Conceptual Biology & Medicine

The goal of our interdisciplinary team is to explore the conceptual and foundational bases of today’s biology and medicine. We reach this aim through what we call  « Philosophy in biology »,  an innovative way to combine the contributions of philosophy of biology, experimental biology, and medical biology. We are focused first and foremost on the immune system, cancer, aging, and the microbiota (particularly through our ERC-funded IDEM project), although we also work on conceptual issues related to evolutionary biology, ecology, developmental biology, physiology, and the medical sciences in general.

Our team currently works on four main projects:

  • 1.1. Understanding the triggering of an immune response

    Our aim is to offer, through the articulation of conceptual, experimental, and medical perspectives, a better characterization of how the immune system is activated. What triggers an effector or a regulatory immune response? How can concepts, theories, and models help us understand how the immune system is activated? One aspect of this investigation is the assessment of the “discontinuity theory” (Pradeu, Jaeger and Vivier 2013; Pradeu and Vivier 2016; Pradeu 2019), which states that effector immune responses are triggered by sudden changes in the molecular patterns with which immune receptors interact.

    People involved: Julie Déchanet-Merville, Hannah Kaminski, Maria Mamani, Jean-François Moreau, Thomas Pradeu, Marie-Elise Truchetet.

    Partners: Gérard Eberl, Eric Vivier.

  • 1.2. Immunity and the constant construction and maintenance of biological boundaries.

    Recent data show that the immune system is not just a system of elimination and defence, but is involved, much more broadly, in development, regulation, and repair. One key problem is to determine how the immune system constantly patrols and repairs biological boundaries, such as the epithelium and the endothelium. We are particularly interested in how innate lymphoid cells (ILCs) and gammadelta T cells are involved in this process. We are developing, with Patrick Blanco’s group, a translational program exploring the role of ILC2s in controlling and maintaining the endothelium, both in physiological and pathological conditions, including in fibrosis and systemic sclerosis.

    People involved: Patrick Blanco, Cécile Contin-Bordes, Paôline Laurent (PhD student), Valérie Jolivel (postdoc), Pauline Manicki, Jean-François Moreau, Thomas Pradeu, Marie-Elise Truchetet.

    This project was funded by the IDEX programme of the University of Bordeaux.

  • 1.3. Immunity, mobility, and aging

    Initiated by Jean-François Moreau, this project is based on the idea that mobility is central to immunity. In the transition from unicellularity to multicellularity, all cells have mostly lost their mobility – except for the immune cells. We are interested in better characterizing this link between immunity and mobility, and the way it emerged through evolution. On this ground, we propose a novel hypothesis about aging and immunosenescence, based on the idea that the increasing stiffness and cross-linking of the senescent ECM lead to progressive immunodeficiency via an age-related decrease in T cell mobility and the death of these cells.

    People involved: Jean-François Moreau, Thomas Pradeu.

    Partners: Claudio Franceschi and his lab (Bologna)

  • 1.4. Key conceptual challenges in current immunology

    This project consists in better defining immunolological concepts that both lack precision and are central in the field. The aim of our collaborative work associating philosophers of science and immunologists is to clarify such concepts so as to make them more operational in actual experimental and medical practice. Important examples of our work here include the exploration of immunological memory, self and nonself, constitutive defense, immunological exhaustion, the function of immunity in prokaryotes, and so on.

  • 1.5. Artificial intelligence in the biomedical sciences, especially immunology

    In 2021 we are starting a collaboration between our team, Patrick Blanco’s team in the lab and at the Bordeaux Hospital (especially Guillaume Martinroche, an MD working on AI), Olivier Saut’s lab (MONC, Institut de mathématiques, CNRS and Inria, Bordeaux, a lab specialized in data-driven medicine) and Fridolin Gross (ETH Zürich and Univ. Kassel), on the uses of artificial intelligence in the biomedical sciences, especially immunology. The initial step consists in implementing and assessing a machine learning assisted version of the antinuclear-antibody (ANA) test, a diagnostic test that is used as an indicator for the body’s autoimmune response, to be applied in clinical practice. We hope to expand this highly collaborative research program in the near future.

    Within Thomas Pradeu’s ERC Starting Grant project (2015-2020), entitled “IDEM” (for “Immunology, Development, and the Microbiota: Understanding the Continuous Construction of the Organism”), we aim at understanding how the microbiota is involved in the construction and maintenance of the host organism.

    IDEM consists of four areas:

    • Identity, internalism and externalism in the biological sciences

      Lynn Chiu (Sept 2015-Sept 2017)

    • Disentangling the causes of development

      Leonardo Bich (Sept 2016-Sept 2018)

    • The “holobiont” and its construction through the integration of microbes

      Derek Skillings (Sept 2016-Sept 2019)

    • The role of the immune system in the maintenance and construction of the organism

      Lynn Chiu (Sept 2017-Sept 2019)

    In total, 4 were hired in this project. For further information, please visit the ERC IDEM’s webpage.

    In collaboration with medical doctors of the Pellegrin Hospital, we formed two teams working on the microbiota: one works on immune-microbiota interactions; the other organizes meetings with internal and external speakers.

    We attempt to propose a refined definition of the notion of tumor microenvironment, at the interface between cancer biology, developmental biology, immunology, and studies on angiogenesis.

