We address three fundamental questions: What does it mean for an entity to be living? What is the role of inter-organismic collaboration in evolution? What is a biological individual? Our central argument is that life arises when lineage-forming entities collaborate in metabolism. By conceiving of metabolism as a collaborative process performed by functional wholes, which are associations of a variety of lineage-forming entities, we avoid the standard tension between reproduction and metabolism in discussions of life – a tension particularly evident (...) in discussions of whether viruses are alive. Our perspective assumes no sharp distinction between life and non-life, and does not equate life exclusively with cellular or organismal status. We reach this conclusion through an analysis of the capabilities of a spectrum of biological entities, in which we include the pivotal case of viruses as well as prions, plasmids, organelles, intracellular and extracellular symbionts, unicellular and multicellular life-forms. The usual criterion for classifying many of the entities of our continuum as non-living is autonomy. This emphasis on autonomy is problematic, however, because even paradigmatic biological individuals, such as large animals, are dependent on symbiotic associations with many other organisms. These composite individuals constitute the metabolic wholes on which selection acts. Finally, our account treats cooperation and competition not as polar opposites but as points on a continuum of collaboration. We suggest that competitive relations are a transitional state, with multi-lineage metabolic wholes eventually outcompeting selfish competitors, and that this process sometimes leads to the emergence of new types or levels of wholes. Our view of life as a continuum of variably structured collaborative systems leaves open the possibility that a variety of forms of organized matter – from chemical systems to ecosystems – might be usefully understood as living entities. (shrink)

The Tree of Life has traditionally been understood to represent the history of species lineages. However, recently researchers have suggested that it might be better interpreted as representing the history of cellular lineages, sometimes called the Tree of Cells. This paper examines and evaluates reasons offered against this cellular interpretation of the Tree of Life. It argues that some such reasons are bad reasons, based either on a false attribution of essentialism, on a misunderstanding of the problem of lineage identity, (...) or on a limited view of scientific representation. I suggest that debate about the Tree of Cells and other successors to the traditional Tree of Life should be formulated in terms of the purposes these representations may serve. In pursuing this strategy, we see that the Tree of Cells cannot serve one purpose suggested for it: as an explanation for the hierarchical nature of taxonomy. We then explore whether, instead, the tree may play an important role in the dynamic modeling of evolution. As highly-integrated complex systems, cells may influence which lineage components can successfully transfer into them and how they change once integrated. Only if they do in fact have a substantial role to play in this process might the Tree of Cells have some claim to be the Tree of Life. (shrink)

One of intuitions driving the acceptance of a neat structured tree of life is the assumption that organisms and the lineages they form have somewhat stable spatial and temporal boundaries. The phenomenon of symbiosis shows us that such ‘fixist’ assumptions does not correspond to how the natural world actually works. The implications of lateral gene transfer (LGT) have been discussed elsewhere; I wish to stress a related point. I will focus on lateral function transfer (LFT) and will argue, using examples (...) of what many would call ‘superorganisms’, that the emergence of symbiotic individuals revives the importance of functional and adaptationist thinking in how we conceptualize the lineages of biological individuals. The consequence of the argument is that, if we really want to hold onto tree of life thinking, we had better accept that new saplings appear and disappear all the time. (shrink)

According to a once influential view of selection, it consists of repeated cycles of replication and interaction. It has been argued that this view is wrong: replication is not necessary for evolution by natural selection. I analyze the nine most influential arguments for this claim and defend the replication–interaction conception of selection against these objections. In order to do so, however, the replication–interaction conception of selection needs to be modified significantly. My proposal is that replication is not the copying of (...) an entity, the replicator, but the copying of a property. Thus, we can have a replication process without there being a replicator that is being copied. (shrink)

Selectionist evolutionary theory has often been faulted for not making novel predictions that are surprising, risky, and correct. I argue that it in fact exhibits the theoretical virtue of predictive capacity in addition to two other virtues: explanatory unification and model fitting. Two case studies show the predictive capacity of selectionist evolutionary theory: parallel evolutionary change in E. coli, and the origin of eukaryotic cells through endosymbiosis.

