The definition of biological individuality is one of the most discussed topics in philosophy of biology, but current debate has focused almost exclusively on evolution-based accounts. Moreover, several participants in this debate consider the notions of a biological individual and an organism as equivalent. In this paper, I show that the debates would be considerably enriched and clarified if philosophers took into account two elements. First, physiological fields are crucial for the understanding of biological individuality. Second, the category of biological (...) individuals should be divided into two subcategories: physiological individuals and evolutionary individuals, which suggests that the notions of organism and biological individual should not be used interchangeably. I suggest that the combination of an evolutionary and a physiological perspective will enable biologists and philosophers to supply an account of biological individuality that will be both more comprehensive and more in accordance with scientific practices. (shrink)

Bourrat and Griffiths :33, 2018) have recently argued that most of the evidence presented by holobiont defenders to support the thesis that holobionts are evolutionary individuals is not to the point and is not even adequate to discriminate multispecies evolutionary individuals from other multispecies assemblages that would not be considered evolutionary individuals by most holobiont defenders. They further argue that an adequate criterion to distinguish the two categories is fitness alignment, presenting the notion of fitness boundedness as a criterion that (...) allows divorcing true multispecies evolutionary individuals from other multispecies assemblages and provides an adequate criterion to single out genuine evolutionary multispecies assemblages. A consequence of their criterion is that holobionts, as conventionally defined by hologenome defenders, are not evolutionary individuals except in very rare cases, and for very specific host-symbiont associations. This paper is a critical response to Bourrat and Griffiths’ arguments and a defence of the arguments presented by holobiont defenders. Drawing upon the case of the hologenomic basis of the evolution of sanguivory in vampire bats, I argue that Bourrat and Griffiths overlook some aspects of the biological nature of the microbiome that justifies the thesis that holobionts are evolutionarily different to other multispecies assemblages. I argue that the hologenome theory of evolution should not define the hologenome as a collection of genomes, but as the sum of the host genome plus some traits of the microbiome which together constitute an evolutionary individual, a conception I refer to as the stability of traits conception of the hologenome. Based on that conception I argue that the evidence presented by holobiont defenders is to the point, and supports the thesis that holobionts are evolutionary individuals. In this sense, the paper offers an account of the holobiont that aims to foster a dialogue between hologenome advocates and hologenome critics. (shrink)

Biological individuality is a notoriously thorny topic for biologists and philosophers of biology. In this paper we argue that biological individuality presents multiple, interconnected questions for biologists and philosophers that together form a problem agenda. Using a case study of an interdisciplinary research group in ecology, behavioral and evolutionary biology, we claim that a debate on biological individuality that seeks to account for diverse practices in the biological sciences should be broadened to include and give prominence to questions about uniqueness (...) and temporality. We show that broadening the problem agenda of biological individuality draws attention to underrecognized philosophical issues and discussions and thereby organizes and enriches the existing debate. (shrink)

Biological individuality is a major topic of discussion in biology and philosophy of biology. Recently, several objections have been raised against traditional accounts of biological individuality, including the objections of monism, theory-centrism, ahistoricity, disciplinary isolationism, and the multiplication of conceptual uncertainties. In this introduction, I will examine the current philosophical landscape about biological individuality, and show how the contributions gathered in this special issue address these five objections. Overall, the aim of this issue is to offer a more diverse, unifying, (...) and scientifically informed conception of what a biological individual is. (shrink)

Contemporary biological research has suggested that some host–microbiome multispecies systems (referred to as “holobionts”) can in certain circumstances evolve as unique biological individual, thus being a unit of selection in evolution. If this is so, then it is arguably the case that some biological adaptations have evolved at the level of the multispecies system, what we call hologenomic adaptations. However, no research has yet been devoted to investigating their nature, or how these adaptations can be distinguished from adaptations at the (...) species-level (genomic adaptations). In this paper, we cover this gap by investigating the nature of hologenomic adaptations. By drawing on the case of the evolution of sanguivory diet in vampire bats, we argue that a trait constitutes a hologenomic adaptation when its evolution can only be explained if the holobiont is considered the biological individual that manifests this adaptation, while the bacterial taxa that bear the trait are only opportunistic beneficiaries of it. We then use the philosophical notions of emergence and inter-identity to explain the nature of this form of individuality and argue why it is special of holobionts. Overall, our paper illustrates how the use of philosophical concepts can illuminate scientific discussions, in the trend of what has recently been called metaphysics of biology. (shrink)

