What happens when you eat an apple? The answer is vastly more complex than you imagine.

Every apple contains thousands of antioxidants whose names, beyond a few like vitamin C, are unfamiliar to us, and each of these powerful chemicals has the potential to play an important role in supporting our health. They impact thousands upon thousands of metabolic reactions inside the human body. But calculating the specific influence of each of these chemicals isn't nearly sufficient to explain the effect of the apple as a whole. Because almost every chemical can affect every other chemical, there is an almost infinite number of possible biological consequences—and that's just from an apple.

Nutritional science, long stuck in a reductionist mindset, is at the cusp of a revolution. The traditional gold standard of nutrition research has been to study one chemical at a time in an attempt to determine its particular impact on the human body. These sorts of studies are helpful...