Excerpt

The immune system is a distributed complex adaptive system that makes decisions on a daily basis about how to respond to intruders, to commensals, and to itself. These decisions are typically remembered for life. Lifelong immunity typically protects us from a large variety of pathogens in our environment. The absence of immunity to the commensal bacteria in our microbiomes is essential for our physiological health, and the absence of immunity to our own tissues prevents us from suffering from autoimmune disease. These “cognitive” properties of deciding and remembering are typically attributed to the adaptive immune system, that is, the lymphocytes, which are circulating white blood cells, expressing a randomly made receptor, with which they can potentially bind proteins that they encounter while patroling the body. The proteins (or peptides) that lymphocytes bind to with high affinity are called antigens (or epitopes), and lymphocytes tend to be “specific” for a particular antigen because their random receptor only binds to a very small fraction (typically 1 : 105 to 1 : 106) of the proteins in their environment. Lymphocytes specifically binding to a novel antigen—that is, those involved in a high-affinity interaction—trigger a process of cell division and differentiation, and expand into a large clone of “effector cells,” all expressing the same receptor. This process is called “clonal expansion.” Together these effector cells are capable of binding and clearing the antigen.

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