From what I have experienced, I think the confusion regarding the disease is how "autoimmune" is defined by the person.
Autoimmunity, it seems is generally thought of as a permanent condition that is hopelessly tied to genetics or some other irreversible problem. Possibly, this could be the case in some. I think autoimmunity is nothing more than a physical state that can be triggered for any number of reasons. In another words, the magic bullet is not going to be found because there are multiple causes. On the other hand, if you can identify, and eliminate the cause, you have a shot of reversing the disease. But, even that is not as straight forward as it would seem.
When an autoimmune state is reached, and allowed to go on for years, the pathogens that cause symptoms of whatever disease autoimmunity results in are well established and now are very difficult for even a restored immune system to eliminate.
In my particular case, I have reason to believe one or more strains of mycoplasma may be the cause of my autoimmunity. I am not 100% certain, but that seems to be the case at this time. It seems to have a dual role as it also causes symptoms whenit reaches a certain threshold.
This infection allows other pathogens to proliferate, and were well established. The coinfections that are also responsible for other symptoms are a strain of E-Coli, MAP, H-Pylori. There may be others also.
My current thinking is that autoimmunity likely has multiple causes, but is not always or may never be irreversible. I don't know for sure because of so many possible causes. Lyme disease from the Borrelia Burgdorferi bacteria can cause autoimmunity. You may or may not develope Crohns from this state, but the autoimmune state will result in further disease of some kind. Remove the pathogen and then Crohns symptoms are often eliminated.
I am not presenting this as fact, but the premise I am treating under. I put it out there for others to prove or disprove. I am taking theory from many sources and testing directly on myself using an old alternative treatment. I use personal results or failures to develope the running hypothesis for my own disease.
Take it or leave it. Just what I think I have deduced from being ill and getting well. If I am wrong, or my self treatment fails, I will suffer the consequence. If I am correct, and my treatment works, I will do fine. Time will answer the question one way or another.
I hope everyone can get control of their disease, one way or another.
Dan