Mammals are usually considered unproblematic as biological individuals. This article contends the opposite. Once we consider pregnancy, criteria for biological individuality are not easily applicab...

Debates concerning the units and levels of selection have persisted for over fifty years. One major question in this literature is whether units and levels of selection are genuine, in the sense that they are objective features of the world, or merely reflect the interests and goals of an observer. Scientists and philosophers have proposed a range of answers to this question. This Element introduces this literature and proposes a novel contribution. It defends a realist stance and offers a way (...) of delineating genuine levels of selection by invoking the notion of a functional unit. (shrink)

How many individuals are present where we see a pregnant individual? Within a substance ontological framework, there are exactly two possible answers to this question. The standard answer—two individuals—is typically championed by scholars endorsing the predominant Containment View of pregnancy, according to which the foetus resides in the gestating organism like in a container. The alternative answer—one individual—has recently found support in the Parthood View, according to which the foetus is a part of the gestating organism. Here I propose a (...) third answer: a pregnant individual is neither two individuals nor one individual but something in between one and two. This is because organisms are better understood as processes than as substances. With a special focus on the Parthood View, I explain why a Process View of pregnancy, according to which a pregnant individual is a bifurcating hypercomplex process, surpasses the substance ontological approaches. (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)

In this paper, I introduce the notion of ‘philosophy moves’: prominent tropes featured in contemporary academic philosophy. Moves are more than patterns—they are tools for advancing and enriching philosophical debates. By recognizing these patterns in the philosophical literature, we collect an ensemble of moves for deployment in novel contexts, each with the potential to forge new paths of philosophical investigation through a given topic. The moves featured in this paper are constructive and progressive, with the potential to push past stalemates (...) and open a wider conceptual landscape. Following a presentation of five exemplars taken from the philosophy of biology literature, I show how different moves could be made within a current interdisciplinary debate. Overall, I aim to demonstrate that recognizing these patterns is insightful pedagogically and potentially useful when used as part of one’s philosophical methodology. (shrink)

Mammalian placental pregnancy is a neglected problem case for theories of organismality. This example is closer to home than those typically discussed within philosophy of biology. I apply evolutio...

In dicephalus conjoined twinning, it appears that two heads share a body; in cephalopagus, it appears that two bodies share a head. How many human animals are present in these cases? One answer is that there are two in both cases—conjoined twins are precisely that, conjoined twins. Another is that the number of humans corresponds to the number of bodies—so there is one in dicephalus and two in cephalopagus. I show that both of these answers are incorrect. Prominent accounts of (...) biological individuation, which treat the organism as an integrated whole, reveal that in these and other cases of conjoined twinning the ‘twins’ share a single human animal. This has a number of consequences for the debate about what we are. First, if animalism is true, individuals of our kind can be—and are—profoundly psychologically divided. Second, cephalopagus twinning does not divide animalism from its rivals, as has been claimed. Finally, animalists can reply to a vicious species of the ‘too many thinkers’ problem to which they are allegedly uniquely vulnerable. (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.

