What is so special about thinking; after all, we all do it!

Understanding the adaptive immune system can be simplified by treating it as three linked modules, the generation of the recognitive repertoire, the sorting of the repertoire by purging anti-self, and the coupling of the repertoire to appropriate effector mechanisms. Each of these modules has a unique database and a logic that is determined by evolutionary considerations founded on value versus harm. Selection cannot operate to perfection, only to adequacy, meaning not limiting to the procreation of the species. Consequently, this system has limits in that it fails, by human standards, to adequately protect against a variety of pathogens and, even when protecting successfully against others, all too often initiates autoimmunity and innocent bystander pathology. What evolution trivializes defines the subject called clinical immunology. If we wish to deal with the pathology that evolution views to be of an acceptable frequency, then we had best first understand what it did give us as a sufficiently functional system, namely the decision pathways of the three modules and in what ways their protective outputs are limited.