The immune system can be viewed as the evolutionary solution to the ever present risk of microbial infection ( Rose and Mackay, 2014). By taking a fresh look at these two processes together we can envision their evolutionary basis and understand the need for regulatory devices to prevent molecular mimicry from progressing to autoimmune disease. If molecular mimicry were not common, protective adaptive immunity could not be all-encompassing. Molecular mimicry, the sharing of epitopes among self and non-self antigens, is extraordinary common and provides the evidence that complete deletion of self-reactive clones is rare. For comprehensive, protective adaptive immunity, full deletion is necessarily a rare event. If we did have complete clonal deletion, there would be major voids, the infamous “black holes”, in our immune repertoire. Clonal deletion originated as a critical element of the clonal selection theory of antibody formation in order to explain tolerance of self. In this article, I trace the historic background of clonal deletion and molecular mimicry, two major pillars underlying our present understanding of autoimmunity and autoimmune disease.
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