This paper reviews Rosenberg’s and McShea’s textbook in philosophy of biology, entitled Philosophy of Biology. A Contemporary Introduction. I insist on the excellent quality of this textbook, then I turn to more critical comments, which deal mainly with what philosophy of biology is, and what it should be.

The theory of evolution by natural selection is, perhaps, the crowning intellectual achievement of the biological sciences. There is, however, considerable debate about which entity or entities are selected and what it is that fits them for that role. This article aims to clarify what is at issue in these debates by identifying four distinct, though often confused, concerns and then identifying how the debates on what constitute the units of selection depend to a significant degree on which of these (...) four questions a thinker regards as central. (shrink)

Philosophical discussions of species have focused on multicellular, sexual animals and have often neglected to consider unicellular organisms like bacteria. This article begins to fill this gap by considering what species concepts, if any, apply neatly to the bacterial world. First, I argue that the biological species concept cannot be applied to bacteria because of the variable rates of genetic transfer between populations, depending in part on which gene type is prioritized. Second, I present a critique of phylogenetic bacterial species, (...) arguing that phylogenetic bacterial classification requires a questionable metaphysical commitment to the existence of essential genes. I conclude by considering how microbiologists have dealt with these biological complexities by using more pragmatic and not exclusively evolutionary accounts of species. I argue that this pragmatism is not borne of laziness but rather of the substantial conceptual problems in classifying bacteria based on any evolutionary standard. (shrink)

In their recent book, Ladyman and Wiesner (What is a complex system?, Yale University Press, 2020) delineate the bounds of the exciting interdisciplinary field of complexity science. In this work, they provide examples of generally accepted complex systems and common features which these possess to varying degrees. In this paper, I plan to extend their list to include the formal study of natural language, i.e. linguistics. In fact, I will argue that language exhibits many of the hallmarks of a complex (...) system, specifically a complex biological system. Thus, my aim is to advocate contra the the ‘Minimalist Program’ (Chomsky, The minimalist program, MIT Press, Cambridge, 1995), which motivates simple underlying mechanisms (i.e. Merge) in their idealisations, that biolinguistics should embrace a ‘Maximalist Program’ in which multiple subfields contribute component explanations to an emerging whole. (shrink)

Since the last decades of the twentieth and the beginning of the twenty-first century, the use of metaphysics by philosophers when approaching conceptual problems in biology has increased. Some philosophers call this tendency in philosophy of biology ‘Metaphysics of Biology’. In this paper, I aim at characterizing Metaphysics of Biology by paying attention to the diverse ways philosophers use metaphysics when addressing conceptual problems in biology. I will claim that there are two different modes of doing Metaphysics of Biology, namely (...) Metaphysics for Biology and Metaphysics in Biology. (shrink)

While philosophers of science have marginally discussed concepts such as ‘nutrient’, ‘naturalness’, ‘food’, or the ‘molecularization’ of nutrition, they have yet to seriously engage with the nutrition sciences. In this paper, I offer one way to begin this engagement by investigating conceptual challenges facing the burgeoning field of nutritional ecology and the question of how organisms construct a ‘balanced’ diet. To provide clarity, I propose the distinction between nutrient balance as a property of foods or dietary patterns and nutrient balancing (...) as an evolved capacity to regulate nutrient intake. This distinction raises conceptual and empirical issues, such as what properties constitute this capacity and whether they are the same in all organisms. Additionally, while scientists use the term ‘balancing’, its intension and extension need further clarification. Based on the literature, the properties of external nutrient detection, internal sensing of nutrient levels, and organismal regulation could provide a basic recipe for nutrient balancing. Next, using an evolutionary lens, I examine nutrient acquisition in some prokaryotes, slime molds, simple multicellular eukaryotes, and in the quirks of multicellular metabolism to raise questions about the origins and universality of balancing. Finally, I build on this explication of balance and balancing by considering how obesity and cancer might respectively elucidate problems of organismal nutrient imbalances versus disrupted cellular nutrient balancing. (shrink)

