Alan Love

“Functional homology” appears regularly in different areas of biological research and yet it is apparently a contradiction in terms—homology concerns identity of structure regardless of form and function. I argue that despite this conceptual tension there is a legitimate conception of ‘homology of function’, which can be recovered by utilizing a distinction from pre-Darwinian physiology (use versus activity) to identify an appropriate meaning of ‘function’. This account is directly applicable to molecular developmental biology and shares a connection to the theme of hierarchy in homology. I situate ‘homology of function’ within existing definitions and criteria for structural assessments of homology, and introduce a criterion of ‘organization’ for judging function homologues, which focuses on hierarchically interconnected interdependencies (similar to relative position and connection for skeletal elements in structural homology). This analysis of biological concepts has at least three broad philosophical consequences: (1) it provides the grounds for the study of behavior and psychological categories as homologues; (2) it demonstrates that philosophers who take selected effect function as primary effectively ignore large portions of comparative, structural, and experimental research, thereby misconstruing biological reasoning and knowledge; and, (3) it underwrites causal generalizations, which illuminates inferences made from model organisms in experimental biology.

Idealization is a reasoning strategy that biologists use to describe, model and explain that purposefully departs from features known to be present in nature. Similar to other strategies of scientific reasoning, idealization combines distinctive strengths alongside of latent weaknesses. The study of ontogeny in model organisms is usually executed by establishing a set of normal stages for embryonic development, which enables researchers in different laboratory contexts to have standardized comparisons of experimental results. Normal stages are a form of idealization because they intentionally ignore known variation in development, including variation associated with phenotypic plasticity (e.g. via strict control of environmental variables). This is a tension between the phenomenon of plasticity and the practice of staging that has consequences for evolutionary developmental investigation because variation is conceptually removed as a part of rendering model organisms experimentally tractable. Two compensatory tactics for mitigating these consequences are discussed: employing a diversity of model organisms and adopting alternative periodizations.

Günter Wagner’s Homology, Genes, and Evolutionary Innovation collects and synthesizes a vast array of empirical data, theoretical models, and conceptual analysis to set out a progressive research program with a central theoretical commitment: the genetic theory of homology. This research program diverges from standard approaches in evolutionary biology, provides sharpened contours to explanations of the origin of novelty, and expands the conceptual repertoire of evolutionary developmental biology. I concentrate on four aspects of the book in this essay review: the genetic theory of homology and character identity networks; the implications for how we explain evolutionary novelties; the expanded set of concepts surrounding homology, and the epistemological conflicts between Wagner’s viewpoint and functionally-oriented evolutionary biology, as well as differences with other Evo–devo researchers. Together these have ramifications for how we interpret different explanatory approaches to evolutionary phenomena and understand relationships between the usefulness of concepts and the reality they represent

Although the role of morphology in evolutionary theory remains a subject of debate, assessing the contributions of morphological investigation to evolutionary developmental biology (Evo-devo) is a more circumscribed issue of direct relevance to ongoing research. Historical studies of morphologically oriented researchers and the formation of the Modern Synthesis in the Anglo-American context identify a recurring theme: the synthetic theory of evolution did not capture multiple levels of biological organization. When this feature is incorporated into a philosophical framework for explaining the origin of evolutionary innovations and novelties (a core domain of inquiry in Evo-devo) two specific roles for morphology can be described: (1) the conceptualization and operational identification of the targets of explanation; and (2) the elucidation of causal interactions at higher levels of organization during ontogeny and through evolutionary time. These roles are critical components of any adequate explanation of innovation and novelty though not exhaustive of the parts played by morphology in evolutionary investigation. They also invite reflection on what counts as an evolutionary cause in contemporary evolutionary biology.

Evolutionary developmental biology (or developmental evolution) is in the middle stages of its “development.” Its early ontogeny cannot be traced back to fertilization but pivotal developmental events included Gould’s (1977) treatment of heterochrony, Riedl’s (1978) analysis of “burden”, the Dahlem conference of 1981, a British Society of Developmental Biologists Symposium, as well as books that incorporated developmental genetics into older comparative themes. A major inductive process began with the discovery of widespread phylogenetic conservation in homeobox-containing genes. One interpretation of these early developmental dynamics holds that an increasingly prominent problem agenda (e.g., how do novel structures and functions originate?), inherited from long-standing research programs in comparative embryology, morphology, and paleontology, was handed a powerful set of experimental tools from the lineage of experimental embryology. This allowed for an experimental probing of development and its evolution in an unprecedented fashion. Although the relationship between evolution and development has exhibited a protracted and complex history, we are still in the process of comprehending these early stages of “modern” EvoDevo’s ontogeny.

