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Philosophy of Biology: Towards a classification of stem cells by L. Laplane and E. Solary



The characteristic properties of stem cells – notably their ability to self-renew and to differentiate – have meant that they have traditionally been viewed as distinct from most other types of cells. However, recent research has blurred the line between stem cells and other cells by showing that the former display a range of behaviors in different tissues and at different stages of development. The authors use the tools of metaphysics to describe a classification scheme for stem cells, and to highlight what their inherent diversity means for cancer treatment. Read more here.

Why science needs philosophy – new article in PNAS

The latest edition of PNAS features an article co-written by philosophers and scientist pleading for a closer collaboration between their respective disciplines. The article entitled "Why science needs philosophy" argues that despite tight historical links between science and philosophy, present-day scientists often perceive philosophy as completely different from, and even antagonistic to, science. However philosophy can have an important and productive impact on science.

The authors give three examples taken from various fields of the contemporary life sciences. Each bears on cutting-edge scientific research, and each has been explicitly acknowledged by practicing researchers as a useful contribution to science. From there the authors develop in what forms philosphy can help advance science. Read the full article here.

CRISPR-Cas immunity: beyond nonself and defence by T. Pradeu and J.-F. Moreau


The journal Biology & Philosophy has published a special issue on the philosophy of CRISPR-Cas. Thomas Pradeu has written the introduction and together with Jean-François Moreau he presents a commentary to Eugene Koonin's target paper.

In the commentary Pradeu and Moreau defend an extended view of CRISPR-Cas immunity by arguing that CRISPR-Cas includes, but cannot be reduced to, defence against nonself. CRISPR-Cas systems can target endogenous elements (for example in DNA repair) and tolerate exogenous elements (for example some phages). They conclude that the vocabulary of “defence” and “nonself” might be misleading when describing CRISPR-Cas systems (PDF of final draft).

The epigenetics of inflammaging, new review in Seminars in Immunol. by Nadini, Moreau et al.

A growing amount of evidences indicates that inflammaging – the chronic, low grade inflammation state characteristic of the elderly – is the result of genetic as well as environmental or stochastic factors.

In their latest review Christine Nadini, Jean-François Moreau, Noémie Gensous, Francesco Ravaioli, Paolo Garagnani and Maria Giulia Bacalini take a closer look how age related epigenetic changes promote inflammaging. Furthermore they discuss the role on envioronmental and microbial stimuli and how they can affect the rate of inflammaging via epigenetic mechanisms.

Find the full article here.

The Multiple Layers of the Tumor Environment, new paper by Laplane et al.

If and how a tumor develops, depends in large part on its surroundings. While scientists agree on the importance of the tumor environment (TE), there is no consensus on how to define and spatially delineate it.
A new paper by Lucie Laplane, Dorothée Duluc, Nicolas Larmonier, Thomas Pradeu and Andreas Bikfalvi lays out six clearly defined layers that surround the tumor: (i) the tumor cell-only environment, (ii) the niche, and the (iii) confined, (iv) proximal, (v) peripheral, and (vi) organismal tumor environment. The authors show the different tumor-promoting or -suppressing mechanisms at work in the different layers and how they impact therapeutic approaches.

Click here for more information: The Multiple Layers of the Tumor Environment
Click here for the PDF

Dissecting the meanings of physiology, new paper by Lemoine & Pradeu in Physiology

Lemoine M. & Pradeu T. (2018)
Dissecting the meanings of ‘Physiology’ to assess the vitality of the discipline
Physiology 33(4), 236-245. (Open Access PDF) (PDF of final draft).

The vitality of physiology is currently under debate. Some say that physiology is a dying discipline in the era of molecular medicine and systems biology, whereas others claim that physiology remains a key biological and medical discipline, due in part to its integrative nature. In this conceptual review, we argue that any assessment of the vitality of physiology depends heavily on the definition of this discipline adopted. We examine two main conceptions of physiology, one focusing on its object (what physiology is about), and the other on the methods used (how physiologists study the biological reality). We contend that physiology no longer encompasses all biological disciplines and may no longer be the only synoptic biological science. However, far from indicating a sterility of this discipline, this situation should drive physiology to re-invent its relationship with these other biological domains.

Immunological memory, New paper by Pradeu & Du Pasquier in Immunological Reviews

Immunological memory: What’s in a name?

Thomas Pradeu & Louis Du Pasquier

Immunological Reviews (May 2018), Volume 283, Issue 1 (Special Issue: Immunologic Memory),

Pages 7-20.



Immunological memory is one of the core topics of contemporary immunology. Yet there are many discussions about what this concept precisely means, which components of the immune system display it, and in which phyla it exists. Recent years have seen the multiplication of claims that immunological memory can be found in “innate” immune cells and in many phyla beyond vertebrates (including invertebrates, plants, but also bacteria and archaea), as well as the multiplication of concepts to account for these phenomena, such as “innate immune memory” or “trained immunity”. The aim of this critical review is to analyze these recent claims and concepts, and to distinguish ideas that have often been misleadingly associated, such as memory, adaptive immunity, and specificity. We argue that immunological memory is a gradual and multidimensional phenomenon, irreducible to any simple dichotomy, and we show why adopting this new view matters from an experimental and therapeutic point of view.

Robustness in the tissue reconstruction system, New paper by Truchetet & Pradeu

New paper by M-E. Truchetet & T. Pradeu, Re-thinking our understanding of immunity: Robustness in the tissue reconstruction system. Seminars in Immunology (2018). (PDF of final draft).


Robustness, understood as the maintenance of specific functionalities of a given system against internal and external perturbations, is pervasive in today’s biology. Yet precise applications of this notion to the immune system have been scarce. Here we show that the concept of robustness sheds light on tissue repair, and particularly on the crucial role the immune system plays in this process. We describe the specific mechanisms, including plasticity and redundancy, by which robustness is achieved in the tissue reconstruction system (TRS). In turn, tissue repair offers a very important test case for assessing the usefulness of the concept of robustness, and identifying different varieties of robustness.

Tissue repair
Tissue regeneration

Towards a General Theory of Immunity? New paper by Eberl & Pradeu

New paper in Trends in Immunology (2018), by Gérard Eberl (Institut Pasteur, Paris) & Thomas Pradeu (ImmunoConcept, Bordeaux)

Theories are indispensable to organize immunological data into coherent, explanatory, and predictive frameworks. We propose to combine different models to develop a unifying theory of immunity which situates immunology in the wider context of physiology. We believe that the immune system will be increasingly understood as a central component of a network of partner physiological systems that interconnect to maintain homeostasis.

Protective Microbiota & Co-Immunity, New OA paper by Chiu, Bazin, et al.

New paper by Lynn Chiu, Thomas Bazin (co-first authors), Marie-Elise Truchetet, Thierry Schaeverbeke, Laurence Delhaes &  Thomas Pradeu
Frontiers in Immunology (Dec 2017). Full text in Open Access.

Resident microbiota do not just shape host immunity, they can also contribute to host protection against pathogens and infectious diseases. Previous reviews of the protective roles of the microbiota have focused exclusively on colonization resistance localized within a microenvironment. This review shows that the protection against pathogens also involves the mitigation of pathogenic impact without eliminating the pathogens (i.e., “disease tolerance”) and the containment of microorganisms to prevent pathogenic spread. Protective microorganisms can have an impact beyond their niche, interfering with the entry, establishment, growth, and spread of pathogenic microorganisms. More fundamentally, we propose a series of conceptual clarifications in support of the idea of a “co-immunity,” where an organism is protected by both its own immune system and components of its microbiota.