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)

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)

The hologenome concept of evolution is a hypothesis about the evolution of animals and plants. It asserts that the evolution of animals and plants was partially triggered by their interactions with their symbiotic microbiomes. In that vein, the hologenome concept posits that the holobiont (animal host + symbionts of the microbiome) is a unit of selection. -/- The hologenome concept has been severely criticized on the basis that selection on holobionts would only be possible if there were a tight transgenerational (...) host-genotype-to-symbiont-genotype connection. As our current evidence suggests that this is not the case for most of the symbiont species that compose the microbiome of animals and plants, the opportunity for holobiont selection is very low in relation to the opportunity for selection on each of the species that compose the host microbiome. Therefore, holobiont selection will always be disrupted ‘from below’, by selection on each of the species that compose the microbiome. -/- This thesis constitutes a conceptual effort to defend philosophically the hologenome concept. I argue that the criticism according to which holobiont selection requires tight transgenerational host-genotype-to-symbiont-genotype connection is grounded on a metaphysical view of the world according to which the biological hierarchy needs to be nested, such that each new level of selection includes every entity from below. Applied to hologenomes, it entails that the hologenome is a collection of genomes, and selection of hologenomes is assumed to entail cospeciation of the host with the species that constitute its microbiome. -/- Against that interpretation, I propose the ‘stability of traits’ account, according to which hologenome evolution is the result of the action of natural selection in a non-nested hierarchical world. In that vein, hologenome evolution does not entail cospeciation, and thus it does not require tight transgenerational host-genotype-to-symbiont-genotype connection. By embracing a multilevel selection perspective, I argue that hologenome evolution results from the simultaneous action of natural selection on each of the lineages that compose the microbiome, and on the assemblage composed by the host genome plus the functional traits of its microbiome. Hologenome selection occurs when the evolution of the traits of the microbiome result from their effects on the fitness of the host, and it can take the form of multilevel selection 1, or multilevel selection 2. In both cases, hologenome selection entails the evolution of microbiome traits, as well as evolution of the host genome, rather than cospeciation of lineages. (shrink)

A crucial question for a process view of life is how to identify a process and how to follow it through time. The genidentity view can contribute decisively to this project. It says that the identity through time of an entity X is given by a well-identified series of continuous states of affairs. Genidentity helps address the problem of diachronic identity in the living world. This chapter describes the centrality of the concept of genidentity for David Hull and proposes an (...) extension of Hull’s view to the ubiquitous phenomenon of symbiosis. Finally, using immunology as a key example, it shows that the genidentity view suggests that the main interest of a process approach is epistemological rather than ontological and that its principal claim is one of priority, namely that processes precede and define things, and not vice versa. (shrink)

We assess the arguments for recognising functionally integrated multispecies consortia as genuine biological individuals, including cases of so-called ‘holobionts’. We provide two examples in which the same core biochemical processes that sustain life are distributed across a consortium of individuals of different species. Although the same chemistry features in both examples, proponents of the holobiont as unit of evolution would recognize one of the two cases as a multispecies individual whilst they would consider the other as a compelling case of (...) ecological dependence between separate individuals. Some widely used arguments in support of the ‘holobiont’ concept apply equally to both cases, suggesting that those arguments have misidentified what is at stake when seeking to identify a new level of biological individuality. One important aspect of biological individuality is evolutionary individuality. In line with other work on the evolution of individuality, we show that our cases can be distinguished by focusing on the fitness alignment between the partners of the consortia. We conclude that much of the evidence currently presented for the ubiquity and importance of multi-species individuals is simply not to the point, at least unless the issue of biological individuality is firmly divorced from the question of evolutionary individuality. (shrink)

