Alejandro Fábregas-Tejeda

The organism-environment pairing plays a prominent role in the way different biological theories and models are structured, and scientific practices are carried out. However, understanding how this relationship has been construed and on which epistemic and ontological pillars it stands on remains an open problem that has not been sufficiently investigated by historians and philosophers of science. Against this background, this monograph offers a systematic, comprehensive reappraisal of the organism-environment pairing in biology from the standpoint of integrated history and philosophy of science (&HPS).

The organism-environment pairing plays a prominent role in the way different biological theories and models are structured, and scientific practices are carried out. However, understanding how this relationship has been construed and on which epistemic and ontological pillars it stands on remains an open problem that has not been sufficiently investigated by historians and philosophers of science. Against this background, this monograph offers a systematic, comprehensive re-appraisal of the organism-environment pairing in biology from the standpoint of integrated history and philosophy of science (&HPS).

In recent years, discussions on the epistemology of model organism-based research have emerged in the philosophy of science. A key topic of discussion is how the epistemic insights gained from model organisms differ from those gained through other experimental organisms used in laboratory and field research. Here, we argue that model organisms are epistemically special due to their nature as ontogenetically changeable, standardized, and evolved material model carriers. These characteristics afford six important kinds of modeling versatility that biologists marshal in their investigations: (i) synchronic target versatility; (ii) synchronic scope versatility; (iii) diachronic target versatility; (iv) diachronic scope versatility; (v) manipulation versatility; and (vi) discovery versatility. In presenting these dimensions of modeling versatility, we also clarify key notions such as ‘representational target,’ ‘representational scope,’ and ‘representational power’ as these apply to modeling practices that involve model organisms.

In this article, we mobilize and refine the DEKI account of scientific representation to contend that model organisms are not models tout court but model ‘carriers,’ only abstracted and selected ‘parts’ of which are included in biological models. These parts correspond to phenomena of interest that are interpreted as mechanisms or other kinds of causal processes within certain theoretical domains. The models can then be used to represent similar target phenomena in other organisms. Our proposal paves the way to reconcile opposing positions apropos the representational status of model organisms and build a more robust epistemology of model organism-based research.

This chapter sketches, in a programmatic spirit, the possible contours of a metaphilosophy of science—a second-order discourse and inquiry into the concepts, assumptions, aims, and methods that underpin philosophy of science itself. Such a project, open to collective pursuit, can clarify the discipline's current landscape, promote critical self-reflexivity, and open new possibilities for its future. After providing background notes, I survey key issues—ranging from the methods and aims of philosophy of science to recurrent descriptive and normative debates—and examine their interrelations, before concluding with proposals for fostering metaphilosophy of science through local, mid-term, and long-term initiatives.

Trait individuation is an epistemically indispensable and heuristically fruitful practice in biological science. However, important ontological issues transcend an epistemology-only reading of what trait individuation entails (e.g., adaptation and homology), prompting scholars to advance models and frameworks to grapple with this problem. Here, I articulate two challenges that arise when advancing theories and frameworks to tackle trait individuation: the _synchronicity_ and the _diachronicity_ challenges. The synchronicity challenge involves specifying the traits an organism has at a given moment in ontogeny, whereas the diachronicity challenge involves understanding the causal processes that drive trait individuation in development and tracing these units across time. To delve deeper, I introduce extant functionalist and structuralist perspectives on trait individuation and evaluate how they address both challenges. Overcoming these challenges is necessary for such accounts to fulfill their theoretical promise of individuating the traits that organisms have in an ontologically sound way.

