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This chapter presents a genetic theory of homology that addresses the most challenging problem when attempting to explain character identity; namely, unquestionable homologies (that is, character identities across species) are often associated with extensive variations in the developmental pathways and mechanisms that produce these characters. To resolve this problem, the chapter reviews some of the relevant facts from developmental genetics and then proposes a model that explains these patterns and serves as a guide for further research into the developmental evolution of morphological characters. It shows that the function of homeotic genes offers insights into what might be the developmental genetic basis of character identity. It argues that the distinction between character identity and character states is reflected in the genetic architecture of development in which character identity has a different genetic substrate than character states. This approach leads to the concept of character identity networks.

This chapter proposes a conceptual roadmap to homology, with the goal of supporting the research program of developmental evolution that seeks to explain the patterns of phenotypic diversity. It offers a mechanistic developmental and evolutionary explanation of the evolution of body plans and the origin of character identities. It also examines the difference between the origin of homologs (that is, novelties) and their modification by natural selection (that is, adaptation); the limits of homology, focusing on the lack of individuality of body parts; homologous genes; characters and character states; variational modalities; character identity and repeated body parts; and character swarms. Finally, it considers alternative conceptualizations of homology, conceptual liberalism, and how to sort patterns of morphological variation.

This chapter investigates the evolutionary and developmental biology of digits, focusing on what these appendages can teach us about character identity and character origination. The idea that digits have individuality and that it is meaningful to distinguish between the thumb, the index finger, and all the other digits is both intuitive and controversial. With it arise questions regarding how digits evolved, how they were gained, lost, and then possibly regained, and whether or not they had changed place in the limb. The chapter first considers the origin of digits, with emphasis on the issue of the nature of the pentadactyl limb, before discussing the developmental and morphological heterogeneity of the tetrapod hand. It also examines digit loss and re-evolution in amniotes, the pentadactyl autopodium type, and developmental developmental genetics of digit identity. It suggests that the “tetrapod limb” is likely the result of a dynamic evolution of character identities.

This book has argued for the reality of a class of biological entities that have a hard time finding their place in a theory of evolution based on genetics and population biology. These entities, or developmental types, include cell types, homologs, and body plans. The book has also provided examples that already have empirical data to see whether such ideas are contradicted by known facts about certain well-studied organ systems, like limbs, skin appendages, and flowers. This concluding chapter summarizes the book's central claims about homology, characters and character identity, and cooperativity in gene regulatory networks. It also discusses some of the lessons derived from reviewing the literature on these paradigms of devo-evo research as well as the challenges inherent in this perspective of developmental evolution.

This chapter discusses the ontological status of fictional characters and the logical constraints on creating characters. Drawing on Jerrold Levinson's arguments for the creation of musical works, it proposes that fictional characters are initiated types, grounded in acts of storytelling, although not essentially bound to any one, even if tied to a reasonably determinate historico-cultural context. Character identity is interest-relative and a character's variant identity conditions determine which of its properties are essential. Fictional characters are created just to the extent that their grounding narratives are created, narratives which allow for indexicality in character identification. The literary dimension is also explored, accommodating symbolic, value-laden, and interpretation-dependent factors.

This chapter examines the molecular genetics of evolutionary novelties. In particular, it investigates which molecular mechanisms might be involved in the origination of novel gene regulatory networks (and, thus, character identity networks) and what these mechanisms imply for the origin of novel characters. The chapter begins with a discussion of the complex problem of the evolution of transcriptional regulation by focusing on the evolution of cis-regulatory elements (CREs) and the evolution of transcription factor proteins. It then asks whether novel pigment spots, such as the Drosophila wing spots, are novelties. It also explores an evolutionary novelty known as sex comb and the role of transposable elements in the origin of novel CREs. Finally, it considers the role of gene duplications, the evolution of micro-RNAs (miRNAs), and the possibility of a mechanistic difference between adaptation and innovation.

This book examines homology, the correspondence of characters from different species or even within the same organism, from a mechanistic perspective. Homology is explained by derivation from a common ancestor that had the same character or trait. This explanation applies at least to characters from different species. Accordingly, this concept has applications in many fields of biology by referring to morphological characters, behaviors, proteins and genes, gene regulatory networks, and developmental mechanisms and processes. The book considers one class of homology relationships, that between morphological characters, and describes the so-called character identity networks. It argues that the evolutionary origin of characters and body plans is the origin of those gene regulatory networks that underlie character identity.

This chapter examines the developmental mechanisms underlying evolutionary novelties. It first considers the role of the environment in evolutionary innovations, with particular emphasis on how environmental perturbations result in the release of cryptic genetic variation. It then explores where the positional information for novel characters comes from before explaining derived mechanical stimuli and the origin of novelties in the avian hind limb skeleton. It also discusses the origin of character identity networks and the evolution of novel signaling centers, focusing on two novel morphological characters: the butterfly eyespot and the turtle carapace. Finally, it reflects on the developmental biology of novelties, emphasizing the complex and multifaceted nature of the evolutionary changes in the developmental mechanisms that contribute to the origin of novel body parts.

This chapter focuses on the evolutionary processes underlying fins and limbs. Some of the most momentous periods in the history of the human lineage involved evolutionary changes to the paired appendages. Modifications of the hind limb and foot were key during the evolution of bipedal locomotion and the erect posture that is characteristic of humans. Evolutionary biologists have devoted a lot of time and effort in studying both the origin of paired fins and the transformation of fins to tetrapod limbs. The chapter first considers fossil evidence and recent developmental evidence on the origin of paired fins before discussing the fin–limb transition. It also reflects on the nature of character identity and suggests that the origin and evolution of fins and limbs reveal an intriguing pattern of serial homology, identity, and innovation that contradicts the notion of hierarchical homology.