Multicellular organisms contain numerous symbiotic microorganisms, collectively called microbiomes. Recently, microbiomic research has shown that these microorganisms are responsible for the proper functioning of many of the systems (digestive, immune, nervous, etc.) of multicellular organisms. This has inclined some scholars to argue that it is about time to reconceptualise the organism and to develop a concept that would place the greatest emphasis on the vital role of microorganisms in the life of plants and animals. We believe that, unfortunately, there is (...) a problem with this suggestion, since there is no such thing as a universal concept of the organism which could constitute a basis for all biological sciences. Rather, the opposite is true: numerous alternative definitions exist. Therefore, comprehending how microbiomics is changing our understanding of organisms may be a very complex matter. In this paper we will demonstrate that this pluralism proves that claims about a change in our understanding of organisms can be treated as both true and untrue. Mainly, we assert that the existing concepts differ substantially, and that only some of them have to be reconsidered in order to incorporate the discoveries of microbiomics, while others are already flexible enough to do so. Taking into account the plurality of conceptualisations within different branches of modern biology, we will conduct our discussion using the developmental and the cooperation–conflict concepts of the organism. Then we will explain our results by referring to the recent philosophical debate on the nature of the concept of the organism within biology. (shrink)

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)

Is it possible, and in the first place is it even desirable, to define what "development" means and to determine the scope of the field called "developmental biology"? Though these questions appeared crucial for the founders of "developmental biology" in the 1950s, there seems to be no consensus today about the need to address them. Here, in a combined biological, philosophical, and historical approach, we ask whether it is possible and useful to define biological development, and, if such a definition (...) is indeed possible and useful, which definition can be considered as the most satisfactory. (shrink)

Copyright © 2007 Elsevier Ltd All rights reserved.

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)

Building upon a non-standard understanding of evolutionary process focusing on variation and persistence, I will argue that communities and ecosystems can evolve by natural selection as emergent individuals. Evolutionary biology has relied ever increasingly on the modeling of population dynamics. Most have taken for granted that we all agree on what is a population. Recent work has reexamined this perceived consensus. I will argue that there are good reasons to restrict the term “population” to collections of monophyletically related replicators and (...) interactors, which explains why many existing models in population biology exclude by definition many genuine evolving biological individuals such as communities and ecosystems. By studying a case of community evolution (a symbiotic termite–fungus community), we will see that it is variation that is important to evolutionary processes, not populations. Variation within a population is only one of many types of variation that can lead to evolution by natural selection. The upshot of focusing on variation is that cases of community and ecosystem adaptive change become tractable in evolutionary terms. I will show that complex emergent individuals such as communities and ecosystems cannot be fully accommodated by conventional population/reproduction models but can be accommodated by variation/persistence models. (shrink)

Science is now studying biodiversity on a massive scale. These studies are occurring not just at the scale of larger plants and animals, but also at the scale of minute entities such as bacteria and viruses. This expansion has led to the development of a specific sub-field of “microbial diversity”. In this paper, I investigate how microbial diversity faces two of the classical issues encountered by the concept of “ biodiversity ”: the issues of defining the units of biodiversity and (...) of choosing a mathematical measure of diversity. I also show that the extension of the scope of biodiversity to microbial entities such as viruses and many other not-clearly-alive entities raises yet another foundational issue: that of defining a “lower-limit” of biodiversity. (shrink)

