Knees do have problems caused to them. Can be a multitude of reasons- many of which require a medical diagnosis.
My problem started over 40 years ago and is still with me. My problem is the kneecap and pain around that but I can suffer it unless I have put some sideways strain or jolting on the knee. Pain can then come immediately or a couple of days after.
I accommodate it by NEVER running and by setting the bike up to lessen the strain on the knees. --Sideways remember and I always ride the bike with the toes pointing in. For others it may have to be toes pointing out.
Several years ago we had a rider join us and he had pain come in after a couple of hours. He was recommended to build up his quad muscles by a physio and we didn't see him for a few months. When he did come back he had exercised the quads and we took him on a gentle ride. 6 weeks later he was up to 50 milers with no pain.
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How long was I in the army? Five foot seven.
Spike Milligan