This chapter draws on insights from non-equilibrium thermodynamics to demonstrate the ontological inadequacy of the machine conception of the organism. The thermodynamic character of living systems underlies the importance of metabolism and calls for the adoption of a processual view, exemplified by the Heraclitean metaphor of the stream of life. This alternative conception is explored in its various historical formulations and the extent to which it captures the nature of living systems is examined. Following this, the chapter considers the metaphysical (...) implications of reconceptualizing the organism from complex machine to flowing stream. What do we learn when we reject the mechanical and embrace the processual? Three key lessons for biological ontology are identified. The first is that activity is a necessary condition for existence. The second is that persistence is grounded in the continuous self-maintenance of form. And the third is that order does not entail design. (shrink)

This chapter argues that scientific and philosophical progress in our understanding of the living world requires that we abandon a metaphysics of things in favour of one centred on processes. We identify three main empirical motivations for adopting a process ontology in biology: metabolic turnover, life cycles, and ecological interdependence. We show how taking a processual stance in the philosophy of biology enables us to ground existing critiques of essentialism, reductionism, and mechanicism, all of which have traditionally been associated with (...) substance ontology. We illustrate the consequences of embracing an ontology of processes in biology by considering some of its implications for physiology, genetics, evolution, and medicine. And we attempt to locate the subsequent chapters of the book in relation to the position we defend. (shrink)

The “land community” (or “biotic community”) that features centrally in Aldo Leopold’s Land Ethic has typically been equated with the concept of “ecosystem.” Moreover, some have challenged this central Leopoldean concept given the multitude of meanings of the term “ecosystem” and the changes the term has undergone since Leopold’s time (see, e.g., Shrader-Frechette 1996). Even one of Leopold’s primary defenders, J. Baird Callicott, asserts that there are difficulties in identifying the boundaries of ecosystems and suggests that we recognize that their (...) boundaries are determined by scientific questions ecologists pose (Callicott 2013). I argue that we need to rethink Leopold’s concept of land community in the following ways. First, we should recognize that Leopold’s views are not identical to those of his contemporaries (e.g., Clements, Elton), although they resemble those of some subsequent ecologists, including some of our contemporaries (e.g., O’Neill 2001, Post et al. 2007, Hastings and Gross 2012). Second, the land community concept does not map cleanly onto the concept of “ecosystem”; it also incorporates elements of the “community” concept in community ecology by emphasizing the interactions between organisms and not just the matter/energy flow of the ecosystem concept. Third, the boundary question can be illuminated by considering some of the recent literature on the nature of biological individuals (in particular, Odenbaugh 2007; Hamilton, Smith, and Haber 2009; Millstein 2009), focusing on concentrations of causal relations as determinative of the boundaries of the land community qua individual. There are challenges to be worked out, particularly when the interactions of community members do not map cleanly onto matter/energy flows, but I argue that these challenges can be resolved. The result is a defensible land community concept that is ontologically robust enough to be a locus of moral obligation while being consistent with contemporary ecological theory and practice. (shrink)

This paper argues that the medical conception of health as absence of disease is a value-free theoretical notion. Its main elements are biological function and statistical normality, in contrast to various other ideas prominent in the literature on health. Apart from universal environmental injuries, diseases are internal states that depress a functional ability below species-typical levels. Health as freedom from disease is then statistical normality of function, i.e., the ability to perform all typical physiological functions with at least typical efficiency. (...) This conception of health is as value-free as statements of biological function. The view that health is essentially value-laden, held by most writers on the topic, seems to have one of two sources: an assumption that health judgments must be practical judgments about the treatment of patients, or a commitment to "positive" health beyond the absence of disease. I suggest that the assumption is mistaken, the commitment possibly misdescribed. (shrink)

Population health has recently grown from a series of loosely connected critiques of twentieth-century public health and medicine into a theoretical framework with a corresponding field of research—population health science. Its approach is to promote the public’s health through improving everyday human life: affordable nutritious food, clean air, safe places where children can play, living wages, etc. It recognizes that addressing contemporary health challenges such as the prevalence of type 2 diabetes will take much more than good hospitals and public (...) health departments. -/- Blending philosophy of science/medicine, public health ethics and history, this book offers a framework that explains, analyses and largely endorses the features that define this relatively new field. Presenting a philosophical perspective, Valles helps to clarify what these features are and why they matter, including: searching for health’s “upstream” causes in social life, embracing a professional commitment to studying and ameliorating the staggering health inequities in and between populations; and reforming scientific practices to foster humility and respect among the many scientists and non- scientists who must work collaboratively to promote health. -/- Featuring illustrative case studies from around the globe at the end of all main chapters, this radical monograph is written to be accessible to all scholars and advanced students who have an interest in health—from public health students to professional philosophers. (shrink)