In recent years there have been a number of calls for integrating developmental and organismal phenomena into evolutionary theory. This so-called Extended Evolutionary Synthesis (EES) argues that evolutionary theory should not primarily explain certain evolutionary phenomena by highlighting genes and populations but organisms instead, in particular how their development and behavior biases and drives evolutionary change. Here, we offer a new historiography that focuses less on the differences between the EES and the Modern Synthesis but seeks to provide a better understanding about which theoretical and explanatory traditions the organism-centered framework of the EES draws on. This concerns especially three currently resurfacing explanatory roles granted to organisms in evolution: organisms should allow (1) contextualizing parts in development, especially genes, (2) focusing on reciprocal organism-environment relations (in contrast to, e.g., gene-environment interactions), and (3) understand the role of agency in evolution. Through this analysis, we show that the EES advances a revival of older explanatory roles granted to the organism in evolutionary research, which became marginalized in the second half of the twentieth century. This new perspective helps to re-center contemporary theoretical debates towards relevant questions of explanatory standards in evolutionary biology.

The research programme ‘basal cognition’ adopts an evolutionary perspective for studying biological cognition. This entails investigating possible cognitive processes in ‘simple’–often non-neuronal–organisms as a means to discover conserved mechanisms and adaptive capacities underwriting cognition in more complex (neuronal) organisms. However, by pulling in the opposite direction of a tradition that views cognition as something that is unique to neuronal organisms, basal cognition has been met with a fair amount of scepticism by philosophers and scientists. The very idea of approaching cognition by way of investigating the behaviour and underlying mechanisms in, say, bacteria, has been seen as preposterous and harmful to both cognitive science and biology. This paper aims to temper such scepticism to a certain degree by drawing parallels with how the evolution of ‘development,’ another loaded concept that refers to a not-so-easily definable, contested bundle of phenomena, has been fruitfully approached in Evolutionary Developmental Biology (Evo-Devo). Through this comparison, we identify four promising features of the basal cognition approach. These features suggest that sweeping scepticism may be unwarranted. However, each of them comes with important epistemic cautionary notes that should not be disregarded. By presenting these twofold considerations as potential ways to integrate a fully evolutionary perspective into basal cognition, this paper seeks to provide clarity and direction for the advancement of this research programme.

Niche construction is the process of organisms changing themselves or their environment—or their relationship with their environment—in ways that affect the evolutionary trajectory of their population. These evolutionary trajectory changes are traditionally understood to be triggered by changes in selection pressures. Niche construction thus necessarily involves organisms altering selection pressures. In this paper, we argue that changes in selection pressures is not the only way organisms can influence the evolutionary futures of their population. We propose that organisms can also affect drift probabilities, and that such changes should be considered niche construction. Drift probabilities can be modulated by altering population size or by affecting driftability (individual variance in possible reproductive outcomes). We consider both and provide examples of how niche construction can stabilize, increase, or dampen drift probabilities. Finally, we revisit and broaden the traditional definition of niche construction. We hold that organismic activities that modify drift probabilities should count as niche construction, even if selection pressures remain unaltered.

In a recent development of what may be called biological philosophy of science, scholars have proposed that aligning notions of research environments with biological concepts of environment holds great promise for understanding the socio-material contexts in and through which science happens. Here, I explore the prospects and potential shortcomings of building sound research environment concepts by contrasting them with biological environment concepts. In doing so, I emphasize the importance of adhering to two central desiderata: the need to clarify what is being environed (i.e., what the counter relatum of an environment is) and what is doing the environing (i.e., what type of environmental partition is instantiated). Subsequently, I juxtapose two biological construals of environment—organismal environments and population environments—with possible articulations of what ‘research environments’ might stand for, and I maintain that each presents distinct epistemic upshots and limitations. More generally, I argue that there are two broad relations that could exist between biological and research environments: ontological parallels and ontic discordance. Finally, employing the visual metaphor of epistemic parallax, I conclude by conveying some lessons and cautionary notes arising from these comparisons and the importation of biological environment concepts into philosophy of science. While environment concepts may come with epistemic purchase, we should be careful when ontologizing them.

