Trial and error and enough statistics. Ignoring lab tests on rats, basically if you see that on some region in the world, we can observe that people are getting ill in repeatable way, that doesn’t follow any genetic deformation, any usual known paths of disease spreading and any pollution, but they all have similar diet, then it is a good idea to alter this diet and see what will happen
Trial and error mostly. Nearly all vitamin and mineral deficiencies have historically been identified by figuring out what healthy people ate and what the affected people ate, and narrowing it down. That’s how they figured out scurvy was caused by vitamin C deficiency. They narrowed it down to lack of fruits and veggies until they figured out that it was lemons and oranges that worked.
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