The paper begins with a retrospective of the debates on the origin of life: the virus or the cell? The virus needs a cell for replication, instead the cell is a more evolved form on the evolutionary scale of life. In addition, the study of viruses raises pressing conceptual and philosophical questions about their nature, their classification, and their place in the biological world. The subject of pandemics is approached starting from the existentialism of Albert Camus and Sartre, the replacement (...) of the exclusion ritual with the disciplinary mechanism of Michel Foucault, and about the Gaia hypothesis, developed by James Lovelock and supported in the current pandemic by Bruno Latour. The social dimensions of pandemics, their connection to global warming, which has led to an increase in infectious diseases, and the deforestation of large areas, which have caused viruses to migrate from their native area (their "reservoir") are highlighted below. The ethics of pandemics is approached from several philosophical points of view, of which the most important in a crisis of such global dimensions is utilitarianism which involves maximizing benefits for society in direct conflict with the usual (Kantian) view of respect for people as individuals. After a retrospective of the COVID-19 virus that caused the current pandemic, its life cycle and its history, with an emphasis on the philosophy of death, the concept of biopower initially developed by Foucault is discussed, with reference to the practice of modern states of control of the populations and the debate generated by Giorgio Agamben who states that what is manifested in this pandemic is the growing tendency to use the state of emergency as a normal paradigm of government. An interesting and much debated approach is the one generated by the works of Slavoj Žižek, who states that the current pandemic has led to the bankruptcy of the current "barbaric" capitalism, wondering if the path that humanity will take is a neo-communism. Another important negative effect is desocialization, with the conclusion of some philosophers that we cannot exist independently of our relationships with others, that a person's humanity depends on the humanity of those around him. The last section is dedicated to forecasting what the world will look like after the pandemic, and there are already signs of a paradigm shift, including the sudden disappearance of the "wall" ideology: a cough was enough to make it suddenly impossible to avoid the responsibility that every individual has it towards all living beings for the simple fact that he is part of this world, and of the desire to be part of it. The whole is always involved in part, because everything is, in a sense, in everything and in nature there are no autonomous regions that are an exception. The COVID-19 pandemic seems to restore the supremacy that once belonged to politics. One of the virtues of the virus is its ability to generate a more sober idea of ​​freedom: to be free means to do what needs to be done in a specific situation. -/- CONTENTS: -/- Abstract Introduction 1 Viruses 1.1 Ontology 2 Pandemics 2.1 Social dimensions 2.2 Ethics 3 COVID-19 3.1 Biopolitics 3.2 Neocommunism 3.3 Desocialising 4 Forecasting Bibliography -/- DOI: 10.13140/RG.2.2.31039.74405/1. (shrink)

Lucrarea debutează cu o retrospectivă a dezbaterilor privind originea vieții: virusul sau celula? Virusul are nevoie de celulă pentru replicare, în schimb celula este o formă mai evoluată pe scara evoluționistă a vieții. În plus, studiul virușilor ridică întrebări conceptuale și filozofice presante despre natura lor, clasificarea lor, și locul lor în lumea biologică. Subiectul pandemiilor este abordat pornind de la existențialismul lui Albert Camus și Sartre, înlocuirea ritualului de excludere cu mecanismul disciplinar al lui Michel Foucault, și despre ipoteza (...) Gaia, dezvoltată de James Lovelock și susținută în actuala pandemie de Bruno Latour. În continuare sunt evidențiate dimensiunile sociale ale pandemiilor, legătura lor cu încălzirea globală care a dus la o creștere a bolilor infecțioase, și despădurirea unor zone întinse, care au determinat virușii să migreze din zona lor nativă („rezervorul” lor). Etica pandemiilor este abordată din mai multe puncte de vedere filosofice, din care cel mai important într-o criză de asemenea dimensiuni globale este utilitarismul care presupune maximizarea beneficiilor pentru societate în conflict direct cu viziunea obișnuită (kantiană) privind respectul față de persoane ca indivizi. După o retrospectivă a virusul COVID-19 care a cauzat actuala pandemie, a ciclului său de viață și a istoriei sale, cu accent pe filosofia morții, este discutat conceptul de bioputere dezvoltat inițial de Foucault, cu referire la practica statelor naționale moderne de control al populațiilor și dezbaterea generată de Giorgio Agamben care afirmă că ceea ce se manifestă în această pandemie este tendința crescândă de a folosi starea de excepție ca o paradigmă normală de guvernare. O altă abordare de interes și foarte dezbătută este cea generată de lucrările lui Slavoj Žižek, care afirmă că actuala pandemie a dus la falimentul actualului capitalism ”barbar”, întrebându-se dacă nu cumva drumul pe care îl va lua omenirea este un neo-comunism. Un alt efect negativ important este desocializarea, cu concluzia unor filosofi că nu putem exista independent de relațiile noastre cu ceilalți, că umanitatea unei persoane depinde de umanitatea celor din jurul ei. Ultima secțiune este dedicată previziunilor despre cum va arăta lumea după pandemie, existând deja semne ale unei schimbări de paradigmă, inclusiv dispariția bruscă a ideologiei legate de „ziduri”: o tuse a fost suficientă pentru a face dintr-o dată imposibilă evitarea responsabilității pe care fiecare individ o are față de toate ființele vii pentru simplul fapt că este parte a acestei lumi, și a dorinței de a fi parte a ei. Întregul este întotdeauna implicat în parte, pentru că totul este, într-un anumit sens, în tot și în natură nu există regiuni autonome care să constituie o excepție. Pandemia COVID-19 pare să restabilească supremația care a aparținut cândva politicii. Una din virtuțile virusului este capacitatea acestuia de a genera o idee mai sobră de libertate: a fi liber înseamnă a face ceea ce trebuie făcut într-o situație specifică. -/- CUPRINS: -/- Abstract Introducere 1 Viruși 1.1 Ontologia 2 Pandemii 2.1 Dimensiuni sociale 2.2 Etica 3 COVID-19 3.1 Biopolitica 3.2 Neocomunism 3.3 Desocializarea 4 Previziuni Bibliografie -/- DOI: 10.13140/RG.2.2.27611.39205 . (shrink)

