This paper attempts to reconcile the conceptual conflict between typological and population thinking to provide a philosophical foundation for extended evolutionary synthesis. Typological thinking has been considered a pre-Darwinian, essentialist dogma incompatible with population thinking, which is the core notion of Darwinism. More recent philosophical and historical studies suggest that a non-essentialist form of typology has some advantages in the study of evolutionary biology. However, even if we adopt such an epistemological interpretation of typological thinking, there still remains an epistemological (...) and methodological conflict between these two styles of thinking. How can we relate typological thinking with population thinking in pursuit of more integrated or interconnected research into evolutionary biology? I propose that homology thinking, which is another style of thinking that recognizes homologous characters, provides a common basis for typological representations of character states and for character dynamics in an evolving population. Good examples of this bridging role are found in teratology and breeding, where variation and novelty are recognized in developmental and morphological traits, gene expression patterns, and so on. Essentialism-free, dynamic views of homology have great potential to reconcile typological and population thinking and to set the stage for the EES. (shrink)

The metaphysical nature of homologies has been variously characterized as natural kind, individualist, and pluralist-pragmatic. In this essay, I aim to build on the work of proponents of a natural kinds ontology for homologies using Richard Boyd’s influential HPC account of natural kinds. I aim to advance this position by showing the unique fit of extending the HPC account to homologies, deflecting individualist critiques, as well as the pluralist-pragmatic alternative, showing that homologies have a determinate metaphysical character as kinds. As (...) an important extension of this position, I attempt to explain away how the mistaken metaphysics of the individualist, and derivatively the pluralist-pragmatic approach that contextually embraces it, can facilitate certain elements of biological practice. (shrink)

Feinberg and Mallatt, in their presentation of neurobiological naturalism, have suggested that visual consciousness was acquired by early vertebrates and inherited by a wide range of descendants, and that its neural basis has shifted to nonhomologous nervous structures during evolution. However, their evolutionary scenario of visual consciousness relies on the assumption that visual consciousness is closely linked with survival, which is not commonly accepted in current consciousness research. We suggest an alternative idea that visual consciousness is linked to a specific (...) class of agency, consequently justifying their phylogenetic claim. We also examine the implication of their phylogenetic claim: visual consciousness is homologous across vertebrates, but its neural basis is not. This apparent incongruence illustrates a general phenomenon of homology, and that the resulting hierarchical view of visual consciousness and its neural basis can be straightforwardly accommodated by neurobiological naturalism. Throughout these discussions, we aim to address the potential theoretical issues in neurobiological naturalism and refine the picture illustrated by Feinberg and Mallatt regarding phylogenetic distribution and trajectories of visual consciousness. (shrink)

Advances in developmental genetics and evo-devo in the last several decades have enabled the growth of novel developmental approaches to the classic theme of homology. These approaches depart from the more standard phylogenetic view by contending that homology between morphological characters depends on developmental-genetic individuation and explanation. This article provides a systematic re-examination of the relationship between developmental and phylogenetic homology in light of current evidence from developmental and evolutionary genetics and genomics. I present a qualitative model of the processes (...) that cause de-coupling of morphological and molecular evolution by developmental system drift (DSD), and hypothesize that DSD is a widespread and regular stochastic process that is predictable from parameters such as population size, pleiotropy, and regulatory redundancy. These theoretical findings support an integrative approach in which models of DSD aid in determining when developmental-genetic explanations of homology apply and when other explanations such as stabilizing selection are needed. I argue that a phylogenetic monism about the definition and criteria of homology supports the integration of different explanations into a theory of homology better than pluralism does. (shrink)

There have been repeated attempts in the history of comparative biology to provide a mechanistic account of morphological homology. However, it is well-established that homologues can develop from diverse sets of developmental causes, appearing not to share any core causal architecture that underwrites character identity. We address this challenge with a new conceptual model of Character Identity Mechanisms. ChIMs are cohesive mechanisms with a recognizable causal profile that allows them to be traced through evolution as homologues despite having a diverse (...) etiological organization. Our model hypothesizes that anatomical units at different levels of organization—cell types, tissues, and organs—have level-specific ChIMs with different conserved parts, activities, and organization. Relying on a methodology of conceptual engineering, we show how the ChIM concept advances our understanding of the developmental basis of morphological characters, while forging an important link between comparative and mechanistic biology. (shrink)