This chapter contains section titled: The Old Problem (Agenda) of the Ontogeny of Form Explaining the Ontogeny of Form Epistemological Issues: Representation Epistemological Issues: Explanation Epistemological Issues: Methodology Unexplored Issues and Summary Acknowledgment References.

Reductionism encompasses a set of ontological, epistemological, and methodological claims about the relation of different scientific domains. The basic question of reduction is whether the properties, concepts, explanations, or methods from one scientific domain (typically at higher levels of organization) can be deduced from or explained by the properties, concepts, explanations, or methods from another domain of science (typically one about lower levels of organization). Reduction is germane to a variety of issues in philosophy of science, including the structure of (...) scientific theories, the relations between different scientific disciplines, the nature of explanation, the diversity of methodology, and the very idea of theoretical progress, as well as to numerous topics in metaphysics and philosophy of mind, such as emergence, mereology, and supervenience. (shrink)

It is a common complaint that antireductionist arguments are primarily negative. Here I describe an alternative nonreductionist epistemology based on considerations taken from multidisciplinary research in biology. The core of this framework consists in seeing investigation as coordinated around sets of problems (problem agendas) that have associated criteria of explanatory adequacy. These ideas are developed in a case study, the explanation of evolutionary innovations and novelties, which demonstrates the applicability and fruitfulness of this nonreductionist epistemological perspective. This account also bears (...) on questions of conceptual change and theory structure in philosophy of science. †To contact the author, please write to: Department of Philosophy, University of Minnesota, 831 Heller Hall, 271 19th Ave. S., Minneapolis, MN 55455; e‐mail: [email protected]. (shrink)

Developmental biology is the science that investigates how a variety of interacting processes generate an organism’s heterogeneous shapes, size, and structural features that arise on the trajectory from embryo to adult, or more generally throughout a life cycle. It represents an exemplary area of contemporary experimental biology that focuses on phenomena that have puzzled natural philosophers and scientists for more than two millennia. Philosophers of biology have shown interest in developmental biology due to the potential relevance of development for understanding (...) evolution, the theme of reductionism in genetic explanations, and via increased attention to the details of particular research programs, such as stem cell biology. Developmental biology displays a rich array of material and conceptual practices that can be analyzed to better understand the scientific reasoning exhibited in experimental life science. This entry briefly reviews some central phenomena of ontogeny and then explores four domains that represent some of the import and promise of conceptual reflection on the epistemology of developmental biology. (shrink)

“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. (shrink)

The goal of this paper is to encourage a reconfiguration of the discussion about typology in biology away from the metaphysics of essentialism and toward the epistemology of classifying natural phenomena for the purposes of empirical inquiry. First, I briefly review arguments concerning ‘typological thinking’, essentialism, species, and natural kinds, highlighting their predominantly metaphysical nature. Second, I use a distinction between the aims, strategies, and tactics of science to suggest how a shift from metaphysics to epistemology might be accomplished. Typological (...) thinking can be understood as a scientific tactic that involves representing natural phenomena using idealizations and approximations, which facilitates explanation, investigation, and theorizing via abstraction and generalization. Third, a variety of typologies from different areas of biology are introduced to emphasize the diversity of this representational reasoning. One particular example is used to examine how there can be epistemological conflict between typology and evolutionary analysis. This demonstrates that alternative strategies of typological thinking arise due to the divergent explanatory goals of researchers working in different disciplines with disparate methodologies. I conclude with several research questions that emerge from an epistemological reconfiguration of typology. (shrink)

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. (shrink)

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. (shrink)

This volume explores questions about conceptual change from both scientific and philosophical viewpoints by analyzing the recent history of evolutionary developmental biology. It features revised papers that originated from the workshop "Conceptual Change in Biological Science: Evolutionary Developmental Biology, 1981-2011" held at the Max Planck Institute for the History of Science in Berlin in July 2010. The Preface has been written by Ron Amundson. In these papers, philosophers and biologists compare and contrast key concepts in evolutionary developmental biology and their (...) development since the original, seminal Dahlem conference on evolution and development held in Berlin in 1981. Many of the original scientific participants from the 1981 conference are also contributors to this new volume and, in conjunction with other expert biologists and philosophers specializing on these topics, provide an authoritative, comprehensive view on the subject. Taken together, the papers supply novel perspectives on how and why the conceptual landscape has shifted and stabilized in particular ways, yielding insights into the dynamic epistemic changes that have occurred over the past three decades. This volume will appeal to philosophers of biology studying conceptual change, evolutionary developmental biologists focused on comprehending the genesis of their field and evaluating its future directions, and historians of biology examining this period when the intersection of evolution and development rose again to prominence in biological science. (shrink)