Existing accounts of mechanistic causation are not suited for understanding causation in biological and neural mechanisms because they do not have the resources to capture the unique causal structure of control heterarchies. In this paper, we provide a new account on which the causal powers of mechanisms are grounded by time-dependent, variable constraints. Constraints can also serve as a key bridge concept between the mechanistic approach to explanation and underappreciated work in theoretical biology that sheds light on how biological systems (...) channel energy to actively respond to the environment in adaptive ways, perform work, and fulfill the requirements to maintain themselves far from equilibrium. We show how the framework applies to several concrete examples of control in simple organisms as well as the nervous system of complex organisms. (shrink)

In their paper “How Causal are Microbiomes? A Comparison with the Helicobacter pylori Explanation of Ulcers,” Lynch, Parke, and O’Malley successfully argue that certain causal attributions made to the microbiome have not satisfied Koch’s postulates nor the interventionist framework. However, their argument involves an implicit assumption that cases such as H. pylori are sufficiently similar to cases involving the microbiome, such that causal attributions to both should be evaluated according to the same causal framework. Our commentary targets this assumption. First, (...) we introduce the historical circumstances that led to the formulation of Koch’s postulates in order to differentiate the case of the microbiome from that of infectious bacteria. Then, we introduce the concept of the holobiont, the idea that hosts and their symbionts should be conceptualized as a metaphysical and biological unit. Finally, using the holobiont concept, we argue that Koch’s postulates and the interventionist framework are ill-equipped to handle the microbiome. We conclude by suggesting that a revision of what counts as microbiological causality within the holobiont is justified. (shrink)

Phylogenetic models traditionally represent the history of life as having a strictly-branching tree structure. However, it is becoming increasingly clear that the history of life is often not strictly-branching; lateral gene transfer, endosymbiosis, and hybridization, for example, can all produce lateral branching events. There is thus motivation to allow phylogenetic models to have a reticulate structure. One proposal involves the reconciliation of genealogical discordance. Briefly, this method uses patterns of disagreement – discordance – between trees of different genes to add (...) lateral branching events to phylogenetic trees of taxa, and to estimate the most likely cause of these events. I use this practice to argue for: (1) a need for expanded accounts of multiple-models idealization, (2) a distinction between automatic and manual de-idealization, and (3) recognition that idealization may serve the meso-level aims of science in a different way than hitherto acknowledged. (shrink)

On the basis of findings from developmental biology, some researchers have argued that evolutionary theory needs to be significantly updated. Advocates of such a “developmental update” have, among other things, suggested that we need to re-conceptualize units of selection, that we should expand our view of inheritance to include environmental as well as genetic and epigenetic factors, that we should think of organisms and their environment as involved in reciprocal causation, and that we should reevaluate the rates of evolutionary change. (...) However, many of these same conclusions could be reached on the basis of other evidence, namely from microbiology. In this paper, I ask why microbiological evidence has not had a similarly large influence on calls to update biological theory, and argue that there is no principled reason to focus on developmental as opposed to microbiological evidence in support of these revisions to evolutionary theory. I suggest that the focus on developmental biology is more likely attributable to historical accident. I will also discuss some possible room for overlap between developmental and microbiology, despite the historical separation of these two subdisciplines. (shrink)

If there is a single discipline of science calling the basic concepts of biology into question, it is without doubt microbiology. Indeed, developments in microbiology have recently forced us to rethink such fundamental concepts as the organism, individual, and genome. In this paper I show how microorganisms are changing our understanding of natural aggregations and develop the concept of a Darwinian population to embrace these discoveries. I start by showing that it is hard to set the boundaries of a Darwinian (...) population, and I suggest thinking of a Darwinian population as a relative property of a Darwinian individual. Then I argue, in contrast to the commonly held view, that Darwinian populations are multispecies units, and that in order to accept the multispecies account of Darwinian populations we have to separate fitness from natural selection. Finally, I show how all these ideas provide a theoretical framework leading to a more precise understanding of the ecology of endosymbiosis than is afforded by poetic metaphors such as ‘slavery’. (shrink)

