This chapter draws on what I call map thinking – philosophical reflection on mapping and map use – to shed light on representational processes in the life sciences. In particular, it relies on the analogy between mapping and representation or knowledge in general. I first identify three map analogies, which I call literal, causal, and extreme-scale. I then show how these analogies help us to understand three cases, not previously analysed in this light: the evolution of Darwin’s finches according to Peter and Rosemary Grant, Kurt Kohn’s biochemical causal maps, and the extreme-scale gene expression maps of the Allen Human Brain Atlas. Viewing these research programs through a cartographic lens illuminates their purposes and methods, while also helping us look differently at traditional maps and geospatial ontologies.