Resident microbiota do not just shape host immunity, they can also contribute to host protection against pathogens and infectious diseases. Previous reviews of the protective roles of the microbiota have focused exclusively on colonization resistance localized within a microenvironment. This review shows that the protection against pathogens also involves the mitigation of pathogenic impact without eliminating the pathogens (i.e., “disease tolerance”) and the containment of microorganisms to prevent pathogenic spread. Protective microorganisms can have an impact beyond their niche, interfering with (...) the entry, establishment, growth, and spread of pathogenic microorganisms. More fundamentally, we propose a series of conceptual clarifications in support of the idea of a “co-immunity,” where an organism is protected by both its own immune system and components of its microbiota. -/- . (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)

Problems raised by complex life cycles for standard summaries of evolutionary processes, and for concepts of individuality in biology, are described. I then outline a framework that can be used to compare life cycles. This framework treats reproduction as a combination of production and recurrence and organizes life cycles according to the distribution of steps in which multiplication, bottlenecks, and sex occur. I also discuss fitness and its measurement in complex life cycles and consider some phenomena that raise complications and (...) difficulties for my framework. (shrink)

Though viruses have generally been characterized by their pathogenic and more generally harmful effects, many examples of mutualistic viruses exist. Here I explain how the idea of mutualistic viruses has been defended in recent virology, and I explore four important conceptual and practical consequences of this idea. I ask to what extent this research modifies the way scientists might search for new viruses, our notion of how the host immune system interacts with microbes, the development of new therapeutic approaches, and, (...) finally, the role played by the criterion of autonomy in our understanding of living things. Overall, I suggest that the recognition of mutualistic viruses plays a major role in a wider ongoing revision of our conception of viruses. (shrink)

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)

Griffiths and Stotz’s Genetics and Philosophy: An Introduction offers a very good overview of scientific and philosophical issues raised by present-day genetics. Examining, in particular, the questions of how a “gene” should be defined and what a gene does from a causal point of view, the authors explore the different domains of the life sciences in which genetics has come to play a decisive role, from Mendelian genetics to molecular genetics, behavioural genetics, and evolution. In this review, I highlight what (...) I consider as the two main theses of the book, namely: genes are better conceived as tools; genes become causes only in a context. I situate these two theses in the wider perspective of developmental systems theory. This leads me to emphasize that Griffiths and Stotz reflect very well an on going process in genetics, which I call the “epigenetization” of genetics, i.e., the growing interest in the complex processes by which gene activation is regulated. I then make a factual objection, which is that Griffiths and Stotz have almost entirely neglected the perspective of ecological developmental biology, and more precisely recent work on developmental symbioses, and I suggest that this omission is unfortunate in so far as an examination of developmental symbioses would have considerably strengthened Griffiths and Stotz’s own conclusions. (shrink)

Regeneration capabilities are found in most or all animals. Whether regeneration is part of the development of an animal or a distinct phenomenon independent of development is a debatable question. If we consider regeneration as a process belonging to development, similarly to embryogenesis or metamorphosis, the existence of regenerative capabilities in adults can be seen as an argument in favor of the theory that development continues throughout the life of animals. Here I perform a comparative analysis of regeneration versus “classical” (...) developmental processes in animals in order to determine to what extent these processes are inclusive or distinct. I identify the existence of regeneration-specific processes, i.e., processes that occur during the regeneration, but not the initial development, of a given structure. In addition, I find that seemingly similar processes acting during development and regeneration may have differential molecular and cellular bases. I thus conclude that there are significant differences between regeneration processes in adult animals and developmental processes occurring during earlier phases of the life cycle. The existence of regenerative capabilities in adult animals can therefore not be used as an argument in favor of the idea that development spans the whole life. (shrink)