Contemporary biology has inherited two key assumptions from the Modern Synthesis about the nature of population lineages: sexual reproduction is the exemplar for how individuals in population lineages inherit traits from their parents, and random mating is the exemplar for reproductive interaction. While these assumptions have been extremely fruitful for a number of fields, such as population genetics and phylogenetics, they are increasingly unviable for studying the full diversity and evolution of life. I introduce the “mixture” account of population lineages (...) that escapes these assumptions by dissolving the Modern Synthesis’s sharp line separating reproduction and development and characterizing reproductive integration in population lineages by the ephemerality of isolated subgroups rather than random mating. The mixture account provides a single criterion for reproductive integration that accommodates both sexual and asexual reproduction, unifying their treatment under Kevin de Queiroz’s generalized lineage concept of species. The account also provides a new basis for empirically assessing the effect of random mating as an idealization on the empirical adequacy of population genetic models. (shrink)

Both concepts of the holobiont and the immune system are at the heart of an ongoing scientific and philosophical examination concerning questions of the organism’s individuality and identity as well as the relations between organisms and their environment. Examining the holobiont, the question of boundaries and individuality is challenging because it is both an assemblage of organisms with physiological cohesive aspects. I discuss the concept of immunity and the immune system function from the holobiont perspective. Because of the host-microbial close (...) relations of codependence and interdependence, the holobiont is more often than not confused with the host, as the host is the domain in which this entity exists. I discuss the holobiont unique ecological characteristics of microbial assemblages connected to a host in a network of interactions in which the host is one of the organisms in the community but also its landscape. Therefore, I suggest viewing the holobiont as a host-ecosystem and discuss the implication of such a view on the concept of immunity and the meaning of protection. Furthermore, I show that viewing the holobiont as a host ecosystem opens the possibility of using the same ecological definition of boundaries and immunity dealing with an ecological system. Thus, the holobiont’s boundaries and immunity are defined by the persistence of its complex system of interactions integrating existing and new interactions. This way of thinking presents a notion of immunity that materializes as the result of the complex interdependence relations between the different organisms composing the holobiont similar to that of an ecosystem. Taking this view further, I discuss the notion of immunogenicity that is ontologically heterogeneous with various causal explanations of the processes of tolerance and targeted immune response. Finally, I discuss the possible conceptualization of already existing and new biomedical practices. (shrink)

While unicellular microbes such as phytoplankton (marine algae) have long been considered immortal unless eaten by predators, recent research suggests that under specific conditions entire populations of phytoplankton actively kill themselves; their assumed atemporality is being revised as marine ecologists recognize phytoplankton’s important role in the global carbon cycle. Drawing on empirical research into programmed cell death in marine microbes, this article explores how, in their study of microbial death, scientists change not only our understanding of microbial temporality, but also (...) reconstruct the relationship between life and death, biological individuality and assumptions about a natural teleology associated with bounded biological systems and genetic programmes. Reading this research together with a Derridean deconstruction of the limit between human and other animals with respect to death, this article explores how the deconstruction of individuality from within biology may suggest alternatives to our anthropocentric notion of time and embodiment. (shrink)

Philosophers use historical case studies to support wide-ranging claims about science. This practice is often criticized as problematic. In this paper we suggest that the function of case studies can be understood and justified by analogy to a well-established practice in biology: the investigation of model organisms. We argue that inferences based on case studies are no more problematic than inferences from model organisms to larger classes of organisms in biology. We demonstrate our view in detail by reference to a (...) case study with a long history: Semmelweis’s discovery of the cause of childbed fever. (shrink)

Which domains of biology do philosophers of biology primarily study? The fact that philosophy of biology has been dominated by an interest for evolutionary biology is widely admitted, but it has not been strictly demonstrated. Here I analyse the topics of all the papers published in Biology & Philosophy, just as the journal celebrates its thirtieth anniversary. I then compare the distribution of biological topics in Biology & Philosophy with that of the scientific journal Proceedings of the National Academy of (...) Science of the USA, focusing on the recent period 2003–2015. This comparison reveals a significant mismatch between the distributions of these topics. I examine plausible explanations for that mismatch. Finally, I argue that many biological topics underrepresented in philosophy of biology raise important philosophical issues and should therefore play a more central role in future philosophy of biology. (shrink)

Viruses have been virtually absent from philosophy of biology. In this editorial introduction, we explain why we think viruses are philosophically important. We focus on six issues, and we show how they relate to classic questions of philosophy of biology and even general philosophy.

