First things first: It's still a bad idea to drink alcohol while you're on medication. However, it's not for the reasons you may think. Some doctors suggest that the advice to not mix antibiotics with alcohol came from the 1950s, when penicillin first started getting used to combat syphilis.
Doctors at the time thought that the bad influence of alcohol could undo their expensive new treatment, so they asked patients to abstain from alcohol until they were cleared up. It's been shown that people engage in riskier sexual activity while intoxicated, so they weren't that far off from the mark.
However, with the rare exception of a few types of antibiotics, alcohol doesn't interfere with the effects of medicine that much. That said, it's still a generally bad idea to mix them, because you might forget to take your dose. Alcohol's effects on the body also get exaggerated.
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