Thomas Pradeu

CNRS & University Of Bordeaux
  •  22
    Reuniting philosophy and science to advance cancer research
    with Bertrand Daignan-Fornier, Andrew Ewald, Pierre-Luc Germain, Samir Okasha, Anya Plutynski, Sébastien Benzekry, Marta Bertolaso, Mina Bissell, Joel S. Brown, Benjamin Chin-Yee, Ian Chin-Yee, Hans Clevers, Laurent Cognet, Marie Darrason, Emmanuel Farge, Jean Feunteun, Jérôme Galon, Elodie Giroux, Sara Green, Fridolin Gross, Fanny Jaulin, Rob Knight, Ezio Laconi, Nicolas Larmonier, Carlo Maley, Alberto Mantovani, Violaine Moreau, Pierre Nassoy, Elena Rondeau, David Santamaria, Catherine M. Sawai, Andrei Seluanov, Gregory D. Sepich-Poore, Vanja Sisirak, Eric Solary, Sarah Yvonnet, and Lucie Laplane
    Biological Reviews 98 (5): 1668-1686. 2023.
    Cancers rely on multiple, heterogeneous processes at different scales, pertaining to many biomedical fields. Therefore, understanding cancer is necessarily an interdisciplinary task that requires placing specialised experimental and clinical research into a broader conceptual, theoretical, and methodological framework. Without such a framework, oncology will collect piecemeal results, with scant dialogue between the different scientific communities studying cancer. We argue that one important wa…Read more
  •  12
    Redrawing therapeutic boundaries: microbiota and cancer
    with Jonathan Sholl, Gregory Sepich-Poore, and Rob Knight
    Trends in Cancer 8 (2): 87-97. 2022.
    The unexpected roles of the microbiota in cancer challenge explanations of carcinogenesis that focus on tumor-intrinsic properties. Most tumors contain bacteria and viruses, and the host’s proximal and distal microbiota influence both cancer incidence and therapeutic responsiveness. Continuing the history of cancer–microbe research, these findings raise a key question: to what extent is the microbiota relevant for clinical oncology? We approach this by critically evaluating three issues: how the…Read more
  •  2
    In this contribution, I show that Jean Gayon’s work operates an original synthesis between the history of scienceHistory of science, the philosophy of science and the life sciences. I propose that the philosophy of biology as it has been constructed since the 1970s could usefully draw inspiration from this synthesis to develop a much richer and more open analysis of current biological sciences. While the philosophy of biology is very strongly dominated by the biology of evolution, the history of…Read more
  •  14
    Host-Microbiota Co-immunity: An Intimate Relationship That Goes Beyond Protection
    with Thomas Bazin and Lynn Chiu
    Philosophy, Theory, and Practice in Biology 14 (3). 2022.
    Resident microorganisms, known as the microbiota, are essential for many physiological functions including protection against pathogens. Microbiota is indeed required for proper immune system development and function, and can also host-independently protect against infections. Thus, a co-constructed view of host protection involving both host and microbiota, named ’co-immunity,’ has been proposed, and the idea of an ’immunological holobiont’ has been suggested. Yet this view of co-immunity might…Read more
  •  13
    The presence and role of microbes in human cancers has come full circle in the last century. Tumors are no longer considered aseptic, but implications for cancer biology and oncology remain underappreciated. Opportunities to identify and build translational diagnostics, prognostics, and therapeutics that exploit cancer's second genome—the metagenome—are manifold, but require careful consideration of microbial experimental idiosyncrasies that are distinct from host‐centric methods. Furthermore, t…Read more
  •  68
    The visibility of philosophy of science in the sciences, 1980–2018
    with Mahdi Khelfaoui, Yves Gingras, and Mael Lemoine
    Synthese 199 (3-4): 1-31. 2021.
    In this paper, we provide a macro level analysis of the visibility of philosophy of science in the sciences over the last four decades. Our quantitative analysis of publications and citations of philosophy of science papers, published in 17 main journals representing the discipline, contributes to the longstanding debate on the influence of philosophy of science on the sciences. It reveals the global structure of relationships that philosophy of science maintains with science, technology, engine…Read more
  •  28
    Une objectivité kaléidoscopique : construire l'image scientifique du monde
    with Pierre-Alain Braillard, Alexandre Guay, and Cyrille Imbert
    Philosophie 110 (3): 46-71. 2011.
    Dans Science, Perception and Reality, Sellars distingue l’image manifeste de l’homme et l’image scientifique de l’homme. La première est obtenue à partir de la façon dont nous prenons conscience de nous-mêmes comme humains dans le monde. La seconde correspond à ce que les différentes sciences nous amènent à postuler sur la manière dont l’homme est constitué. Van Fraassen, lui, étend au monde ces concepts...
