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Recognizing Known IntrudersThe vertebrate immune system recognizes particular antigens (viruses and other undesirable foreign substances) by means of antibodies and immune cell receptors which bind to epitopes (small portions of the antigen, consisting of at least 4 to 6 amino acids). It is interesting to note that an exact match to the entire antigen is not attempted; in fact, it is almost certainly a physical impossibility. No antibody molecule or immune-cell receptor could be perfectly specific to a given antigen because matching occurs at surfaces, not throughout volumes. T cell receptors can see the inner portions of antigen, but only after the antigen has been consumed by a macrophage or other cell, which then presents pieces of the antigen on it surface, where they can be seen by other cells. Similarly, in the computer immune system, a particular virus is not recognized via an exact match; rather, it is recognized via an exact or fuzzy match to a relatively short sequence of bytes occurring in the virus (a ``signature'', as described in section 2). Although matching to a small portion of the virus is not necessitated in this case by the laws of chemistry, it has some important advantages. In particular,
The issues of efficiency and variant recognition are relevant for biology as well. For both biological and computer immune systems, an ability to recognize variants is essential because viruses tend to mutate frequently. If an exact match were required, immunity to one variant of a virus would confer no protection against a slightly different variant. Similarly, vaccines would not work, because they rely on the biological immune system's ability to synthesize antibodies to tamed or killed viruses that are similar in form to the more virulent one that the individual is being immunized against.
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