Reduction and reductionism have been central philosophical topics in analytic philosophy of science for more than six decades. Together they encompass a diversity of issues from metaphysics and epistemology. This article provides an introduction to the topic that illuminates how contemporary epistemological discussions took their shape historically and limns the contours of concrete cases of reduction in specific natural sciences. The unity of science and the impulse to accomplish compositional reduction in accord with a layer-cake vision of the sciences, the seminal contributions of Ernest Nagel on theory reduction and how they strongly conditioned subsequent philosophical discussions, and the detailed issues pertaining to different accounts of reduction that arise in both physical and biological science (e.g., limit-case and part-whole reduction in physics, the difference-making principle in genetics, and mechanisms in molecular biology) are explored. The conclusion argues that the epistemological heterogeneity and patchwork organization of the natural sciences encourages a pluralist stance about reduction.

Although natural philosophers have long been interested in individuality, it has been of interest to contemporary philosophers of biology because of its role in different aspects of evolutionary biology. These debates include whether species are individuals or classes, what counts as a unit of selection, and how transitions in individuality occur evolutionarily. Philosophical analyses are often conducted in terms of metaphysics (“what is an individual?”), rather than epistemology (“how can and do researchers conceptualize individuals so as to address some of their scientific goals?”). We review several philosophical distinctions in order to shift attention from metaphysics to epistemology. Many controversies involve epistemological differences rather than metaphysical disagreement. This implies that a pluralist stance about individuality in biology is warranted and has metaphysical consequences because the pluralism emerges from the diversity of scientific interests that investigate the complexity of living phenomena.

Exploring history pertinent to evolutionary developmental biology (hereafter, Evo-devo) is an exciting prospect given its current status as a cutting-edge field of research. The first and obvious question concerns where to begin searching for materials and sources. Since this new discipline adopts a moniker that intentionally juxtaposes ‘evolution’ and development’, individuals, disciplines, and institutional contexts relevant to the history of evolutionary studies and investigations of ontogeny prompt themselves. Each of these topics has received attention from historians and thus there is both primary and secondary material from which to draw. For example, many historians have documented the historical trajectories of genetics and embryology, their split, and various relations (or lack thereof), especially in the first three decades of the 20th century.

One foundational question in contemporarybiology is how to `rejoin evolution anddevelopment. The emerging research program(evolutionary developmental biology or`evo-devo) requires a meshing of disciplines,concepts, and explanations that have beendeveloped largely in independence over the pastcentury. In the attempt to comprehend thepresent separation between evolution anddevelopment much attention has been paid to thesplit between genetics and embryology in theearly part of the 20th century with itscodification in the exclusion of embryologyfrom the Modern Synthesis. This encourages acharacterization of evolutionary developmentalbiology as the marriage of evolutionary theoryand embryology via developmental genetics. Butthere remains a largely untold story about thesignificance of morphology and comparativeanatomy (also minimized in the ModernSynthesis). Functional and evolutionarymorphology are critical for understanding thedevelopment of a concept central toevolutionary developmental biology,evolutionary innovation. Highlighting thediscipline of morphology and the concepts ofinnovation and novelty provides an alternativeway of conceptualizing the `evo and the `devoto be synthesized.

The larval arms of echinoid plutei are used for locomotion and feeding. They are composed of internal calcite skeletal rods covered by an ectoderm layer bearing a ciliary band. Skeletogenesis includes an autonomous molecular differentiation program in primary mesenchyme cells (PMCs), initiated when PMCs leave the vegetal plate for the blastocoel, and a patterning of the differentiated skeletal units that requires molecular cues from the overlaying ectoderm. The arms represent a larval feature that arose in the echinoid lineage during the Paleozoic and offers a subject for the study of gene co-option in the evolution of novel larval features. We isolated new molecular markers in two closely related but differently developing species, Heliocidaris tuberculata and Heliocidaris erythrogramma. We report the expression of a larval arm-associated ectoderm gene tetraspanin, as well as two new PMC markers, advillin and carbonic anhydrase. Tetraspanin localizes to the animal half of blastula stage H. tuberculata and then undergoes a restriction into the putative oral ectoderm and future location of the postoral arms, where it continues to be expressed at the leading edge of both the postoral and anterolateral arms. In H. erythrogramma, its expression initiates in the animal half of blastulae and expands over the entire ectoderm from gastrulation onward. Advillin and carbonic anhydrase are upregulated in the PMCs postgastrulation and localized to the leading edge of the growing larval arms of H. tuberculata but do not exhibit coordinated expression in H. erythrogramma larvae. The tight spatiotemporal regulation of these genes in H. tuberculata along with other ontogenetic and phylogenetic evidence suggest that pluteus arms are novel larval organs, distinguishable from the processes of skeletogenesis per se. The dissociation of expression control in H. erythrogramma suggest that coordinate gene expression in H. tuberculata evolved as part of the evolution of pluteus arms, and is not required for larval or adult development.

