Pyrogens work in quite a cool way, in the sense that they directly affect your brain and make it do things. You probably have heard about the blood-brain barrier, an ingenious contraption that stops most cells and substances (and pathogens of course) from entering the very delicate tissues of your brain, to keep it safe from damage and disturbance. But there are regions of your brain where this barrier is partially penetrable by pyrogens. If they enter and interact with your brain they trigger a complex chain of events that basically cranks up the temperature by changing the internal
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