The yeast and bacteria present in fermentation is visible when it’s multiplying in the billions. People would collect the “mother” from a good fermentation and use it in the next. In selecting for the best yeasts and bacteria people bred strains that diverged from wild strains. Some might even call this domestication. This all happened well before germ theory. People knew what yeasts and bacteria were, they just didn’t know that it was made of billions of microscopic cells.
Think of it this way,
You don’t need to know gravity works for it to do its job. You drop a ball, it falls to the ground.
Likewise if you crush grapes and let them sit they will ferment. You have wine.
You don’t need to know that there is natural yeast on the grape that eats the sugars in the grape converting it to alchohol.
You just need to know if you if you crush grapes, let them sit, and eat/drink them it makes you feel funny.
Most medieval and before cultures didn’t really know why a lot of things happened, they just knew that they did happen. Call it a blessing from God(s). They essentially found out that the process we know to be fermentation happened under certain conditions and then that knowledge was passed on down the generations. Its pretty crazy to think that until maybe 300 years ago we didn’t really know why anything happened, just that it did.
There was a very interesting superstition before they knew all the science behind distilling, when they brought in a new still to replace the old, they would hit it with a hammer to put dents in it to match the old as a superstitious thing, and now we know that in fact, the size and shape of the still do play a part in how it works, so doing this actually had a function, they just didn’t necessarily know it.
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