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CronoDAS comments on Causal Diagrams and Causal Models - Less Wrong
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There are a lot of drugs that people develop tolerances to when used over long periods of time (the body's various feedback mechanisms recalibrate themselves to compensate for the drug's presence), but I can't say with any authority that this applies to mild stimulant use and weight loss.
I'm pretty sure tolerance to caffeine is a thing, judging from what I see on other people. (I usually abstain from drinking anything with caffeine at least on weekends and holidays to prevent that from happening to me.)
Yes, the literature seems to pretty solidly support caffeine tolerance (which is one of the reasons it's not as useful as most people think).