It started from people noticing that this leaf made you energetic when you chewed it. We also have learned over time that many of the compounds that come from plants are soluble in certain things but not others. So you did different solvent extractions, water based, hydrocarbon based, alcohol based and so on. This was stuff being done centuries ago from people experimenting. Then you would find that what ever it was that made you energetic was in the hydrocarbon extraction or the alcohol extraction. We also learned in chemistry how to take things which were dissolved into a solvent and precipitate it out using other chemicals. It was all experimentation and testing.
In the modern era, we have things like spectrometers, pH meters, specific gravity bulbs, chemistry books n so on to get extract readings and processes. We know how much of Substance A we pulled out of the leaf slurry by measuring and weighing everything at every step. There are a few episodes in Breaking Bad that covered this when Walter was checking mass of final product and noticed it was slightly lower than it should be based on all the mass of the chemicals going in. There was a small mass unaccounted for because it was going into Jessie’s pocket.
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