    We also explore the concept of cancer as a process of decohesion of the multicellular individual, an idea that combines cancer biology, immunology, developmental biology, evolutionary biology, and ecology. We investigate the role of the immune system as a system that maintains the cohesion of the biological individual, and how this process is disturbed in cancer.

    Cancer is one of the diseases that come with aging. At the epidemiological level, age is the most ‘explanatory’ factor of most cancers. However, this remains vague and elusive at the biological level. Which processes are associated with an increasing risk of cancer? We look for a conceptually precise theory of aging that would help understand the patterns of incidence of cancer. Beyond that, we hope this theory to be able to also account for patterns of incidence of other diseases.

    We have received funding from the Siric BRIO and we are part of the program “Intercellular COMMUnication in CANcer biology and Therapy” (COMMUCAN).

    Currently we are participating in the construction of a new interdisciplinary research program, directed by Julie Déchanet-Merville.

    People involved: Dorothée Duluc, Nicolas Larmonier, Maël Lemoine, Thomas Pradeu, Elena Rondeau, Vanja Sissirak.

    People from other labs involved: Andreas Bikfalvi (Inserm), Lucie Laplane (IHPST & IGR).

    Philosophers of medicine have investigated the broader framework of concepts of health and disease, with very general terms such as ‘function’ and ‘dysfunction’, ‘reference class’, ’norms’, ‘risk factor’, and the like. They have not investigated so much the more specific concepts of the biological sciences of health and disease, such as ‘homeostasis’, ‘robustness’ or ‘regulation’.
    More specifically, we focus on the strong association, at the population level, of the process of aging and the incidence of diseases. To do that, we investigate concepts such as ‘antagonistic pleiotropy’, ’senescence’, ‘intrinsic factor of death’, and explanatory hypotheses, models and theories of aging.

    This project is coordinated by Maël Lemoine, Professor at the University of Bordeaux.

    Participants are Jean-François Moreau, Simon Okholm

    CONTEXT

    Our team is a pillar of the Institute for Philosophy in Biology and Medicine (PhilInBioMed), an interdisciplinary institute located at the University of Bordeaux, France, and a national and international network of interdisciplinary institutes. PhilInBioMed aims at promoting philosophy in the biological and medical sciences.

    TEAM

    Team leaders: Thomas PRADEU (Research Professor) & Maël LEMOINE (Professor)

    Activities

    Institute for Philosophy in Biology and Medicine (PhilInBioMed)

    PhilInBioMed is both an interdisciplinary institute located at the University of Bordeaux, France, and a national and international network of interdisciplinary institutes. PhilInBioMed aims at promoting philosophy in the biological and medical sciences, a co-production of knowledge by the direct interactions of philosophers, biologists, and medical doctors.

    More information here.

    Contact: Thomas Pradeu

    Philosophy in Biology & Medicine Seminars

    The Philosophy & Biology Seminar is held once a month at the University of Bordeaux. Details and Program.

    Contact: Thomas Pradeu

    Microbiota Seminar

    The Microbiota seminar explores conceptual, theoretical, experimental, and medical issues concerning research on the microbiota.

    Contact: Thomas Pradeu

    Team Meetings

    Twice a month, a member of the team presents their work.

    FORMER MEMBERS

    > Leonardo BICH (Now Ramon y Cajal senior researcher at the University of the Basque Country, Spain)

    • > Imane BARBARA (Project Manager)
    •  > Wiebke BRETTING (Now Project Manager in a Bordeaux hospital-hosted project)

    > Lynn CHIU (Now Media and Communications Officer, Konrad Lorenz Institute for Evolution and Cognition Research (KLI) & Extended Evolutionary Synthesis research project, University of St. Andrews)

    • > Nicolas DUSSECH (Intern in Biology)

    > Katarzyna HOOKS (Now Postdoctoral researcher)

    > Valérie JOLIVEL (Now Associate Professor of Biology in Strasbourg)

    > Paôline LAURENT (Now Postdoctoral researcher in New York)

    > Maureen O’MALLEY (Now Senior researcher at the University of Sydney)

    > Derek SKILLINGS (Now Assistant Professor of Philosophy at UNC Greensboro, USA)

    RECENT VISITORS

    • Mina BISSELL, Professor of Biology, University of Berkeley, USA.
    • Peter GODFREY-SMITH, Professor in Philosophy of Science, University of Sydney, Australia
    • Deborah GORDON, Professor of Biology, Stanford University, USA
    • Paul GRIFFITHS, Professor in Philosophy of Science, University of Sydney, Australia
    • Fridolin GROSS, Postdoctoral researcher, University of Kassel, Germany
    • Valerie HARDCASTLE, Professor of Philosophy and Psychology, University of Cincinnati, USA
    • Alberto MANTOVANI, Professor of Medicine, Humanitas, Italy.
    • Jacob STEGENGA, Lecturer in Philosophy of Science, University of Cambridge, UK
    • Adrian STENCEL, PhD Student Jagiellonian University, Krakow, Poland
    • Martin ZACH (visiting PhD student from Oct.-Dec. 2019 and will be an EPSA Fellow in our team in the near future)
    • Javier SUAREZ, Postdoctoral Researcher, University of Bielefeld, Germany

    PUBLICATIONS

    2017

    2016

    FUNDING

    COLLABORATIONS