Causal relations among components and activities are intentionally misrepresented in mechanistic explanations found routinely across the life sciences. Since several mechanists explicitly advocate accurately representing factors that make a difference to the outcome, these idealizations conflict with the stated rationale for mechanistic explanation. We argue that these idealizations signal an overlooked feature of reasoning in molecular and cell biology—mechanistic explanations do not occur in isolation—and suggest that explanatory practices within the mechanistic tradition share commonalities with model-based approaches prevalent in population (...) biology. (shrink)

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. (shrink)

Many biologists and philosophers have worried that importing models of reasoning from the physical sciences obscures our understanding of reasoning in the life sciences. In this paper we discuss one example that partially validates this concern: part-whole reductive explanations. Biology and physics tend to incorporate different models of temporality in part-whole reductive explanations. This results from differential emphases on compositional and causal facets of reductive explanations, which have not been distinguished reliably in prior philosophical analyses. Keeping these two facets distinct (...) facilitates the identifi cation of two further aspects of reductive explanation: intrinsicality and fundamentality. Our account provides resources for discriminating between different types of reductive explanation and suggests a new approach to comprehending similarities and differences in the explanatory reasoning found in biology and physics. (shrink)

Using the context of controversies surrounding evolutionary developmental biology (EvoDevo) and the possibility of an Extended Evolutionary Synthesis, I provide an account of theory structure as idealized theory presentations that are always incomplete (partial) and shaped by their conceptual content (material rather than formal organization). These two characteristics are salient because the goals that organize and regulate scientific practice, including the activity of using a theory, are heterogeneous. This means that the same theory can be structured differently, in part because (...) theory presentations (as idealizations) intentionally depart from different features known to be present in a theory. Since there are diverse and potentially incompatible theory structures derived from heterogeneous goals found in scientific practices, a question arises about the absence of a unifying theory structure in the background. The notion of a “theory façade” offers a fruitful perspective on this potentially unsettling result. (shrink)

The Routledge Handbook of Mechanisms and Mechanical Philosophy is an outstanding reference source to the key topics, problems, and debates in this exciting subject and is the first collection of its kind. Comprising over thirty chapters by a team of international contributors, the Handbook is divided into four Parts: Historical perspectives on mechanisms The nature of mechanisms Mechanisms and the philosophy of science Disciplinary perspectives on mechanisms. Within these Parts central topics and problems are examined, including the rise of mechanical (...) philosophy in the seventeenth century; what mechanisms are made of and how they are organized; mechanisms and laws and regularities; how mechanisms are discovered and explained; dynamical systems theory; and disciplinary perspectives from physics, chemistry, biology, biomedicine, ecology, neuroscience, and the social sciences. Essential reading for students and researchers in philosophy of science, the Handbook will also be of interest to those in related fields, such as metaphysics, philosophy of psychology, and history of science. (shrink)

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. (shrink)

Model organisms are central to contemporary biology and studies of embryogenesis in particular. Biologists utilize only a small number of species to experimentally elucidate the phenomena and mechanisms of development. Critics have questioned whether these experimental models are good representatives of their targets because of the inherent biases involved in their selection (e.g., rapid development and short generation time). A standard response is that the manipulative molecular techniques available for experimental analysis mitigate, if not counterbalance, this concern. But the most (...) powerful investigative techniques and molecular methods are applicable to single-celled organisms (‘microbes’). Why not use unicellular rather than multicellular model organisms, which are the standard for developmental biology? To claim that microbes are not good representatives takes us back to the original criticism leveled against model organisms. Using empirical case studies of microbes modeling ontogeny, we break out of this circle of reasoning by showing: (a) that the criterion of representation is more complex than earlier discussions have emphasized; and, (b) that different aspects of manipulability are comparable in importance to representation when deciding if a model organism is a good model. These aspects of manipulability harbor the prospect of enhancing representation. The result is a better understanding of how developmental biologists conceptualize research using experimental models and suggestions for underappreciated avenues of inquiry using microbes. More generally, it demonstrates how the practical aspects of experimental biology must be scrutinized in order to understand the associated scientific reasoning. (shrink)

