The difference between the protein markers your immune system is looking for and your own cells isn’t all that much. If you want to have an immune system that doesn’t target healthy cells you need a system that can tag exactly which cells are the bad ones. The only way to do that effectively is to have a memory of exactly which cells are good and exactly which ones are bad.
Even with such a complex and specific system in place, autoimmune diseases are still fairly common.
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