Biological explanations are often designed to elucidate the general causal relationships that transcend species boundaries. According to popular recent accounts of explanation in biology, successful causal explanation involves specifying a regular causal mechanism. However, because mechanisms describe types of causal chains and types of phenomena, this account of explanation has a harder time answering questions about why and when individuals and populations vary and/or deviate from typical causal chain of events or display differences in the phenomenon. This account of explanation also has a hard time telling us when a certain explanation should apply—it gives us the explanation, given a certain phenomenon, but does not really tell us how to determine whether we are looking at an instance of that type of phenomenon in the first place. These difficulties with mechanistic accounts of explanation are exacerbated when we consider the relationship between the phenomenon and the mechanism that explains it during the process of discovering or filling in the mechanism. Although explanations on this view are explanations of a given phenomenon, just how this phenomenon is characterized can change as we acquire new evidence about both the phenomenon itself and the mechanism that explains the phenomenon. Thus, although it is certainly extremely useful and important to discover, describe, and explain regularities and generalizations, it is also important to understand why, how, and when these generalizations fail to explain. It is thus important to have an account of how to determine the domain of an explanation—the range of instances over which we can expect an explanation to extend—and how to determine whether or not a particular instance of a phenomenon is of a type of phenomenon for which we have described a type of mechanism. This dissertation thus seeks to take seriously the idea that choices made by researchers can shape the explanation, and explores some of the consequences this idea has on our scientific pursuits. The overall goal of this dissertation is thus to draw attention to a set of issues that arise simply as a consequence of the structure of and method of giving explanations in many areas of biology. My hope is that by drawing attention to these issues and describing the particular ways that they can affect our scientific projects we can have another way of evaluating scientific claims, especially interdisciplinary claims that involve giving multi-level explanatio