In Immunity, Alfred Tauber sets forth a new theory of immunology that rejects the common principle of self and non-self, and the immune system's role as a protector of the self from external threats. Rather than serving to defend an independent entity, he argues, immunity participates in a large, complex eco-system of porous and flexible boundaries. Tauber's new approach to immunology necessitates a new biology in which symbiosis is the rule, not the exception.

Holobionts are symbiotic assemblages composed by a macrobe host plus its symbiotic microbiota. In recent years, the ontological status of holobionts has created a great amount of controversy among philosophers and biologists: are holobionts biological individuals or are they rather ecological communities of independent individuals that interact together? Chiu and Eberl have recently developed an eco-immunity account of the holobiont wherein holobionts are neither biological individuals nor ecological communities, but hybrids between a host and its microbiota. According to their account, (...) the microbiota is not a proper part of the holobiont. Yet, it should be regarded as a set of scaffolds that support the individuality of the host. In this paper, we approach Chiu and Eberl’s account from a metaphysical perspective and argue that, contrary to what the authors claim, the eco-immunity account entails that the microorganisms that compose the host’s microbiota are proper parts of the holobiont. Second, we argue that by claiming that holobionts are hybrids, and therefore, not biological individuals, the authors seem to be assuming a controversial position about the ontology of hybrids, which are conventionally characterized as a type of biological individual. In doing so, our paper aligns with the contemporary tendency to incorporate metaphysical resources to shed light on current biological debates and builds on that to provide additional support to the consideration of holobionts as biological individuals from an eco-immunity perspective. (shrink)

It is now widely accepted that microorganisms play many important roles in the lives of plants and animals. Every macroorganism has been shaped in some way by microorganisms. The recognition of the ubiquity and importance of microorganisms has led some to argue for a revolution in how we understand biological individuality and the primary units of natural selection. The term “holobiont” was introduced as a name for the biological unit made up by a host and all of its associated microorganisms, (...) and much of this new debate about biological individuality has focused on whether holobionts are integrated individuals or communities. In this paper, I show how parts of the holobiont can span both characterizations. I argue that most holobionts share more affinities with communities than they do with organisms, and that, except for maybe in rare cases, holobionts do not meet the criteria for being organisms, evolutionary individuals, or units of selection. (shrink)

Taking the case of H. pylori and ulcer, Lynch et al., demonstrate how framing Koch’s postulate by an interventionist account clarifies the latter’s explanatory strength in proportionality with the weaknesses in specificity and stability due to the influence of background conditions. They suggest this approach as an efficient way to bypass the enigma of background conditions and microbial activity in the microbiome’s causal relations. However, it is the background conditions and the microbial interactions in the stomach that determine whether the (...) presence of H. pylori results in an ulcer. I agree with their analysis of the problems and challenges with the microbiome causal explanation but argue that their suggested framework is insufficient without a proper understanding and inclusion of the background conditions and microbial interactions. The reductionist approach fits well within the model of causal explanation that centers on one causal entity. However, such a model is weak in specificity and is too broad because it does not address the factors of microbial activity and background conditions. I argue that for a better causal explanation with explanatory strength in specificity, it is essential to include the background conditions and microbial interactions. Furthermore, I argue that this inclusion changes the framework of the causal relations from looking for the causal entity to looking at the causal process. (shrink)

Over the last three decades, studies in microbiology have exposed a world of diverse and dynamic interactions. Through metagenomic sequencing, complex bacterial communities became visible and proved important for many biological phenomena. As a result of discovering the connection between microorganisms and organisms’ survival, the notion of the holobiont has become prominent and has been suggested as a biological individual. The view of the holobiont as an individual, commonly known as the Hologenome Theory, focuses on the interactions and relations between (...) the host and its symbionts in the host’s development and evolution. Today, the holobiont is at the heart of the debate on the nature of the biological individual, a debate which is connected to the same question about the nature of the individual organism. (shrink)