The Riddle of Organismal Agency brings together historians, philosophers and scientists for an interdisciplinary re-assessment of one of the long-standing problems in the scientific understanding of life. Marshalling insights from diverse sciences including physiology, comparative psychology, developmental biology, and evolutionary biology, the book provides an up-to-date survey of approaches to non-human organisms as agents, capable of performing activities serving their own goals such as surviving or reproducing, and whose doings in the world are thus to be explained teleologically. From an Integrated History and Philosophy of Science perspective, the book contributes to a better conceptual and theoretical understanding of organismal agency, advancing some suggestions on how to study it empirically and how to frame it in relation to wider scientific and philosophical traditions. It also provides new historical entry points for examining the deployment, trajectories and challenges of agential views of organisms in the history of biology and philosophy. This book will be of interest to philosophers of biology; historians of science; biologists interested in analysing the active roles of organisms in development, ecological interactions, and evolution; philosophers and practitioners of the cognitive sciences; and philosophers and historians of philosophy working on purposiveness and teleology.

In recent years, biologists and philosophers of science have argued that evolutionary theory should incorporate more seriously the idea of ‘reciprocal causation.’ This notion refers to feedback loops whereby organisms change their experiences of the environment or alter the physical properties of their surroundings. In these loops, in particular niche constructing activities are central, since they may alter selection pressures acting on organisms, and thus affect their evolutionary trajectories. This paper discusses long-standing problems that emerge when studying such reciprocal causal processes between organisms and environments. By comparing past approaches to reciprocal causation from the early twentieth century with contemporary ones in niche construction theory, we identify two central reoccurring problems: All of these approaches have not been able to provide a conceptual framework that allows maintaining meaningful boundaries between organisms and environments, instead of merging the two, and integrating experiential and physical kinds of reciprocal causation. By building on case studies of niche construction research, we provide a model that is able to solve these two problems. It allows distinguishing between mutually interacting organisms and environments in complex scenarios, as well as integrating various forms of experiential and physical niche construction.

Dietary changes can alter the human microbiome with potential detrimental consequences for health. Given that environment, health, and evolution are interconnected, we ask: Could diet‐driven microbiome perturbations have consequences that extend beyond their immediate impact on human health? We address this question in the context of the urgent health challenges posed by global climate change. Drawing on recent studies, we propose that not only can diet‐driven microbiome changes lead to dysbiosis, they can also shape life‐history traits and fuel human evolution. We posit that dietary shifts prompt mismatched microbiome‐host genetics configurations that modulate human longevity and reproductive success. These mismatches can also induce a heritable intra‐holobiont stress response, which encourages the holobiont to re‐establish equilibrium within the changed nutritional environment. Thus, while mismatches between climate change‐related genetic and epigenetic configurations within the holobiont increase the risk and severity of diseases, they may also affect life‐history traits and facilitate adaptive responses. These propositions form a framework that can help systematize and address climate‐related dietary challenges for policy and health interventions.

Against the common historiographic narratives of evolutionary biology, the first decades of the 20th century were theoretically far richer than usually assumed. This especially refers to the hitherto neglected role that early theoretical biologists played in introducing visionary research perspectives and concepts before the institutionalization of the Modern Synthesis. Here, we present one of these scholars, the German theoretical biologist and ecomorphologist Hans Böker, by reviewing his 1935 paper “Artumwandlung durch Umkonstruktion, Umkonstruktion durch aktives Reagieren der Organismen”, published in the inaugural volume of the journal Acta Biotheoretica. While largely forgotten today, this work represents a melting pot of ideas that adumbrate some of today’s most lively debated empirical and conceptual topics in evolutionary biology: the active role of organisms as actors of their own evolution, environmental induction and phenotypic plasticity, genetic assimilation, as well as developmental bias. We discuss Böker’s views on how species change through "Umkonstruktion," and how such reconstruction is exerted through active reactions of organisms to environmental perturbations. In addition, we outline the aims and wider context of his "biological comparative anatomy," including Boker’s reprehensible political affiliation with the Nazi Party. Finally, we highlight some of the historical reasons for why Böker’s views did not have a larger impact in evolutionary biology, but we also recount some of the direct and indirect legacies of his approach in research areas such as ecomorphology and EvoDevo. Böker’s paper is available as supplementary material in the online version of this article, as part of the journal's "Classics in Biological Theory" collection; the first translation of the paper into English, by Alexander Böhm and Jan Baedke, is also being published in this volume.

