ERC Starting Grant Project (2015-2020)

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

Principal investigator (PI): Thomas Pradeu


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

Four postdocs and one PhD student will be hired.

For a full description of the project and related activities, see: ERC IDEM


International Workshop (Bordeaux, France, June 14-16, 2016):

30 years after The Dialectical Biologist:
New Frontiers in Ecological Developmental Biology and
Microbiota-Host Co-Construction

In memory of Richard Levins (1930-2016)

See description: Dialectical Biologist Workshop


Two additional Postdoc Positions have been fulfilled

(Starting date: October 2016)

See description of Development Postdoc and Holobiont Postdoc


One Postdoc Position has been fulfilled (Starting date: October 2015) (see Internalism-Externalism Postdoc).

One Postdoc Position and one PhD Position will be available in September 2017



Project presentation

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, a fundamentally interdisciplinary project at the crossroads of philosophy and biology, aims at:

(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; and

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

>>> For a full description of the project, see Detailed research statement.



IDEM examines four main themes. 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 (except for Postdoc #1) they will spend at least six months in a partner scientific lab of outstanding international reputation, under the supervision of the lab head.



Team member normally based in Partner scientific lab (and scientific supervisor) for the 6-month stay
Identity, internalism and externalism in the biological sciences


(Sept 2015-Sept 2017)

Centre for immunology, Bordeaux

Centre for immunology, Bordeaux

(Julie Déchanet-Merville)

Disentangling the causes of development


(Sept 2016-Sept 2018)

Centre for immunology, Bordeaux

Developmental Biology Lab, Villefranche-sur-Mer

(Evelyn Houliston)

The “holobiont” and its construction through the integration of microbes PD3 (Sept 2016-Sept 2019) Centre for immunology, Bordeaux

Microenvironment and Immunity Lab, Institut Pasteur, Paris

(Gérard Eberl)

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

PD4 (Sept 2017-Sept 2019)

+ PhD (Sept 2017-Sept 2020)

Centre for immunology, Bordeaux

CIML, Marseille

(Eric Vivier)





  • PI: Thomas Pradeu
  • Postdoc 1: Lynn Chiu (starts Oct 1, 2015)
  • Postdocs 2, 3, 4 & PhD
  • In addition, one immunology PhD student (Paôline Laurent) and one immunology postdoc (Valérie Jolivel) work under the supervision of Thomas Pradeu, in collaboration with immunologists of the lab.
  • In March 2016, Maureen O'Malley (formerly at the University of Sydney), has been recruited by the University of Bordeaux for at least three years and has joined our group.
  • In total, our team will therefore be constituted of 9 people.


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



  • 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 will build on already strong interactions with the following teams/people:

  • In immunology:
    • Eric Vivier (CIML, Marseille-Luminy, France)
    • Gérard Eberl (Microenvironment and Immunity Lab, Pasteur Institute, Paris, France)
  • In microbiology:
    • Margaret McFall-Ngai (University of Hawai, USA)
    • Eric Bapteste (“Aire” Lab, CNRS & UPMC, Paris, France).
  • In developmental biology:
    • 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).
  • In philosophy of biology:
    • Maureen O’Malley (University of Bordeaux & CNRS, 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 Gayon, Philippe Huneman, Max Kistler
    • Melinda Fagan 
    • Matt Haber
    • Sara Green
    • Direct collaborations will be developed with the "Philosophy of Developmental Biology" group, initiated by Thomas Pradeu in 2009.


>>> For questions or queries, please contact Thomas Pradeu.