In this paper I examine a dispositional property that has been receiving increased attention in biology, evolvability. First, I identify three compatible but distinct investigative approaches, distinguish two interpretations of evolvability, and treat the difference between dispositions of individuals versus populations. Second, I explore the relevance of philosophical distinctions about dispositions for evolvability, isolating the assumption that dispositions are intrinsically located. I conclude that some instances of evolvability cannot be understood as purely intrinsic to populations and suggest alternative strategies for (...) resolving this difficulty. (shrink)

Represents the most comprehensive and current survey of the various challenges to the Modern Synthesis theory of evolution. Incorporates a variety of theoretical and disciplinary perspectives, from evolutionary biologists, historians and philosophers of science. These essays constitute the state of the art in the current debate on the status of the Modern Synthesis.

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. (shrink)

Erratum to Using the context of controversies surrounding evolutionary developmental biology (EvoDevo) and the possibility of an Extended Evolutionary Synthesis, I provide an account of theory structure as idealized theory presentations that are always incomplete (partial) and shaped by their conceptual content (material rather than formal organization). These two characteristics are salient because the goals that organize and regulate scientific practice, including the activity of using a theory, are heterogeneous. This means that the same theory can be structured differently, in (...) part because theory presentations (as idealizations) intentionally depart from different features known to be present in a theory. Since there are diverse and potentially incompatible theory structures derived from heterogeneous goals found in scientific practices, a question arises about the absence of a unifying theory structure in the background. The notion of a “theory façade” offers a fruitful perspective on this potentially unsettling result. (shrink)

The ubiquity of top-down causal explanations within and across the sciences is prima facie evidence for the existence of top-down causation. Much debate has been focused on whether top-down causation is coherent or in conflict with reductionism. Less attention has been given to the question of whether these representations of hierarchical relations pick out a single, common hierarchy. A negative answer to this question undermines a commonplace view that the world is divided into stratified ‘levels’ of organization and suggests that (...) attributions of causal responsibility in different hierarchical representations may not have a meaningful basis for comparison. Representations used in top-down and bottom-up explanations are primarily ‘local’ and tied to distinct domains of science, illustrated here by protein structure and folding. This locality suggests that no single metaphysical account of hierarchy for causal relations to obtain within emerges from the epistemology of scientific explanation. Instead, a pluralist perspective is recommended—many different kinds of top-down causation (explanation) can exist alongside many different kinds of bottom-up causation (explanation). Pluralism makes plausible why different senses of top-down causation can be coherent and not in conflict with reductionism, thereby illustrating a productive interface between philosophical analysis and scientific inquiry. (shrink)

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. (shrink)

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. (shrink)

Evolutionary developmental biology (Evo-devo) is a loose conglomeration of research programs in the life sciences with two main axes: (a) the evolution of development, or inquiry into the pattern and processes of how ontogeny varies and changes over time; and, (b) the developmental basis of evolution, or inquiry into the causal impact of ontogenetic processes on evolutionary trajectories—both in terms of constraint and facilitation. Philosophical issues are found along both axes surrounding concepts such as evolvability, novelty, and modularity. The developmental (...) basis of evolution has garnered much attention because it speaks to the possibility of revising a standard construal of evolutionary theory, but the evolution of development harbors its own conceptual questions. This article addresses the heterogeneity of Evo-devo’s conglomerate structure (including disagreements over its individuation), as well as the concepts and controversies of philosophical interest pertaining to the evolution of development and the developmental basis of evolution. Future research will benefit from a shift away from global theorizing toward the scientific practices of Evo-devo. (shrink)

According to Joshua Alexander, philosophers use intuitions routinely as a form of evidence to test philosophical theories but experimental philosophy demonstrates that these intuitions are unreliable and unrepresentative.1 According to Herman Cappelen, philosophers never use intuitions as evidence (despite the vacuous sentential leader ‘intuitively’) and experimental philosophy lacks a rationale for its much-touted existence.2 That two books are diametrically opposed on methodology in philosophy is not noteworthy. But eyebrows might be raised at such contradictory accounts of the phenomenology of philosophical (...) inquiry. What is it that (analytic) philosophers do? Why is it so difficult to achieve consensus on the professional activities in which we engage? (shrink)

