The problem of plant individuality is something which has vexed botanists throughout the ages, with fashion swinging back and forth from treating plants as communities of individuals (Darwin 1800 ; Braun and Stone 1853 ; Münch 1938 ) to treating them as organisms in their own right, and although the latter view has dominated mainstream thought most recently (Harper 1977 ; Cook 1985 ; Ariew and Lewontin 2004 ), a lively debate conducted mostly in Scandinavian journals proves that the issues (...) are far from being resolved (Tuomi and Vuorisalo 1989b ; Fagerström 1992 ; Pan and Price 2001 ). In this paper I settle the matter once and for all, by showing which elements of each side are correct. (shrink)

The historiography of immunology since 1999 is reviewed, in part as a response to claims by historians such as Thomas Söderqvist the field was still immature at the time. First addressed are the difficulties, past and present, surrounding the disciplinary definition of immunology, which is followed by a commentary on the recent scholarship devoted to the concept of the immune self. The new literature on broad immunological topics is examined and assessed, and specific charges leveled against the paucity of certain (...) types of histories, e.g. biographical and institutional histories, are evaluated. In conclusion, there are compelling indications that the history of immunology has moved past the initial tentative stages identified in the earlier reviews to become a bustling, pluripotent discipline, much like the subject of its scrutiny, and that it continues to develop in many new and exciting directions. (shrink)

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

In this commentary of Koonin’s target paper, we defend an extended view of CRISPR-Cas immunity by arguing that CRISPR-Cas includes, but cannot be reduced to, defence against nonself. CRISPR-Cas systems can target endogenous elements and tolerate exogenous elements. We conclude that the vocabulary of “defence” and “nonself” might be misleading when describing CRISPR-Cas systems.

This special issue of Biological Theory is focused on development; it raises the problem of the temporal and spatial boundaries of development. From a temporal point of view, when does development start and stop? From a spatial point of view, what is it exactly that "develops", and is it possible to delineate clearly the developing entity? This issue explores the possible answers to these questions, and thus sheds light on the definition of development itself.

Darwin’s classic ‘Origin of Species’ (Darwin 1859) described forces of selection acting upon individuals, but there remains a great deal of controversy about what exactly the status and definition of a biological individual is. Recently some authors have argued that the individual is dispensable – that an inability to pin it down is not problematic because little rests on it anyway. The aim of this paper is to show that there is a real problem of biological individuality, and an urgent (...) need to arbitrate over the current plethora of solutions to it. (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)

Thomas Pradeu’s The Limits of the Self provides a precise account of biological identity developed from the central concepts of immunology. Yet the central concepts most relevant to this task are themselves deemed inadequate, suffering from ambiguity and imprecision. Pradeu seeks to remedy this by proposing a new guiding theory for immunology, the continuity theory. From this, an account of biological identity is provided in terms of uniqueness and individuality, ultimately leading to a defense of the heterogeneous organism as expressing (...) the highest degree of individuality. (shrink)

In recent years, immune systems have sparked considerable interest within the philosophy of science. One issue that has received increased attention is whether other phyla besides vertebrates display an adaptive immune system. Particularly the discovery of CRISPR-Cas9-based systems has triggered a discussion about how to classify adaptive immune systems. One question that has not been addressed yet is the transgenerational aspect of the CRISPR-Cas9-based response. If immunity is acquired and inherited, how to distinguish evolutionary from immunological adaptation? To shed light (...) on this issue and obtain conceptual clarity, I will investigate the inheritance of small RNA responses to pathogens in the nematode C. elegans as a further potential instantiation of a transgenerational adaptive immune system. I will explore how to make sense of systems that lie at the crossroads between genetic, immunological, and evolutionary spheres and explore the consequences of a transgenerational perspective on immune systems for immunology and its philosophy. (shrink)

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

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)

All living organisms are under stress imposed by their surrounding environments. They must adapt to their stressors to live and survive. At the forefront of this adaptation is a defense system called immunity. Immunity, as the most ancient cognitive apparatus with memory function, is present in all living organisms. In previous reports, minimal cognitive function was defined as a “biologized” concept—namely, perception of elements in a milieu, integration of perceived information, reaction according to integrated information, and memory of that experience. (...) In this study, I aim to explore the essential feature of immunity by synthesizing scientific facts and “metaphysicalizing” them with logical reasoning. As a result of my analysis, I have realized the essential element in immunity: the capacity to preserve the existence of organisms by regulating their physiology and pathology. Having further analyzed immunity with special reference to the philosophy of Baruch Spinoza and George Canguilhem, _conatus_ (“appetite”, to be precise) with normative activities is deeply embedded in immunity and may constitute its essential feature. Given that _conatus_ and normativity imply mental elements, including the judgment of good and bad or health and disease, it is possible to conclude that the essential function of immunity includes cognition with normative connotations. This inclusive view encourages us to rethink the fundamental nature and philosophical implications of immunity from the cognitive perspective. (shrink)

This article traces the ubiquitous geopolitical metaphors used by researchers in the field of pregnancy-related microchimerism. In this research domain, immunologists and medical geneticists locate ‘non-self’ cells in women by marking Y chromosomes in cells derived from their sons. In the course of this research trajectory, experiments have yielded a number of surprises, beginning with the very presence of these cells in women decades after pregnancy. This finding confounded the expectations predicted by classical immunology, which posits the destruction of such (...) ‘foreign’ entities. Once they were known to be present, fetal cells were implicated in pathological and destructive activity. In a series of reorientations in which metaphor, theory and practice are entangled with matter, the characterization of these cells has shifted from invaders to insurgent foreigners to assimilated productive immigrants. The article reflects on this rich domain of material-semiotic practice to demonstrate that the case of fetomaternal cell trafficking contributes to a growing uneasiness with dominant ontologies of bodies as bounded, defended, pure collectives of homogeneous inhabitants. (shrink)

Immunology — though deeply experimental in everyday practice — is also a theoretical discipline. Recent advances in the understanding of innate immunity, how it is triggered and how it shares features that have previously been uniquely ascribed to the adaptive immune system, can contribute to the refinement of the theoretical framework of immunology. In particular, natural killer cells and macrophages are activated by transient modifications, but adapt to long-lasting modifications that occur in the surrounding tissue environment. This process facilitates the (...) maintenance of self-tolerance while permitting efficient immune responses. In this Essay we extend this idea to other components of the immune system and we propose some general principles that lay the foundations for a unifying theory of immunity — the discontinuity theory. According to this theoretical framework, effector immune responses (namely, activated responses that lead to the potential elimination of the target antigen) are induced by an antigenic discontinuity; that is, by the sudden modification of molecular motifs with which immune cells interact. (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)

The issue of what is proper to nature, or life itself, is central to critical accounts of biomedicine and its complex interrelations with social, political and economic forces. These engagements, namely biopolitical accounts of medical practices and ethical-political critiques of biomedical discourse, grapple with the indistinction between the political and biological that biomedicine enacts. Making a significant contribution to both literatures, Ed Cohen’s A Body Worth Defending argues that the emergence of the concept of biological immunity signals the entry of (...) politics into life itself and, as such, constitutes a concrete example of biopolitics. This article examines Cohen’s account of how the political becomes biological, and the view of life it assumes. Seeking to open up the question of biology, it draws on the work of Georges Canguilhem, and New Materialist accounts of matter–meaning entanglement, to offer a reading of knowledge and life, or politics and biology, as ontologically entangled. (shrink)