Immunity, DEvelopment, and the Microbiota (IDEM): Understanding the Continuous Construction of Biological Identity

ercIDEM is an ERC-funded project (2015-2020) located at the interface between philosophy of biology and biology. Hosted by the CNRS in Bordeaux, France, IDEM is conducted by Thomas Pradeu.


Megan Diddie

Credit: Megan Diddie

IDEM (“Immunity, DEvelopment, and the Microbiota”) explores the problem of biological identity at the interface between immunology, microbiology, and developmental biology.

Biological Identity at the Crossroads

The problem of biological identity (what counts as one individual organism, and what makes each individual organism the “same” though it constantly changes through time?) has a long history both in philosophy and in science. Recent data coming from immunology, microbiology and developmental biology may revolutionize our conception of the construction of biological identity through time, by showing that this construction depends crucially on environmental factors and, most importantly, on a constant dialogue with symbiotic microorganisms integrated into the organism (the “microbiota”).

IDEM aims at exploring how research done on the microbiota at the interface between developmental biology, microbiology and immunology impacts our conception of biological identity, and providing a new understanding of the way living things are continuously constructed through time and interact with their biotic environment.

A fundamentally interdisciplinary project at the crossroads of philosophy and biology:

  • (i) assessing from a conceptual and historical point of view the reality of this proclaimed “revolution” in today’s biology

  • (ii) understanding the exact mechanisms by which developmental processes in organisms depend on microbial symbionts

  • (iii) asking whether the role of the immune system (usually seen as a system that rejects genetically foreign elements from the body) in the maintenance of the organism needs to be reevaluated

  • (iv) determining how traditional conceptions of biological individuality may be modified by current research on the microbiota


Former Team Members

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

Lynn CHIU (Associated Researcher of ImmunoConcept, University of Bordeaux/CNRS)

Derek SKILLINGS (Starting from Fall 2019: Assistant Professor of Philosophy at UNC Greensboro, USA)


Funding and opportunities

  • ERC project IDEM has received €1,454,000 in financing.
  • This funding will make it possible to hire 4 postdocs and 1 PhD, and to ensure to all IDEM members that they will have excellent working conditions: a desk and all office facilities, online access to journals, the possibility to be involved in lab experiments, the opportunity to spend several months in world-leading partner labs (CIML, Pasteur Institute, Marine station of Villefranche), funds to participate in international conferences and workshops, etc.


  • IDEM research is done mainly at the University of Bordeaux, France, and more precisely in the Immunology Lab, which is part of the College of Health Sciences. Though IDEM’s focus is first and foremost on the domain of philosophy of biology, it will benefit greatly from its direct environment, which is one of the most important communities of biologists and medical doctors in France.
  • The research team will gather twice a month, to make possible a close oversight of the PhD student and post-docs and to develop constant synergies. It is expected that the PhD student and post-docs involved in IDEM will finish the project with excellent CVs and wide international recognition, with at least 2 co-authored papers (with scientists and/or philosophers), and 2 single-authored papers.
  • The team will benefit from regular interactions with excellent philosophers (both locally and internationally), and, perhaps more originally, excellent scientists and medical doctors.


IDEM examines four main themes. 

  • > Identity, internalism and externalism in the biological sciences
  • > Disentangling the causes of development
  • > The “holobiont” and its construction through the integration of microbes
  • > The role of the immune system in the maintenance and construction of the organism

Each theme will be explored by one or several team members (postdocs/PhD), under the supervision of Thomas Pradeu (principal investigator).

All team members will be normally based at the University of Bordeaux with the PI, but they will spend at least six months in a partner scientific lab of outstanding international reputation, under the supervision of the lab head.


workshop will be organized every year, one on each of the four sub-projects.

  • summer school, probably devoted to “The interactions between development and immunity in the microbiota era”, will be organized at the end of Year 4.
  • On the fifth year an international conference will be the occasion to present the results of IDEM to a wide scientific community.

5th of May 2020, Bordeaux

Microbiota and Development


Thomas Bosch, University of Kiel, Germany
Nadine Cerf-Bensussan, IMAGINE Insitut, France
Scott Gilbert, Swarthmore College, USA
Margeret McFall-Ngai, University of Hawai’i, USA

Date do be set

Role of the immune system in the maintenance of the organism

Save the date: July 1-5 2019

Summer school on: Microbiota, Symbiosis, and Individuality: Conceptual and Philosophical Issues

For more details click here.

May 6th – 7th 2020

International Conference on Immunity, Development, and the Microbiota


  • Eric Vivier (CIML, Marseille-Luminy, France)
    • Gérard Eberl (Microenvironment and Immunity Lab, Pasteur Institute, Paris, France)
  • Margaret McFall-Ngai (University of Hawai, USA)
    • Eric Bapteste (“Aire” Lab, CNRS & UPMC, Paris, France).
  • Evelyn Houliston (Developmental Biology Lab, Marine station of Villefranche-sur-Mer, France)
  • Scott Gilbert (Swarthmore College, USA, and Helsinki Evo-Devo Lab, University of Helsinki, Finland)
  • Alessandro Minelli (University of Padova, Italy)
  • Michel Vervoort (Paris-Diderot University, France).
  • John Dupré (University of Exeter, UK)
  • Peter Godfrey-Smith (CUNY, USA)
  • Alan Love (University of Minnesota, USA)
  • Jim Griesemer (UC Davis, USA)
  • Elliott Sober (University of Wisconsin Madison, USA)
  • Ellen Clarke (All Souls, Oxford University, UK)
  • Marc Ereshefsky (University of Calgary, Canada)
  • At IHPST (Paris): Jean GayonPhilippe HunemanMax Kistler
  • Melinda Fagan 
  • Matt Haber 
  • Sara Green