I'm feeling much better today; amazing what the immune system will do if you just let it do its job stress-free. Getting sick has reminded me of a question I think of every time I get sick: why do we get muscle aches when we are ill?
There are two ways to approach this question. One is to ask why, evolutionarily, do we get muscle aches while sick (the ultimate question), and the other is to ask what, mechanistically, is causing our muscle aches (the proximate question). It's easy to come up with realistic hypotheses at the ultimate level explaining muscle aches. They may simply be a direct result of the viral infection and have no overall adaptive value (i.e. they're an unpleasant side effect). Alternatively, they might be adaptive in that they're a strong reminder to our conscious selves that we should sit down and stop doing whatever we're trying to do and let the immune system work. For instance, thanks to my sore muscles I needed little extra motivation to spend most of yesterday on the couch or in bed.
However, I've never seen a good physiological explanation for why we get muscle aches during/after viral infections. Are they being caused directly by the virus? Is it some response of our immune system (or other organ systems) to the infection? Any ideas would be wonderful!