The immune system provides accessible data about the evolution, the organizational operation and the end function of a complex system; immunology exemplifies the evolution, the organizational sociology and the end function of complex systems’ research. I shall discuss select issues related both to the system and to the science that studies the system. The system: Evolution (from innate to adaptive immunity); Organization (degeneracy of recognitions and interactions; pleiotropic and redundant agents); End function (body protection or body maintenance). The science: Evolution (from clonal selection to systems biology; the quest for optimums); Organization (molecular biology versus physiology); End function (prevention and cure of disease).