<p>Two competing approaches, namely the New Mechanism/Mechanistic Philosophy and the “counterfactual + interventionist” (CF + I) approach, have dominated recent debates in philosophy of science. This article argues that the two approaches are underpinned by two logics of experiment. More concretely, there are two types and hence two logics of experiment in biology and medicine: a mechanism-oriented one and a populational one. The former seeks to identify and establish mechanisms or pathways (including entities, activities, and interactions) behind biological phenomena, whereas the latter seeks to establish whether and how much specific factors or variables impact outcomes at the populational level. These two types of experiment operate upon two different logics, and the word “experiment” means quite different things for them. Explicitly differentiating the two logics of experiment yields critical implications for a host of philosophical issues, including whether natural selection is a mechanism and whether the Hodgkin-Huxley model is explanatory.</p>