To substantiate and illustrate the centrality of molecular archaeology in bridging the divide between the natural sciences and the humanities, this chapter draws upon laboratory research on ‘fermentation’ and ‘ancient medicine’. Fermentation is probably the first energy system on Earth, which is embodied in the physiology of all animals including humans. It is probably the first biotechnology discovered and utilized by our species. In short, humans coevolved with microorganisms, then harnessed them to our purposes in many innovative ways—to provide alcohol as an energy source and for dissolving botanical compounds which have medicinal properties. Arguably, the most important fermentation system used by humankind was to make fermented beverages. As the universal medicine, social lubricant, mind-altering substance, religious symbol, artistic inspiration, and highly valued commodity, fermented beverages around the world became the focus of religious cults, pharmacopoeias, cuisines, economies, and society.