Recently claims have been made for radical new insights in the field of invertebrate immunology that involve memory, specificity and/or maternal transfer of immunocompetence. For evidence these claims rely on phenomena, such as survival or reproductive capacity, observed at the level of the whole organism. The allure of these apparently revelatory hypotheses is that they are contrary to established views of innate immunity. They draw implicit analogy to adaptive responses in jawed vertebrates and the terminology used creates an incomplete and (...) misleading picture. We argue that the case for adaptive immunity in invertebrates based only on such phenomena is weak and flawed, as it can only be upheld if supported by descriptions of the underlying mechanisms. We caution against a reliance on this approach as a means of advancing this field—highlighting, as an example, some negative commercial implications of adopting this approach. BioEssays 29:1138–1146, 2007. © 2007 Wiley Periodicals, Inc. (shrink)

The main objective of immunology is to establish why and when an immune response occurs, that is, to determine a criterion of immunogenicity. According to the consensus view, the proper criterion of immunogenicity lies in the discrimination between self and nonself. Here we challenge this consensus by suggesting a simpler and more comprehensive criterion, the criterion of continuity. Moreover, we show that this criterion may be considered as an interpretation of the immune 'self'. We conclude that immunologists can continue to (...) speak of the self, provided that they admit that the self/nonself discrimination is not an adequate criterion of immunogenicity. (shrink)

Contemporary immunology has established its fundamental theory as a biological expression of personal identity, wherein the "immune self" is defended by the immune system. Protection of this agent putatively requires a cognitive capacity by which the self and the foreign are perceived and thereby discriminated; from such information, discernment of the environment is achieved and activation of pathways leading to an immune response may be initiated. This so-called cognitive paradigm embeds such functions as "perception," "recognition," "learning," and "memory" to characterize (...) immune processes, but the conceptual character of such functions has meanings that vary with the particular theory adopted. When different formulations of cognition are considered, immunology's conceptual infrastructure shifts: Extensions of conventional psychological understanding of representational cognition based on a subject-object dichotomy support notions of immune agency; alternatively, formulations of perception that dispense with representations and attendant notions of agency reconfigure the predicate epistemology dominating current immune theory. Reviewing immunological literature of the past five decades, these two understandings of perception – representational and non-representational – offer competing views of immune cognitive functions. These, in turn, provide competing philosophical understandings of immunology's conceptual foundations, which reflect parallel controversies dominating current debates in philosophy of mind and attendant discussions about personal identity. (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 multicellular eukaryotes with multiple species of persistent symbionts. They are not individuals in the genetic sense— composed of and regulated by the same genome—but they are anatomical, physiological, developmental, immunological, and evolutionary units, evolved from a shared relationship between different species. We argue that many of the interactions between human and microbiota symbionts and the reproductive process of a new holobiont are best understood as instances of reciprocal scaffolding of developmental processes and mutual construction of developmental, ecological, and (...) evolutionary niches. Our examples show that mother, fetus, and different symbiotic microbial communities induce or constitute conditions for the development and reproduction of one another. These include the direct induction of maternal or fetus physiological changes, the restructuring of ecological relations between communities, and evolutionary selection against undesirable competitors. The mutual scaffolding and niche constructing processes start early—prior to amniotic rupture. We are evolutionarily, physiologically, and developmentally integrated holobiont systems, strung together through mutual reliance and mutual construction. Bringing the processes of niche construction and developmental scaffolding together to interpret holobiont birth conceptually scaffolds two new directions for research: in niche construction, identifying the evolutionary implications of organisms actively constructing multiple overlapping niches and scaffolds, and in Evolutionary Developmental Biology, characterizing evolutionary and ecological processes as developmental causes. (shrink)

This Element presents a philosophical exploration of the concept of the 'model organism' in contemporary biology. Thinking about model organisms enables us to examine how living organisms have been brought into the laboratory and used to gain a better understanding of biology, and to explore the research practices, commitments, and norms underlying this understanding. We contend that model organisms are key components of a distinctive way of doing research. We focus on what makes model organisms an important type of model, (...) and how the use of these models has shaped biological knowledge, including how model organisms represent, how they are used as tools for intervention, and how the representational commitments linked to their use as models affect the research practices associated with them. This title is available as Open Access on Cambridge Core. (shrink)

This book explores the ways in which the spatio-temporal contingency of human life is being conceived in different fields of research. Specifically, it looks at the relationship between the situatedness of human life, the situation or place in which human life is supposed to be situated, and the dimensions of space and time in which both situation and place are usually themselves supposed to be situated. Over the last two or three decades, the spatio-temporal contingency of human life has become (...) an important topic of research in a broad range of different disciplines including the social sciences, the cultural sciences, the cognitive sciences, and philosophy. However, this research topic is referred to in quite different ways: while some researchers refer to it in terms of “situation”, emphasizing the “situatedness” of human experience and action, others refer to it in terms of “place”, emphasizing the “power of place” and advocating a “topological” or “topographical turn” in the context of a larger “spatial turn”. Interdisciplinary exchange is so far hampered by the fact that the notions referred to and the relationships between them are usually not sufficiently questioned. This book addresses these issues by bringing together contributions on the spatio-temporal contingency of human life from different fields of research. (shrink)

