" Because characters and the conception of characters are central to all studies of evolution, and because evolution is the central organizing principle of biology, this book will appeal to a wide cross-section of biologists.

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)

Understanding the evolutionary role of environmentally induced phenotypic variation (i.e., plasticity) is an important issue in developmental evolution. A major physiological response to environmental change is cellular stress, which is counteracted by generic stress reactions detoxifying the cell. A model, stress‐induced evolutionary innovation (SIEI), whereby ancestral stress reactions and their corresponding pathways can be transformed into novel structural components of body plans, such as new cell types, is described. Previous findings suggest that the cell differentiation cascade of a cell type (...) critical to pregnancy in humans, the decidual stromal cell, evolved from a cellular stress reaction. It is hypothesized that the stress reaction in these cells was elicited ancestrally via inflammation caused by embryo attachment. The present study proposes that SIEI is a distinct form of plasticity‐based evolutionary change leading to the origin of novel structures rather than adaptive transformation of pre‐existing characters. (shrink)

A number of biologists and philosophers have noted the diversity of interpretations of evolvability in contemporary evolutionary research. Different clusters of research defined by co-citation patterns or shared methodological orientation sometimes concentrate on distinct conceptions of evolvability. We examine five different activities where the notion of evolvability plays conceptual roles in evolutionary biological investigation: setting a research agenda, characterization, explanation, prediction, and control. Our analysis of representative examples demonstrates how different conceptual roles of evolvability are quasi-independent and yet exhibit important (...) relationships across scientific activities. It also provides us with the resources to detail two distinct strategies for how evolvability can help to synthesize disparate areas of research and thereby potentially serve as a unifying concept in evolutionary biology. (shrink)

Two welcome extensions of evolutionary thinking have come to prominence over the last thirty years: the so-called ’extended evolutionary synthesis’ (EES) and debate about biological kinds and individuals. These two agendas have, however, remained orthogonal to one another. The EES has mostly restricted itself to widening the explanations of adaptation offered by the preceding ’modern evolutionary synthesis’ by including additional mechanisms of inheritance and variation; while discussion of biological kinds has turned toward philosophical questions of essential vs. contingent properties of (...) life forms and realist vs. epistemological approaches to categorization and classification. Here we attempt to broaden the explanatory scope of evolutionary theory by linking these two agendas. We expand on the mechanistic orientation of the EES, using new understandings of networked systems of components in order to engage the distinct intellectual challenge of the origination of “historical kinds”. With this phrase we designate a subset of natural kinds that acquires, through evolutionary processes, a quasi-independent lineage-history. Such kinds emerge in both biology and culture, and we enlarge the limited number of historical kinds that have thus far been recognized in evolutionary biology in a series of paradigmatic exemplars, from genes and cell types to rituals and music. For each exemplar we discern specific mechanisms by which it arose and persists; comparing these, we suggest a general unity in the ways in which diverse historical kinds originate. (shrink)

In this paper we argue that an operational organism concept can help to overcome the structural deficiency of mathematical models in biology. In our opinion, the structural deficiency of mathematical models lies mainly in our inability to identify functionally relevant biological characters in biological systems, and not so much in a lack of adequate mathematical representations of biological processes. We argue that the problem of character identification in biological systems is linked to the question of a properly formulated organism concept. (...) Lastly, we demonstrate how a decomposition of an organism into independent characters in the context of a specific biological process--such as adaptation by means of natural selection--depends on the dynamical properties and invariance conditions of the equations that describe this process. (shrink)

In the 20th century, genetic explanatory approaches became dominant in both developmental and evolutionary biological research. By contrast, physical approaches, which appeal to properties such as mechanical forces, were largely relegated to the margins, despite important advances in modeling. Recently, there have been renewed attempts to find balanced viewpoints that integrate both biological physics and molecular genetics into explanations of developmental and evolutionary phenomena. Here we introduce the 2017 SICB symposium “Physical and Genetic Mechanisms for Evolutionary Novelty” that was dedicated (...) to exploring empirical cases where both biological physics and developmental genetic considerations are crucial. To further contextualize these case studies, we offer two theoretical frameworks for integrating genetic and physical explanations: combining complementary perspectives and comprehensive unification. We conclude by arguing that intentional reflection on conceptual questions about investigation, explanation, and integration is critical to achieving significant empirical and theoretical advances in our understanding of how novel forms originate across the tree of life. (shrink)

Why do humans menstruate while most mammals do not? Here, we present our answer to this long‐debated question, arguing that (i) menstruation occurs as a mechanistic consequence of hormone‐induced differentiation of the endometrium (referred to as spontaneous decidualization, or SD); (ii) SD evolved because of maternal–fetal conflict; and (iii) SD evolved by genetic assimilation of the decidualization reaction, which is induced by the fetus in non‐menstruating species. The idea that menstruation occurs as a consequence of SD has been proposed in (...) the past, but here we present a novel hypothesis on how SD evolved. We argue that decidualization became genetically stabilized in menstruating lineages, allowing females to prepare for pregnancy without any signal from the fetus. We present three models for the evolution of SD by genetic assimilation, based on recent advances in our understanding of the mechanisms of endometrial differentiation and implantation. Testing these models will ultimately shed light on the evolutionary significance of menstruation, as well as on the etiology of human reproductive disorders like endometriosis and recurrent pregnancy loss. (shrink)

This paper responds to the essay reviews by David Haig, Alan Love and Rachel Brown of my recently published book “Homology, Genes and Evolutionary Innovation”. The issues addressed here relate to: the notion of classes and individuals, issues of explanatory value of adaptive and structuralist explanations in evolutionary biology, the role of homology in evolutionary theory, the limits of a pluralist stance vis a vis alternative explanations of homology, as well as the question whether and to what extend the perspective (...) laid out in HGEI can be or should be transferred to other branches of study, like comparative behavioral biology. (shrink)

In this paper we argue that an operational organism concept can help to overcome the structural deficiency of mathematical models in biology. In our opinion, the structural deficiency of mathematical models lies mainly in our inability to identify functionally relevant biological characters in biological systems, and not so much in a lack of adequate mathematical representations of biological processes. We argue that the problem of character identification in biological systems is linked to the question of a properly formulated organism concept. (...) Lastly, we demonstrate how a decomposition of an organism into independent characters in the context of a specific biological process—such as adaptation by means of natural selection—depends on the dynamical properties and invariance conditions of the equations that describe this process. (shrink)

This paper argues in defense of theanti-reductionist consensus in the philosophy ofbiology. More specifically, it takes issues with AlexRosenberg's recent challenge of this position. Weargue that the results of modern developmentalgenetics rather than eliminating the need forfunctional kinds in explanations of developmentactually reinforce their importance.