An introduction to the philosophy of biology, with application to specific current problems. The course focuses on two major strands of thinking seeking answers to two fundamental and to some extent complementary questions: “How do we know?” [epistemology] and “What things really exist in the world?” [ontology]. These two themes have the most important impact on the practice of science, as they pertain to the nature of the scientific enterprise and how it works [epistemology and philosophy of science], as well as what scientists consider part of reality [science-related ontology: unicorns and phlogiston, NO; atoms, electrons, YES; but what about species and genes? Do they have the same status as atoms?]. In each of these fields of philosophy we outline the main positions and discuss how they apply to past and current debates in biology—in particular, but not exclusively, evolutionary biology.