Thomas Pradeu

This volume is the best available tool to compare and appraise the different approaches of today’s biology and their conceptual frameworks, serving as a springboard for new research on a clarified conceptual basis. It is expected to constitute a key reference work for biologists and philosophers of biology, as well as for all scientists interested in understanding what is at stake in the present transformations of biological models and theories. The volume is distinguished by including, for the first time, self-reflections and exchanges of views on practice and theoretical attitudes by important participants in recent biological debates. The questions of how biological models and theories are constructed, how concepts are chosen and how different models can be articulated, are asked. Then the book explores some of these convergences between different models or theoretical frameworks. Confronting views on adaptive complexity are investigated, as well as the role of self-organization in evolution; niche construction meets developmental biology; the promises of the emergent field of ecological-evolutionary-development are examined. In sum, this book is a marvellous account of the dynamism of today’s theoretical biology. Foreword: Carving Nature at its Joints? Richard Lewontin Chapter 1: Introduction Anouk Barberousse, Michel Morange, Thomas Pradeu Chapter 2: Articulating Different Modes of Explanation: The Present Boundary in Biological Research Michel Morange Chapter 3: Compromising Positions: The Minding of Matter Susan Oyama Chapter 4:ions, Idealizations, and Evolutionary Biology Peter Godfrey-Smith Chapter 5: The Adequacy of Model Systems for Evo-Devo: Modeling the Formation Of Organisms / Modeling the Formation Of Society Scott F. Gilbert Chapter 6: Niche Construction in Evolution, Ecosystems and Developmental Biology John Odling-Smee Chapter 7: Novelty, Plasticity and Niche Construction: The Influence of Phenotypic Variation on Evolution Kim Sterelny Chapter 8: The Evolution of Complexity Mark A. Bedau Chapter 9: Self-Organization, Self-Assembly, and the Origin of Life Evelyn Fox Keller Chapter 10: Self-Organization and Complexity in Evolutionary Theory, or, In this Life the Bread Always Falls Jammy Side Down Michael Ruse.

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.

The concept of genidentity has been proposed as a way to better understand identity through time, especially in physics and biology. The genidentity view is utterly anti-substantialist in so far as it suggests that the identity of X through time does not presuppose whatsoever the existence of a permanent “core” or “substrate” of X. Yet applications of this concept to real science have been scarce and unsatisfying. In this paper, our aim is to show that a well-defined concept of functional genidentity can be crucial to shed light on identity through time in classical physics and especially in biology. Finally, we show that understanding identity on the basis of continuity suggests a move towards an ontology of processes.

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?

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.

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.

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.

Le Précis de philosophie des sciences vise à présenter, de manière pédagogique, l'état actuel des grandes questions et des grands domaines de la philosophie des sciences. C'est un ouvrage de niveau "intermédiaire", entre les ouvrages d'initiation et les ouvrages de recherche. Il peut être utilisé comme manuel pour des cours de philosophie des sciences au niveau Master, ainsi que dans le cadre de la préparation aux nouvelles épreuves d'épistémologie des CAPES scientifiques. Il a notamment pour vocation de servir de support de cours pour des enseignements en épistémologie et philosophie des sciences de niveau L3, M1 et M2.

What are individuals? How can they be identified? These are crucial questions for philosophers and scientists alike. Criteria of individuality seem to differ markedly between metaphysics and the empirical sciences - and this might well explain why no work has hitherto attempted to relate the contributions of metaphysics, physics and biology on this question. This timely volume brings together various strands of research into 'individuality', examining how different sciences handle the issue, and reflecting on how this scientific work relates to metaphysical concerns. The collection makes a major contribution to clarifying and overcoming obstacles to the construction of a general conception of the individual adequate for both physics and biology, and perhaps even beyond.

In this paper, I address the question of what the Developmental Systems Theory (DST) aims at explaining. I distinguish two lines of thought in DST, one which deals specifically with development, and tries to explain the development of the individual organism, and the other which presents itself as a reconceptualization of evolution, and tries to explain the evolution of populations of developmental systems (organism-environment units). I emphasize that, despite the claiming 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 the 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.

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.

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