In his insightful review, Eugene V. Koonin discusses various aspects of CRISPR-Cas systems with a strong focus on their qualities as "adaptive immune systems". The CRISPR-Cas system is most famous for its application as a gene-editing tool. Koonin provides a deeper insight into its biological function in bacteria, which is to immunize the cell against parasite DNA. I shall comment on one issue discussed in the text, in two steps. First, I shall elaborate on CRISPR-Cas systems and their supposed Lamarckian (...) character. Criteria for calling biological phenomena genuinely Lamarckian will be narrowed down and then applied to the CRISPR-Cas system, considering interference-driven spacer acquisition as an instantiation of a truly Lamarckian paradigm. Second, I shall consider whether Lamarckian and "canonical" instances of inheritance are a case of theoretical pluralism, being two non-reducible, yet interconnected paradigms. (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)

The discovery of RNA interference in 1998 has made a lasting impact on biological research. Identifying the regulatory role of small RNAs changed the modes of molecular biological inquiry as well as biologists' understanding of genetic regulation. This article examines the early years of small RNA biology's success story. I query which factors had to come together so that small RNA research came into life in the blink of an eye. I primarily look at scientific repertoires as facilitators of rapid (...) scientific change. I show that for a short period of time, between the years 1998 and 2002, different model organism communities, investigative strategies, technological innovations, and research interests could be successfully aligned to take small RNA research off the ground. I discuss how the keystone discoveries were situated in specific experimental traditions and what strategies were employed to establish these discoveries as more general phenomena. Providing thus a practice-based approach of rapid scientific change, I ask how to relate the change in propositional bits of scientific knowledge with changes in scientific practice. (shrink)

The CRISPR-Cas systems of bacterial and archaeal adaptive immunity have become a household name among biologists and even the general public thanks to the unprecedented success of the new generation of genome editing tools utilizing Cas proteins. However, the fundamental biological features of CRISPR-Cas are of no lesser interest and have major impacts on our understanding of the evolution of antivirus defense, host-parasite coevolution, self versus non-self discrimination and mechanisms of adaptation. CRISPR-Cas systems present the best known case in point (...) for Lamarckian evolution, i.e. generation of heritable, adaptive genomic changes in response to encounters with external factors, in this case, foreign nucleic acids. CRISPR-Cas systems employ multiple mechanisms of self versus non-self discrimination but, as is the case with immune systems in general, are nevertheless costly because autoimmunity cannot be eliminated completely. In addition to the autoimmunity, the fitness cost of CRISPR-Cas systems appears to be determined by their inhibitory effect on horizontal gene transfer, curtailing evolutionary innovation. Hence the dynamic evolution of CRISPR-Cas loci that are frequently lost and acquired by archaea and bacteria. Another fundamental biological feature of CRISPR-Cas is its intimate connection with programmed cell death and dormancy induction in microbes. In this and, possibly, other immune systems, active immune response appears to be coupled to a different form of defense, namely, “altruistic” shutdown of cellular functions resulting in protection of neighboring cells. Finally, analysis of the evolutionary connections of Cas proteins reveals multiple contributions of mobile genetic elements to the origin of various components of CRISPR-Cas systems, furthermore, different biological systems that function by genome manipulation appear to have evolved convergently from unrelated MGE. The shared features of adaptive defense systems and MGE, namely the ability to recognize and cleave unique sites in genomes, make them ideal candidates for genome editing and engineering tools. (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.

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)

Immunology is central to contemporary biology and medicine, but it also provides novel philosophical insights. Its most significant contribution to philosophy concerns the understanding of biological individuality: what a biological individual is, what makes it unique, how its boundaries are established and what ensures its identity through time. Immunology also offers answers to some of the most interesting philosophical questions. What is the definition of life? How are bodily systems delineated? How do the mind and the body interact? In this (...) Element, Thomas Pradeu considers the ways in which immunology can shed light on these and other important philosophical issues. This title is also available as Open Access on Cambridge Core. (shrink)

It has long been taken for granted that the immune system’s capacity to protect an individual from infection and disease depends on the power of the system to distinguish between self and nonself. However, accumulating data have undermined this fundamental concept. Evidence against the self/nonself discrimination model left researchers in need of a new overarching framework able to capture the immune system’s reactivity. Here, I highlight that along with the self/nonself model, another powerful representation of the immune system’s reactivity has (...) been developed in the twentieth century immunology. According to this alternative view, the immune system is not a killer of nonself strangers but a peace-maker helping to establish harmony with the environment. The balance view of the system has never become part of the dominant paradigm. However, it is gaining more and more currency as new research develops. Advances in mucosal immunology confirm that instead of distinguishing between self and foreign the immune system reacts to microbial, chemical and self-induced alterations to produce responses that counterbalance effects of these changes. (shrink)

Recent findings have provided evidence for the existence of non‐vertebrate acquired immunity. We survey these findings and propose that all living organisms must express both innate and acquired immunity. This is opposed to the paradigm that only vertebrates manifest the two forms of immune mechanism; other species are thought to use innate immunity alone. We suggest new definitions of innate and acquired immunity, based on whether immune recognition molecules are encoded in the inherited genome or are generated through somatic processes. (...) We reason that both forms of immunity are similarly ancient, and have co‐evolved in response to lifestyle, cost‐benefit tradeoffs and symbiosis versus parasitism. However, different species have evolved different immune solutions that are not necessarily genetically related, but serve a similar general function – allowing individuals to learn from their own immune experience; survival of species is contingent on the acquired immune experience of its individuals. (shrink)