysfunction of organs is not due to a misguided immune response targeting healthy tissue but rather a lack of nutrients required for normal organ function.
Cause of nutritional deficiencies: Underlying infections feed off nutrients in the body. The immune system subsequently uses up energy and nutrients in fighting the infections.
Treatments based on Orthomolecular Theory
Replenishing depleted nutrients that are necessary for optimal immune and organ function: High-dose supplementation with nutrients restores the immune system and the proper functioning of organs.
Replenishing depleted nutrients that are necessary for optimal immune and organ function: High-dose supplementation with nutrients restores the immune system and the proper functioning of organs.
Cellular Energy Theory
Description of Autoimmune Diseases based on Cellular Energy Theory
Cellular energy understanding of autoimmune diseases: In autoimmune disease, cells overly rely on anaerobic glycolysis (rather than oxidative phosphorylation) to create energy.
Oxidative phosphorylation: Oxidative phosphorylation is an efficient but slow way for cells to create energy when there is oxygen present. We largely think of oxidative phosphorylation as the preferred mechanism of creating energy.
Anaerobic glycolysis: Anaerobic glycolysis is a less efficient but faster way for cells to create energy and does not require oxygen. A byproduct of anaerobic glycolysis is lactate. A familiar example of the body adopting anaerobic glycolysis is in sprinting, where the body must generate energy quickly with a reducing oxygen supply and we feel the burn of lactate (often loosely referred to as lactic acid) in our legs.
Energy generation by immune cells: Our immune cells (i.e., our cells that fight infections, such as macrophages and T cells) prefer to generate energy through slow oxidative phosphorylation when at rest and through fast anaerobic glycolysis when actively fighting infection.
Advantages of anaerobic glycolysis in fighting infection: During an immune response, immune cells rely on anaerobic glycolysis to rapidly produce energy. They need this rapid energy to multiply, travel to the site of infection and fight the infection. Additionally, immune cells make use of the byproducts of anaerobic glycolysis in fighting infection. Finally, infections often occur in low-oxygen environments, such as inflamed or damaged tissues, and anaerobic glycolysis enables immune cells to operate effectively even when oxygen is scarce.
Problem with excess anaerobic glycolysis in fighting infection: An excessive buildup of lactate in anaerobic glycolysis becomes problematic. An excess level of lactate can arise through a cycle whereby the lactate from anaerobic glycolysis fuels inflammation, the inflammation keeps the originally activated immune cells in an active state and activates other resting immune cells, and even more lactate is produced through anaerobic glycolysis. The high level of lactate damages tissue through various mechanisms, such as by creating an acidic environment, impairing tissue repair, and signalling for the production of cytokines.
Excess anaerobic glycolysis outside the immune system: All cells, not just immune cells, can switch between oxidative phosphorylation and anaerobic glycolysis for energy production. Ideally, cells rely on oxidative phosphorylation as it is more efficient (requires far less glucose) and has less-harmful byproducts. However, oxidative phosphorylation requires functional mitochondria and several key nutrients, such as vitamin B1 (thiamine), which is essential for enzymes in the TCA cycle. A lack of these nutrients forces many cells to primarily adopt anaerobic glycolysis, which as discussed above, results in a continuous immune response.
Cellular energy understanding of autoimmune diseases: In autoimmune disease, cells overly rely on anaerobic glycolysis (rather than oxidative phosphorylation) to create energy.
Oxidative phosphorylation: Oxidative phosphorylation is an efficient but slow way for cells to create energy when there is oxygen present. We largely think of oxidative phosphorylation as the preferred mechanism of creating energy.
Anaerobic glycolysis: Anaerobic glycolysis is a less efficient but faster way for cells to create energy and does not require oxygen. A byproduct of anaerobic glycolysis is lactate. A familiar example of the body adopting anaerobic glycolysis is in sprinting, where the body must generate energy quickly with a reducing oxygen supply and we feel the burn of lactate (often loosely referred to as lactic acid) in our legs.
Energy generation by immune cells: Our immune cells (i.e., our cells that fight infections, such as macrophages and T cells) prefer to generate energy through slow oxidative phosphorylation when at rest and through fast anaerobic glycolysis when actively fighting infection.
Advantages of anaerobic glycolysis in fighting infection: During an immune response, immune cells rely on anaerobic glycolysis to rapidly produce energy. They need this rapid energy to multiply, travel to the site of infection and fight the infection. Additionally, immune cells make use of the byproducts of anaerobic glycolysis in fighting infection. Finally, infections often occur in low-oxygen environments, such as inflamed or damaged tissues, and anaerobic glycolysis enables immune cells to operate effectively even when oxygen is scarce.
