I have argued that in a reasonably healthy person, autoimmunity begins with normal immunity to a Franken-structure, like Franken-myelin, altered in at least two ways by B12 deficiency: the presence of methylmalonic acid among the lipids, and the under-methylation of the lipids (too little choline, e.g.). Regular immunity creates a lot of inflammation in the still normal surrounding structures, and regular immunity evolves into “autoimmunity”. Here I want to add that the autoimmune reaction may be “directed to” (have higher affinity for) an inflamed structure rather natural structure. The physical alterations of the structure under inflammation may change its shape enough that antibodies can be generated against it that are initially not in fact really good antibodies to a purely wild type structure in a non-inflamed environment, but of course these antibodies would have a measurable reactivity even against a purely wild type structure. Antibody-antigen reactions are never perfectly specific.
In any person in which the direction of evolution of the antibodies tends toward recognition of ever subtler structural alterations due to lower levels of inflammation, does that process finally yield antibodies with enough cross-reactivity with wild-type structures to be properly called “autoimmune”?
Now when a person is outright unhealthy or outright poorly nourished or suffering local toxicities in regions where antibodies are being generated, these requirements are not necessary – the very process of shuffling antibody gene segments and making test antibodies and selecting against defective (auto-) antibodies can be defective under these conditions. That is, real autoimmunity evolves in a milieu with more serious underlying problems, much bigger than say mere B12 deficiency.
However, anyone deficient in B12 cannot possibly be merely deficient in B12, as I have argued and hopefully demonstrated before. A person deficient enough in B12 to be accumulating methylmalonic acid in his tissues is deficient in other important substances, and likely so at more than just one location in his body. It is also likely that such a person has excesses of substances other than just methylmalonic acid. Imbalances of all sorts are the rule when nutrition is catch as catch can, as it so often is in modern America.