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)

Kin selection and multilevel selection are alternative approaches for studying the evolution of social behaviour, the relation between which has long been a source of controversy. Many recent theorists regard the two approaches as ultimately equivalent, on the grounds that gene frequency change can be correctly expressed using either. However, this shows only that the two are formally equivalent, not that they offer equally good causal representations of the evolutionary process. This article articulates the notion of an ‘adequate causal representation’ (...) using causal graphs, and then seeks to identify circumstances under which kin and multilevel selection do and do not satisfy the test of causal adequacy. 1 Introduction2 The KS and MLS Approaches2.1 The MLS decomposition2.2 The KS decomposition3 Equivalence and Causality4 Two Problem Cases4.1 The non-social trait case4.2 Genotypic selection with meiotic drive5 Casual Adequacy: A Graphical Approach5.1 The basic idea5.2 Graphs with individual and group variables5.3 Cases where KS is causally adequate5.4 Cases where MLS is causally adequate6 Discussion6.1 Relation to previous work. (shrink)

Ecological communities are seldom, if ever, biological individuals. They lack causal boundaries as the populations that constitute communities are not congruent and rarely have persistent functional roles regulating the communities’ higher-level properties. Instead we should represent ecological communities indexically, by identifying ecological communities via the network of weak causal interactions between populations that unfurl from a starting set of populations. This precisification of ecological communities helps identify how community properties remain invariant, and why they have robust characteristics. This respects the (...) diversity and aggregational nature of these complex systems while still vindicating them as units worthy of investigation. (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)

Individuality is an important concept in biology, yet there are many non-equivalent criteria of individuality expressed in different kinds of biological individuals. This article evaluates these different kinds in terms of their capacity to support explanatory generalizations over the systems they individuate. Viewing the problem of individuality from this perspective promotes a splitting strategy in which different kinds make different epistemic trade-offs that suit them for different explanatory roles. I argue that evolutionary individuals, interpreted as forming a functional kind, face (...) difficulties of individuation and explanatory power that are mitigated by relying on more structurally based properties and non-evolutionary kinds. 1Introduction2Kinds of Biological Individuals3Evolutionary Individuals and Functional Kinds4Evolutionary versus Non-evolutionary Kinds of Individuals 4.1Physiological individuality4.2Ecological individuality4.3Developmental individuality5Conclusion. (shrink)

What are the prospects for a monistic view of biological individuality given the multiple epistemic roles the concept must satisfy? In this paper, I examine the epistemic adequacy of two recent accounts based on the capacity to undergo natural selection. One is from Ellen Clarke, and the other is by Peter Godfrey-Smith. Clarke’s position reflects a strong monism, in that she aims to characterize individuality in purely functional terms and refrains from privileging any specific material properties as important in their (...) own right. I argue that Clarke’s functionalism impairs the epistemic adequacy of her account compared to a middle-ground position taken by Godfrey-Smith. In comparing Clarke and Godfrey-Smith’s account, two pathways emerge to pluralism about biological individuality. The first develops from the contrast between functionalist and materialist approaches, and the second from an underlying temporal structure involved in using evolutionary processes to define individuality. (shrink)

Theoreticians that defend a form of realism regarding natural kinds minimally entertain the belief that the world features divisions into kinds and that the natural kind concept is a useful tool for philosophy of science. The objective of this paper is to challenge these assumptions. First, we challenge realism toward natural kinds by showing that the main arguments for their existence, which rely on the epistemic success of natural kinds, are unsatisfactory. Second, we show that, whether they exist or not, (...) natural kinds are expendable when it comes to describing and analyzing scientific explanations accurately. (shrink)

An understanding of the factors behind the evolution of multicellularity is one of today’s frontiers in evolutionary biology. This is because multicellular organisms are made of one subset of cells with the capacity to transmit genes to the next generation and another subset responsible for maintaining the functionality of the organism, but incapable of transmitting genes to the next generation. The question arises: why do somatic cells sacrifice their lives for the sake of germline cells? How is germ/soma separation maintained? (...) One conventional answer refers to inclusive fitness theory, according to which somatic cells sacrifice themselves altruistically, because in so doing they enhance the transmission of their genes by virtue of their genetic relatedness to germline cells. In the present article we will argue that this explanation ignores the key role of policing mechanisms in maintaining the germ/soma divide. Based on the pervasiveness of the latter, we argue that the role of altruistic mechanisms in the evolution of multicellularity is limited and that our understanding of this evolution must be enriched through the consideration of coercion mechanisms. (shrink)