Problem with excess anaerobic glycolysis in fighting infection: An excessive buildup of lactate in anaerobic glycolysis becomes problematic. An excess level of lactate can arise through a cycle whereby the lactate from anaerobic glycolysis fuels inflammation, the inflammation keeps the originally activated immune cells in an active state and activates other resting immune cells, and even more lactate is produced through anaerobic glycolysis. The high level of lactate damages tissue through various mechanisms, such as by creating an acidic environment, impairing tissue repair, and signalling for the production of cytokines.
Excess anaerobic glycolysis outside the immune system: All cells, not just immune cells, can switch between oxidative phosphorylation and anaerobic glycolysis for energy production. Ideally, cells rely on oxidative phosphorylation as it is more efficient (requires far less glucose) and has less-harmful byproducts. However, oxidative phosphorylation requires functional mitochondria and several key nutrients, such as vitamin B1 (thiamine), which is essential for enzymes in the TCA cycle. A lack of these nutrients forces many cells to primarily adopt anaerobic glycolysis, which as discussed above, results in a continuous immune response.
Treatments based on Cellular Energy Theory
High-dose vitamin B1 (thiamine/benfotiamine) supplementation: High doses of vitamin B1 are supplemented with a B-complex to ensure cells can generate energy through oxidative phosphorylation.
Effectiveness across a wide range of diseases: High dosing with vitamin B1 has been highly successful in addressing a wide range of diseases. Moreover, it is interesting to note that the symptoms of a wide range of diseases match those of severe vitamin B1 deficiency (beriberi).
High-dose vitamin B1 (thiamine/benfotiamine) supplementation: High doses of vitamin B1 are supplemented with a B-complex to ensure cells can generate energy through oxidative phosphorylation.
Effectiveness across a wide range of diseases: High dosing with vitamin B1 has been highly successful in addressing a wide range of diseases. Moreover, it is interesting to note that the symptoms of a wide range of diseases match those of severe vitamin B1 deficiency (beriberi).
Potential Overlap of Different Explanations for Auto-immune Disorders
There is potentially overlap between the above explanations for auto-immune disorders:
Overlap between different explanations: One can easily imagine the situation that an underlying parasitic or bacterial infection is robbing the body of nutrients, and the immune system is using the last of some of its nutrients in fighting the infection. Both the immune system and the body in general enter a state of anaerobic glycolysis, producing lactate that damages the body and keeps the immune system activated. The immune system causes collateral damage to the body. From the doctor’s point of view, the immune system is “attacking” the body.
Difference in treatments: The difference between mainstream theory and other theories is that the latter theories present solutions to addressing the underlying causes of auto-immune disorders, such as treating the infection and supplementing with high doses of depleted nutrients.
Other Inflammatory Diseases
There are other inflammatory diseases that are not considered auto-immune diseases in mainstream theory because the underlying infection is known or another cause of the inflammation, such as an irritant, is known.
Examples of inflammation diseases for which infections are known: Rheumatic fever, which develops as a complication of a streptococcal (bacterial) throat infection; reactive arthritis, which can follow infections caused by Chlamydia, Shigella, or other bacteria; and Lyme disease, which refers to infection with the bacterium Borrelia burgdorferi.
Examples of inflammation diseases with other known triggers: Asthma and COPD, which are caused by allergens or irritants; gout, resulting from the buildup of uric acid crystals in the bloodstream; and osteoarthritis, which arises from mechanical wear and joint damage.
There is potentially overlap between the above explanations for auto-immune disorders:
Overlap between different explanations: One can easily imagine the situation that an underlying parasitic or bacterial infection is robbing the body of nutrients, and the immune system is using the last of some of its nutrients in fighting the infection. Both the immune system and the body in general enter a state of anaerobic glycolysis, producing lactate that damages the body and keeps the immune system activated. The immune system causes collateral damage to the body. From the doctor’s point of view, the immune system is “attacking” the body.
Difference in treatments: The difference between mainstream theory and other theories is that the latter theories present solutions to addressing the underlying causes of auto-immune disorders, such as treating the infection and supplementing with high doses of depleted nutrients.
Other Inflammatory Diseases
There are other inflammatory diseases that are not considered auto-immune diseases in mainstream theory because the underlying infection is known or another cause of the inflammation, such as an irritant, is known.
Examples of inflammation diseases for which infections are known: Rheumatic fever, which develops as a complication of a streptococcal (bacterial) throat infection; reactive arthritis, which can follow infections caused by Chlamydia, Shigella, or other bacteria; and Lyme disease, which refers to infection with the bacterium Borrelia burgdorferi.
Examples of inflammation diseases with other known triggers: Asthma and COPD, which are caused by allergens or irritants; gout, resulting from the buildup of uric acid crystals in the bloodstream; and osteoarthritis, which arises from mechanical wear and joint damage.