Alan Love

The star-nosed mole is aptly named. Its distinctive snout consists of 22 tendrils ringing a pair of nostrils and, from some angles, the entire setup resembles a misshapen star. The tendrils are fleshy and look a bit like fingers, and, like fingers, they have a certain dexterity. But why? Why does the mole have such a singular appendage as opposed to something more ordinary? What is the function or purpose of this bizarre structure? From the dedicated work of Ken Catania, of Vanderbilt University, and colleagues, it appears that the appendage facilitates rapid handling of small prey items, making it advantageous for an organism whose diet consists of tiny invertebrates. We might therefore hazard that this feature arose evolutionarily because it conferred this benefit. But the matter is difficult to resolve, because current utility does not permit a straightforward inference of a reason for existence. A correction has been published: BioScience, Volume 72, Issue 7, July 2022, Page 708

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.

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.

A central topic in research at the intersection of development and evolution is the origin of novel traits. Despite progress on understanding how developmental mechanisms underlie patterns of diversity in the history of life, the problem of novelty continues to challenge researchers. Here we argue that research on evolutionary novelty and the closely associated phenomenon of co-option can be reframed fruitfully by: (1) specifying a conceptual model of mechanisms that underwrite character identity, (2) providing a richer and more empirically precise notion of co-option that goes beyond common appeals to “deep homology”, and (3) attending to the nature of experimental interventions that can determine whether and how the co-option of identity mechanisms can help to explain novel character origins. This reframing has the potential to channel future investigation to make substantive progress on the problem of evolutionary novelty. To illustrate this potential, we apply our reframing to two case studies: treehopper helmets and beetle horns.

Given the pervasiveness of gene sharing in evolution and the extent of homology across the tree of life, why is everything not homologous with everything else? The continuity and overlapping genetic contributions to diverse traits across lineages seem to imply that no discrete determination of homology is possible. Although some argue that the widespread overlap in parts and processes should be acknowledged as “partial” homology, this threatens a broad base of presumed comparative morphological knowledge accepted by most biologists. Following a long scientific tradition, we advocate a strategy of “theoretical articulation” that introduces further distinctions to existing concepts to produce increased contrastive resolution among the labels used to represent biological phenomena. We pursue this strategy by drawing on successful patterns of reasoning from serial homology at the level of gene sequences to generate an enriched characterization of serial homology as a hierarchical, phylogenetic concept. Specifically, we propose that the concept of serial homology should be applied primarily to repeated but developmentally individualized body parts, such as cell types, differentiated body segments, or epidermal appendages. For these characters, a phylogenetic history can be reconstructed, similar to families of paralogous genes, endowing the notion of serial homology with a hierarchical, phylogenetic interpretation. On this basis, we propose a five-fold theoretical classification that permits a more fine-grained mapping of diverse trait-types. This facilitates answering the question of why everything is not homologous with everything else, as well as how novelty is possible given that any new character possesses evolutionary precursors. We illustrate the fecundity of our account by reference to debates over insect wing serial homologs and vertebrate paired appendages.

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.

Throughout his life, John Tyler Bonner contributed to major transformations in the fields of developmental and evolutionary biology. He pondered the evolution of complexity and the significance of randomness in evolution, and was instrumental in the formation of evolutionary developmental biology. His contributions were vast, ranging from highly technical scientific articles to numerous books written for a broad audience. This historical vignette gathers reflections by several prominent researchers on the greatness of John Bonner and the implications of his work.

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.

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.

Philosophers have traditionally focused on the nature of scientific explanation while ignoring the process by which features of the world are formulated as discrete explanantia and explananda. However, the characterization of phenomena is an important activity in its own right, and is intertwined with evaluations of the appropriateness and sufficiency of explanatory strategies. We explore this entanglement of characterization and explanation using an extended case study from deep time: research into the Cambrian explosion. Our analysis focuses on three spheres of research that together illustrate key features of characterization for complex phenomena, including open-endedness, interdisciplinarity, and a concern with explananda and explanantia alike. In addition, they suggest a pair of substantive claims: (1) characterizations of complex phenomena are frequently contested along several dimensions of descriptive understanding, and (2) the dynamics of characterization for complex phenomena are poorly described by models that treat recharacterization primarily as a response to explanatory failures.

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.

A disposition or dispositional property is a capacity, ability, or potential to display or exhibit some outcome. Evolvability refers to a disposition to evolve. This chapter discusses why the dispositional nature of evolvability matters—why philosophical distinctions about dispositions can have scientific implications. To that end, we build a conceptual toolkit with vocabulary from prior philosophical analyses using a different disposition: protein foldability. We then apply this toolkit to address several methodological questions related to evolvability. What entities are the bearers of evolvability? What features causally contribute to the disposition of evolvability? How does evolvability manifest? The various possible answers to these questions available from philosophical distinctions suggest key implications for why the concept of evolvability as a disposition is useful in evolutionary research. These include (1) securing scientific virtues (e.g., explanatory depth and generalization, prediction or retrodiction, and control or manipulation) and (2) fostering interdisciplinary collaboration through the coordination of definitional diversity and different types of inquiry. Together these facilitate concentration on a variety of research questions at different levels of organization and on distinct time scales, all of which should be expected for a complex dispositional property such as evolvability.