According to the mainstream position in the bioethical definition of death debate, death is to be equated with the cessation of an organism. Given such a perspective, some bioethicists uphold the position that brain-dead patients are dead, while others claim that they are alive. Regardless of the specific opinion on the status of brain-dead patients, the mere bioethical concept of death, according to many bioethicists, has the merit of being unanimous and univocal, as well as grounded in biology. In the (...) present article, we challenge such a thesis. We provide evidence that theoretical biology operates with a plurality of equally valid organismic concepts, which imply different conclusions regarding the organismal status of a brain-dead patient. Moreover, the theoretical biology concepts of an organism are very distant from the view on an organism that appears by way of bioethicists theorizing on death. We conclude that if death is to be understood as the cessation of an organism, there is no single correct answer to the question of whether a brain-dead patient is alive or dead. (shrink)

The Problem of Biological Individuality is the problem of how to count organisms. Whilst counting organisms may seem easy, the biological world is full of difficult cases such as colonial siphonophores and aspen tree groves. One of the main solutions to the Problem of Biological Individuality is the Physiological Approach. Drawing on an argument made by Eric Olson in the personal identity debate, I argue that the Physiological Approach faces a metaphysical problem - the ‘Foetus Problem’. This paper illustrates how (...) metaphysics can contribute to debates about organisms in the philosophy of biology. (shrink)

Much of the debate over the definition and criteria for determining our death has focused on disagreement over the correct biological account of death, i.e., what it means for any organism to die. In this paper, we argue that this exclusive focus on the biology of death is misguided, because it ignores ethical and social factors that bear on the acceptability of criteria for determining our death. We propose that attention shift from strictly biological considerations to ethical and social considerations (...) that bear on the determination of what we call “civil death.” We argue for acceptance of a neurological criterion for determining death on grounds that it is the most reasonable way to synthesize biological, ethical, and social considerations about our death.. (shrink)

What changes when an evolutionary transition in individuality takes place? Many different answers have been given, in respect of different cases of actual transition, but some have suggested a general answer: that a major transition is a change in the extent to which selection acts at one hierarchical level rather than another. The current paper evaluates some different ways to develop this general answer as a way to characterise the property ‘evolutionary individuality’; and offers a justification of the option taken (...) in Clarke :413–435, 2013)—to define evolutionary individuality in terms of an object’s capacity to undergo selection at its own level. In addition, I suggest a method by which the property can be measured and argue that a problem which is often considered to be fatal to that method—the problem of ‘cross-level by-products’—can be avoided. (shrink)

Various results show the ‘formal equivalence’ of kin and group selectionist methodologies, but this does not preclude there being a real and useful distinction between kin and group selection processes. I distinguish individual- and population-centred approaches to drawing such a distinction, and I proceed to develop the latter. On the account I advance, the differences between kin and group selection are differences of degree in the structural properties of populations. A spatial metaphor provides a useful framework for thinking about these (...) differences: kin and group selection may be conceptualized as large, overlapping regions of K - G space. I then consider some implications of the account, defend it from possible objections, and further argue that the structural features characteristic of both kin and group selection may recur at multiple levels of biological organization. (shrink)

This article defends lineage pluralism; the view that biological lineages are not a single, unified type of entity. I analyze aspects of evolutionary theory, phylogenetics, and developmental biology to show that these areas appeal to distinct notions of lineage. I formulate three arguments for lineage pluralism. These arguments undercut the main motivations for lineage monism; the view that biological lineages are a single, unified type of entity. Although this view is rarely made explicit, it is often assumed in philosophy and (...) biology. Hence, this article sheds light on this monistic assumption and shows why lineage pluralism should be adopted instead. (shrink)