This paper analyzes recent attempts to reject reproduction with lineage formation as a necessary condition for evolution by means of natural selection :560–570, 2008; Stud Hist Philos Sci Part C Stud Hist Philos Biol Biomed Sci 42:106–114, 2011; Bourrat in Biol Philos 29:517–538, 2014; Br J Philos Sci 66:883–903, 2015; Charbonneau in Philos Sci 81:727–740, 2014; Doolittle and Inkpen in Proc Natl Acad Sci 115:4006–4014, 2018). Building on the strengths of these attempts and avoiding their pitfalls, it is argued that (...) a robust formulation of evolution by natural selection without reproduction can be established. The main contribution of this paper is a reformulation of Lewontin’s three principles stating that minimal evolution by natural selection occurs when two conditions are met in a population: fitness-related variation and memory. Paradigmatic evolution by natural selection, which can generate adaptations, takes place when an additional condition is present, namely regeneration. (shrink)

. Early microbiome research found numerous associations between microbial community patterns and host physiological states. These findings hinted at community-level explanations. “Top-down” experiments, working with whole communities, strengthened these explanatory expectations. Now, “bottom-up” mechanism-seeking approaches are dissecting communities to focus on specific microbes carrying out particular biochemical activities. To understand the interplay between methodological and explanatory scales, we examine claims of “dysbiosis,” when host illness is proposed as the consequence of a community state. Our analysis concludes with general observations about (...) how methodologies relate to explanations, and the implications for microbiome research. (shrink)

Contrary to the common-sense view and positivist aspirations, scientific concepts are often imprecise. Many of these concepts are ambiguous, vague, or have an under-specified meaning. In this paper, I discuss how imprecise concepts promote integration in biology and thus benefit science. Previous discussions of this issue focus on the concepts of molecular gene and evolutionary novelty. The concept of molecular gene helps biologists integrate explanatory practices, while the notion of evolutionary novelty helps them integrate research questions into an interdisciplinary problem (...) New directions in the philosophy of science, Springer, Dordrecht, 2014). In what follows, I compare molecular gene and evolutionary novelty to another imprecise concept, namely biological lineage. This concept promotes two other types of scientific integration: it helps biologists integrate theoretical principles and methodologies into different areas of biology. The concept of biological lineage facilitates these types of integration because it is broad and under-specified in ways that the concepts of molecular gene and evolutionary novelty are not. Hence, I use the concept of biological lineage as a case study to reveal types of integration that have been overlooked by philosophers. This case study also shows that even very imprecise concepts can be beneficial to scientific practice. (shrink)

In a pioneering book, Philosophy of Microbiology, Maureen O’Malley argues for the philosophical importance of microbes through an examination of their impact on ecosystems, evolution, biological classification, collaborative behavior, and multicellular organisms. She identifies many understudied conceptual issues in the study of microbes. If philosophers follow her lead, the philosophy of biology will be expanded and enriched.

The history of twentieth-century life sciences is not exactly a new topic. However, in view of the increasingly rapid development of the life sciences themselves over the past decades, some of the well-established narratives are worth revisiting. Taking stock of where we stand on these issues was the aim of a conference in 2015, entitled “Perspectives for the History of Life Sciences”. The papers in this topical collection are based on work presented and discussed at and around this meeting. Just (...) as the conference, the collection aims at exploring fields in the history of life sciences that appear understudied, sources that have been overlooked, and novel ways of engaging with this material. The papers convened in this collection may not be representative of the field as a whole; but we feel that they do indicate some elements that have received emphasis in recent years, and may become more central in the years to come, such as the history of previously neglected contexts and domains of the life sciences, the question of continuity and change on the level of practices, the history of complexity and diversity in twentieth-century life sciences and the reconsideration of the relationship between history and philosophy of life sciences. (shrink)

The definitions and conceptualizations of health, and the management of healthcare have been challenged by the current global scenarios (e.g., new diseases, new geographical distribution of diseases, effects of climate change on health, etc.) and by the ongoing scholarship in humanities and science. In this paper we question the mainstream definition of health adopted by the WHO—‘a state of complete physical, mental and social well-being and not merely the absence of disease or infirmity’ (WHO in Preamble to the constitution of (...) the World Health Organization as adopted by the international health conference, The World Health Organization, 1948)—and its role in providing tools to understand what health is in the contemporary context. More specifically, we argue that this context requires to take into account the role of the environment both in medical theory and in the healthcare practice. To do so, we analyse WHO documents dated 1984 and 1986 which define health as ‘coping with the environment’. We develop the idea of ‘coping with the environment’, by focusing on two cardinal concepts: adaptation in public health and adaptivity in philosophy of biology. We argue that the notions of adaptation and adaptivity can be of major benefit for the characterization of health, and have practical implications. We explore some of these implications by discussing two recent case studies of adaptivity in public health, which can be valuable to further develop adaptive strategies in the current pandemic scenario: community-centred care and microbiologically healthier buildings. (shrink)