Biologists and philosophers of science have recently called for an extension of evolutionary theory. This so-called ‘extended evolutionary synthesis’ seeks to integrate developmental processes, extra-genetic forms of inheritance, and niche construction into evolutionary theory in a central way. While there is often agreement in evolutionary biology over the existence of these phenomena, their explanatory relevance is questioned. Advocates of EES posit that their perspective offers better explanations than those provided by ‘standard evolutionary theory’. Still, why this would be the case is unclear. Usually, such claims assume that EES’s superior explanatory status arises from the pluralist structure of EES, its different problem agenda, and a growing body of evidence for the evolutionary relevance of developmental phenomena. However, what is usually neglected in this debate is a discussion of what the explanatory standards of EES actually are, and how they differ from prevailing standards in SET. In other words, what is considered to be a good explanation in EES versus SET? To answer this question, we present a theoretical framework that evaluates the explanatory power of different evolutionary explanations of the same phenomena. This account is able to identify criteria for why and when evolutionary explanations of EES are better than those of SET. Such evaluations will enable evolutionary biology to find potential grounds for theoretical integration.

Contemporary evolutionary biology comprises a plural landscape of multiple co-existent conceptual frameworks and strenuous voices that disagree on the nature and scope of evolutionary theory. Since the mid-eighties, some of these conceptual frameworks have denounced the ontologies of the Modern Synthesis and of the updated Standard Theory of Evolution as unfinished or even flawed. In this paper, we analyze and compare two of those conceptual frameworks, namely Niles Eldredge’s Hierarchy Theory of Evolution (with its extended ontology of evolutionary entities) and the Extended Evolutionary Synthesis (with its proposal of an extended ontology of evolutionary processes), in an attempt to map some epistemic bridges (e.g. compatible views of causation; niche construction) and some conceptual rifts (e.g. extra-genetic inheritance; different perspectives on macroevolution; contrasting standpoints held in the “externalism–internalism” debate) that exist between them. This paper seeks to encourage theoretical, philosophical and historiographical discussions about pluralism or the possible unification of contemporary evolutionary biology.

The Extended Evolutionary Synthesis (EES) debate is gaining ground in contemporary evolutionary biology. In parallel, a number of philosophical standpoints have emerged in an attempt to clarify what exactly is represented by the EES. For Massimo Pigliucci, we are in the wake of the newest instantiation of a persisting Kuhnian paradigm; in contrast, Telmo Pievani has contended that the transition to an EES could be best represented as a progressive reformation of a prior Lakatosian scientific research program, with the extension of its Neo-Darwinian core and the addition of a brand-new protective belt of assumptions and auxiliary hypotheses. Here, we argue that those philosophical vantage points are not the only ways to interpret what current proposals to ‘extend’ the Modern Synthesis-derived ‘standard evolutionary theory’ (SET) entail in terms of theoretical change in evolutionary biology. We specifically propose the image of the emergent EES as a vast network of models and interweaved representations that, instantiated in diverse practices, are connected and related in multiple ways. Under that assumption, the EES could be articulated around a paraconsistent network of evolutionary theories (including some elements of the SET), as well as models, practices and representation systems of contemporary evolutionary biology, with edges and nodes that change their position and centrality as a consequence of the co-construction and stabilization of facts and historical discussions revolving around the epistemic goals of this area of the life sciences. We then critically examine the purported structure of the EES—published by Laland and collaborators in 2015—in light of our own network-based proposal. Finally, we consider which epistemic units of Evo-Devo are present or still missing from the EES, in preparation for further analyses of the topic of explanatory integration in this conceptual framework.