EXPLAINING EVOLUTIONARY INNOVATION AND NOVELTY: A HISTORICAL AND PHILOSOPHICAL STUDY OF BIOLOGICAL CONCEPTS by Alan Christopher Love BS in Biology, Massachusetts Institute of Technology, 1995 MA in Philosophy, University of Pittsburgh, 2002 MA in Biology, Indiana University, Bloomington, 2004 Submitted to the Graduate Faculty of Arts and Sciences in partial fulfillment of the requirements for the degree of Doctor of Philosophy in History and Philosophy of Science University of Pittsburgh 2005 UNIVERSITY OF PITTSBURGH FACULTY OF ARTS AND SCIENCES This dissertation was presented by Alan Christopher Love It was defended on June 22, 2005 and approved by Sandra D. Mitchell, PhD Professor of History and Philosophy of Science, University of Pittsburgh Robert C. Olby, PhD Professor of History and Philosophy of Science, University of Pittsburgh Rudolf A. Raff, PhD Professor of Biology, Indiana University, Bloomington Günter P. Wagner, PhD Professor of Ecology and Evolutionary Biology, Yale University James G. Lennox, PhD Dissertation Director Professor of History and Philosophy of Science, University of Pittsburgh ii Copyright by Alan Christopher Love 2005 iii EXPLAINING EVOLUTIONARY INNOVATION AND NOVELTY: A HISTORICAL AND PHILOSOPHICAL STUDY OF BIOLOGICAL CONCEPTS Alan Christopher Love, PhD University of Pittsburgh, 2005 Abstract Explaining evolutionary novelties (such as feathers or neural crest cells) is a central item on the research agenda of evolutionary developmental biology (Evo-devo). Proponents of Evo- devo have claimed that the origin of innovation and novelty constitute a distinct research problem, ignored by evolutionary theory during the latter half of the 20th century, and that Evo- devo as a synthesis of biological disciplines is in a unique position to address this problem. In order to answer historical and philosophical questions attending these claims, two philosophical tools were developed. The first, conceptual clusters, captures the joint deployment of concepts in the offering of scientific explanations and allows for a novel definition of conceptual change. The second, problem agendas, captures the multifaceted nature of explanatory domains in biological science and their diachronic stability. The value of problem agendas as an analytical unit is illustrated through the examples of avian feather and flight origination. Historical research shows that explanations of innovation and novelty were not ignored. They were situated in disciplines such as comparative embryology, morphology, and paleontology (exemplified in the research of N.J. Berrill, D.D. Davis, and W.K. Gregory), which were overlooked because of a historiography emphasizing the relations between genetics and iv experimental embryology. This identified the origin of Evo-devo tools (developmental genetics) but missed the source of its problem agenda. The structure of developmental genetic explanations of innovations and novelties is compared and contrasted with those of other disciplinary approaches, past and present. Applying the tool of conceptual clusters to these explanations reveals a unique form of conceptual change over the past five decades: a change in the causal and evidential concepts appealed to in explanations. Specification of the criteria of explanatory adequacy for the problem agenda of innovation and novelty indicates that Evo-devo qua disciplinary synthesis requires more attention to the construction of integrated explanations from its constituent disciplines besides developmental genetics. A model for explanations integrating multiple disciplinary contributions is provided. The phylogenetic approach to philosophy of science utilized in this study is relevant to philosophical studies of other sciences and meets numerous criteria of adequacy for analyses of conceptual change. v TABLE OF CONTENTS ACKNOWLEDGMENTS ...........................................................................................................xiii PREFACE.................................................................................................................................... xvi 1. ANALYTICAL TOOLS AND METHODOLOGY: CONCEPTS AND HISTORY............. 1 1.1. Introduction and Subject Matter of the Dissertation....................................................... 1 1.2. Tracking Conceptual Differences in Explanations: Conceptual Clusters....................... 7 1.2.1. Methodological Considerations .............................................................................. 7 1.2.2. Explicating Conceptual Clusters: Toolkits ........................................................... 10 1.2.3. Explicating Conceptual Clusters: Neighborhoods................................................ 17 1.2.4. A Comparison ....................................................................................................... 21 1.2.5. Isolating and Characterizing the Significance of Conceptual Clusters................. 23 1.3. Conceptual Differences Across Time: A Phylogenetic Approach to Philosophy of Science ...................................................................................................................................... 30 1.3.1. Historiographic Issues and Philosophical Method................................................ 30 1.3.2. The Phylogenetic Approach to Philosophy of Science......................................... 35 1.3.3. Normative Import of Philosophical Analysis ....................................................... 39 1.4. Situating the Argument: Concepts, Conceptual Change, and Historical Epistemology41 1.4.1. Theories of Concepts ............................................................................................ 41 1.4.2. The Problem of Conceptual Change..................................................................... 46 1.4.3. Historical Epistemology........................................................................................ 50 1.5. Summaries and the Road Ahead................................................................................... 54 2. THE PROBLEM AGENDA OF EVOLUTIONARY INNOVATION AND NOVELTY .. 58 2.1. Introduction: Problems in Focus and Individuation ..................................................... 58 2.2. Problem Agendas.......................................................................................................... 62 2.3. The Problem Agenda of Evolutionary Innovation and Novelty ................................... 71 2.3.1. Individuating the Problem Agenda ....................................................................... 71 2.3.1.1. Two Caveats on Natural Selection and the Intrinsic/Extrinsic Dichotomy .. 81 2.3.2. Characterizing the Problem Agenda ..................................................................... 83 2.3.2.1. Form and Function........................................................................................ 83 2.3.2.2. Level of Biological Hierarchy or Organization ............................................ 87 2.3.2.3. Degree of Generality..................................................................................... 90 2.3.2.4. Analytical Results ......................................................................................... 94 2.4. Problem Agendas and Problems as Units in Philosophy of Science ............................ 97 2.4.1. Prior Accounts of Problems in Philosophy of Science ......................................... 98 2.4.2. Domains and Fields: Units and Relations in Philosophy of Science.................. 106 2.4.3. Incommensurability, ‘Values’ in Science, and ‘Standards’ in Special Sciences 111 2.5. Recapitulation ............................................................................................................. 113 3. AVIAN ILLUSTRATIONS: THE ORIGINS OF FEATHERS AND FLIGHT ................ 116 3.1. Introduction................................................................................................................. 116 3.2. Explaining the Origin of Avian Form: Feathers ......................................................... 120 vi 3.2.1.1. What is the explanandum phenomenon? .................................................... 120 3.2.1.2. How is the origin of the feature a qualitative departure from an ancestral condition? 122 3.2.2. What is the particular phylogenetic juncture under consideration for this feature? What is the disciplinary contribution of systematics? ........................................................ 122 3.2.3. What is the contribution of paleontology for understanding the kinds of variation available at the phylogenetic juncture in question? ............................................................ 124 3.2.4. How is there a discrepancy between states of variation past and present? What is the contribution of ontogenetic studies to understanding the developmental accessibility between ancestor and descendant genotype-phenotype relations? ..................................... 126 3.2.5. How does the application of the distinctions between form, function, and character bear on analyzing the origin of this feature? What is the disciplinary contribution of morphological investigation? ......................................................................................... 132 3.2.6. How does the recognition of distinct levels of biological organization apply to the origin of this feature? Can we distinguish pertinent compositional and procedural hierarchies, either developmentally (spatially) or evolutionarily (temporally)? ................ 134 3.2.7. How does