This article uses the case study of ethnobiological classification to develop a positive and a negative thesis about the state of natural kind debates. On the one hand, I argue that current accounts of natural kinds can be integrated in a multidimensional framework that advances understanding of classificatory practices in ethnobiology. On the other hand, I argue that such a multidimensional framework does not leave any substantial work for the notion “natural kind” and that attempts to formulate a general account (...) of naturalness have become an obstacle to understanding classificatory practices. (shrink)

Biologists who work on the pig (_Sus scrofa_) take advantage of its similarity to humans by constructing the inferential and material means to traffic data, information and knowledge across the species barrier. Their research has been funded due to its perceived value for agriculture and medicine. Improving selective breeding practices, for instance, has been a driver of genomics research. The pig is also an animal model for biomedical research and practice, and is proposed as a source of organs for cross-species (...) transplantation: xenotransplantation. Genomics research has informed transplantation biology, which has itself motivated developments in genomics. Both have generated models of correspondences between the genomes of pigs and humans. Concerning genomics, I detail how researchers traverse species boundaries to develop representations of the pig genome, alongside ensuring that such representations are sufficiently porcine. In transplantation biology, the representations of the genomes of humans and pigs are used to detect and investigate immunologically-pertinent differences between the two species. These key differences can then be removed, to ‘humanise’ donor pigs so that they can become a safe and effective source of organs. In both of these endeavours, there is a tension between practices that ‘humanise’ the pig (or representations thereof) through using resources from human genomics, and the need to ‘dehumanise’ the pig to maintain distinctions for legal, ethical and scientific reasons. This paper assesses the ways in which this tension has been managed, observing the differences between its realisations across comparative pig genomics and transplantation biology, and considering the consequences of this. (shrink)

Godfrey-Smith’s environmental complexity thesis is most often applied to multicellular animals and the complexity of their macroscopic environments to explain how cognition evolved. We think that the ECT may be less suited to explain the origins of the animal bodily organization, including this organization’s potentiality for dealing with complex macroscopic environments. We argue that acquiring the fundamental sensorimotor features of the animal body may be better explained as a consequence of dealing with internal bodily—rather than environmental complexity. To press and (...) elucidate this option, we develop the notion of an animal sensorimotor organization that derives from an internal coordination account for the evolution of early nervous systems. The ASMO notion is a reply to the question how a collection of single cells can become integrated such that the resulting multicellular organization becomes sensitive to and can manipulate macroscopic features of both the animal body and its environment. In this account, epithelial contractile tissues play the central role in the organization behind complex animal bodies. In this paper, we relate the ASMO concept to recent work on epithelia, which provides empirical evidence that supports central assumptions behind the ASMO notion. Second, we discuss to what extent the notion applies to basic animal architectures, exemplified by sponges and jellyfish. We conclude that the features exhibited by the ASMO are plausibly explained by internal constraints acting on and within this multicellular organization, providing a challenge for the role the ECT plays in this context. (shrink)

The human microbiome is changing the way experts and non-experts think about germs and microorganisms. This essay is a gender analysis of contemporary discourses surrounding the human reproductive microbiome, specifically the vaginal microbiota and the penile microbiota. I first historically situate the human reproductive microbiome within the germ theory of disease. Then, I draw on Heather Paxson’s Foucauldian and Latourian concept of microbiopolitics to argue that microbiopolitics is not only about how humans should live with microorganisms; but it also impacts (...) how humans and microbes live together as gendered beings. I illustrate this gendering through two figures: the microbial mother and the independent organ. (shrink)

Biological lineages move through time, space, and each other. As they do, they diversify, diverge, and grade away from and into one another. One result of this is genealogical discordance; i.e., the lineages of a biological entity may have different histories. We see this on numerous levels, from microbial networks, to holobionts, to population-level lineages. This paper considers how genealogical discordance impacts our study of species. More specifically, I consider this in the context of three framing questions: (1) How, if (...) at all, does genealogical discordance challenge, modify, or revise how we conceive of species? (2) How has growing appreciation of genealogical discordance impacted scientific practice? Of systematics in particular? (3) How do lineages at different levels diverge and diversify? All told, genealogical discordance enriches and complicates our taxonomic ontology, as well as the practice of reconstructing phylogenies. This presents both challenges and opportunities for the study of divergence and diversification. (shrink)

We present two case studies from contemporary biology in which we observe conflicts between established and emerging approaches. The first case study discusses the relation between molecular biology and systems biology regarding the explanation of cellular processes, while the second deals with phylogenetic systematics and the challenge posed by recent network approaches to established ideas of evolutionary processes. We show that the emergence of new fields is in both cases driven by the development of high-throughput data generation technologies and the (...) transfer of modeling techniques from other fields. New and emerging views are characterized by different philosophies of nature, i.e. by different ontological and methodological assumptions and epistemic values and virtues. This results in a kind of conflict we call “epistemic competition” that manifests in two ways: On the one hand, opponents engage in mutual critique and defense of their fundamental assumptions. On the other hand, they compete for the acceptance and integration of the knowledge they provide by a broader scientific community. Despite an initial rhetoric of replacement, the views as well as the respective audiences come to be seen as more clearly distinct during the course of the debate. Hence, we observe—contrary to many other accounts of scientific change—that conflict results in the formation of new niches of research, leading to co-existence and perceived complementarity of approaches. Our model thus contributes to the understanding of the pluralization of the scientific landscape. (shrink)