Although contemporary metaphysics has recently undergone a neo-Aristotelian revival wherein dispositions, or capacities are now commonplace in empirically grounded ontologies, being routinely utilised in theories of causality and modality, a central Aristotelian concept has yet to be given serious attention – the doctrine of hylomorphism. The reason for this is clear: while the Aristotelian ontological distinction between actuality and potentiality has proven to be a fruitful conceptual framework with which to model the operation of the natural world, the distinction between (...) form and matter has yet to similarly earn its keep. In this chapter, I offer a first step toward showing that the hylomorphic framework is up to that task. To do so, I return to the birthplace of that doctrine - the biological realm. Utilising recent advances in developmental biology, I argue that the hylomorphic framework is an empirically adequate and conceptually rich explanatory schema with which to model the nature of organisms. (shrink)

Humans are a kind of animal, and it is a natural and sensible idea that the way to understand what it is for a human person to persist over time is to reflect on what it is for an animal to persist. This paper accepts this strategy. However, especially in the light of a range of recent biological findings, the persistence of animals turns out to be much more problematic than is generally supposed. The main philosophical premise of the paper (...) is that living systems generally are best treated as processes rather than things. These processes prove to be so complexly intertwined and interdependent, that there is no unique, objective way of distinguishing the individuals from which they are composed. For this reason the animalist perspective, it is argued, problematizes as much as it resolves the problem of personal identity. Traditional concerns with responsibility and reactive attitudes provide an intelligible and defensible motivation for distinguishing the individuals we standardly assume as the explanandum in these discussions. But, from a biological point of view, the underlying individualism is a contingent perspective, as much justified by these concerns as providing an objective grounding for them. (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)

Synthetic biology promises to eliminate the distinction between biology and engineering by delivering a philosophically interesting new kind of entity: a biological organism that is wholly designed and constructed by humans. The possibility of such organisms raises interesting questions in three domains: the analysis of (1) biological functions, (2) engineering functions, and (3) health and disease. This paper identifies and systematically answers these questions. This does not only establish how we should think about functions and health and disease in synthetic (...) biological organisms, but it also reveals insights that are of broader relevance: (1) aetiological accounts of biological function need to omit or reinterpret reference to natural selection. This results in complete continuity between aetiological analyses of function in engineering and philosophy; (2) considering synthetic biology prompts interesting further questions about heritability, ancestry, and biological individuals; and (3) accounts of disease as biological dysfunction do not straightforwardly map onto our intuitive health and disease judgments regarding non‐human animals. In response to the latter point I examine three possible avenues, and tentatively defend one on behalf of the ‘disease as dysfunction’ theorist. (shrink)

All disciplines must define their basic units and core processes. In evolutionary biology, the core process is natural selection and the basic unit of selection and adaptation is the individual. To operationalize the theory of natural selection we must count individuals, as they are the bearers of fitness. While canonical individuals have often been taken to be multicellular organisms, the hierarchy of life shows that new kinds of individuals have evolved. A variety of criteria have been used to define biological (...) individuality. Some criteria rely on the presence/absence of a particular property while others advocate an approach that reflects the process of natural selection. The plethora of approaches to classifying individuality has resulted in confusion regarding how to study individuality in a given taxon. (shrink)

Immunology and its philosophy are a primary source for thinking about biological individuality. Through its discriminatory function, the immune system is believed to delineate organism and environment within one generation, thus defining the physiological individual. Based on the paradigmatic instantiations of immune systems, immune interactions and, thus, the physiological individual are believed to last only for one generation. However, in recent years, transgenerationally persisting immune responses have been reported in several phyla, but the consequences for physiological individuality have not yet (...) been explored. In this article, I will introduce an invertebrate immune system that is RNA-based and operates through a heritable silencing/licensing paradigm. I will discuss how such a perspective on immune systems can illuminate our conceptions of individuality. I will particularly introduce an account of immunological individuality that is not restricted to one generation. (shrink)

