A wealth of evidence suggests that pathogens may play a role--perhaps even a causal one--in chronic diseases like Alzheimer's or MS. Proving that theory, however, is another matter. Every step of the research is fraught with controversy, from isolating the pathogens to determining how they might cause the disease to sorting out how a host's genetic profile influences the course of disease. And because these illnesses are chronic, scientists have to confront frustrating questions about cause and effect that don't come up with acute illnesses like Ebola or the mumps.