Microbial diversity has become a leitmotiv of contemporary microbiology, as epitomized in the concept of the microbiome, with significant consequences for the classification of microbes. In this paper, I contrast microbiology’s current diversity ideal with its influential predecessor in the twentieth century, that of purity, as epitomized in Robert Koch’s bacteriological culture methods. Purity and diversity, the two polar opposites with regard to making sense of the microbial world, have been operationalized in microbiological practice by tools such as the “clean” (...) Petri dish versus the “dirty” Winogradsky column, the latter a container that mimics, in the laboratory, the natural environment that teems with diverse microbial life. By tracing the impact of the practices and concepts of purity and diversity on microbial classification through a history of techniques, tools, and manuals, I show the shifts in these concepts over the last century. Juxtaposing the dominant purity ideal with the more restricted, but continuously articulated, diversity ideal in microbial ecology not only provides a fresh perspective on microbial classification that goes beyond its intellectual history, but also contextualizes the present focus on diversity. By covering the period of a century, this paper outlines a revised longue durée historiography that takes its inspiration from artifacts, such as Petri dish and the Winogradsky column, and thereby simple, but influential technologies that often remain invisible. This enables the problem of historical continuity in modern science to be addressed and the accelerationist narratives of its development to be countered. (shrink)

Historical analyses of what metabolism has been conceived of, how concepts of metabolism were related to disciplines such as nineteenth-century nutritional physiology or twentieth-century biochemistry, and how their genealogies relate to the current developments may be helpful to understand the various, at times polemic, ways in which the boundaries between metabolism and heredity have been re-drawn. Against this background, a small number of scholars gathered in Berlin for a workshop that equally aimed at bringing new stories to the fore, and (...) at considering seemingly known ones in a new light. Some aspects of the discussions are summarized in this paper. (shrink)

The paper links discussions of two topics: biological individuality and the simplest forms of mentality. I discuss several attempts to locate the boundary between metabolic activity and ‘minimal cognition.’ I then look at differences between the kinds of individuality present in unicellular life, multicellular life in general, and animals of several kinds. Nervous systems, which are clearly relevant to cognition and subjectivity, also play an important role in the form of individuality seen in animals. The last part of the paper (...) links these biological transitions to the evolutionary history of subjective experience. (shrink)

Ontologies of living things are increasingly grounded on the concepts and practices of current life science. Biological development is a process, undergone by living things, which begins with a single cell and (in an important class of cases) ends with formation of a multicellular organism. The process of development is thus prima facie central for ideas about biological individuality and organismality. However, recent accounts of these concepts do not engage developmental biology. This paper aims to fill the gap, proposing the (...) lineage view of stem cells as an ontological framework for conceptualizing organismal development. This account is grounded on experimental practices of stem cell research, with emphasis on new techniques for generating biological organization in vitro. On the lineage view, a stem cell is the starting point of a cell lineage with a specific organismal source, time-interval of existence, and ‘tree topology’ of branch-points linking the stem to developmental termini. The concept of ‘enkapsis’ accommodates the cell-organism relation within the lineage view; this hierarchical notion is further explicated by considering the methods and results of stem cell experiments. Results of this examination include a (partial) characterization of stem cells’ developmental versatility, and the context-dependence of developmental processes involving stem cells. (shrink)

Whether we live in a world of autonomous things, or a world of interconnected processes in constant flux, is an ancient philosophical debate. Modern biology provides decisive reasons for embracing the latter view. How does one understand the practices and outputs of science in such a dynamic, ever-changing world - and particularly in an emergency situation such as the COVID-19 pandemic, where scientific knowledge has been regarded as bedrock for decisive social interventions? We argue that key to answering this question (...) is to consider the role of the activity of reification within the research process. Reification consists in the identification of more or less stable features of the flux, and treating these as constituting stable things. As we illustrate with reference to biological and biomedical research on COVID-19, reification is a necessary component of any process of inquiry and comes in at least two forms: means reification, when researchers create objects meant to capture features of the world, or phenomena, in order to be able to study them; and target reification, when researchers infer an understanding of phenomena from an investigation of the epistemic objects created to study them. We note that both objects and phenomena are dynamic processes and argue that have no reason to assume that changes in objects and phenomena track one another. We conclude that failure to acknowledge these forms of reification and their epistemic role in scientific inquiry can have dire consequences for how the resulting knowledge is interpreted and used. (shrink)

Microbes are generally thought of as unicellular organisms, but we know that many microbes live as parts of biofilms—complex, surface-attached microbial communities numbering millions of cells. Some authors have recently argued in favour of reconceiving biofilms as biological entities in their own right. In particular, some have claimed that multispecies biofilms are evolutionary individuals : 10126–10132 2015). Against this view, I defend the conservative consensus that selection acts primarily upon microbial cells.