Despite the iconic roles of coelacanths, cycads, tadpole shrimps, and tuataras as taxa that demonstrate a pattern of morphological stability over geological time, their status as living fossils is contested. We responded to these controversies with a recommendation to rethink the function of the living fossil concept. Concepts in science do useful work beyond categorizing particular items and we argued that the diverse and sometimes conflicting criteria associated with categorizing items as living fossils represent a complex problem space associated with answering a range of questions related to prolonged evolutionary stasis. Turner defends the living concept against a variety of recent skeptics, but his criticism of our approach relies on a misreading of our main argument. This misreading is instructive because it brings into view the value of three central themes for rethinking the living fossil concept—the function of concepts in biology outside of categorization, the methodological importance of distinguishing parts and wholes in conceptualizing evolutionary phenomena, and articulating diverse explanatory goals associated with these phenomena.

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.

Reductionism concerns a set of ontological and epistemological claims, and methodological strictures based on them, about the relationship between two different scientific domains. The critical assumption is that one of these domains is privileged over the other in the sense that the concepts, rules, laws, and other elements of the privileged domain can be used to specify, constitute, or account for those of the other “reduced” domain. This specification often consists of explanation, such that the “reducing” domain is epistemically privileged over the reduced one. Explanations of this type are “reductionist” (or, are “reductions”) and reductionism is then the thesis that such explanations will always be forthcoming or at least are possible in principle. Reductionism is most plausible if the entities of the reduced domain can be interpreted as arising from (e.g., as aggregates of) entities of the reduced domain. This ontological claim is controversial but motivates many reductionist theses and associated scientific research programs. Thus, epistemological and ontological claims about reductionism have the methodological implication that they should govern and guide scientific research. When such research proves to be fruitless over a period of time, the associated reductionist claims themselves become suspect. Although issues connected with reductionism arise in the physical and social sciences, most attention to reductionism in philosophy of science over the last few decades has focused on the biological sciences, especially after the advent of molecular biology made it plausible to believe that biological phenomena can be uniformly explained (in detail) from their physical basis. However, the program of finding such explanations has a long philosophical history often couched in terms of seeking “mechanical,” “mechanistic,” or “materialistic” explanations. The contrast here is with traditional vitalism and various forms of teleology and holism.

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.

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

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.

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.

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.

Phillip Sloan has thoroughly documented the importance of Darwin's general invertebrate research program in the period from 1826 to 1836 and demonstrated how it had an impact on his conversion to transformism. Although Darwin later spent eight years of his life investigating barnacles, this period has received less treatment in studies of Darwin and the development of his thought. The most prominent question for the barnacle period that has been attended to is why Darwin "delayed" in publishing his theory of evolution. A related but distinct question concerns the variety of earlier events and influences that led Darwin to the study of "Cirripedia" in 1846, apart from its role in the trajectory that led to "On the Origin of Species ". In this paper I focus on four specific episodes prior to 1846 that inform a picture of why Darwin had an antecedent interest in barnacles: the orientation to collecting strange and curious invertebrate organisms, as well as the strong affinities of Darwin's invertebrate collecting on the Beagle voyage with the work of John Vaughan Thompson; the critical role of marine invertebrate fossils in Darwin's geological reasoning aboard the Beagle and exemplified in his "Geological Observations of South America;" the strange absence of a "Zoology of the Beagle" volume on invertebrates and Darwin's original intent to publish some of the descriptions himself; and the noteworthy presence of barnacles in Darwin's transformation theorizing between 1837 and 1839. There is a wealth of support for the thesis that Darwin had a strong interest in cirripedes prior to the formal barnacle research, blunting arguments that it was psychological aversion or a feeling of inferiority about his taxonomic abilities that drove Darwin to the cirripedes

Current fears of a “reproducibility crisis” have led researchers, sources of scientific funding, and the public to question both the efficacy and trustworthiness of science. Suggested policy changes have been focused on statistical problems, such as p-hacking, and issues of experimental design and execution. However, “reproducibility” is a broad concept that includes a number of issues. Furthermore, reproducibility failures occur even in fields such as mathematics or computer science that do not have statistical problems or issues with experimental design. Most importantly, these proposed policy changes ignore a core feature of the process of scientific inquiry that occurs after reproducibility failures: the integration of conflicting observations and ideas into a coherent theory.

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 (Hopkins, Weisberg, and Taylor 2016). 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 (Brigandt and Love 2017). 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.

If we set aside personal edification, what reasons remain for a philosopher of science to study the intellectual biography of a famous (or infamous) scientist? This question raises familiar and perhaps tired arguments about the relationship between history of science and philosophy of science, but it is also practical: why take the time to digest almost 600 pages devoted to the controversial German zoologist Ernst Haeckel? A preliminary answer is the author. The historical investigations of Robert Richards have been of ongoing interest to philosophers, whether it be evolutionary explanations of mind and behavior in the nineteenth century (Dennett 1989) or his contentious claims—reinvigorated in the present volume—about Darwin’s commitment to embryonic recapitulation (Lennox 1994). Richards has a knack for unearthing details germane to conceptual reflection, in no small part because of his own philosophical predilections (e.g., a selection model of scientific theory development). Here I entertain three more reasons to follow the injunction tolle lege: the prescient synthesis exemplified in Haeckel’s evolutionary theorizing, the impact of model organism choice, and the critical role of pictures in scientific reasoning accented by Haeckel’s artistic proclivities.

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.

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.