PhD TESIS 2019 EVOLUTION AND THE ARCHITECTURE OF LIFE GIORGIO AIROLDI Director: CRISTIAN SABORIDO ALEJANDRO, UNED Co-Director: DAVIDE VECCHI, Universidade de Lisboa PhD Program in Philosophy Department of Logic, History and Philosophy of Science Faculty of Philosophy UNED iii Acknowledgements I would like to thank Cristian Saborido for his support, both academic and moral!, during the years dedicated to my research and to the writing of this thesis; Davide Vecchi for accepting to be co-director and for providing countless advices and insightful suggestions; and David Teira, who was so kind to read the final draft of this work and to propose some brilliant improvements to its structure and contents. I would also like to thank Víctor Luque, Javier Suarez and all the many students and professors I met during these years in congresses and seminars, and who shared with me their knowledge and researches, which contributed greatly to shaping the ideas behind this work. I am grateful to all members and staff of the department of logic, history and philosophy of science of UNED in Madrid for providing a wonderful working and studying environment, and especially to Clara Bueno for revealing me unknown facts about Primates and Henry Potter. A special thanks to Ana Peel for the reinterpretation of the original frontispiece from I Quattro Libri dell’Architettura of Andrea Palladio. iv Evolution and the Architecture of Life v Contents 1. INTRODUCTION ........................................................................................................................ 3 2. NATURAL SELECTION AND THE VARIETY AND COMPLEXITY OF THE LIVING WORLD ............................................................................................................................................... 15 2.1. DARWIN’S VIEW: SELECTION AS EXPLANANS OF BOTH VARIETY AND COMPLEXITY ....................... 16 2.2. NATURAL SELECTION AND VARIETY ............................................................................................. 19 2.2.1. Population genetics or: why are some phenotypic traits more frequent than others? .................................. 20 2.2.2. Foundational assumptions of population genetics ............................................................................. 22 2.2.3. Population genetics models .......................................................................................................... 24 2.3. NATURAL SELECTION AND PHENOTYPIC COMPLEXITY .................................................................. 29 2.3.1. What is the nature of the link between natural selection and biological complexity? ................................. 30 2.3.2. Two lines of research to explain phenotypic complexity: formal adaptationism and pluralism ..................... 37 2.4. A PROPOSAL TO FORMALISE BIOLOGICAL COMPLEXITY ................................................................. 39 2.4.1. What is complexity? Polysemy of the concept. .................................................................................. 39 2.4.2. Biological complexity: organismal architecture as form and function ...................................................... 46 2.4.3. A model to classify evolutionary complexity changes .......................................................................... 53 2.5. BUT… DOES BIOLOGICAL COMPLEXITY INCREASE IN THE HISTORY OF LIFE? ................................ 60 2.6. CONCLUSIONS ............................................................................................................................... 65 3. ADAPTATIONISM ..................................................................................................................... 67 3.1. KINDS OF ADAPTATIONISM ........................................................................................................... 67 3.2. THE FOUR PILLARS OF EMPIRICAL ADAPTATIONISM ....................................................................... 69 3.2.1. Pillar I - Ubiquity of adaptation ................................................................................................. 69 3.2.2. Pillar II - Continuous, slow and incremental evolutionary change ........................................................ 70 3.2.3. Pillar III - Random and unconstrained variation ............................................................................ 71 3.2.4. Pillar IV - Supremacy of selection ................................................................................................ 72 3.3. WAS DARWIN A DARWINIST? ........................................................................................................ 74 3.3.1. The creative power of selection ...................................................................................................... 74 3.3.2. Optimization ability of selection ................................................................................................... 78 3.3.3. Constraints and selection ............................................................................................................ 80 3.4. FUNCTIONALISM AND EXTERNALISM ............................................................................................ 81 3.5. OPTIMIZATION PROGRAMS. .......................................................................................................... 84 3.6. THE FORMAL DARWINISM PROJECT BY ALAN GRAFEN. ................................................................ 92 3.6.1. Two models, one equilibrium ....................................................................................................... 93 3.6.2. A controversial project ............................................................................................................. 100 3.7. THE FITNESS MATRIX .................................................................................................................. 109 3.8. CONCLUSIONS ............................................................................................................................. 111 4. PLURALISM: BEYOND THE LIMITATION OF ADAPTATIONISM ................................. 115 4.1. CRITIQUES TO ADAPTATIONISM .................................................................................................. 116 4.1.1. What natural selection leaves uncovered ....................................................................................... 116 4.1.2. Pluralism and the pillars of adaptationism ................................................................................... 117 4.1.3. An instance of a pluralist program: the Extended Evolutionary Synthesis .......................................... 124 4.1.4. Structuralism and Internalism ................................................................................................... 126 4.1.5. The source of innovation as the basis of our classification of non-adaptationist evolutionary accounts .......... 129 vi Evolution and the Architecture of Life 4.2. GENETIC ACCOUNTS ................................................................................................................... 131 4.2.1. Classical population genetics’ processes: mutation, recombination, and drift .......................................... 131 4.2.2. Wright’s Shifting Balance theory and the metaphor of adaptive landscape ............................................ 133 4.2.3. Punctuated Equilibrium .......................................................................................................... 139 4.2.4. Kimura’s neutral theory of molecular evolution .............................................................................. 143 4.2.5. Andreas Wagner’s Genetic Networks ......................................................................................... 147 4.2.6. Molecular Drive ..................................................................................................................... 156 4.2.7. Final comments on the genetic sources of variation .......................................................................... 156 4.3. PHENOTYPIC ACCOUNTS ............................................................................................................. 157 4.3.1. Exaptations .......................................................................................................................... 157 4.3.2. Phenotypic plasticity and genetic assimilation ................................................................................ 159 4.3.3. Neo-Lamarckian accounts: induced mutations .............................................................................. 167 4.3.4. Epigenetics ............................................................................................................................ 174 4.3.5. Final comments on the phenotypic sources of variations .................................................................... 178 4.4. DEVELOPMENTAL ACCOUNTS ..................................................................................................... 179 4.4.1. Evo-Devo ............................................................................................................................. 179 4.4.2. Developmental constraints. ........................................................................................................ 182 4.4.3. Developmental modularity and evolvability ................................................................................... 185 4.4.4. Final comments on developmental accounts of variation ..................................................................