Custom Tag: Publication

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.

What is metaphysics of science? New paper in Synthese by Guay & Pradeu

Right out of the box: how to situate metaphysics of science in relation to other metaphysical approaches
Alexandre Guay & Thomas Pradeu
Free full text:

Several advocates of the lively field of “metaphysics of science” have recently argued that a naturalistic metaphysics should be based solely on current science, and that it should replace more traditional, intuition-based, forms of metaphysics. The aim of the present paper is to assess that claim by examining the relations between metaphysics of science and general metaphysics. We show that the current metaphysical battlefield is richer and more complex than a simple dichotomy between “metaphysics of science” and “traditional metaphysics”, and that it should instead be understood as a three dimensional “box”, with one axis distinguishing “descriptive metaphysics” from “revisionary metaphysics”, a second axis distinguishing a priori from a posteriori metaphysics, and a third axis distinguishing “commonsense metaphysics”, “traditional metaphysics” and “metaphysics of science”. We use this three-dimensional figure to shed light on the project of current metaphysics of science, and to demonstrate that, in many instances, the target of that project is not defined with enough precision and clarity.

New open access paper on dysbiosis, by Hooks & O’Malley

Hooks K. & O’Malley M. (2017) Dysbiosis and Its Discontents. mBio 8:e01492-17. (Open Access).
Dysbiosis is a key term in human microbiome research, especially when microbiome patterns are associated with disease states. Although some questions have been raised about how this term is applied, its use continues undiminished in the literature. We investigate the ways in which microbiome researchers discuss dysbiosis and then assess the impact of different concepts of dysbiosis on microbiome research. After an overview of the term’s historical roots, we conduct quantitative and qualitative analyses of a large selection of contemporary dysbiosis statements. We categorize both short definitions and longer conceptual statements about dysbiosis. Further analysis allows us to identify the problematic implications of how dysbiosis is used, particularly with regard to causal hypotheses and normal-abnormal distinctions. We suggest that researchers should reflect carefully on the ways in which they discuss dysbiosis, in order for the field to continue to develop greater predictive scope and explanatory depth.

Is defining life pointless?

New paper in Synthese
Is defining life pointless? Operational definitions at the frontiers of biology

by Leonardo Bich & Sara Green.

Despite numerous and increasing attempts to define what life is,there is no consensus on necessary and sufficient conditions for life. Accordingly, some schol- ars have questioned the value of definitions of life and encouraged scientists and philosophers alike to discard the project. As an alternative to this pessimistic conclu- sion, we argue that critically rethinking the nature and uses of definitions can provide new insights into the epistemic roles of definitions of life for different research prac- tices. This paper examines the possible contributions of definitions of life in scientific domains where such definitions are used most (e.g., Synthetic Biology, Origins of Life, Alife, and Astrobiology). Rather than as classificatory tools for demarcation of nat- ural kinds, we highlight the pragmatic utility of what we call operational definitions that serve as theoretical and epistemic tools in scientific practice. In particular, we examine contexts where definitions integrate criteria for life into theoretical models that involve or enable observable operations. We show how these definitions of life play important roles in influencing research agendas and evaluating results, and we argue that to discard the project of defining life is neither sufficiently motivated, nor possible without dismissing important theoretical and practical research.

Definitions of life · Integration · Origins of life · Artificial life · Synthetic biology · Astrobiology · Philosophy of science in practice
First Online: 18 April 2017

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