I examine the feminist epistemic values in science, presented by Helen Longino, and their role in framing microbiome causality in the study of inflammatory bowel disease (IBD). In particular, I show how values presented as feminist give an alternative view in scientific theories—focusing on ontological heterogeneity and mutuality of interactions rather than simplicity and one causal direction—when looking at relations between organisms and microorganisms, and between organisms (particularly humans) and their environment. I identify two approaches in microbiome study, an immunological (...) approach that looks at the microbiome pathogenicity and an ecological approach that studies the microbial activity and functions. I show the puzzles stemming from the traditional background beliefs of the immune self and germ theory in the study of IBD causality. Furthermore, I argue for the benefits of a shift to the ecological view of body-microbe interrelations. I conclude with the benefits and advantages of feminist values over traditional ones, both in creating new ways of understanding organisms’ physiology and immune systems and for future biomedical studies involving microbiome causality. (shrink)

Over the last three decades, studies in microbiology have exposed a world of diverse and dynamic interactions. Through metagenomic sequencing, complex bacterial communities became visible and proved important for many biological phenomena. As a result of discovering the connection between microorganisms and organisms’ survival, the notion of the holobiont has become prominent and has been suggested as a biological individual. The view of the holobiont as an individual, commonly known as the Hologenome Theory, focuses on the interactions and relations between (...) the host and its symbionts in the host’s development and evolution. Today, the holobiont is at the heart of the debate on the nature of the biological individual, a debate which is connected to the same question about the nature of the individual organism. (shrink)

Holobionts, consisting of a host and diverse microbial symbionts, function as distinct biological entities anatomically, metabolically, immunologically, and developmentally. Symbionts can be transmitted from parent to offspring by a variety of vertical and horizontal methods. Holobionts can be considered levels of selection in evolution because they are well-defined interactors, replicators/reproducers, and manifestors of adaptation. An initial mathematical model is presented to help understand how holobionts evolve. The model offered combines the processes of horizontal symbiont transfer, within-host symbiont proliferation, vertical symbiont (...) transmission, and holobiont selection. The model offers equations for the population dynamics and evolution of holobionts whose hologenomes differ in gene copy number, not in allelic or loci identity. The model may readily be extended to include variation among holobionts in the gene identities of both symbionts and host. (shrink)

The organism is one of the fundamental concepts of biology and has been at the center of many discussions about biological individuality, yet what exactly it is can be confusing. The definition that we find generally useful is that an organism is a unit in which all the subunits have evolved to be highly cooperative, with very little conflict. We focus on how often organisms evolve from two or more formerly independent organisms. Two canonical transitions of this type—replicators clustered in (...) cells and endosymbiotic organelles within host cells—demonstrate the reality of this kind of evolutionary transition and suggest conditions that can favor it. These conditions include co-transmission of the partners across generations and rules that strongly regulate and limit conflict, such as a fair meiosis. Recently, much attention has been given to associations of animals with microbes involved in their nutrition. These range from tight endosymbiotic associations like those between aphids and Buchnera bacteria, to the complex communities in animal intestines. Here, starting with a reflection about identity through time, we consider the distinctions between these kinds of animal–bacteria interactions and describe the criteria by which a few can be considered jointly organismal but most cannot. (shrink)

The self/non-self model, first proposed by F.M. Burnet, has dominated immunology for 60 years now. According to this model, any foreign element will trigger an immune reaction in an organism, whereas endogenous elements will not, in normal circumstances, induce an immune reaction. In this paper we show that the self/non-self model is no longer an appropriate explanation of experimental data in immunology, and that this inadequacy may be rooted in an excessively strong metaphysical conception of biological identity. We suggest that (...) another hypothesis, one based on the notion of continuity, gives a better account of immune phenomena. Finally, we underscore the mapping between this metaphysical deflation from self to continuity in immunology and the philosophical debate between substantialism and empiricism about identity. (shrink)

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)

Since the 1950s, the common view of development has been internalist: development is seen as the result of the unfolding of potentialities already present in the egg cell. In this article, I show that this view is incorrect because of the crucial influence of the environment on development. I focus on a fascinating example, that of the role played by symbioses in development, especially bacterial symbioses, a phenomenon found in virtually all organisms (plants, invertebrates, and vertebrates). I claim that we (...) must consequently modify our conception of the boundaries of the developing entity, and I show how immunology can help us in accomplishing this task. I conclude that the developing entity encompasses many elements traditionally seen as “foreign,” while I reject the idea that there is no possible distinction between the organism and its environment. (shrink)

