PhD position in Philosophy of Biology
and/or Philosophy of Medicine
and/or Conceptual/theoretical Biology
Thomas Pradeu’s ERC Starting Grant Project
Topic: “The role of the immune system in the maintenance and construction of the organism”
The University of Bordeaux and the CNRS seek candidates for a three-year PhD position in Philosophy of Biology and/or Philosophy of Medicine and/or Conceptual/theoretical Biology, in the context of Thomas Pradeu’s ERC Starting Grant project, called “Immunity, Development and the Microbiota: Understanding the Continuous Construction of Biological Identity” (IDEM, ERC#637647, 2015-2020).
PhD topic: “The role of the immune system in the maintenance and construction of the organism”.
Location: Immunology lab (https://www.immuconcept.org/), CNRS & University of Bordeaux, Bordeaux, France.
Project’s PI: Thomas Pradeu, head of Conceptual Immunology team (https://www.immuconcept.org/conceptual-immunology/).
Duration: Three years.
Start date: September 1st, 2017, or October 1st, 2017.
Requirements: Master in Philosophy of Biology, or Philosophy of Medicine, or Philosophy of Science more generally, with a strong interest in biology and/or medicine (and, if possible, a degree in biology or medicine), OR a Master in Biological or Biomedical sciences, with a strong interest in conceptual and theoretical investigation. A good knowledge of immunology will be an asset, but it is not necessary.
Application deadline: April 25, 2017.
Website: all details about IDEM project and the PhD position can be found here:
Contact: Thomas Pradeu, firstname.lastname@example.org
Description of project
The immune system has traditionally been conceived as a system of recognition and elimination of foreign living entities, seen as potential pathogens, and hence threats for the integrity of the organism. Yet, in virtually all species, many bacteria are actively tolerated by the immune system, and even participate in host defense against pathogens and in the development of the immune system itself (Mazmanian et al. 2005; Round and Mazmanian 2009). The immune system cannot be understood anymore as a system of rejection; it is instead, in all organisms, a system of selective but constant integration of some living entities (Pradeu 2012). A key challenge for current immunology, therefore, is to determine the mechanisms through which mutualistic microorganisms are tolerated, while pathogenic ones are rejected (Chu and Mazmanian 2013).
Philosophers of biology, philosophers of medicine, and theoretical biologists may play an important role in this discussion, as answers will depend on the adopted theoretical framework. Can the self-nonself theory (Burnet 1969) be accommodated to integrate recent data on the massive presence of symbionts in the host? Or will the danger theory, suggested by Polly Matzinger (2002) and stating that the immune system does not respond to “nonself” but to “danger” signals, constitute a convincing alternative? In collaboration with immunologists, the PI has suggested a different theoretical framework, the “discontinuity theory”, which proposes that immune responses are triggered by rapid molecular changes in the organism (be they of internal or external origin) (Pradeu and Carosella 2006a; Pradeu, Jaeger and Vivier 2013; Pradeu and Vivier 2016). It is not clear, however, how this framework can account for the tolerance of symbiotic bacteria in the newborn, given that the newborn is in fact massively and rapidly colonized at birth, which suggests that its immune system should respond to this rapid phenotypic change. A fundamental objective of IDEM will be, therefore, to characterize both theoretically and experimentally the criteria for the triggering of an effector immune response, and the reasons that explain why the microbiota, far from being rejected by the organism, is actively tolerated.
The question of how to account for tolerance to the microbiota will be part of a larger inquiry about the interactions between immunology and developmental biology. These two fields have too long been considered as having little to say one to the other. But, as Jules Hoffmann showed in his 2011 Nobel Lecture, development and immunity are strongly intertwined, as exemplified by the role of drosophila Toll receptors, or by the action of macrophages and the complement in vertebrates. It is likely that the immune system plays a crucial role in development in all species, as this system can exert a destructive function, for instance through apoptosis (induced cell death), of organic constituents that have become too numerous or superfluous. Indeed, to build an organism often implies to destroy some of its tissues, and it appears that the immune system fulfills this task (Jacobson et al. 1997). Theories currently available in immunology have difficulties in explaining some crucial phenomena studied by developmental biology, from the tolerance of numerous symbiotic bacteria to the very possibility of massive phenotypic changes in the host, such as metamorphosis (a frequent phenomenon in nature), sexual maturation, regeneration, etc. Recent data also suggest that at least some cancers appear through developmental-like mechanisms, as if cancerogenesis was an abnormal “reactivation” of processes usually involved in development (in particular angiogenesis: Tammela et al. 2008); an important question is to understand how the immune system interacts with these developing cancerous tumors. Overall, it will be crucial for IDEM to characterize in detail the interface between immunology and developmental biology, and in particular to assess the discontinuity theory in face of data on the way the organism, throughout its life, can sometimes change very rapidly.