Robert Wilson’s The Eugenic Mind Project is a major achievement of engaged scholarship and socially relevant philosophy and history of science. It exemplifies the virtues of interdisciplinarity. As principal investigator of the Living Archives on Eugenics in Western Canada project, while employed in the Department of Philosophy at the University of Alberta, Wilson encountered a proverbial big ball of mud with questions and issues that involved local individuals living through a painful set of memories and implicated his institutional home in (...) outstanding moral obligations. It is engaged scholarship because it required building relationships with affected persons and taking responsibility for his institution’s legacy, as well as transforming Wilson’s own outlook along the way. It is socially relevant philosophy and history of science because it brings to light issues that remain salient today, especially how eugenic themes are ubiquitous in societal discourse and evinced in everyday decisions. It is interdisciplinary because to accomplish this type of analysis requires intellectual gymnastics that range over diverse domains of research: from standpoint theory and disability studies to oral history and governmental policy; from the evolutionary biology of prosociality and variation to conceptual questions about the categorization of human traits and types. (shrink)

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. (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)

This edited collection showcases some of the best recent research in the philosophy of science. It comprises of thematically arranged papers presented at the 5th conference of the European Philosophy of Science Association (EPSA15), covering a broad variety of topics within general philosophy of science, and philosophical issues pertaining to specific sciences. The collection will appeal to researchers with an interest in the philosophical underpinnings of their own discipline, and to philosophers who wish to study the latest work on the (...) themes discussed. (shrink)

Contributors: Sabina Leonelli Nancy J. Nersessian Michel Janssen Jacob G. Foster James A. Evans Mark A. Bedau Marshall Abrams Gilbert B. Tostevin Salikoko S. Mufwene Massimo Maiocchi Joseph D. Martin Paul E. Smaldino Claes Andersson Anton Törnberg Petter Törnberg Beyond the Meme assembles interdisciplinary perspectives on cultural evolution, providing a nuanced understanding of it as a process in which dynamic structures interact on different scales of size and time. The volume demonstrates how a thick understanding of change in culture emerges (...) from multiple disciplinary vantage points, each of which is required to understand cultural evolution in all its complexity. (shrink)

John Norton’s argument that all formal theories of induction fail raises substantive questions about the philosophical analysis of scientific reasoning. What are the criteria of adequacy for philosophical theories of induction, explanation, or theory structure? Is more than one adequate theory possible? Using a generalized version of Norton’s argument, I demonstrate that the competition between formal and material theories in philosophy of science results from adhering to different criteria of adequacy. This situation encourages an interpretation of “formal” and “material” as (...) indicators of divergent criteria that accompany different philosophical methodologies. I characterize another criterion of adequacy associated with material theories, the avoidance of imported problems, and conclude that one way to negotiate between conflicting criteria is to adopt a pluralist stance toward philosophical theories of scientific reasoning. (shrink)

Philosophical discussions of information and specificity in biology are now commonplace, but no consensus exists about whether the privileging of genetic causation in investigation and explanation...

Review symposium of Alexander Rosenberg’s Darwinian Reductionism: Or, How to Stop Worrying and Love Molecular Biology [2006]. -/- Worry carries with it a connotation of false concern, as in ‘your mother is always worried about you’. And yet some worrying, including that of your mother, turns out to be justified. Alexander Rosenberg’s new book is an extended argument intended to assuage false concerns about reductionism and molecular biology while encouraging a loving embrace of the two.

Scientific explanation is a perennial topic in philosophy of science, but the literature has fragmented into specialized discussions in different scientific disciplines. An increasing attention to scientific practice by philosophers is (in part) responsible for this fragmentation and has put pressure on criteria of adequacy for philosophical accounts of explanation, usually demanding some form of pluralism. This commentary examines the arguments offered by Fagan and Woody with respect to explanation and understanding in scientific practice. I begin by scrutinizing Fagan's concept (...) of collaborative explanation, highlighting its distinctive advantages and expressing concern about several of its assumptions. Then I analyze Woody's attempt to reorient discussions of scientific explanation around functional considerations, elaborating on the wider implications of this methodological recommendation. I conclude with reflections on synergies and tensions that emerge when the two papers are juxtaposed and how these draw attention to critical issues that confront ongoing philosophical analyses of scientific explanation. (shrink)

