Dissertations, Theses, and Capstone Projects

Date of Degree


Document Type


Degree Name





Peter Godfrey-Smith

Committee Members

Massimo Pigliucci

Catherine Wilson

David Papineau

Justin Garson

Subject Categories

Philosophy of Science


explanation, robustness, holobiont, evolution, stochasticity, mechanism


This dissertation is an evaluation of some strategies used for understanding the biological world. It argues that the complexity of living systems challenges the adequacy of traditional approaches to scientific explanation. An examination of the empirical details—especially those at the microscopic and nano scales—highlights the limitations of mechanistic explanation, common habits of causal reasoning, and theories of individuality. According to this analysis, starting with broad generalizations of how the world is, or a single universal theory of how it ought to be investigated or explained, has things entirely backwards. Instead, we ought to start by looking at the important processes, relations, and interactions uncovered by the sciences, carefully building towards general claims. In chapter one, I examine and challenge a dominant characterization of mechanistic explanation. I develop an alternative approach that situates biological processes as falling along a multidimensional gradient—with some processes being paradigmatic cases of mechanisms and some being marginal cases. In chapter two I trace recent developments in biology where the study of robustness has become increasingly important. I develop a general taxonomy of robustness to help clarify links between the study of robustness in different fields, and argue for a shift towards incorporating more top-down, system-level approaches into general accounts of explanation. In chapter three I examine aspects of causal reasoning in biology. I provide a novel distinction between two types of difficulties encountered while reasoning about biological systems. In the face of these problems I argue that approaches to explanation are best seen as heuristics, which focuses our attention on both how our conceptual tools resolve problems, and when and where they can break down. In the final chapter I turn to a debate at the interface of philosophy and biology about whether we need to reevaluate our understanding of the biological world because we—along with every other multicellular organism—are, and always have been, multispecies entities.