Biological systems generate electrons through chemical processes. EMPs cause damage to electronics because the magnetic pulses generated cause an induced current (Maxwell's equations) in the wires, which become overwhelmed and burn up/melt due to the amount of energy contained within the pulse. Since humans don't naturally contain wires, their functions still work because nothing melts internally.
However, there may be other effects that affect neural and physiological processes, or result from chain reactions caused by EMPs, so it's not to say that humans are completely impervious from EMPs.
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