Although sciences are often conceptualized in terms of theory confirmation and hypothesis testing, an equally important dimension of scientific reasoning is the structure of problems that guide inquiry. This problem structure is evident in several concepts central to evolutionary developmental biology (Evo-devo)—constraints, modularity, evolvability, and novelty. Because problems play an important role in biological practice, they should be included in biological pedagogy, especially when treating the issue of scientific controversy. A key feature of resolving controversy is synthesizing methodologies from different biological disciplines to generate empirically adequate explanations. Concentrating on problem structure illuminates this interdisciplinarity in a way that is often ignored when science is taught only from the perspective of theory or hypothesis. These philosophical considerations can assist life science educators in their continuing quest to teach biology to the next generation.

Judgments of plausibility involve appearance of the truth or reasonableness, which is always a function of background knowledge. What anyone will countenance is conditioned by what they already know (or think they know). Marc Kirschner (professor of systems biology at Harvard) and John Gerhart (professor of molecular and cell biology at the University of California—Berkeley) aim to show that molecular, cellular, and developmental processes relevant to the generation of phenotypic variation in anatomy, physiology, and behavior demonstrate how evolutionary processes, especially the origins of novelty, are plausible. The outstanding question for Kirschner and Gerhart concerns not the modification of structures but their origination—a question unanswered by the theoretical framework of the modern synthesis.

Philosophy of Science, 73 (April 2006) pp. 247–257. 0031-8248/2006/7302-0007$10.00 Copyright 2006 by the Philosophy of Science Association. All rights reserved. 247 BOOK REVIEWS Lenny Moss, What Genes Can’t Do . Cambridge, MA: MIT Press (2004), 256 pp., $21.00 (paper). Many philosophers of science will have encountered the core distinction between two different gene concepts found in What Genes Can’t Do . Moss argues that contemporary uses of the term ‘gene’ that denote an infor- mation bearing entity result from the conflation of two concepts (‘Gene- P’ and ‘Gene-D’). These concepts arise out of distinct trajectories in the history of biology (preformation and epigenesis, respectively) but are glued together by the rhetoric of linguistic and textual metaphors (e.g., blueprints and programs). Gene-P picks out an instrumentalist use of ‘gene’ as phenotypic indicator or predictor, whereas Gene-D refers to DNA sequences as developmental template resources for RNA and pro- tein products that play variegated cellular roles in the production of many, distinct phenotypes. A number of critical responses to the distinction are now extant in the literature, but my aim is to answer a different question. Why should philosophers of science who have not read the book be interested in it (besides the fact that it is now available in paperback)? The answer is found at the level of methodology and is relevant to crit- icisms of Moss’s distinction.

Evolutionary developmental biology (Evo-devo) is a vibrant area of contemporary life science that should be (and is) increasingly incorporated into teaching curricula. Although the inclusion of this content is important for biological pedagogy at multiple levels of instruction, there are also philosophical lessons that can be drawn from the scientific practices found in Evo-devo. One feature of particular significance is the interdisciplinary nature of Evo-devo investigations and their resulting explanations. Instead of a single disciplinary approach being the most explanatory or fundamental, different methodologies from biological disciplines must be synthesized to generate empirically adequate explanations. Thus, Evo-devo points toward a non-reductionist epistemology in biology. I review three areas where these synthetic efforts become manifest as a result of Evo-devo’s practices (form versus function reasoning styles; problem-structured investigations; idealizations related to studying model organisms), and then sketch some possible applications to teaching biology. These philosophical considerations provide resources for life science educators to address (and challenge) key aspects of the National Science Education Standards and Benchmarks for Scientific Literacy.

