In biology, the question of origins often refers to the origin of life; however, it is far broader and, in a sense, has far more pervasive ramifications. All organisms carry differences and can be the beginning of a new lineage. This perspective is central to the phylogenetic classification of living beings. In this course, we will discuss this approach from an epistemological angle. We will also show that, beyond the specific method, its epistemology permeates biology, for example, the reporting of experiments. Overall, we will discuss how the historical nature of biological objects can be used as a lever to define them theoretically and how this approach differs profoundly from the ones in physics.