In this essay I first provide an analysis of various community concepts. Second, I evaluate two of the most serious challenges to the existence of communities—gradient and paleoecological analysis respectively—arguing that, properly understood, neither threatens the existence of communities construed interactively. Finally, I apply the same interactive approach to ecosystem ecology, arguing that ecosystems may exist robustly as well. ‡I would like to thank to the participants at the Ecology and Environmental Ethics Conference at the University of Utah, the Philosophy (...) of Ecology Conference hosted by the University of Brisbane, and those participants in a session at the Philosophy of Science Association Meeting in Vancouver, British Columbia for helpful discussions of this essay. Specific thanks go to Mark Colyvan, Greg Cooper, Steve Downes, Chris Elliott, Marc Ereshefsky, Paul Griffiths, Jesse Hendrikse, Greg Mikkelson, Anya Plutynski, Kate Ritchie, Sahotra Sarkar, Kim Sterelny, and Rob Wilson. †To contact the author, please write to: Department of Philosophy, Lewis and Clark College, 0615 SW Palatine Hill Road, Portland, OR 97219; e-mail: [email protected]. (shrink)

Dominant views about the nature of health and disease in bioethics and the philosophy of medicine have presumed the existence of a fixed, stable, individual organism as the bearer of health and disease states, and as such, the appropriate target of medical therapy and ethical concern. However, recent developments in microbial biology, neuroscience, the philosophy of cognitive science, and social and personality psychology (Ickes...

I examine the use of the term function in Aldo Leopold’s land ethic, invoked as (1) the healthy functioning of the land community, which is dependent on (2) the maintenance of the characteristic functions of populations that are parts of the land community. The latter can be understood as referring to interactions between species that are the products of coevolution (such as parasite-host, predator-prey) and, thus, in terms of the “selected effect” account of function. The performance of these functions under (...) certain conditions maintain what Leopold took to be the healthy functioning of a land community. (shrink)

In their book, Defending Biodiversity, Newman, Varner, and Linquist (NVL) cast doubt on whether Leopoldian defenses of biodiversity, in their current form, have been successful. I argue that there is a more accurate interpretation of Leopold that is not subject to the criticisms made by NVL, and that Leopold’s body of work as a whole, including but not limited to the essay “The Land Ethic” in A Sand County Almanac, provides quite a bit of useful guidance and perspective. I begin (...) with a brief summary of some of my own recent work on Leopold. This is intended to orient the reader who is more familiar with J. Baird Callicott’s influential interpretations of Leopold. I then discuss NVL’s Chapter 10 first followed by a discussion of their Chapter 9, responding to their critiques. I then conclude. On the revised interpretation that I have given, Leopold’s land ethic is defended by the method of reflective equilibrium, showing us that the land communities that we are interdependent with have intrinsic value, necessitating preserving their (land) health, which in turn necessitates preserving biodiversity. (shrink)

On most understandings of what an ecosystem is, it is a kind of thing that can be literally, not just metaphorically, healthy or unhealthy. Health is best understood as a kind of well-being; a thing’s health is a matter of retaining those structures and functions that are good for it. While it is true both that what’s good for an ecosystem depends on how we define the system and that how we define the system depends on our interests, these facts (...) do not force us to the conclusion that an ecosystem has no good of its own. Ecosystems and persons can have goods of their own in spite of the fact that the schemes we use to categorize them are matters that we decide upon. (shrink)

Human microbiome research makes causal connections between entire microbial communities and a wide array of traits that range from physiological diseases to psychological states. To evaluate these causal claims, we first examine a well-known single-microbe causal explanation: of Helicobacter pylori causing ulcers. This apparently straightforward causal explanation is not so simple, however. It does not achieve a key explanatory standard in microbiology, of Koch’s postulates, which rely on manipulations of single-microorganism cultures to infer causal relationships to disease. When Koch’s postulates (...) are framed by an interventionist causal framework, it is clearer what the H. pylori explanation achieves and where its explanatory strengths lie. After assessing this ‘simple’, single-microbe case, we apply the interventionist framework to two key areas of microbiome research, in which obesity and mental health states are purportedly explained by microbiomes. Despite the experimental data available, interventionist criteria for explanation show that many of the causal claims generated by microbiome research are weak or misleading. We focus on the stability, specificity and proportionality of proposed microbiome causal explanations, and evaluate how effectively these dimensions of causal explanation are achieved in some promising avenues of research. We suggest some conceptual and explanatory strategies to improve how causal claims about microbiomes are made. (shrink)