Standard microbial evolutionary ontology is organized according to a nested hierarchy of entities at various levels of biological organization. It typically detects and defines these entities in relation to the most stable aspects of evolutionary processes, by identifying lineages evolving by a process of vertical inheritance from an ancestral entity. However, recent advances in microbiology indicate that such an ontology has important limitations. The various dynamics detected within microbiological systems reveal that a focus on the most stable entities (or features (...) of entities) over time inevitably underestimates the extent and nature of microbial diversity. These dynamics are not the outcome of the process of vertical descent alone. Other processes, often involving causal interactions between entities from distinct levels of biological organisation, or operating at different time scales, are responsible not only for the destabilisation of pre-existing entities, but also for the emergence and stabilisation of novel entities in the microbial world. In this article we consider microbial entities as more or less stabilised functional wholes, and sketch a network-based ontology that can represent a diverse set of processes including, for example, as well as phylogenetic relations, interactions that stabilise or destabilise the interacting entities, spatial relations, ecological connections, and genetic exchanges. We use this pluralistic framework for evaluating (i) the existing ontological assumptions in evolution (e.g. whether currently recognized entities are adequate for understanding the causes of change and stabilisation in the microbial world), and (ii) for identifying hidden ontological kinds, essentially invisible from within a more limited perspective. We propose to recognize additional classes of entities that provide new insights into the structure of the microbial world, namely “processually equivalent” entities, “processually versatile” entities, and “stabilized” entities. (shrink)

Our aim in the present paper is to approach the nature of life from the perspective of autonomy, showing that this perspective can be helpful for overcoming the traditional Cartesian gap between the physical and cognitive domains. We first argue that, although the phenomenon of life manifests itself as highly complex and multidimensional, requiring various levels of description, individual organisms constitute the core of this multifarious phenomenology. Thereafter, our discussion focuses on the nature of the organization of individual living entities, (...) proposing autonomy as the main concept to grasp it. In the second part of the article we show how autonomy is also fundamental to explaining major evolutionary transitions, in an attempt to rethink evolution from the point of view of the organizational structure of the entities/organisms involved. This gives further support to the idea of autonomy not only as a key to understanding life in general but also the complex expressions of it that we observe on our planet. Finally, we suggest a possible general principle that underlies those evolutionary transitions, which allow for the open-ended redefinition of autonomous systems: namely, the relative dynamic decoupling that must be articulated among distinct parts, modules or modes of operation in these systems. (shrink)

The dangers of character reification for cladistic inference are explored. The identification and analysis of characters always involves theory-laden abstraction—there is no theory-free “view from nowhere.” Given theory-ladenness, and given a real world with actual objects and processes, how can we separate robustly real biological characters from uncritically reified characters? One way to avoid reification is through the employment of objectivity criteria that give us good methods for identifying robust primary homology statements. I identify six such criteria and explore each (...) with examples. Ultimately, it is important to minimize character reification, because poor character analysis leads to dismal cladograms, even when proper phylogenetic analysis is employed. Given the deep and systemic problems associated with character reification, it is ironic that philosophers have focused almost entirely on phylogenetic analysis and neglected character analysis. (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)

The eukaryote cell is one of the most radical innovations in the history of life, and the circumstances of its emergence are still deeply contested. This paper will outline the recent history of attempts to reveal these origins, with special attention to the argumentative strategies used to support claims about the first eukaryote cell. I will focus on two general models of eukaryogenesis: the phagotrophy model and the syntrophy model. As their labels indicate, they are based on claims about metabolic (...) relationships. The first foregrounds the ability to consume other organisms; the second the ability to enter into symbiotic metabolic arrangements. More importantly, however, the first model argues for the autogenous or self-generated origins of the eukaryote cell, and the second for its exogenous or externally generated origins. Framing cell evolution this way leads each model to assert different priorities in regard to cell-biological versus molecular evidence, cellular versus environmental influences, plausibility versus evolutionary probability, and irreducibility versus the continuity of cell types. My examination of these issues will conclude with broader reflections on the implications of eukaryogenesis studies for a philosophical understanding of scientific contestation. (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.

As Raymond Williams famously declared, nature is one of the most complex words in the English language – and, we may confidently predict, its Germanic relatives including Dutch. The workshop that took place in June 2007 in the Netherlands, from which this volume is derived, was based on an earlier program exploring connections between our concepts of nature and related concepts of science and religion. Though one may not immediately expect these three realms to be interrelated, countless examples suggest otherwise.

