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Vaniver comments on You'll die if you do that - Less Wrong Discussion
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The one that I can think of is cracking your knuckles, which supposedly causes arthritis. It's beyond me how cavitation can cause an autoimmune disease, and seems much more likely to me that people are bothered by the sound and settled on a joint ailment as a deterrent. (Studies have shown there is no link, but that cracking your knuckles is correlated with other hand problems. I suspect that's because people with those problems are more likely to be able to / get relief from cracking their knuckles.)
Osteoarthritis, which is the most common form of arthritis, is not an autoimmune disease; rather it seems to be related to aging, including cumulative wear and tear on joints. (Rheumatoid arthritis is an autoimmune disease.) Cavitation can mess up hydraulics components pretty bad, so I do think this passes the common-sense test. Apparently it doesn't pass the evidence test, though.