We address the controversy in the literature concerning the definition of holobionts and the apparent constraints on their evolution using concepts from community population genetics. The genetics of holobionts, consisting of a host and diverse microbial symbionts, has been neglected in many discussions of the topic, and, where it has been discussed, a gene-centric, species-centric view, based in genomic conflict, has been predominant. Because coevolution takes place between traits or genes in two or more species and not, strictly speaking, between (...) species, it may affect some traits but not others in either host or symbiont. Moreover, when interacting species pairs are embedded in a larger community, indirect ecological effects can alter the expected pairwise dynamics. Mode of symbiont transmission and the degree of host inbreeding both affect the extent of microbial mixing across host lineages and thereby the degree to which selection on one trait of either partner affects other aspects of a holobiont phenotype. We discuss several potential defining criteria for holobionts using community genetics and population genetics models, suggesting their application and limitations. Using community genetics models, we show how conflict between genomes can be self-limiting, while cooperation and mutualism tend to be self-accelerating. It is likely that this bias in the evolutionary dynamics of interaction between hosts and symbionts is an important feature of holobionts. This bias in the evolutionary dynamic could contribute to explaining the absence of cheaters from natural mutualisms, although cheaters are predicted by gene-centered conflict theory to cause the evolutionary instability of mutualisms. Additionally, it may help explain the more frequent origin of mutualisms from parasitic than from free-living systems, an evolutionary trajectory opposite to that predicted by genome conflict theory. (shrink)

Christopher Boorse's Bio Statistical Theory (BST) defines health as the absence of disease, and disease as the adverse departure from normal species functioning. This paper presents a two-pronged problem for this account. First I demonstrate that, in order to accurately account for dynamic physiological functions, Boorse's account of normal function needs to be modified to index functions against situations. I then demonstrate that if functions are indexed against situations, the BST can no longer account for diseases that result from specific (...) environmental factors. The BST is impaled on either horn of this dilemma and therefore must be dismissed. (shrink)

Following a previous elaboration of the concept of weak individuality and some examples of its instances in ecology and biology, the article focuses on general features of the concept, arguing that in any ontological field individuals are understood on the basis of our knowledge of interactions, through the application of these general formulas for extracting individuals from interactions. Then, the specificities of the individuality in the sense of this weak concept are examined in ecology; I conclude by addressing the differences (...) between ecosystems and organisms as they appear in the viewpoint of such concept. (shrink)

Biological reproduction is a material process of intertwined, recursive propagule generation and development, assuming that development produces simple life cycles. Most organisms, however, have more or less complex life cycles. Here, I attempt to reconcile recent articulations of a reproducer account with traditional approaches to complex life cycles by generalizing genetic demarcation criteria for life cycle generations in terms of the “scaffolded” development of hybrid reproducers. I argue that scaffolding provides a general method for identifying developmental bottlenecks and suggests in (...) turn a new way of understanding developmental reaction norms. (shrink)

Given immunity’s general role in the organism’s economy—both in terms of its internal environment as well as mediating its external relations—immune theory has expanded its traditional formulation of preserving individual autonomy to one that includes accounting for nutritional processes and symbiotic relationships that require immune tolerance. When such a full ecological alignment is adopted, the immune system becomes the mediator of both defensive and assimilative environmental intercourse, where a balance of immune rejection and tolerance governs the complex interactions of the (...) organism’s ecological relationships. Accordingly, immunology, which historically had affiliated with the biology of individuals, now becomes a science concerned with the biology of communities. With this translocation, the ontological basis of the organism is undergoing a profound change. Indeed, the recent recognition of the ubiquity of symbiosis has challenged the traditional notions of biological individuality and requires a shift in the metaphysics undergirding biology, in which a philosophy of the organism must be characterized by ecological dialectics “all-the-way-down.”. (shrink)

