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)

In this article, I address the question of what Developmental Systems Theory aims at explaining. I distinguish two lines of thought in DST, one that deals specifically with development and tries to explain the development of the individual organism, and the other that presents itself as a reconceptualization of evolution and tries to explain the evolution of populations of developmental systems. I emphasize that, despite the claim of the contrary by DST proponents, there are two very different definitions of the (...) “developmental system,” and therefore DST is not a unified theory of evolution and development. I show that DST loses the most interesting aspects of its reconceptualization of development when it tries to reconceptualize evolutionary theory. I suggest that DST is about development per se, and that it fails at offering a new view on evolution. (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)

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)

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

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

No comprehensive theory of development is available yet. Traditionally, we regard the development of animals as a sequence of changes through which an adult multicellular animal is produced, starting from a single cell which is usually a fertilized egg, through increasingly complex stages. However, many phenomena that would not qualify as developmental according to these criteria would nevertheless qualify as developmental in that they imply nontrivial (e.g., non degenerative) changes of form, and/or substantial changes in gene expression. A broad, comparative (...) approach is badly needed. In the Cnidaria, for example, even the boundary between generations is problematic. Describing their life cycle in terms of metagenesis (alternation between polyp generation and medusa generation) or in terms of metamorphosis (polyp as larva or juvenile) are matters of semantics more than biology. The life cycle of other metazoans, described in textbooks in terms of larva-to-adult metamorphosis, is hardly different from a typical metagenetic life cycle of cnidarians. This applies to holometabolous insects and to marine invertebrates like sea urchins, where most of the larval cells are discarded at metamorphosis. The uncertain temporal and spatial boundaries of individual development are also shown by the widespread lack of a strict correspondence between adult and mature. A comprehensive theory of development should start with a zero principle of “developmental inertia,” corresponding to an indeterminate local self-perpetuation of cell-level dynamics. Indeterminate growth, scale-invariance, segmentation, and regeneration provide examples of developmental dynamics close to that. (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)

In this work it is proposed that the conditions of identity for biological organisms are given by the following principle: for all organisms x and y, x = y if and only if x has been caused by the self-preserving activity of y. This principle determines both the inter-temporal identity of organisms and the identity of organism in different possible worlds. It unifies what can be supposed about conditions of identity coming from —at least— three different conceptions about the nature (...) of biological organisms, those of RobertWilson, Thomas Pradeu and Ellen Clarke. These conceptions are presented and compared. (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)