Following Wallace’s suggestion, Darwin framed his theory using Spencer’s expression “survival of the fittest”. Since then, fitness occupies a significant place in the conventional understanding of Darwinism, even though the explicit meaning of the term ‘fitness’ is rarely stated. In this paper I examine some of the different roles that fitness has played in the development of the theory. Whereas the meaning of fitness was originally understood in ecological terms, it took a statistical turn in terms of reproductive success throughout (...) the 20th Century. This has lead to the ever-increasing importance of sexually reproducing organisms and the populations they compose in evolutionary explanations. I will argue that, moving forward, evolutionary theory should look back at its ecological roots in order to be more inclusive in the type of systems it examines. Many biological systems can only be satisfactorily accounted for by offering a non-reproductive account of fitness. This argument will be made by examining biological systems with very small or transient population structures. I argue this has significant consequences for how we define Darwinism, increasing the significance of survival over that of reproduction. (shrink)

This paper examines the species problem in microbiology and its implications for the species problem more generally. Given the different meanings of ‘species’ in microbiology, the use of ‘species’ in biology is more multifarious and problematic than commonly recognized. So much so, that recent work in microbial systematics casts doubt on the existence of a prokaryote species category in nature. It also casts doubt on the existence of a general species category for all of life (one that includes both prokaryotes (...) and eukaryotes). Prokaryote biology also undermines recent attempts to save the species category, such as the suggestion that species are metapopulation lineages and the idea that ‘species’ is a family resemblance concept. (shrink)

Metagenomics is an emerging microbial systems science that is based on the large-scale analysis of the DNA of microbial communities in their natural environments. Studies of metagenomes are revealing the vast scope of biodiversity in a wide range of environments, as well as new functional capacities of individual cells and communities, and the complex evolutionary relationships between them. Our examination of this science focuses on the ontological implications of these studies of metagenomes and metaorganisms, and what they mean for common (...) sense and philosophical understandings of multicellularity, individuality and organism. We show how metagenomics requires us to think in different ways about what human beings are and what their relation to the microbial world is. Metagenomics could also transform the way in which evolutionary processes are understood, with the most basic relationship between cells from both similar and different organisms being far more cooperative and less antagonistic than is widely assumed. In addition to raising fundamental questions about biological ontology, metagenomics generates possibilities for powerful technologies addressed to issues of climate, health and conservation. We conclude with reflections about process-oriented versus entity-oriented analysis in light of current trends towards systems approaches. (shrink)

We discuss the impact of horizontal gene transfer (HGT) on phylogenetic reconstruction and taxonomy. We review the power of HGT as a creative force in assembling new metabolic pathways, and we discuss the impact that HGT has on phylogenetic reconstruction. On one hand, shared derived characters are created through transferred genes that persist in the recipient lineage, either because they were adaptive in the recipient lineage or because they resulted in a functional replacement. On the other hand, taxonomic patterns in (...) microbial phylogenies might also be created through biased gene transfer. The agreement between different molecular phylogenies has encouraged interpretation of the consensus signal as reflecting organismal history or as the tree of cell divisions; however, to date the extent to which the consensus reflects shared organismal ancestry and to which it reflects highways of gene sharing and biased gene transfer remains an open question. Preferential patterns of gene exchange act as a homogenizing force in creating and maintaining microbial groups, generating taxonomic patterns that are indistinguishable to those created by shared ancestry. To understand the evolution of higher bacterial taxonomic units, concepts usually applied in population genetics need to be applied. (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)

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.