Human microbiome research makes causal connections between entire microbial communities and a wide array of traits that range from physiological diseases to psychological states. To evaluate these causal claims, we first examine a well-known single-microbe causal explanation: of Helicobacter pylori causing ulcers. This apparently straightforward causal explanation is not so simple, however. It does not achieve a key explanatory standard in microbiology, of Koch’s postulates, which rely on manipulations of single-microorganism cultures to infer causal relationships to disease. When Koch’s postulates (...) are framed by an interventionist causal framework, it is clearer what the H. pylori explanation achieves and where its explanatory strengths lie. After assessing this ‘simple’, single-microbe case, we apply the interventionist framework to two key areas of microbiome research, in which obesity and mental health states are purportedly explained by microbiomes. Despite the experimental data available, interventionist criteria for explanation show that many of the causal claims generated by microbiome research are weak or misleading. We focus on the stability, specificity and proportionality of proposed microbiome causal explanations, and evaluate how effectively these dimensions of causal explanation are achieved in some promising avenues of research. We suggest some conceptual and explanatory strategies to improve how causal claims about microbiomes are made. (shrink)

Human microbiome research makes causal connections between entire microbial communities and a wide array of traits that range from physiological diseases to psychological states. To evaluate these causal claims, we first examine a well-known single-microbe causal explanation: of Helicobacter pylori causing ulcers. This apparently straightforward causal explanation is not so simple, however. It does not achieve a key explanatory standard in microbiology, of Koch’s postulates, which rely on manipulations of single-microorganism cultures to infer causal relationships to disease. When Koch’s postulates (...) are framed by an interventionist causal framework, it is clearer what the H. pylori explanation achieves and where its explanatory strengths lie. After assessing this ‘simple’, single-microbe case, we apply the interventionist framework to two key areas of microbiome research, in which obesity and mental health states are purportedly explained by microbiomes. Despite the experimental data available, interventionist criteria for explanation show that many of the causal claims generated by microbiome research are weak or misleading. We focus on the stability, specificity and proportionality of proposed microbiome causal explanations, and evaluate how effectively these dimensions of causal explanation are achieved in some promising avenues of research. We suggest some conceptual and explanatory strategies to improve how causal claims about microbiomes are made. (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)

This is one of the first books in a new series that will publish the very best work in the philosophy of biology. The series will be non-sectarian in character, will extend across the broadest range of topics, and will be genuinely interdisciplinary. The Immune Self is a critical study of immunology from its origins at the end of the nineteenth century to its contemporary formulation. The book offers the first extended philosophical critique of immunology, in which the function of (...) the term 'self' that underlies the structure of current immune theory is analysed. However, this analysis is carefully integrated into a broad survey of the major scientific developments in immunology, a discussion of their historical context, and a review of the conceptual arguments that have moulded this sophisticated modern science. (shrink)

Microbes and microbiology are seldom encountered in philosophical accounts of the life sciences. Although microbiology is a well-established science and microbes the basis of life on this planet, neither the organisms nor the science have been seen as philosophically significant. This book will change that. It fills a major gap in the philosophy of biology by examining central philosophical issues in microbiology. Topics are drawn from evolutionary microbiology, microbial ecology, and microbial classification. These discussions are aimed at philosophers and scientists (...) who wish to gain insight into the basic philosophical issues of microbiology. (shrink)

This is one of the first books in a new series that will publish the very best work in the philosophy of biology. The series will be non-sectarian in character, will extend across the broadest range of topics, and will be genuinely interdisciplinary. The Immune Self is a critical study of immunology from its origins at the end of the nineteenth century to its contemporary formulation. The book offers the first extended philosophical critique of immunology, in which the function of (...) the term 'self' that underlies the structure of current immune theory is analysed. However, this analysis is carefully integrated into a broad survey of the major scientific developments in immunology, a discussion of their historical context, and a review of the conceptual arguments that have moulded this sophisticated modern science. (shrink)

The Limits of the Self, will be essential reading for anyone interested in the definition of biological individuality and the understanding of the immune system.

A theoretical physicist and feminist theorist, Karen Barad elaborates her theory of agential realism, a schema that is at once a new epistemology, ontology, and ethics.

