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

Periodic Reporting for period 4 - IDEM (Immunity, DEvelopment and Microbiota: Understanding the Continuous Construction of Biological Identity)

Reporting period: 2020-03-01 to 2020-12-31

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”).

This issue is of great interest for society, as recent work on the microbiota may lead us to re-think significantly our conception of what a human being is. The topic of the microbiota is also fascinating for anyone interested in building a fruitful dialogue between the biomedical sciences and the social sciences.

IDEM is a fundamentally interdisciplinary project at the crossroads of philosophy and biology. The main objectives of the project are:
(i) assessing from a conceptual and historical point of view the reality of the proclaimed “revolution of the microbiota” 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.

Overall, this project is unique in providing a new understanding of the way living things are continuously constructed through time and interact with their biotic environment.
The in-depth examination of all four WPs has been achieved and, overall, the project has been very successful. We have published a high number of papers: a total of 38 papers, most of the time in high-impact science journals (including PNAS, Nature Reviews Immunology, eLife) or in world-leading philosophy journals (including Synthese, Biology & Philosophy, Studies C), in addition to one book published at Cambridge University Press that summarises many of our results and opens up new perspective in the philosophy of the biomedical sciences. Often, papers published by our group were co-authored with scientists and/or medical doctors. We have organized many workshops and conferences, as well as very successful seminars on Philosophy & Biology and on the conceptual and philosophical aspects of current microbiota research. We have also contributed to create a dialogue between different researchers working on the microbiota. All our activities in terms of conferences, workshops, publications and so on, are described in detail on our webpage:

The five postdoctoral researchers who worked on the project in the past have found excellent positions after leaving our lab. Leonardo BICH is Full Professor in San Sebastian (Spain), Derek SKILLINGS is Associate Professor in Philosophy, University of North Carolina at Greensboro (USA), Lynn Chiu is Science Communicator at the School of Biology, University of St. Andrews (UK), Gregor Greslehner is a University Assistant/Postdoc at the Department of Philosophy at the University of Vienna (Austria), and Jonathan Sholl is a postdoctoral researcher at the University of Bordeaux (France), working with Mael Lemoine.
Our group is recognized as a world-leading group of philosophers of science working in close contact with science and medicine. We are indeed "embedded" in a biology and medicine lab (at the CNRS and Bordeaux hospital), and we participate intensively in all lab's activities. This is what we call philosophy "in" science (in contrast with traditional philosophy "of" science). We bring our conceptual, theoretical, and philosophical insights into scientific projects, and contribute to the emergence of new experimental questions and investigations. Building on this expertise, we have launched a national and international network promoting what we have called "Philosophy in Biology and Medicine" (rather than the more classical philosophy "of" biology and medicine) (website: Very few groups in the world have reached this degree of tight connection between philosophy and science. Our work on the microbiota, the immune system, microbiology and other biological and medical aspects is often published in science journals and it is discussed and cited by scientists; to that extent, it has the quite unique feature of contributing and making a difference to science itself.

In the final phase of the project, we did exciting research on the microbiome-immune-cancer connection, a fascinating emerging issue in the biomedical sciences. We teamed up with two of the best experts in the world, both at UCSD (California) and respectively first and last authors on a paper published in the journal Nature in 2020.

Overall, what we are most proud of is this constant, intimate and fruitful interaction with scientists and MDs. We have the feeling that such a degree of cross-fertilization between scientific and philosophical work is rare, and that this achievement has been perfectly recognized by our community. The IDEM project allowed our group to really be on the world map from this point of view.