Some maladies are thought to be "autoimmune," that is, one's immune system supposedly goes wacky and starts attacking its own body. I think this can happen, but only in rare instances, and
perhaps only in transplant cases (which is where it is really attacking a foreign body.)
The way "autoimmune" disorders are typically diagnosed is a blood panel is drawn and immune system disorder is seen based on excessive counts of one or more immune factors, which is typical of many infections. Then, smears and cultures, antigen and antibody tests, biopsies, and other diagnostics are run, but nothing is seen. Disregarding the fact that only a tiny fraction of bacteria, parasites, toxins, fungi, or other pathogens are tested for that could be causing an inflammatory condition such as this, it is assumed that the immune system is attacking the body. The immune system is pretty sophisticated and sensitive. A lot more sophisticated than the current diagnostic capabilities of conventional medicine. It compares DNA or protein coatings of pathogens against its own. If it does not get a match, it puts out a call to arms.
A first line response of the body to infection (especially bacterial and parasitic) is inflammation. Inflammation "calls" immune cells to the scene to combat the invader. I think it is the height of folly to believe that testing for a tiny fraction of possible pathogens and not finding anything is a better barometer of infection than a body's typical response to infection.
In recent years, conventional medicine has found or suspected that there are many disorders actually caused by pathogens, and sometimes common ones, that were not suspected before. Some cases of circulation dysfunction, heart disease, Parkinson's, lupus, MS, and other illnesses are now suspected to be caused by chlamydia, rather common bacteria that appears to get out of control in some people. Inflammatory bowel diseases like IBS are now known to some researchers to be often caused by giardia. Same with Lyme disease and spirochete bacteria. Mycoplasmas are being investigated as being the cause of other chronic disorders, but there are no conventional medical tests which detect them. (Update: there was recently advertised a clinic in California which tests blood samples for 4 types of mycoplasma using a pioneer method.)
Parasites like worms can cause a myriad of problems throughout the body, especially if they "escape" the intestinal tract. The typical test for parasites in the US is a fecal swab. If it comes up negative, the patient is declared to be free of parasites, although this test probably is less than 1% accurate in detecting active parasitic infection in the body. See the article called "Conventional Diagnosis of Parasites" on this web site for more information.
Look how long it took for the establishment to acknowledge that helicobacter pylori is the usual cause of gastric ulcers, even though the fact was proven over forty years ago. As late as the 2000's, some MDs were still prescribing acid blockers. Conventional researchers have found chlamydia trachomatis, yersinia enterocolitica, shigella, y. pseudotuberculosis, and ureaplasma urealyticum as the cause of some inflammatory disease. As far as I know, these bacteria are not typically tested for when attempting to diagnose an "autoimmune" disease. Even then, one of the most sophisticated conventional diagnostics for bacteria, the ALISA antibody test, is only about 30% accurate. It even says right on the results that it shouldn't be used as a diagnostic test.
Lupus, MS, rheumatoid arthritis, scleroderma, and many other inflammatory disorders are now being treated by a handful of forward-thinking doctors with low dose long term antibiotics. See http://rheumatic.org/ They claim great success in most cases, although progress can be slow (probably because they are using low dose instead of high doses of antibiotics). This treatment is based on the work of Thomas McPherson Brown, MD. Don't hold one's breath for effective therapy for these disorders to be prescribed by conventional doctors anytime soon, though.
The normal prescription for inflammatory disorders are strong antiinflammatories like steroids. These can certainly decrease symptoms but since they are covering up the problem and doing nothing to treat it, make it worse in the long run. A more ridiculous prescription for treating a pathogen-induced illness is a drug which decreases immune function. Since there are less immune cells to "call to arms" there is less inflammation. I can think of no better way to allow a pathogen to overrun and destroy tissue more quickly.
Many who are familiar with complementary health measures for "autoimmune" disorders will note that good treatments for many of them are herbs that should, according to conventional medicine, make the disorder worse. Echinacea, cat's claw (uncaria tometosa), goldenseal, pau d'arco, to name a few, are some of the better herbal immune stimulators. Yet they are often found valuable in rheumatoid arthritis, lupus, IBS, circulation dysfunction, heart disease, Parkinson's, scleroderma, and many other disorders, when taken in sufficient dosage. Since they are generally antiinflammatory and antibacterial, they are often appropriate treatments since they provide some palliation while addressing the cause.