Slightly modified excerpt from the section 13.4 Zusammenfassung und Ausblick (translated into englisch): This chapter is based on an analysis of ethical debates on epigenetics and genome editing, debates, in which ethical arguments relating to future generations and justice play a central role. The analysis aims to contextualize new developments in genetic engineering, such as genome and epigenome editing, ethically. At the beginning, the assumptions of "genetic determinism," on which "genetic essentialism" is based, of "epigenetic determinism" as well as "genetic" (...) and "epigenetic exceptionalism" are analyzed and critically discussed. The remarks on the ethical discourse on epigenetics show that the notion of "epigenetic determinism" can sometimes be discerned not only in popular scientific discourse but also in ethical discourse. Ethical debates on epigenetics, however, have distanced themselves from this deterministic understanding. As a result, the focus in the ethical discourse on epigenetics shifts from responsibility for one's own health and that of subsequent generations to justice. What is meant here is justice, for example, in terms of access to healthy environmental conditions, regardless of whether these contribute to health with or without epigenetic agency. An analysis of the discourse on genome editing reveals that it is primarily germline interventions that are being ethically examined, with a concentration on the aspect of inheritance. The question is whether this is accompanied by an implicit "genetic determinism" or even a "genetic essentialism": the determinism could lie in the centrality of the aspect of heritability, since only genetic information is inherited. Does the aspect of heritability and genome modification play a more decisive role in debates on genome editing than the safety issue? Is the problem of embryos and their potential offspring not being able to consent to germline intervention given such a high priority because it is a genetic intervention? Under such a premise of "strong genetic determinism" supplemented by "epigenetic determinism," not only genome editing but also epigenome editing would be ethically relevant precisely because it too would have an influence on the genome. How this influence of genome editing and epigenome editing is ethically evaluated in each case therefore depends initially on whether the assumptions of "genetic" and "epigenetic determinism" are advocated. These assumptions are increasingly viewed critically in ethical discourse because they cannot be confirmed from a scientific perspective. In popular scientific debates in particular, however, they seem to persist, which ultimately also influences the public discussion. Since a broad public discussion is required especially on genome editing, a reflective approach to the various "-isms" analyzed in this chapter is central. DOI: 10.5771/9783748927242. (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)

Recently, there has been a growing interest, both within theoretical biology and the philosophy of biology, in the possibility and desirability of a theory of development. Among the many issues raised within this debate, the questions of the spatial and temporal boundaries of development have received particular attention. In this article, noting that so far the discussion has mostly centered on the processes of morphogenesis and organogenesis, we argue that an important missing element in the equation, namely the development of (...) language and cognition in general, may play an important role in settling the issue of temporal boundaries. After examining the idea that the development of language, cognition, and action are bona fide biological processes, we explore the consequences for a general theory of development of taking them into consideration. (shrink)

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)

Both concepts of the holobiont and the immune system are at the heart of an ongoing scientific and philosophical examination concerning questions of the organism’s individuality and identity as well as the relations between organisms and their environment. Examining the holobiont, the question of boundaries and individuality is challenging because it is both an assemblage of organisms with physiological cohesive aspects. I discuss the concept of immunity and the immune system function from the holobiont perspective. Because of the host-microbial close (...) relations of codependence and interdependence, the holobiont is more often than not confused with the host, as the host is the domain in which this entity exists. I discuss the holobiont unique ecological characteristics of microbial assemblages connected to a host in a network of interactions in which the host is one of the organisms in the community but also its landscape. Therefore, I suggest viewing the holobiont as a host-ecosystem and discuss the implication of such a view on the concept of immunity and the meaning of protection. Furthermore, I show that viewing the holobiont as a host ecosystem opens the possibility of using the same ecological definition of boundaries and immunity dealing with an ecological system. Thus, the holobiont’s boundaries and immunity are defined by the persistence of its complex system of interactions integrating existing and new interactions. This way of thinking presents a notion of immunity that materializes as the result of the complex interdependence relations between the different organisms composing the holobiont similar to that of an ecosystem. Taking this view further, I discuss the notion of immunogenicity that is ontologically heterogeneous with various causal explanations of the processes of tolerance and targeted immune response. Finally, I discuss the possible conceptualization of already existing and new biomedical practices. (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)