Reductive explanations are psychologically seductive; when given two explanations, people prefer the one that refers to lower-level components or processes to account for the phenomena under consideration even when information about these lower levels is irrelevant. Maybe individuals assume that a reductive explanation is what a scientific explanation should look like (e.g., neuroscience should explain psychology) or presume that information about lower-level components or processes is more explanatory (e.g., molecular detail explains better than anatomical detail). Philosophers have been analyzing reduction (...) for more than half a century (Hüttemann and Love 2016), but neither of these possibilities is a consensus view (even if psychologically applicable). Instead, there is widespread agreement that the landscape of reductionism is complicated, especially in biology. Increasing scrutiny of actual practices within biology and other sciences has often provoked the questions (paraphrasing Alasdair MacIntyre): Whose explanation? Which reductionism? Marie Kaiser’s book—Reductive Explanation in the Biological Sciences—is a decisive intervention into these discussions, offering a wealth of helpful distinctions and new analyses with a healthy focus on scientific practices of explanation. (shrink)

Philosophy of Molecular Medicine: Foundational Issues in Theory and Practice aims at a systematic investigation of a number of foundational issues in the field of molecular medicine. The volume is organized around four broad modules focusing, respectively, on the following key aspects: What are the nature, scope, and limits of molecular medicine? How does it provide explanations? How does it represent and model phenomena of interest? How does it infer new knowledge from data and experiments? The essays collected here, authored (...) by prominent scientists and philosophers of science, focus on a handful of mainstream topics in the philosophical literature, such as causation, explanation, modeling, and scientific inference. These previously unpublished contributions shed new light on these traditional topics by integrating them with problems, methods, and results from three prominent areas of contemporary biomedical science: basic research, translational and clinical research, and clinical practice. (shrink)

Review by Alan Love of "Keywords & Concepts in Evolutionary Developmental Biology." Hall, Brian K. and Wendy M. Olson (Eds), Cambridge, Harvard University Press. Hb. 476+xvi pp.

Conceptual analysis aims to uncover the basic criteria of concepts that underwrite categorizing members via the method of cases. However, conceptual analysis has not been very successful and experimental philosophy has increasingly detailed this lack of success. This essay reviews Thinking Off Your Feet: How Empirical Psychology Vindicates Armchair Philosophy by Michael Strevens, which attempts a novel defence of conceptual analysis. It is a strategic intervention that seems to preserve a relatively traditional picture of philosophical inquiry. I concentrate on several (...) assumptions in this intervention that might be questioned and conclude there are good reasons to continue an interrogation of how we understand the philosophical enterprise. Ideally, this might encourage us to rebuild our picture of what philosophy is. (shrink)

The concept of evolvability—the capacity of a population to produce and maintain evolutionarily relevant variation—has become increasingly prominent in evolutionary biology. Paleontology has a long history of investigating questions of evolvability, but paleontological thinking has tended to neglect recent discussions, because many tools used in the current evolvability literature are challenging to apply to the fossil record. The fundamental difficulty is how to disentangle whether the causes of evolutionary patterns arise from variational properties of traits or lineages rather than being (...) due to selection and ecological success. Despite these obstacles, the fossil record offers unique and growing sources of data that capture evolutionary patterns of sustained duration and significance otherwise inaccessible to evolutionary biologists. Additionally, there exist a variety of strategic possibilities for combining prominent neontological approaches to evolvability with those from paleontology. We illustrate three of these possibilities with quantitative genetics, evolutionary developmental biology, and phylogenetic models of macroevolution. In conclusion, we provide a methodological schema that focuses on the conceptualization, measurement, and testing of hypotheses to motivate and provide guidance for future empirical and theoretical studies of evolvability in the fossil record. (shrink)

For several decades, a debate has been waged over how to interpret the significance of fossils from the Burgess Shale and Cambrian Explosion. Stephen Jay Gould argued that if the “tape of life” was rerun, then the resulting lineages would differ radically from what we find today, implying that humans are a happy accident of evolution. Simon Conway Morris argued that if the “tape of life” was rerun, the resulting lineages would be similar to what we now observe, implying that (...) intelligence would still emerge from an evolutionary process. Recent methodological innovations in paleontological practice call into question both positions and suggest that global claims about the history of life, whether in terms of essential contingency or predictable convergence, are unwarranted. (shrink)

