Altered plant-derived amino acids and their influence on human protein structure and subsequent effects on immune function, specific food-derived pathological misfolded prion proteins and their influence on nervous-system function, and-lastly-microRNAs from plant foods and their influence on genetic expression of both enteric bacteria and potentially endogenous cellular function are all examples of the dark matter of nutrition concept. These phenomena are far outside the familiar nutritional boundaries of macro- and micronutrients. We have entered new territory now-the exploration of how food-related substances influence cellular signaling through the modification of genetic expression.