There is currently a great debate about whether the holobiont, i.e. a multicellular host and its residential microorganisms, constitutes a biological individual. We propose that resident microorganisms have a general and important role in the individuality of the host organism, not the holobiont. Drawing upon the Equilibrium Model of Immunity, we argue that microorganisms are scaffolds of immune capacities and processes that determine the constituency and persistence of the host organism. A scaffolding perspective accommodates the contingency and heterogeneity of resident (...) microorganisms while accounting for their necessity and unifying contributions to host individuality. In our symbiotic view of life, holobionts may not be organisms or units of selection, but macroorganisms cannot persist nor function as individuals without their scaffolding microorganisms. (shrink)

The nature and role of the patient in biomedicine comprise issues central to bioethical inquiry. Given its developmental history grounded firmly in a backlash against 20th-century cases of egregious human subjects abuse, contemporary medical bioethics has come to rely on a fundamental assumption: the unit of care is the autonomous self-directing patient. In this article we examine first the structure of the feminist social critique of autonomy. Then we show that a parallel argument can be made against relational autonomy as (...) well, demonstrating how this second concept of autonomy fails to take sufficiently into account an array of biological determinants, particularly those from microbial biology. Finally, in light of this biological critique, we question whether or to what extent any relevant and meaningful view of autonomy can be recovered in the contemporary landscape of bioethics. (shrink)

The received view holds that there is a significant divide between full-blown representational states and so called ‘detectors’, which are mechanisms set off by specific stimuli that trigger a particular effect. The main goal of this paper is to defend the idea that many detectors are genuine representations, a view that I call ‘Strong Liberal Representationalism’. More precisely, I argue that ascribing semantic properties to them contributes to an explanation of behavior, guides research in useful ways and can accommodate misrepresentation.

Recent research on bacteria and other microorganisms has provided interesting insights into the nature of life, cooperation, evolution, individuality or species. In this paper, I focus on the capacity of bacteria to produce molecules that are usually classified as ’signals’ and I defend two claims. First, I argue that certain interactions between bacteria should actually qualify as genuine forms of communication. Second, I use this case study to revise our general theories of signaling. Among other things, I argue that a (...) plausible requirement for a state to qualify as a signal is that it is a minimal cause. (shrink)

The impressive variation amongst biological individuals generates many complexities in addressing the simple-sounding question what is a biological individual? A distinction between evolutionary and physiological individuals is useful in thinking about biological individuals, as is attention to the kinds of groups, such as superorganisms and species, that have sometimes been thought of as biological individuals. More fully understanding the conceptual space that biological individuals occupy also involves considering a range of other concepts, such as life, reproduction, and agency. There has (...) been a focus in some recent discussions by both philosophers and biologists on how evolutionary individuals are created and regulated, as well as continuing work on the evolution of individuality. (shrink)

Philosophy of immunology is a subfield of philosophy of biology dealing with ontological and epistemological issues related to the studies of the immune system. While speculative investigations and abstract analyses have always been part of immune theorizing, until recently philosophers have largely ignored immunology. Yet the implications for understanding the philosophical basis of organismal functions framed by immunity offer new perspectives on fundamental questions of biology and medicine. Developed in the context of history of medicine, theoretical biology, and medical anthropology, (...) philosophy of immunology differs from these related branches of study in its focus on traditional philosophical questions concerning identity, individuality, ecology, cognition, scientific methodology and theory construction. This broad agenda derives from immunology’s multifaceted research program that has developed from its initial clinical challenges of host defense, transplantation, autoimmunity, tumor immunology, and allergy. In addition to these well-established research areas, immunity is now understood to play a central role in other physiological functions, development, ecology, and evolutionary mechanics. Holding together these diverse domains of inquiry lie philosophical commitments oriented by organismal identity. In this regard, pertinent issues are raised concerning cognition (organization of immune perception and information processing), the character of individuality (framed by the ecological context of immune-mediated assimilation and rejection), and the dynamics of complex systems (understood as holistic systems biology). Indeed, immunology, in the context of cognitive science, evolutionary biology, environmental sciences, and development provides multi-focal perspectives for philosophy of science. (shrink)

This afterword to Species and Beyond provides some reflections on species, with special attention to what I think the most significant developments have been in the thinking of biologists and philosophers working on species over the past 25 years, as well as some bad jokes.