Despite emerging attention to Indigenous philosophies both within and outside of feminism, Indigenous logics remain relatively underexplored and underappreciated. By amplifying the voices of recent Indigenous philosophies and literatures, I seek to demonstrate that Indigenous logic is a crucial aspect of Indigenous resurgence as well as political and ethical resistance. Indigenous philosophies provide alternatives to the colonial, masculinist tendencies of classical logic in the form of paraconsistent—many-valued—logics. Specifically, when Indigenous logics embrace the possibility of true contradictions, they highlight aspects of (...) the world rejected and ignored by classical logic and inspire a relational, decolonial imaginary. To demonstrate this, I look to biology, from which Indigenous logics are often explicitly excluded, and consider one problem that would benefit from an Indigenous, paraconsistent analysis: that of the biological individual. This article is an effort to expand the arenas in which allied feminists can responsibly take up and deploy these decolonial logics. (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)

Recently, philosophers have sought to determine the nature of individuals relevant to evolution by natural selection or evolutionary individuals. The Evolutionary Contingency Thesis is a claim about evolution that emphasizes the role of contingency or dependency relations and chance-based factors in how evolution unfolds. In this article, I argue that if we take evolutionary contingency seriously, then we should be pluralists about the types of individuals in selection.

I consider the relationship between scientific practice and the philosophical debate surrounding biological individuality. I argue for the sensitivity account, on which biologists do not require a resolution to the individuality debate. This view puts me in disagreement with much of the literature on biological individuality, where it has become common to claim that there is a relationship of dependence between biologists’ conceptions of individuality and the quality of their empirical work.

Philosophers of biology typically pose questions about individuation by asking “what is an individual?” For example, we ask, “what is an individual species”, “what is an individual organism”, and “what is an individual gene?” In the first part of this chapter, I present my account of the gene concept and how it is used in investigative practices in order to motivate a more pragmatic approach. Instead of asking “what is a gene?”, I ask: “how do biologists individuate genes?”, “for what (...) purposes?”, and “do their practices of individuating genes serve these purposes?" In the second part of this chapter, I propose that we use this approach when analyzing concepts of organisms and biological individuals. Following philosophical pragmatism, I argue that we should abstain from attempts to situate individuation of Darwinian individuals or of holobionts in a philosophy of nature. Instead, we should analyze practices of individuating organisms in terms of three-place relations between the world, ideas, and human purposes and actions. I conclude with three lessons: an ontological, an epistemological, and a meta-philosophical lesson, which I suggest, apply to philosophy of science generally and to philosophy and metaphysics at large. (shrink)

Given the central place organisms occupy in Kant’s account of living nature, it might seem unlikely that his claims about biological wholes could be relevant to current debates over the problem of biological individuality. These debates acknowledge the multiple realizability of biological individuality in vastly different forms, including parts of organisms and complex groups of organisms at various levels of the biological hierarchy, sparking much controversy in attempts to characterize a biological individual. I argue that, far from being irrelevant to (...) this controversy, Kant’s account provides a key insight for addressing the multiple realizability problem. I show how the reciprocal causality between a self-organizing whole and its parts, which Kant thinks characterizes a natural end, is not limited to organisms but is exhibited by numerous types of beings in living nature. Self-organizing wholes of various kinds, and at various biological levels, may count as biological individuals, depending on the degree to which their functionally integrated parts are represented by reflective judgement as a natural end. (shrink)

One Health medicine aims to improve health by focusing on the relations between the health of humans, animals, and the environment. However, One Health does not provide a clear idea of these relations, which are still represented as conceptually separated and not as one health, as the name implies. Inspired by holobiont research, I suggest a new model and conceptual framework for One Health that expands the notion of the biological patient by providing a gradational and dynamic understanding of environments, (...) patients, and their relations. This new model conceptualizes humans and non-humans, individual organisms, and collectives, as belonging to one system that allows for more or less inclusive understandings of patients. As such, it resolves the conceptual tensions of different One Health approaches and supports the implementation of One Health as an interdisciplinary research field. (shrink)