Many philosophers of biology have embraced a version of pluralism in response to the failure of theory reduction but overlook how concepts, methods, and explanatory resources are in fact coordinated, such as in interdisciplinary research where the aim is to integrate different strands into an articulated whole. This is observable for the origin of evolutionary novelty—a complex problem that requires a synthesis of intellectual resources from different fields to arrive at robust answers to multiple allied questions. It is an apt locus for exploring new dimensions of explanatory integration because it necessitates coordination among historical and experimental disciplines . These coordination issues are widespread for the origin of novel morphologies observed in the Cambrian Explosion. Despite an explicit commitment to an integrated, interdisciplinary explanation, some potential disciplinary contributors are excluded. Notable among these exclusions is the physics of ontogeny. We argue that two different dimensions of integration—data and standards—have been insufficiently distinguished. This distinction accounts for why physics-based explanatory contributions to the origin of novelty have been resisted: they do not integrate certain types of data and differ in how they conceptualize the standard of uniformitarianism in historical, causal explanations. Our analysis of these different dimensions of integration contributes to the development of more adequate and integrated explanatory frameworks

Overview The evolution of multicellularity raises questions regarding genomic and developmental commonalities and discordances, selective advantages and disadvantages, physical determinants of development, and the origins of morphological novelties. It also represents a change in the definition of individuality, because a new organism emerges from interactions among single cells. This volume considers these and other questions, with contributions that explore the origins and consequences of the evolution of multicellularity, addressing a range of topics, organisms, and experimental protocols. Each section focuses on selected topics or particular lineages that present a significant insight or challenge. The contributors consider the fossil record of the paleontological circumstances in which animal multicellularity evolved; cooptation, recurrent patterns, modularity, and plausible pathways for multicellular evolution in plants; theoretical approaches to the amoebozoa and fungi (cellular slime molds having long provided a robust model system for exploring the evolution of multicellularity), plants, and animals; genomic toolkits of metazoan multicellularity; and philosophical aspects of the meaning of individuality in light of multicellular evolution. Contributors Maja Adamska, Argyris Arnellos, Juan A. Arias, Eugenio Azpeitia, Mariana Benítez, Adriano Bonforti, John Tyler Bonner, Peter L. Conlin, A. Keith Dunker, Salva Duran-Nebreda, Ana E. Escalante, Valeria Hernández-Hernández, Kunihiko Kaneko, Andrew H. Knoll, Stephan G. König, Daniel J. G. Lahr, Ottoline Leyser, Alan C. Love, Raul Montañez, Emilio Mora van Cauwelaert, Alvaro Moreno, Vidyanand Nanjundiah, Aurora M. Nedelcu, Stuart A. Newman, Karl J. Niklas, William C. Ratcliff, Iñaki Ruiz-Trillo, Ricard Solé

Alan C. LoveDarwinian calisthenicsAn athlete engages in calisthenics as part of basic training and as a preliminary to more advanced or intense activity. Whether it is stretching, lunges, crunches, or push-ups, routine calisthenics provide a baseline of strength and flexibility that prevent a variety of injuries that might otherwise be incurred. Peter Bowler has spent 40 years doing Darwinian calisthenics, researching and writing on the development of evolutionary ideas with special attention to Darwin and subsequent filiations among scientists exploring evolution . Therefore, we would expect that when Bowler engages in a counterfactual history—imagining a world without Darwin—he is able to avoid historical injury and generate novel insights. My assessment is that the results are mixed. Before we can see why, it is necessary to walk briskly through the main contours of his argument.Bowler begins with an apologia for a counterfactual appr ..

This chapter describes the theoretical implications of Extended Synthesis and addresses the methodological options available for determining aspects of theoretical structure. It uses a “bottom-up” approach focused on evolutionary theory in particular, as opposed to a “top-down” strategy that attempts to characterize the structure of all scientific theories. The chapter shows that there are multiple stable components contained within a broad representation of evolutionary theory. It suggests that the philosophical analysis offered in the chapter regarding the structure of evolutionary theory assists attempts to recover coherence through the vehicle of an Extended Synthesis.

A central reason that undergirds the significance of evo-devo is the claim that development was left out of the Modern synthesis. This claim turns out to be quite complicated, both in terms of whether development was genuinely excluded and how to understand the different kinds of embryological research that might have contributed. The present paper reevaluates this central claim by focusing on the practice of model organism choice. Through a survey of examples utilized in the literature of the Modern synthesis, I identify a previously overlooked feature: exclusion of research on marine invertebrates. Understanding the import of this pattern requires interpreting it in terms of two epistemic values operating in biological research: theoretical generality and explanatory completeness. In tandem, these values clarify and enhance the significance of this exclusion. The absence of marine invertebrates implied both a lack of generality in the resulting theory and a lack of completeness with respect to particular evolutionary problems, such as evolvability and the origin of novelty. These problems were salient to embryological researchers aware of the variation and diversity of larval forms in marine invertebrates. In closing, I apply this analysis to model organism choice in evo-devo and discuss its relevance for an extended evolutionary synthesis.