Since, it has become clear that individuality is not to be considered as a given, but rather as something which needs to be explained. How has individuality emerged through evolution, and how has it subsequently been maintained? In particular, why is it that multicellular organisms appeared and persisted, despite the obvious interest of each cell of favoring its own replication? Several biologists see the immune system as one of the key components for explaining the maintenance of multicellular organisms’ individuality. Indeed, (...) the immune system exerts a constant surveillance on all the constituents of the organism, including “cheaters” like tumor cells, which favor their own replication at the expense of the whole organism. In most cases, the immune system eliminates those cheaters. This is the “immune surveillance” hypothesis, first suggested by Burnet and Thomas. In this paper, I account for recent findings on immune surveillance in order to determine the precise role of the immune system in the emergence and maintenance of individuality. This investigation gives rise to a critical question for the domain of biological individuality: should immunity be considered as something unique to multicellular organisms? If it is indeed unique, should the multicellular organism be considered as an individual to a higher degree than any other living entity? If it is not unique, what precisely are the equivalents of the immune system in other living individuals? (shrink)

Non-adjacent or long-distance dependencies (LDDs) are routinely considered to be a distinctive trait of language, which purportedly locates it higher than other sequentially organized signal systems in terms of structural complexity. This paper argues that particular languages display specific resources (e.g. non-interpretive morphological agreement paradigms) that help the brain system responsible for dealing with LDDs to develop the capacity of acquiring and processing expressions with such a human-typical degree of computational complexity. Independently obtained naturalistic data is discussed and put to (...) the service of the idea that the above-mentioned resources exert their developmental role from the outside, but in compliance with other internal resources, ultimately compounding an integrated developmental system. Parallels with other human and nonhuman developmental phenomena are explored, which point to the conclusion that the developmental system of concern can be assimilated to cases currently been conceptualized as ‘cue-response systems’ or ‘developmental hybrids’ within the ecological-developmental paradigm in theoretical biology. Such a conclusion is used to support the idea that both current externalist and internalist concepts fall short of a correct characterization of language. (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)

Many aspects of biology, such as population genetics and senescence, are predicated on identifying individuals and generations. Conventional demarcations of individuals and generations, such as physiological autonomy, unicellular bottlenecks, and alternation of generation, are rife with problems. Do physically separated cuttings or plant ramets constitute separate individuals or generations? Are chimaeras one or more individuals? To resolve these problems, Clarke : 321–361, 2012) proposed that individuals are circumscribed by mechanisms that constrain heritable variance in fitness. Simultaneously, Gorelick and Heng : (...) 1088–1098 2011) showed that sex constrains heritable variance Therefore, for eukaryotes, meiosis and karyogamy provide a consistent way to demarcate individuals and generations. Epigenetic reset associated with meiosis and karyogamy rejuvenates the next generation, but not the parent that engaged in the sex act. Wholesale epigenetic resets that probably only occur with meiosis and karyogamy imply that monozygotic twins are two different individuals, but apomictic progeny are diffuse parts of one disaggregated individual. Mitotic heritability circumscribes an individual, whereas meiotic heritability demarcates new individuals and generations. (shrink)

The paper links discussions of two topics: biological individuality and the simplest forms of mentality. I discuss several attempts to locate the boundary between metabolic activity and ‘minimal cognition.’ I then look at differences between the kinds of individuality present in unicellular life, multicellular life in general, and animals of several kinds. Nervous systems, which are clearly relevant to cognition and subjectivity, also play an important role in the form of individuality seen in animals. The last part of the paper (...) links these biological transitions to the evolutionary history of subjective experience. (shrink)

Two major philosophical movements have sought to fundamentally rethink the relationship between humans and their environment(s): environmental ethics and enactivism. Surprisingly, they virtually never refer to or seek inspiration from each other. The goal of this analysis is to bridge the gap. Our main purpose, then, is to address, from the enactivist angle, the conceptual backbone of environmental ethics, namely the concept of intrinsic value. We argue that intrinsic value does indeed exist, yet its "intrinsicality" does not boil down to (...) being independent of the interests and needs of humans. Rather, it is brought forth by what we callshared enactionof an axiological domain. The latter is built upon such core posits of enactivism as autonomy, enaction, participatory sense-making as well as the most recent concept of loving as knowing proposed by Hanne De Jaegher. (shrink)

