 Within the confines of a single organism, the reaction of the immune system to antigens has all the characteristics of selection processes; however, when the organism dies, all of these adaptations are lost. In some species, females pass on not only the genes for the basic structure of their immune systems but also some of the machinery that past invasions of antigens have produced in them. However, these cells are rapidly removed from the offspring as it develops its own immune system. The reaction of the immune system to antigens departs from gene-based selection in biological evolution in two ways. First, from the organismal perspective, the genes that function in protecting an organism from invaders are not germ-line. They are somatic. Second, the relevant mutation rates are much, much higher in the immune system than in ordinary gene-based selection. Instead of mechanisms existing to discover mutations and repair them, mechanisms exist that encourage mutations—massively so. If the functioning of the immune system is to count as an adaptive process, some changes must be made. One possibility is to clarify what counts as a “germ-line” replicator and reject the notion that extremely low mutation rates are inherent in all selection processes [see the section below on  Challenges to the Replicator].