In the American Scientist, Per Brandtzaeg tells us about how we develop food allergies.
The story of food allergy is a story about how the development of the immune system is tightly linked to the development of our digestive tract or, as scientists and physicians usually refer to it, our gut. A human being is born with an immature immune system and an immature gut, and they grow up together. The immune system takes samples of gut contents and uses them to inform its understanding of the world—an understanding that helps safeguard the digestive system (and the body that houses it) against harmful microorganisms.
The many-layered defenses of the immune system are designed to guard against invaders while sparing our own tissues. Food represents a special challenge to this system: an entire class of alien substances that needs to be welcomed rather than rebuffed. An adult may pass a ton of food through her gut each year, nearly all of it distinct at the molecular level from her own flesh and blood. In addition, strains of normal, or commensal, bacteria in the gut help with digestion and compete with pathogenic strains; these good microbes need to be distinguished from harmful ones. The body’s ability to suppress its killer instinct in the presence of a gut-full of innocuous foreign substances is a phenomenon called oral tolerance. It requires cultivating a state of equilibrium, or homeostasis, that balances aggression and tolerance in the immune system. Intolerance, or failure to suppress the immune response, results in an allergic reaction, sometimes with life-threatening consequences.