John Bonner managed a long and productive career that balanced specialized inquiry into cellular slime molds with general investigations of big questions in evolutionary biology, such as the origins of multicellular development and the evolution of complexity. This commentary engages with his final paper (“The evolution of evolution”), which argues that the evolutionary process has changed through the history of life. In particular, Bonner emphasizes the possibility that natural selection plays different roles at different size scales. I identify some underlying (...) assumptions in his argument and evaluate its cogency to both foster future discussion and emulate the intellectual example set by Bonner over a lifetime. This endeavor is important beyond Bonner's own theoretical disposition because similar issues are visible in controversies about the possibility of an extended evolutionary synthesis. (shrink)

It is widely accepted that stressful conditions can facilitate evolutionary change. The mechanisms elucidated thus far accomplish this with a generic increase in heritable variation that facilitates more rapid adaptive evolution, often via plastic modifications of existing characters. Through scrutiny of different meanings of stress in biological research, and an explicit recognition that stressors must be characterized relative to their effect on capacities for maintaining functional integrity, we distinguish between: (1) previously identified stress-responsive mechanisms that facilitate evolution by maintaining an (...) adaptive fit with the environment, and (2) the co-option of stress-responsive mechanisms that are specific to stressors leading to the origin of novelties via compensation. Unlike standard accounts of gene co-option that identify component sources of evolutionary change, our model documents the cost-benefit trade-offs and thereby explains how one mechanism—an immediate response to acute stress—is transformed evolutionarily into another—routine protection from recurring stressors. We illustrate our argument with examples from cell type origination as well as processes and structures at higher levels of organization. These examples suggest a general principle of evolutionary origination based on the capacity to switch between regulatory states related to reproduction and proliferation versus survival and differentiation. (shrink)

The questions raised for the study of marine invertebrate larvae have implications for the evolution of development, the life histories of animals, and life in the sea more generally. These questions began to coalesce in the 19th century around two main factors. The first was the discovery of marine larvae. Through careful observation, investigators detected and confirmed that the development of animals exhibited stages surprisingly different from the previously known adults and adult-like juveniles. Famous examples include the demonstration that barnacles (...) were arthropods because of a shared larval form (Thompson 1830), the characterization of bilateral echinoderm larvae by Johannes Müller (summarized in Huxley 1851), and the unexpected chordate affinities of tunicates. Subsequent studies also demonstrated that adults with similar morphological features could have radically different larval forms and life histories. (shrink)

The inapplicability of variations on theory reduction in the context of genetics and their irrelevance to ongoing research has led to an anti-reductionist consensus in philosophy of biology. One response to this situation is to focus on forms of reductive explanation that better correspond to actual scientific reasoning (e.g. part–whole relations). Working from this perspective, we explore three different aspects (intrinsicality, fundamentality, and temporality) that arise from distinct facets of reductive explanation: composition and causation. Concentrating on these aspects generates new (...) forms of reductive explanation and conditions for their success or failure in biology and other sciences. This analysis is illustrated using the case of protein folding in molecular biology, which demonstrates its applicability and relevance, as well as illuminating the complexity of reductive reasoning in a specific biological context. (shrink)

According to many biologists, explaining the evolution of morphological novelty and behavioral innovation are central endeavors in contemporary evolutionary biology. These endeavors are inherently multidisciplinary but also have involved a high degree of controversy. One key source of controversy is the definitional diversity associated with the concept of evolutionary novelty, which can lead to contradictory claims (a novel trait according to one definition is not a novel trait according to another). We argue that this diversity should be interpreted in light (...) of a different epistemic role played by the concept of evolutionary novelty—the structuring of a problem space or setting of an explanatory agenda—rather than the concept’s capacity to categorize traits as novel. This distinctive role is consistent with the definitional diversity and shows that the concept of novelty benefits ongoing investigation by focusing attention on answering different questions related to comprehending the origins of novelty. A review of recent theoretical and empirical work on evolutionary novelty confirms this interpretation. (shrink)

Accounting for the evolutionary origins of morphological novelty is one of the core challenges of contemporary evolutionary biology. A successful explanatory framework requires the integration of different biological disciplines, but the relationships between developmental biology and standard evolutionary biology remain contested. There is also disagreement about how to define the concept of evolutionary novelty. These issues were the subjects of a workshop held in November 2009 at the University of Alberta. We report on the discussion and results of this workshop, (...) addressing questions about (i) how to define evolutionary novelty and understand its significance, (ii) how to interpret evolutionary developmental biology as a synthesis and its relation to neo-Darwinian evolutionary theory, and (iii) how to integrate disparate biological approaches in general. (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)