Can we be realists about a general category but pluralists about concepts relating to that category? I argue that paleobiological methods of delineating species are not affected by differing species concepts, and that this underwrites an argument that species concept pluralists should be species category realists. First, the criteria by which paleobiologists delineate species are ‘indifferent’ to the species category. That is, their method for identifying species applies equally to any species concept. To identify a new species, paleobiologists show that (...) interspecies processes, such as phenotypic plasticity, sexual dimorphism, or ontogenetic diversity, are a worse explanation of the variance between specimens than intraspecies processes. As opposed to operating under a single or plurality of species concepts, then, paleobiologists use abductive inferences, which would be required regardless of any particular species concept. Second, paleobiologists are frequently interested in large-scale, long-term morphological patterns in the fossil record, and resolving the fine-grained differences which result from different species concepts is irrelevant at those scales. I argue that this claim about paleobiological practice supports what I call ‘indifference realism’ about the species category. The indifference realist argues that when legitimate investigation is indifferent to a plurality of concepts, we should be realists about the category those concepts pertain to. (shrink)

This is a highly welcome book that offers a fresh perspective on the philosophy of biology. It is of interest to both philosophers and biologists and to experienced readers as well as novices. The book is structured into four sections ‘Science’, ‘Biology’, ‘Microbes’ and ‘Humans’ and consists of a collection of articles written by John Dupré over the past few years.

This paper appraises the role of critical-feminist figurations within the environmental humanities, focusing on the capacity of figures to produce situated environmental knowledges and pose site-specific ethical obligations. We turn to four environments—the home, the skies, the seas and the microscopic—to examine the work that various figures do in these contexts. We elucidate how diverse figures—ranging from companion animals to birds, undersea creatures and bugs—reflect productive traffic between longstanding concerns in feminist theory and the environmental humanities, and generate new insights (...) related to situated knowledges, feminist care-ethics and the politics of everyday sensory encounters. We also argue, however, that certain figures have tested the limits of theoretical approaches which have emerged as the product of dialogue between feminist theory and environmental studies. In particular, we explore how particular figures have complicated ethical questions of how to intervene in broad environmental threats borne of anthropogenic activities, and of who or what to include in relational ethical frameworks. (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)

This paper will begin with some very broad and general considerations about the kind of biological entities we are. This exercise is motivated by the belief that the view of what we—multicellular eukaryotic organisms—are that is widely assumed by biologists, medical scientists and the general public, is an extremely limited one. It cannot be assumed a priori that a more sophisticated view will make a major difference to the science or practice of medicine, and there are areas of medicine to (...) which it is probably largely irrelevant. However, in this case there are important implications for medicine, or so I shall argue. In particular, it enables us to appreciate fully the potential medical significance of some of the most exciting contemporary advances in general biology, in such fields as epigenetics, metagenomics, and systems biology; and part of this significance is that these advances have raised serious doubts about how we should understand the biological individuals that medicine is generally assumed to aim to treat. (shrink)

The human intestinal ecosystem, previously called the gut microflora is now known as the Human Gut Microbiota. Microbiome research has emphasized the potential role of this ecosystem in human homeostasis, offering unexpected opportunities in therapeutics, far beyond digestive diseases. It has also highlighted ethical, social and commercial concerns related to the gut microbiota. As diet factors are accepted to be the major regulator of the gut microbiota, the modulation of its composition, either by antibiotics or by food intake, should be (...) regarded as a fascinating tool for improving the human health. Scientists, the food industry, consumers and policymakers alike are involved in this new field of nutrition. Defining how knowledge about the HGM is being translated into public perception has never been addressed before. This raises the question of metaphors associated with the HGM, and how they could be used to improve public understanding, and to influence individual decision-making on healthcare policy. This article suggests that a meeting of stakeholders from the social sciences, basic research and the food industry, taking an epistemological approach to the HGM, is needed to foster close, innovative partnerships that will help shape public perception and enable novel behavioural interventions that would benefit public health. (shrink)

This paper presents an account of the biological populations that can undergo paradigmatic natural selection. I argue for, and develop Peter Godfrey-Smith’s claim that reproductive competition is a core attribute of such populations. However, as Godfrey-Smith notes, it is not the only important attribute. I suggest what the missing element is, co-opting elements of Alan Templeton’s notion of exchangeability. The final framework is then compared to two recent discussions regarding biological populations proposed by Roberta Millstein and Jacob Stegenga.