I have always found it somewhat confusing that evolutionary principles can be applied to medicine in so many ways. From the start of my work with George Williams, it has seemed clear that our attempts to ask why natural selection left the body vulnerable to so many diseases are fundamentally different from applications of population genetics or phylogenetic trees. Finally, in preparing an article with Stephen Stearns, I came up with a framework that seems helpful.
First it is essential to be clear about the kind of question:
1. What is the phylogeny of the trait?
2. How has the trait given a selective advantage?
Second, it is important to distinguish five different objects of explanation:
1. Human (or other focus species) phenotypic trait
2. Human (or other focus species) gene
3. Pathogen phenotypic trait
4. Pathogen gene
5. Somatic cell lines such as cancer or immune cells
This fleshes out into a rather nice table that defines ten ways evolutionary biology can be applied to medicine.
The full article is available free from Evolutionary Applications.
Nesse, R. M., & Stearns, S. C. (2008). The great opportunity: Evolutionary applications to medicine and public health. Evolutionary Applications 1(1), 28-48.