Ethnobiology has a long tradition of metaphysical debates about the “naturalness,” “objectivity”, “reality”, and “universality” of classifications. Especially the work of Brent Berlin has been influential in developing a “convergence metaphysics” that explains cross-cultural similarities of knowledge systems through shared recognition of objective discontinuities in nature. Despite its influence on the development of the field, convergence metaphysics has largely fallen out of favor as contemporary ethnobiologists tend to emphasize the locality and diversity of classificatory practices. The aim of this article (...) is twofold: First, I provide a historical account of the rise and fall of convergence metaphysics in ethnobiology. I show how convergence metaphysics emerged as an innovative theoretical program in the wake of the “cognitive revolution” and the “modern evolutionary synthesis” but failed to incorporate both theoretical insights and political concerns that gained prominence in the 1980s and 1990s. Second, I develop a positive proposal of how to engage with metaphysical issues in ethnobiology. By integrating traditional research on convergence of classifications with more nuanced accounts of distinctly local categories, a revamped metaphysics of ethnobiological classification can make substantial contributions to debates about ontological difference in anthropology and about the relation between applied and theoretical ethnobiology. (shrink)

In this review, we describe some of the central philosophical issues facing origins-of-life research and provide a targeted history of the developments that have led to the multidisciplinary field of origins-of-life studies. We outline these issues and developments to guide researchers and students from all fields. With respect to philosophy, we provide brief summaries of debates with respect to (1) definitions (or theories) of life, what life is and how research should be conducted in the absence of an accepted theory (...) of life, (2) the distinctions between synthetic, historical, and universal projects in origins-of-life studies, issues with strategies for inferring the origins of life, such as (3) the nature of the first living entities (the “bottom up” approach) and (4) how to infer the nature of the last universal common ancestor (the “top down” approach), and (5) the status of origins of life as a science. Each of these debates influences the others. Although there are clusters of researchers that agree on some answers to these issues, each of these debates is still open. With respect to history, we outline several independent paths that have led to some of the approaches now prevalent in origins-of-life studies. These include one path from early views of life through the scientific revolutions brought about by Linnaeus (von Linn.), Wöhler, Miller, and others. In this approach, new theories, tools, and evidence guide new thoughts about the nature of life and its origin.We also describe another family of paths motivated by a” circularity” approach to life, which is guided by such thinkers as Maturana & Varela, Gánti, Rosen, and others. These views echo ideas developed by Kant and Aristotle, though they do so using modern science in ways that produce exciting avenues of investigation. By exploring the history of these ideas, we can see how many of the issues that currently interest us have been guided by the contexts in which the ideas were developed. The disciplinary backgrounds of each of these scholars has influenced the questions they sought to answer, the experiments they envisioned, and the kinds of data they collected. We conclude by encouraging scientists and scholars in the humanities and social sciences to explore ways in which they can interact to provide a deeper understanding of the conceptual assumptions, structure, and history of origins-of-life research. This may be useful to help frame future research agendas and bring awareness to the multifaceted issues facing this challenging scientific question. (shrink)

L'étude des virus soulève des questions conceptuelles et philosophiques pressantes sur leur nature, leur classification et leur place dans le monde biologique. Un ensemble majeur de problèmes concerne l'individualité et l'identité diachronique d'un virus: qu'est-ce que le virus, la particule virale (virion) ou l'ensemble du cycle viral? L'identification correcte du virus a des conséquences ontologiques importantes, également liées au lieu et au moment où les entités biologiques commencent et se terminent. DOI: 10.13140/RG.2.2.32904.24327.

Studiul virușilor ridică întrebări conceptuale și filozofice presante despre natura lor, clasificarea lor, și locul lor în lumea biologică. Un set major de probleme se referă la individualitatea și identitatea diacronică a unui virus: ce anume este virusul, particula virală (virionul) sau întregul ciclu viral? Identificarea corectă a virusului are consecințe ontologice semnificative, legate și de locul și momentul în care încep și se termină entitățile biologice. DOI: 10.13140/RG.2.2.29715.09760.

The study of viruses raises pressing conceptual and philosophical questions about their nature, their classification, and their place in the biological world. A major set of problems concerns the individuality and diachronic identity of a virus: what is the virus, the viral particle (virion) or the entire viral cycle? The correct identification of the virus has significant ontological consequences, also related to the place and time when biological entities begin and end. DOI: 10.13140/RG.2.2.35874.66241.

In this chapter, I am concerned with the concept of Intra-individual Genetic Hetereogeneity (IGH) and its potential influence on biodiversity estimates. Definitions of biological individuality are often indirectly dependent on genetic sampling -and vice versa. Genetic sampling typically focuses on a particular locus or set of loci, found in the the mitochondrial, chloroplast or nuclear genome. If ecological function or evolutionary individuality can be defined on the level of multiple divergent genomes, as I shall argue is the case in IGH, (...) our current genetic sampling strategies and analytic approaches may miss out on relevant biodiversity. Now that more and more examples of IGH are available, it is becoming possible to investigate the positive and negative effects of IGH on the functioning and evolution of multicellular individuals more systematically. I consider some examples and argue that studying diversity through the lens of IGH facilitates thinking not in terms of units, but in terms of interactions between biological entities. This, in turn, enables a fresh take on the ecological and evolutionary significance of biological diversity. (shrink)