Essentially, parasites were inside the body of most human beings over our evolutionary history, up until the last 100 years. The parasites secrete immune-modifying molecules[1]. And because we don't have parasites as often anymore, autoimmune disorders have exploded in prevalence.
The thinking is that, in the same way that human beings and guinea pigs lost the ability to synthesize vitamin C because it was always available, some people lost the ability to regulate their immune system because parasites were just that pervasive. In other words, our ancestors lost genetic machinery that modulated their immune response because the parasites they had provided that service already. So losing those genes had no effect on their fitness.
It's not a widely accepted theory, but it certainly challenges the notion of self in relation to parasites.