  •  84
    Understanding viruses: Philosophical investigations
    with Gladys Kostyrka and John Dupré
    Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 59 57-63. 2016.
    Viruses have been virtually absent from philosophy of biology. In this editorial introduction, we explain why we think viruses are philosophically important. We focus on six issues, and we show how they relate to classic questions of philosophy of biology and even general philosophy.
  •  238
    Understanding Multicellularity: The Functional Organization of the Intercellular Space
    with Leonardo Bich and Jean-Francois Moreau
    Frontiers in Physiology 10. 2019.
    The aim of this paper is to provide a theoretical framework to understand how multicellular systems realize functionally integrated physiological entities by organizing their intercellular space. From a perspective centered on physiology and integration, biological systems are often characterized as organized in such a way that they realize metabolic self-production and self-maintenance. The existence and activity of their components rely on the network they realize and on the continuous managem…Read more
  •  16
    Philosophy of Immunology
    Cambridge University Press. 2020.
    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 delineat…Read more
  •  66
    The Boundaries of Development
    with Lucie Laplane, Michel Morange, Antonine Nicoglou, and Michel Vervoort
    Biological Theory 6 (1). 2011.
    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
  •  163
    Immune-mediated repair: a matter of repair
    with Paôline Laurent, Marie-Elise Truchetet, Valérie Jolivel, Pauline Manicki, and Lynn Chiu
    Frontiers in Immunology 8 454. 2017.
  •  22
    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.
  •  72
    Genidentity and Biological Processes
    In Daniel J. Nicholson & John Dupré (eds.), Everything Flows: Towards a Processual Philosophy of Biology, Oxford University Press. 2018.
    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 v…Read more
  •  35
    CRISPR-Cas immunity: beyond nonself and defence
    with Jean-François Moreau
    Biology and Philosophy 34 (1): 6. 2019.
    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.
  •  3
    This chapter introduces the main issues and themes of the volume. Approaches to individuality from metaphysics and philosophy of science are contrasted. Recent philosophical developments regarding concepts of biological and physical individuality are exposed. These research trends show how philosophy of physics and philosophy of biology address differently the question of what an individual is. Five main divergences are identified: the centrality of part-whole questions, the issue of identical i…Read more
  •  157
    Several advocates of the lively field of “metaphysics of science” have recently argued that a naturalistic metaphysics should be based solely on current science, and that it should replace more traditional, intuition-based, forms of metaphysics. The aim of the present paper is to assess that claim by examining the relations between metaphysics of science and general metaphysics. We show that the current metaphysical battlefield is richer and more complex than a simple dichotomy between “metaphys…Read more
  •  456
    Ontologies of Living Beings: Introduction
    Philosophy, Theory, and Practice in Biology 9 (4). 2017.
    Part of a special issue, Ontologies of Living Beings, guest-edited by A. M. Ferner and Thomas Pradeu
  •  45
    Thirty years of Biology & Philosophy: philosophy of which biology?
    Biology and Philosophy 32 (2): 149-167. 2017.
    Which domains of biology do philosophers of biology primarily study? The fact that philosophy of biology has been dominated by an interest for evolutionary biology is widely admitted, but it has not been strictly demonstrated. Here I analyse the topics of all the papers published in Biology & Philosophy, just as the journal celebrates its thirtieth anniversary. I then compare the distribution of biological topics in Biology & Philosophy with that of the scientific journal Proceedings of the Nati…Read more
  •  299
    Protective Microbiota: From Localized to Long-Reaching Co-Immunity
    with Lynn Chiu, Thomas Bazin, Marie-Elise Truchetet, Thierry Schaeverbeke, and Laurence Delhaes
    Frontiers Immunology 8 1678. 2017.
    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 pre…Read more
  •  77
    The Limits of the Self, will be essential reading for anyone interested in the definition of biological individuality and the understanding of the immune system.
  •  9
    Towards a Theory of Development (edited book)
    with Alessandro Minelli
    Oxford University Press UK. 2014.
    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 genera…Read more
  • Quand et pourquoi une réponse immunitaire est-elle déclenchée?
    Bulletin de la Société Française D’Immunologie 115 7--7. 2007.
  •  74
    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 s…Read more
  •  55
    Mutualistic viruses and the heteronomy of life
    Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 59 80-88. 2016.
    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…Read more
  •  2
    First human face allograft: early report. Commentary
    with Patrick Warnke, Carosella H., D. Edgardo, Bernard Devauchelle, Lionel Badet, Benoit Lengele, Emmanuel Morelon, Sylvie Testelin, Mauricette Michallet, Cédric D'Hauthuille, and Others
    Lancet 368 (9531). 2006.
  • Immune System
    Science 325 393--393. 2009.
  •  29
    The Organism in Developmental Systems Theory
    Biological Theory 5 (3): 216-222. 2009.
    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 d…Read more