According to immunology’s prevailing paradigm, immunity is based on self/nonself discrimination and thus requires a construction of identity. Two orientations vie for dominance: The original conception, conceived in the context of infectious diseases, regards the organism as insular and autonomous, an entity that requires defense of its borders. An alternate view places the organism firmly in its environment in which both benign and onerous encounters occur. On this latter relational account, active tolerance allows for cooperative relationships with other organisms in (...) the larger ecological economy. These contending orientations —one derived from biomedicine and the other from the ecological sciences— have drawn the attention of social scientists and culture critics. On the one hand, feminists have portrayed immune theory as based upon borrowed social notions of identity that reflect male aggressive values and thus distort more balanced accounts of immunity; and, on the other hand, other commentary projects immune theory as a framework in which analysis of Western societies putatively reveals analogous patterns of ‘self’ and ‘other’ interactions, where autoimmunity and immunization are understood as expressions of the insular understanding of identity. Here, a meta-interpretation is presented that shows how these critiques place the immune self on a spectrum stretching from its formulation as an autonomous agent, a modernist conception of the independent individual, to a postmodern portrayal in which this conception of selfhood has been deconstructed. Accordingly, immunology is drawn into a wide-ranging debate about agency, where differing interpretations of immunity serves as a template in which competing understandings of human social intercourse is modeled.Según el paradigma dominante en inmunología, la inmunidad está basada en la discriminación entre yo/noyo y requiere, por tanto, una construcción de la identidad. Dos orientaciones compiten por dominar: la concepción original, concebida en el contexto de las enfermedades infecciosas contempla al organismo como aislado y autónomo, como una entidad que necesita defender sus fronteras. Una visión alternativa sitúa firmemente al organismo en su entorno, en el cual suceden tanto encuentros beneficiosos como costosos. En este enfoque relacional, la tolerancia activa permite relaciones cooperativas con otros organismos en una economía ecológica más amplia. Estas orientaciones en liza —una derivada de la biomedicina y otra de las ciencias ecológicas— han llamado la atención de los científicos sociales y de los críticos de la cultura. Por una parte, el feminismo ha descrito la teoría inmunológica como basada en nociones sociales prestadas de identidad que reflejan los valores agresivos del macho y que, de este modo, impiden una explicación más equilibrada de la inmunidad. Por otra parte, otro comentario proyecta la teoría inmunológica como un marco en el que el análisis de las sociedades occidentales revela aparentemente patrones análogos de interacciones ‘yo’ y ‘otros’, en las que la autoinmunidad y la inmunización son entendidas como expresiones de la comprensión insular de la identidad. Se ofrece aquí una meta-representación que muestra cómo estas críticas sitúan al yo inmune en un espectro que va desde su formulación cómo un agente autónomo, una concepción modernista del individuo independiente, a una visión postmoderna en la que esta concepción de la identidad ha sido deconstruida. De acuerdo con esto, la inmunología recoge un amplio debate sobre la agencia en el que diferentes interpretaciones de la inmunidad sirven como molde en el que se modelan comprensiones competidoras de la comprensión de las relaciones sociales humanas. (shrink)

The question “What is an organism?”, formerly considered as essential in biology, has now been increasingly replaced by a larger question, “What is a biological individual?”. On the grounds that i) individuation is theory-dependent, and ii) physiology does not offer a theory, biologists and philosophers of biology have claimed that it is the theory of evolution by natural selection which tells us what counts as a biological individual. Here I show that one physiological field, immunology, offers a theory, which makes (...) possible a biological individuation based on physiological grounds. I give a new answer to the question of the individuation of an organism by linking together the evolutionary and the immunological approaches to biological individuation. (shrink)

Given one conception of biological individuality (evolutionary, physiological, etc.), can a holobiont – that is the host + its symbiotic (mutualistic, commensalist and parasitic) microbiome – be simultaneously a biological individual and an ecological community? Herein, we support this possibility by arguing that the notion of biological individuality is part‐dependent. In our account, the individuality of a biological ensemble should not only be determined by the conception of biological individuality in use, but also by the biological characteristics of the part (...) of the ensemble under investigation. In the specific case of holobionts, evaluations of their individuality should be made either host‐relative or microbe‐relative. We support the claim that biological individuality is part‐dependent by drawing upon recent empirical evidence regarding the physiology of hosts and microbes, and the recent characterization of the ‘demibiont’. Our account shows that contemporary disagreements about the individuality of the holobiont derive from an incorrect understanding of the ontology of biological individuality. We show that collaboration between philosophers and biologists can be very fruitful in attempts to solve some contemporary biological debates. (shrink)