The aim of the present paper is to explore whether seasonal outbreaks of infectious diseases may be linked to changes in host microbiomes. This is a very important issue, because one way to have more control over seasonal outbreaks is to understand the factors that underlie them. In this paper, I will evaluate the relevance of the microbiome as one of such factors. The paper is based on two pillars of reasoning. Firstly, on the idea that microbiomes play an important (...) role in their hosts’ defence against infectious diseases. Secondly, on the idea that microbiomes are not stable, but change seasonally. These two ideas are combined in order to argue that seasonal changes in a given microbiome may influence the functionality of the host's immune system and consequently make it easier for infectious agents to infect the host at certain times of year. I will argue that, while this is only a theoretical possibility, certain studies may back up such claims. Furthermore, I will show that this does not necessarily contradict other hypotheses aimed at explaining seasonal outbreaks; in fact, it may even enhance them. (shrink)

The tacit standard view that development ends once reproductive capacity is acquired (reproductive boundary, or ‘‘RB,’’ thesis) has recently been challenged by biologists and philosophers of biology arguing that development continues until death (death boundary, or ‘‘DB,’’ thesis). The relevance of these two theses is difficult to assess because the fact that there is no precise definition of development makes the determination of its temporal boundaries problematic. Taking into account this difficulty, this article tries to develop a new species-dependent perspective (...) on temporal boundaries of development. This species-dependent account stands against both RB and DB theses since neither of them reflects the differences between species in the temporality of their development. In this perspective, I propose to use stem cells as a tool to analyze (1) the different developmental capacities of an organism during its life; and (2) the different developmental temporal capacities between species. In particular, I will show that stem cells enable four distinct temporal developmental patterns to be distinguished, i.e., four distinct temporal boundaries of development in the living. I show how these four patterns can be interpreted differently depending on the perspective one has on the definition of development. (shrink)

Developmental biology is expanding into several new areas. One new area of study concerns the production of adult-onset phenotypes by exposure of the fetus or neonate to environmental agents. These agents include maternal nutrients, developmental modulators (endocrine disruptors), and maternal care. In all three cases, a major mechanism for the generation of the altered phenotype is chromatin modification. Nutrient conditions, developmental modulators, and even maternal care appear to alter DNA methylation and other associated changes in chromatin that regulate gene expression. (...) This brings a new, under-appreciated, dimension of gene regulation into developmental biology, and it also demonstrates the poverty of the nature versus nurture framework for discussing phenotype production. Moreover, while such epigenetic mechanisms undermine genetic determinism, they add a layer of probabilistic biological causality for the maintenance of social inequalities. (shrink)

Abstract“Development” suggests that there is something that is developing, or changing over time. We can ask about temporal boundaries of that developmental process, asking when development begins or ends and whether it has defined stages along the way, for example. We can ask about spatial boundaries as well: where does the developing object start and end? For this article, I ask about the boundary definition of the developing organism in particular. What is an individual organism, and what defines it as (...) the same organism as it changes over time? In particular, how has this been answered historically: how have researchers described and explained what an individual developing organism is? This article explores ideas and approaches especially starting in the late 19th century, and in particular looks at the role of “organization.”. (shrink)

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.

This paper aims to clarify the consequences of new scientific and philosophical approaches for the practical-theoretical framework of modern developmental biology. I highlight normal development, and the instructive-permissive distinction, as key parts of this framework which shape how variation is conceptualised and managed. Furthermore, I establish the different dimensions of biological variation: the units, temporality and mode of variation. Using the analytical frame established by this, I interpret a selection of examples as challenges to the instructive-permissive distinction. These examples include (...) the phenomena of developmental plasticity and transdifferentiation, the role of the microbiome in development, and new methodological approaches to standardisation and the assessment of causes. Furthermore, I argue that investigations into organismal development should investigate the effects of a wider range of kinds of variation including variation in the units, modes and temporalities of development. I close by examining various possible opportunities for producing and using normal development free of the assumptions of the instructive-permissive distinction. These opportunities are afforded by recent developments, which include new ways of producing standards incorporating more natural variation and being based on function rather than structure, and the ability to produce, store, and process large quantities of data. (shrink)