Cover -- Title -- Copyright -- Dedication -- CONTENTS -- Preface -- Introduction What This Book Aims to Do and What It Is Not -- Part I: Concepts and Mechanisms -- Chapter 1 The Intellectual Challenge of Morphological Evolution: A Case for Variational Structuralism -- Contrasting Ontologies -- Facts and Ideas about Bodies -- Re-focusing on the Role of Development -- The Emergence of Molecular Structuralism -- The Enigma of Developmental Variation -- Chapter 2 A Conceptual Roadmap to Homology -- Two Observations: Sameness and Continuity -- A Detour into Genetics: Homologous Genes -- Character Identity and Character States -- Characters and Character States: Who Is Who? -- Variational Modalities: More Than One Way of Being a Certain Character -- Character Identity and Repeated Body Parts: Serial Homology -- Character Swarms: Persistent Cases of Partial Individuality -- Alternative Conceptualizations of Homology -- A Case for Conceptual Liberalism -- Sorting Patterns of Morphological Variation -- Chapter 3 A Genetic Theory of Homology -- Why Continuity of Genetic Information Is Not Enough -- Lessons from the Variable Development of Homologs -- Homeotic Genes and Character Identity -- A Model: Character Identity Networks -- Variation and Conservation of Segment Development -- Eye Development and the ey/so/eya/dac (ESED) Networks -- The Role of Protein-Protein Interactions -- Characteristics of Character Identity Networks -- Chapter 4 Evolutionary Novelties: The Origin of Homologs -- Modes of Evolution -- Revisiting the Conceptual Roadmap: Which Way to Novelty? -- Phenomenological Modes for the Origin of Type I Novelties -- From Phenomenology to Explanation -- Explaining Robustness and Canalization -- Natural Selection and the Origin of Novelties: A Roundup -- Chapter 5 Developmental Mechanisms for Evolutionary Novelties.

The Environment's Role in Evolutionary Innovations -- Where Does the Positional Information for Novel Characters Come From? -- Derived Mechanical Stimuli and the Origin of Novelties in the Avian Hind Limb Skeleton -- The Origin of Character Identity Networks -- The Evolution of Novel Signaling Centers -- The Developmental Biology of Novelties: Reflections -- Chapter 6 The Genetics of Evolutionary Novelties -- Evolution of cis-Regulatory Elements -- Are Novel Pigment Spots Novelties, and Why Does It Matter? -- Sex Combs: The Origin of a ChIN -- Origin of Novel cis-Regulatory Elements: Transposable Elements -- The Role of Gene Duplications -- Evolution of Transcription Factor Proteins -- The Evolution of miRNAs -- A Material Difference between Innovation and Adaptation? -- Chapter 7 The Long Shadow of Metaphysics on Research Programs -- Metaphysics as the Sister of Science -- Classes and Individuals -- Individuals and Natural Kinds -- Definitions and Models -- Part II : Paradigms and Research Programs -- Chapter 8 Cell Types and Their Origins -- Developmental Genetics of Cell Types -- The Evolutionary Origin of Cell Types -- Case Studies of Cell Typogenesis -- Concluding Reflections -- Chapter 9 Skin and a Few of Its Derivatives -- Developmental Evolution of Amniote Skin and Skin Appendages -- Mammalian Skin Derivatives: Hairs and Breasts -- Devo-Evo of Bird Skin: Scales into Feathers -- Origin of Feathers -- Chapter 10 Fins and Limbs -- Paired Fins -- From Fins to Limbs -- Concluding Reflection on the Nature of Character Identity -- Chapter 11 Digits and Digit Identity -- The Origin of Digits -- Digits Come and Go: Is There a Pentadactyl Ground Plan? -- Developmental and Morphological Heterogeneity of the Tetrapod Hand -- Digit Loss and Re-evolution in Amniotes -- The Pentadactyl Autopodium (PDA) Type -- Developmental Genetics of Digit Identity.

Digit Identity: Real or Imaginary? -- A Fingerpost on the Nature of Character Identity -- Chapter 12 Flowers -- What Is a Flower? -- Angiosperm Phylogeny and Flower Character Evolution -- Genetics of Canonical Flower Development -- The Developmental Genetic Architecture of the Flower Bauplan -- Flower Variation and Novel Flower Organ Identities -- The Origin of the Bisexual Flower Developmental Type -- Perianth Evolution and the Origin of Petals -- Genetics of Organ Identity: Challenges from Gene Duplication -- Summary and Conclusions -- Chapter 13 Lessons and Challenges -- What Are the Core Claims of This Model of Homology? -- Characters Are Real But Historically Limited -- Homology Is Not Hierarchical -- The Quasi-Cartesian Model of Character Identity -- Character Individuality and Gene Regulatory Network Cooperativity -- Open Questions and Difficulties -- Population, Tree, and Homology Thinking -- References -- Index.