This article proposes two conditions to assess whether an entity at a level of description is a unit of selection qua interactor. These two conditions make it possible to (1) distinguish biologically relevant entities from arbitrary ones and (2) distinguish units that can _potentially_ enter a selection process from those that have already done so. I show that the classical approaches used in the literature on units and levels of selection do not fare well with respect to either or both (...) of these desiderata. (shrink)

The philosophy of biology is witnessing an increasing enthusiasm for what can be called “individuals thinking”. Individuals thinking is a perspective on the metaphysics of biological entities according to which conceiving of them as individuals rather than kinds enables us to expose ongoing metaphysical debates as focusing on the wrong question, and to achieve better accounts of the metaphysics of biological entities. In this paper, I examine two cases of individuals thinking, the claim that species are individuals and the claim (...) that life on Earth is an individual. I argue that these claims fail to do the metaphysical work that one would want them to do. I highlight problems with the specific claims as well as with the general notion of ‘individual’, and argue that naturalistic metaphysicians of biology should think of the metaphysical status of theoretical entities, such as species and life, as fundamentally theory-dependent. This implies a metaphysical pluralism, that allows that in some theories species, life, and other such entities may feature as individuals, whereas in others they may feature as kinds. (shrink)

In this introductory article to the special issue on Multi-level semiosis we attempt to stage the background for qualifying the notion of “multi-levelness” when considering communication processes and semiosis in all life forms, i.e. from the cellular to the organismic level. While structures are organized hierarchically, communication processes require a kind of processual organization that may be better described as being heterarchical. Theoretically, the challenge arises in the temporal domain, that is, in the developmental and evolutionary dimension of dynamic semiotic (...) processes. We discuss the importance of this fundamental difference in order to explain how levels, domains and orders of magnitude, on the one hand, and synchronic and diachronic processes, on the other, contribute to the overall organization of every living being. To account for such multi-level organization, semiotic freedom is assumed to be a scalar property that endows living systems at different levels and domains with the capacity to ponder selectively the overall structural coherence and functional compatibility of their heterarchical processing, which is increasingly less conditioned by the underlying molecular determinism. (shrink)

Cognitive science has been beset for thirty years by foundational disputes about the nature and extension of cognition—e.g. whether cognition is necessarily representational, whether cognitive processes extend outside the brain or body, and whether plants or microbes have them. Whereas previous philosophical work aimed to settle these disputes, I aim to understand what conception of cognition scientists could share given that they disagree so fundamentally. To this end, I develop a number of variations on traditional conceptual explication, and defend a (...) novel explication of cognition called the sensitive management hypothesis. -/- Since expert judgments about the extension of “cognition” vary so much, I argue that there is value in explication that accurately models the variance in judgments rather than taking sides or treating that variance as noise. I say of explications that accomplish this that they are ecumenically extensionally adequate. Thus, rather than adjudicating whether, say, plants can have cognitive processes like humans, an ecumenically adequate explication should classify these cases differently: human cognitive processes as paradigmatically cognitive, and plant processes as controversially cognitive. -/- I achieve ecumenical adequacy by articulating conceptual explications with parameters, or terms that can be assigned a number of distinct interpretations based on the background commitments of participants in a discourse. For example, an explication might require that cognition cause “behavior,” and imply that plant processes are cognitive or not depending on whether anything plants do can be considered “behavior.” Parameterization provides a unified treatment of embattled concepts by isolating topics of disagreement in a small number of parameters. -/- I incorporate these innovations into an account on which cognition is the “sensitive management of organismal behavior.” The sensitive management hypothesis is ecumenically extensionally adequate, accurately classifying a broad variety of cases as paradigmatically or controversially cognitive phenomena. I also describe an extremely permissive version of the sensitive management hypothesis, arguing that it has the potential to explain several features of cognitive scientific discourse, including various facts about the way cognitive scientists ascribe representations to cognitive systems. (shrink)

