This chapter seeks to explore possible explanations for the rise in allergies and immune reactivities and the epidemic proportions of autoimmune disease. A major hypothesis is that this modern sort of plague derives from the modern civilization in which most of the world now lives. The technological advances of progress inevitably bring with them changes in lifestyle and diet, which can affect our immune system in various ways. Individuals today are surrounded and bombarded by genetically modified foods completely different from what their ancestors used to eat and an unending torrent of chemicals that not only pervade the environment around them but are in the very food and drink that they consume daily without a second thought. Thus, the necessary homeostatic balance between type 1 and type 2 T helper cells (Th1 and Th2) can be swayed toward pathogenesis by, ironically, too hygienic a lifestyle.

Likewise, the balance of the commensal bacteria in the gut microbiome can be disturbed by environmental triggers, which may lead to intestinal permeability, immune reactivity, and autoimmunity. Xenobiotics (haptens) in food can form neo-antigens or adducts, leading to autoimmunity and cancer. The increased use of food additives to make our food look better, taste better, last longer, and be cheaper and easier to grow has come with an accompanying rise in reports of food reactivities and autoimmune disorders. It has been proven that many of the common foods that are universally eaten without a second thought are actually cross-reactive with different tissues of the human body, and this includes the brain. It seems all too easy, then, for the healthy relationship and mechanisms between the brain and the immune system to succumb to the overwhelming assault mounted by the environmental triggers of today’s modern world. What is required is a way to detect the beginnings of these environmental attacks, which leave traces or biomarkers, so that years of suffering from immune reactivity or autoimmune disease may be avoided or prevented by early diagnosis and proper therapeutic action.