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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
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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.

The definition of the tumor microenvironment

The members of this interdisciplinary project attempt to propose a refined definition of the notion of tumor microenvironment, at the interface between cancer biology, developmental biology, immunology, and studies on angiogenesis.
People involved: Andreas Bikfalvi (Inserm), Dorothée Duluc, Lucie Laplane (IHPST & IGR), Nicolas Larmonier, Thomas Pradeu.
More information about this project here.

Immunity, mobility, and aging

Initiated by Jean-François Moreau, this project is based on the idea that mobility is central to immunity. In the transition from unicellularity to multicellularity, all cells have mostly lost their mobility – except for the immune cells. We are interested in better characterizing this link between immunity and mobility, and the way it emerged through evolution. On this ground, we propose a novel hypothesis about aging and immunosenescence, based on the idea that the increasing stiffness and cross-linking of the senescent ECM lead to progressive immunodeficiency via an age-related decrease in T cell mobility and the death of these cells.
People involved in Bordeaux: Jean-François Moreau, Leonardo Bich, Thomas Pradeu.
PI: Jean-François Moreau
Partners: Daniel Choquet, Claudio Franceschi.

Immunity and the constant construction and maintenance of biological boundaries

Recent data show that the immune system is not just a system of elimination and defence, but is involved, much more broadly, in development, regulation, and repair. One key problem is to determine how the immune system constantly patrols and repairs biological boundaries, such as the epithelium and the endothelium. We are particularly interested in how innate lymphoid cells (ILCs) and gammadelta T cells are involved in this process. We are developing, with Patrick Blanco’s group, a translational program exploring the role of ILC2s in controlling and maintaining the endothelium, both in physiological and pathological conditions, including in fibrosis and systemic sclerosis.
People involved in Bordeaux: Patrick Blanco, Cécile Contin-Bordes, Julie Déchanet-Merville, Paôline Laurent (PhD student), Valérie Jolivel (postdoc), Pauline Manicki, Jean-François Moreau, Thomas Pradeu, Marie-Elise Truchetet.
PI: Thomas Pradeu
This project is funded by the IDEX programme of the University of Bordeaux and Thomas Pradeu’s group at ImmunoConcept.

Understanding immunogenicity

Understanding the triggering of an immune response

The aim of this interdisciplinary project is to offer, through the articulation of conceptual, experimental, and medical perspectives, a better characterization of how the immune system is activated. What triggers an effector or a regulatory immune response? How can concepts, theories, and models help us understand how the immune system is activated? One aspect of this investigation is the assessment of the “discontinuity theory” Pradeu, Jaeger and Vivier 2013; Pradeu and Vivier 2016), which states that effector immune responses are triggered by sudden changes in the molecular patterns with which immune receptors interact.

People involved in Bordeaux: Julie Déchanet-Merville, Hannah Kaminsky, Maria Mamani, Jean-François Moreau, Thomas Pradeu, Marie-Elise Truchetet.
PI: Thomas Pradeu
Partners: Gérard Eberl (Institut Pasteur), Eric Vivier (CIML).
More information about this project here.

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