According to many philosophical accounts, health is related to the functions and capacities of biological parts. But how do we decide what constitutes the health subject (that is, the bearer of health and disease states) and its biological parts whose functions are relevant for assessing its health? Current science, especially microbiome science, complicating the boundaries between organisms and their environments undermines any straightforward answer. This article explains why this question matters, delineates a few broad options, offers arguments against one option, (...) and draws some modest implications for philosophical accounts of human health. (shrink)

Evolutionary Transitions in Individuality have been responsible for the major transitions in levels of selection and individuality in natural history, such as the origins of prokaryotic and eukaryotic cells, multicellular organisms, and eusocial insects. The integrated hierarchical organization of life thereby emerged as groups of individuals repeatedly evolved into new and more complex kinds of individuals. The Social Protocell Hypothesis proposes that the integrated hierarchical organization of human culture can also be understood as the outcome of an ETI—one that produced (...) a “cultural organism” from a substrate of socially learned traditions that were contained in growing and dividing social communities. The SPH predicts that a threshold degree of evolutionary individuality would have been achieved by 2.0–2.5 Mya, followed by an increasing degree of evolutionary individuality as the ETI unfolded. We here assess the SPH by applying a battery of criteria—developed to assess evolutionary individuality in biological units—to cultural units across the evolutionary history of Homo. We find an increasing agreement with these criteria, which buttresses the claim that an ETI occurred in the cultural realm. (shrink)

The units or levels of selection debate concerns the question of what kind of biological systems are stable enough that part of their evolution is a result of the process of natural selection acting at their level. Traditionally, the debate has concerned at least two different, though related, questions: the question of the level at which interaction with the environment occurs, and the question of the level at which reproduction occurs. In recent years, biologists and philosophers have discussed a new (...) aspect of this debate, namely the possibility that certain multi-species consortia formed by a host and its microbiome may act as a unit of selection. This thesis, however, has not been without criticism, as it is doubtful that such consortia could meet the conditions required to achieve the degree of stability that would allow them to experience natural selection. The purpose of this paper is to systematically examine such criticisms and to defend the thesis that the holobiont/hologenome can act as a genuine level of selection both in the form of an interactor and in the form of a reproducer. To do so, it will be argued that the microbiome should be characterized in functional rather than taxonomic terms. (shrink)

Cancer—and scientific research on cancer—raises a variety of compelling philosophical questions. This entry will focus on four topics, which philosophers of science have begun to explore and debate. First, scientific classifications of cancer have as yet failed to yield a unified taxonomy. There is a diversity of classificatory schemes for cancer, and while some are hierarchical, others appear to be “cross-cutting,” or non-nested. This literature thus raises a variety of questions about the nature of the disease and disease classification. Second, (...) philosophers of science have historically taken the aim of science to be arriving at true theories. However, scientists studying cancer come from a variety of disciplines, with different scientific as well as practical aims. Perhaps it is not surprising, then, that historians and philosophers of science do not seem to agree on how best to characterize the aim and structure of cancer research; it is far from clear whether the appropriate characterization of the aim is arriving at true theories, or even whether the proper units of analysis are “theories”, or instead, “models”, “explanatory frameworks”, “research programs”, “paradigms”, or perhaps, “experimental traditions”. With the rise of “big data” science—such as the Cancer Genome Atlas Project (or TCGA)—and “systems” approaches to the study of disease, both philosophers and historians of science are rethinking how best to describe and explain these distinctive kinds of scientific inquiry. -/- Third, cancer is in part a byproduct of our developmental and life history, as well as our evolutionary history. Cancer progression can be compared to a reversion of development, or, to the evolution of multicellularity. Thus, cancer raises intriguing questions about how we conceive of “functions”, “development”, and the role of our evolutionary history and particularly, selective trade-offs, in vulnerability to disease. -/- Last but not least, cancer research provides a case study for consideration of the roles of values at the science-policy interface. Epidemiological and toxicological research on cancer’s causes informs toxics law and regulatory policy, which raises a variety of questions about the nature of evidence and inductive risk in such contexts. (shrink)