Thomas Pradeu

Is it possible to explain and predict the development of living things? What is development? Articulate answers to these seemingly innocuous questions are far from straightforward. To date, no systematic, targeted effort has been made to construct a unifying theory of development. This novel work offers a unique exploration of the foundations of ontogeny by asking how the development of living things should be understood. It explores the key concepts of developmental biology, asks whether general principles of development can be discovered, and examines the role of models and theories.The two editors have assembled a team of leading contributors who are representative of the scientific and philosophical community within which a diversity of thoughts are growing, and out of which a theory of development may eventually emerge. They analyse a wealth of approaches to concepts, models and theories of development, such as gene regulatory networks, accounts based on systems biology and on physics of soft matter, the different articulations of evolution and development, symbiont-induced development, as well as the widely discussed concepts of positional information and morphogenetic field, the idea of a

The Developmental Systems Theory (DST) presented by its proponents as a challenging approach in biology is aimed at transforming the workings of the life sciences from both a theoretical and experimental point of view (see, in particular, Oyama [1985] 2000; Oyama et al. 2001). Even though some may have the impression that the enthusiasm surrounding DST has faded in very recent years, some of the key concepts, ideas, and visions of DST have in fact pervaded biology and philosophy of biology. It seems crucial to us both to establish which of these ideas are truly specific to DST, and to shift through these ideas in order to determine the criticisms they have drawn, or may draw (e.g., Sterelny et al. 1996; Griesemer 2000; Sterelny 2000; Kitcher 2001; Keller 2005; Waters 2007)

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.

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

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

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.

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.