Dr. Miller cites research in her article that all point in the same direction—healthy "living" soils make for food with better nutrient content. And by "living," I mean soils that are teeming with microorganisms such as bacteria, fungi, protozoa, and microscopic roundworms called nematodes.
Far from being scourges to be avoided at all cost, microorganisms are an essential component of life. We now understand that it is the cooperationbetween these microorganisms, the soil's biome, and the plants' roots, called rhizosphere that is ultimately responsible for allowing the plant to absorb nutrients from the soil in which it's grown.
Insects and weeds also have their place in this circle of life. According to soil scientist Dr. Arden Andersen, insects are nature's garbage collectors. Thanks to their specialized digestive systems, which differ from ours, they remove that which is not fit for us to eat—things we cannot digest.
And weeds are nature's way of evolving the soil—it's an intermediate plant that mobilizes nutrients in order to alter the soil, making it more suitable for the next evolutionary level of plants to grow in it.
Once you understand this natural cycle, it allows you to address food quality, weeds, insects, and plant disease at its point of origination, without ever resorting to chemical herbicides, pesticides, fungicides, synthetic fertilizers, or genetic engineering.
Understanding about the bugs - in your gut and in the soil your food comes from - is going to be the next wave in understanding how to be a thriving human being.