Another consideration in inflammatory disorders is organ function. There must be sufficient cleansing capacity to be able to fight inflammatory disorders since "trash" like metabolic byproducts in the tissues inhibits immune function and may provide more food for bacteria, fungi, or parasites. It is therefore necessary to ensure the lymphs, kidneys, liver, and colon are working well. Whether an herbal or conventional antibiotic regimen will be used, cleaning the organs is a valuable exercise.
Parasites can sometimes cause inflammation directly and can greatly increase histamine response to bacteria or other pathogens, and allergens or other toxins. As one conventional medicine study determined when the correlation between schistosoma mansoni (blood flukes) and lupus and rheumatoid arthritis was studied: "Antibodies against nuclear material in s. mansoni are probably a consequence of heavy disturbance of the immune system in this chronic infection with great permanent antigen load. It is a matter of discussion, whether production of these antibodies is induced by nuclear material from the host or from the parasite." This parasite is easy to detect since it produces a well known antigen in the blood. Yet, how often is the test run when trying to find the cause of rheumatoid arthritis or SLE?
The "Conventional Diagnosis of Parasites" article describes the expensive and time-consuming methods that must be used to rule out parasite involvement. I think it easier, and certainly cheaper and less time consuming, to merely treat for parasites, since most of the herbs used are also beneficial against bacteria and fungi and without side effects. The liver, kidneys, and lymphs should be clean before attempting to deparasitize since it may strain these organs.
Toxins absorbed or ingested into the body can also wreak havoc on the immune system. Some of the toxins produced by pathogens can be tested for, but are probably not tested in over 99.9% of cases when they could be suspect. Toxic metals, solvents, and other poisons are tested for even less, although it is known that excessive amounts of toxic metals like mercury in the tissues can cause immune system dysfunction. So can aspartame, which causes symptoms indistinguishable from MS in some cases and can cause blood sugar problems when used long term (probably when there are insufficient vitamins (like B6) and minerals which help to detoxify the wood alcohol (major pancreas toxin) and phenylalinine (brain and nervous system toxin when used to excess)). It can take up to 18 months of completely avoiding toxins like aspartame and mercury before they are reduced to neglible levels in body tissues.
White cells will usually "attack" a toxin which is in the tissue, trying to remove it, assuming the immune system is not completely exhausted from fighting pathogens and toxins, which can happen in some cases. Not suspecting or attempting to diagnose a toxin, one might think the immune system was attacking the body's tissues, when it is really doing what it should - attempting to remove the offending substance. Avoiding ingestion and absorption of toxins is the best regimen. Any Hulda Clark book, or the Toxin Avoidance section, gives details.
Any problems in the dental area must be addressed for success in fighting infections coming from the mouth. Toxic dental materials can be a direct problem, as can dental bacteria and their toxins which can infect root canals and other areas of the mouth. Bob's Dental Awareness website discusses these problems. An excerpt from the site:
"The new and latest scientific research implicating toxic compounds emitted by mercury amalgam fillings and root canal teeth anaerobic bacteria show definite links to systemic diseases such as CFS, fibromyalgia, ALS, MS, lupus, multichemical senstivity, Parkinson's, endocarditis, and more. Research by notable scientists at leading Universities has unveiled a lack of knowledge within organized dentistry about the hazards of todays dental procedures and a complete lack of concern over the patient's well being. Research and clinical trials have indicated that the toxins excreted by anaerobic bacteria may be the cause of the onset of as much as 85% of the systemic diseases in this country alone. It is a proven and accepted fact that these dental induced toxins inhibit or destroy key enzymes needed for cell reproduction and energy conversion. These toxins also destroy key cellular proteins in the cerebral spinal fluid which allows these and other toxins to destroy nerves and mutate other cellular tissues. This website is designed to get you in touch with the facts with hyperlinks to the National Medical Library, websites of noted research scientists and my personal research into these dental induced problems."
Other problems with chronic disease can be caused by slow elimination. Many disorders are greatly exacerbated if there is not sufficient elimination. If the colon is not kept clean, toxins are reabsorbed before they are eliminated. Slow elimination also provides an ideal breeding ground for pathogens, adding more toxins and the increased risk of them crossing the intestinal barrier.
To combat autoimmune disorders, I would use cleansing and antiseptic regimens.