The Concept of Levels of Organization in the Biological Sciences PhD Thesis Submitted August 2014 Revised June 2015 Daniel Stephen Brooks Department of Philosophy Bielefeld University Reviewers: Martin Carrier, Maria Kronfeldner Dedicated in friendship to Jan and Magga “He who has suffer'd you to impose on him knows you.” Table of Contents Table of Contents........................................................................................................................1 Chapter One: The Intuitive Appeal and Ubiquity of 'Levels of Organization'............................5 1.1 Introduction ................................................................................................................5 1.2 Analyzing 'Levels of Organization' in Biological Science..........................................7 1.2.1 Level Claims.....................................................................................................10 1.2.2 Wimsatt’s Characterization of Levels ..............................................................14 1.3 Initial Distinctions.....................................................................................................16 1.3.1 Erroneous Concepts of Levels...........................................................................18 1.4 Depictions of Levels in Biological Textbooks...........................................................20 1.4.1 The Character of 'Levels' in Biological Science................................................24 1.4.2 The Significance of 'Levels' in Biological Science...........................................30 1.5 The Concept of Hierarchy.........................................................................................34 1.5.1 'Hierarchy' Does Not Exhaust 'Levels of Organization'....................................37 1.6 The Structure of This Dissertation.............................................................................40 Chapter Two: Philosophical Conceptions of Levels.................................................................43 2.1 Introduction...............................................................................................................43 2.2 The Layer-Cake Account of Levels...........................................................................43 2.2.1 Global Scope and Comprehensive Character....................................................46 2.2.2 Stepwise Compositional Continuity .................................................................47 2.2.3 Linearity of Levels Strata..................................................................................50 2.2.4 Correspondence Between Nature and Science..................................................52 2.2.5 The Continued Influence of the Layer-Cake Account.......................................55 2.3 The Mechanistic Account of Levels..........................................................................59 2.3.1 Local Scope and Radically Contextualized Character......................................62 2.3.2 Principled Rejection of Correspondence Between Science and Nature...66 2.3.3 Branching Structure ..........................................................................................68 2.3.4 Constitutive Relevance......................................................................................69 2.4 Conclusion.................................................................................................................71 Chapter Three: Levels Skepticism............................................................................................76 3.1 Introduction...............................................................................................................76 3.2 Levels – A Flawed, Misleading, and Irrelevant Concept? ........................................76 3.2.1 The Levels Concept is Flawed..........................................................................77 3.2.2 The Levels Concept is Misleading....................................................................81 3.2.3 Are Levels of Organization Irrelevant to Science?...........................................84 3.3 Considerations of Levels Skepticism.........................................................................86 3.3.1 A Straw-Man Conception of Levels..................................................................86 3.3.2 Guilt by Association: The Layer-Cake Account as the Default Conception of Levels..............................................................................................................................89 3.3.3 Association of 'Levels' with 'Layer-cake Levels'...............................................90 3.3.4 Association of 'Levels' with Layer-Cake Reductionism....................................92 3.4 Conclusion ................................................................................................................98 Chapter Four: A Fragmentary Concept...................................................................................101 4.1 Introduction.............................................................................................................101 4.2 Semantic Variation and the Levels Concept............................................................103 4.2.1 Fragments of the Levels Concept ...................................................................107 4.2.2 A Common Standard for Comparing Level Claims in Biology......................109 4.3 A Framework for Analyzing Semantic Variation in Biological Concepts...............113 4.3.1 Components of Semantic Content and the Molecular Gene Concept.............116 4.3.2 Epistemic Goals of Concept Usage.................................................................119 4.3.3 Unifying Fragmentary Concepts under their Epistemic Goal.........................121 4.4 The Epistemic Goal of 'Levels of Organization'......................................................126 4.4.1 How Levels of Organization Structure Problems ..........................................128 4.4.2 Descriptive Level Claims................................................................................128 4.4.3 Hypothetical Level Claims .............................................................................130 4.5 Case Study for the Use of Levels: The Explanation of Oxidative Phosphorylation133 4.5.1 Ox-phos as a Multi-level Phenomenon...........................................................135 4.5.2 The Shift from Chemical to Biological Problem............................................138 4.6 Conclusion...............................................................................................................147 Chapter Five: The Organicist Roots of the Levels Concept....................................................149 5.1 Introduction.............................................................................................................149 5.2 The Historical Context of the Levels Concept........................................................154 5.3 The Organicist Program and the Levels Concept....................................................161 5.3.1 The Tenets of the Organicist Program.............................................................161 5.3.2 The Organicists' Use of the Levels Concept ..................................................171 5.3.3 The Epistemic Goal behind the Organicists' Use of Levels ...........................177 5.4 The Integrative Account of Levels of Organization................................................184 5.4.1 Global Scope and Contextualized Character...................................................187 5.4.2 Incomplete Epistemic Continuity in Levels of Organization..........................191 5.4.3 Weak Association Between Science and Nature.............................................195 5.5 Integrative Levels & Layer-cake Levels..................................................................199 5.6 Organicist Influence on Mitchell’s Chemiosmotic Hypothesis...............................202 5.7 Conclusion ..............................................................................................................205 General Conclusion.................................................................................................................208 References...............................................................................................................................211 Acknowledgments...................................................................................................................224 Table of Figures Figure 1.1 Different Overlapping K-Decompositions...............................................................11 Figure 1.2 Levels of Organization in Campbell Biology..........................................................22 Figure 1.3 Common Definitional Criteria for Levels................................................................26 Figure 1.4 Levels of Organization in Solomon et al.'s Biology................................................27 Figure 1.5 Formal Hierarchies..................................................................................................36 Figure 1.6 Types of Branching Structures in Hierarchies.........................................................37 Figure 2.1 Layer-Cake Account of Levels................................................................................45 Figure 2.2 Microreduction Relations in the Layer-cake Account.............................................48 Figure 2.3 Multi-level Mechanisms..........................................................................................62