Hypothesis

If a child raised in a pathogen free environment has more allergies and is worse at dealing with autoimmune diseases, then the primary factor is experience at fighting diseases and ignoring more minor problems, because the immune system is so complex. It is likely that many parts of the immune system are activated as pathogens arrive in the system (such as suppressor T-cells), and these may not be able to function as well without regular “practice”, which is given by minor pathogens.