These two questions (how can the immune system tolerate the massive entry of microorganisms during host development, and how can the immune system tolerate rapid changes in host phenotype) will constitute a crucial basis to renew the problem of the role of the immune system in the delineation of the organism and the construction of its identity through time.
These challenges can be explored from the direct point of view of immunology and philosophy of immunology, but they can also be raised from the perspective of related domains or approaches, including the following: developmental biology; microbiology; cancerology; systems medicine; personalized medicine; etc.
Thus, the major questions raised by the PhD researcher involved in this project will be:
- – What role does the immune system play in the integration and the tolerance of mutualistic microbes?
- – Which is the most appropriate theoretical framework in immunology to account for the tolerance of mutualistic microbes?
- – How does the immune system cope with rapid phenotypic changes in the organism?
- – What role does the immune system play in the maintenance of biological identity through time?
- – What is the exact role of the immune system in tumor progression and elimination?
- – How does current immunology shed light on questions such as systems approaches in medicine and personalized medicine?
This research will be done in close connection with the postdoctoral researcher who will be recruited at the same time to work on the same project.
– IDEM research is done mainly at the University of Bordeaux, France, and more precisely in the Immunology Lab (https://www.immuconcept.org/), which is part of the CNRS, the College of Health Sciences, and the Pellegrin Hospital (the main hospital in Bordeaux). 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 PhD will have the opportunity to do some experimental work in our ImmunoConcEpT lab, or in a partner scientific lab.
- – More generally, a unique feature of the IDEM environment is the opportunity to do some empirical work, via extensive interactions with experimental biologists and medical doctors, both in the ImmunoConcEpT Lab and at the hospital.
- – Thomas Pradeu’s group (https://www.immuconcept.org/conceptual-immunology/) is currently constituted of 9 people:
- Group leader: Thomas PRADEU (Permanent researcher CNRS, philosophy of biology and theoretical immunology)
- Leonardo BICH (Postdoc ERC IDEM, philosophy of biology)
- Lynn CHIU (Postdoc ERC IDEM, philosophy of biology)
- Katarzyna HOOKS (Postdoc IDEX University of Bordeaux, bioinformatics)
- Valérie JOLIVEL (Postdoc, University of Bordeaux, Immunology)
- Paôline LAURENT (PhD student, University of Bordeaux, Immunology)
- Jean-François MOREAU (MD, Professor in Medicine, Bordeaux hospital & University of Bordeaux)
- Maureen O’MALLEY (Senior researcher IDEX University of Bordeaux, philosophy of microbiology)
- Derek SKILLINGS (Postdoc ERC IDEM, philosophy of biology)
- – The group offers an extremely dynamic research environment, with a monthly seminar, many international visitors, interdisciplinary reading groups and seminars, etc. (see our webpage for more details).
- – The recruited PhD student will have excellent working conditions, including a desk and all office facilities, online access to journals, the possibility to be involved in lab experiments, funds to participate in international conferences and workshops, and funds to organize local events.
- Interested candidates might want to contact Leonardo Bich, Lynn Chiu, and Derek Skillings – all postdocs in the project (see above for links to their pages and contact info).
Practical activities and requirements
- – Master in Philosophy of Biology, or Philosophy of Medicine, or Philosophy of Science more generally, with a strong interest in biology and/or medicine (and, if possible, a degree in biology or medicine), OR a Master in Biology, with a strong interest in conceptual and theoretical investigation. A good knowledge of immunology will be an asset, but it is not
- – The recruited PhD student will be expected to participate in seminars, reading groups, and other aspects of the research life.
- – The recruited PhD student will be expected to publish several papers, including papers written in collaboration with scientists (at least 2 co-authored papers with scientists and/or philosophers, and 2 single-authored papers). A major aim of IDEM is the publication of co-authored papers in high-profile scientific journals.
- – Residency in Bordeaux is mandatory.
- – Everyday presence in the lab from 9am to 5pm is mandatory.
- – Salary: approximately €1,400 per month (net salary before income taxes).
- – Vacation: The PhD student will be entitled to a total of 44 days’ vacation per year.
- – Language: IDEM will be conducted in English. Fluency in French is therefore not mandatory.
Applications (in English) should include:
- – a cover letter;
- – a CV;
- – (if applicable) a list of publications;
- – a sample of written work of up to 10,000 words (for example, an excerpt of a Master dissertation);
- – a description of planned research activity of 1,000-1,500 words.
Applications, in one PDF document, will be sent by email to: email@example.com
(before April 25, 2017). Hard copy applications are not accepted.
Additionally, two confidential letters of reference should be sent to the same address from the referees directly.
The CNRS is an equal opportunity employer and encourages women to apply for positions.