Program September 2016-July 2017:
The seminar is held once a month at the University of Bordeaux (Carreire-Segalen campus, 146 rue Léo Saignat), usually on Tuesdays, from 12pm to 1pm.
September 15, 2016, from 1:30pm to 2:30pm, Salle de conférence du Service de néphrologie (CHU Bordeaux)
NB: because the room is not easy to find, we have a meeting point: 1:15pm at the entrance of the university library (BUSVS).
Peter Godfrey-Smith (City University of New York, USA & HPS, University of Sydney, Australia)
Individuality and Minimal Cognition
The paper links discussions of two topics, biological individuality and the simplest forms of mentality. I discuss several attempts to locate the boundary between metabolic activity and ‘minimal cognition.’ I then look at differences between the kinds of individuality present in unicellular life, multicellular life in general, and animals of several kinds. Nervous systems, which are clearly relevant to cognition and subjectivity, also play an important role in the kind of individuality seen in animals. The last part of the paper links the biological transitions discussed earlier to the evolutionary history of subjective experience.
October 18, 2016, 12pm-1pm, salle de conférence de l’Espace Santé
Sara Green (University of Copenhagen, Denmark)
Systems Biology – The Future of Medicine?
Systems biology is expected to radically shape the future of medicine. In this talk I specifically address the implications of P4 medicine (defined as personalized, predictive, preventive and participatory) that draw on models from systems biology for large-scale integration of patient-specific data. Proponents of P4 medicine argue that computational integration and analysis of “big data” will revolutionize our health care systems, in particular primary care-based disease prevention. While many ambitions remain visionary, steps to personalize medicine are already taken via personalized genomics, mobile health technologies and pilot projects. An important aim of P4 medicine is to enable disease prevention among healthy persons through detection of risk factors. I present the results of collaborative analysis combining a view from general practice (MD Henrik Vogt) with a philosophy of science perspective. We examine the current status of P4 medicine in light of historical and current challenges to predictive and preventive medicine, including overdiagnosis and overtreatment. Moreover, we ask whether it is likely that in silico integration of patient-specific data will be able to better deal such challenges and to turn risk predictions into disease-preventive actions in a wider social context. Given the lack of evidence that P4 medicine can tip the balance between benefits and harms in preventive medicine, we raise concerns about the current promotion of P4 medicine as a solution to the current challenges in public health.
November 22, 2016, 12pm-1pm, nouvelle salle de vidéoconférence de la BU (Map)
François Duchesneau (Professor of Philosophy, University of Montreal, Canada)
The cell as an elementary organism: from Schwann to Brücke and Kölliker
This presentation is about the way cell physiology (Cellularphysiologie) was born. Indeed, Schwann invented the cell theory in 1839, but his views on the cell were rapidly challenged and transformed. On the one hand, the principle of formation of cells by a sort of crystallization was replaced by a principle of replication by division of existing organic structures (Omnis cellula e cellula) (Remak 1855; Virchow 1855, 1858). On the other hand, starting from the 1860s, the concept of the cell as an “elementary organism” (Elementarorganismus) was proposed and developed by physiologists like Brücke, Schultze and Kölliker. What did they exactly mean by this new notion? What was the theoretical framework connected with it? How did it translate into a methodology of functional analysis for the cell physiology, which originated therefrom?
December 6, 2016, 12pm-1pm, nouvelle salle de vidéoconférence de la BU (Map)
Purificación Lopez-Garcia (Unité d’Ecologie, Systématique et Evolution, CNRS UMR 8079, Université Paris-Sud)
Molecular views on the microbial world challenge old misconceptions about biological evolution
Life and (biological) evolution are indissoluble. Evolution is the outcome of both, Darwinian processes implying reproduction with variation upon which natural selection acts, and drift. These processes are universal and underlie the biological diversity patterns that we see today. Understanding the mechanisms governing biological evolution leads to refuting some pervasive misconceptions on biological evolution. Among the most obstinate are the idea that complexity necessarily increases along evolution, that simple equals primitive or that bacteria and other unicellular organisms are less evolved than animals and plants. I will argue against these false assumptions, which are largely based on our biased perception of the microbial world. These biases can now be largely overcome thanks to the use of molecular approaches. I will also comment on the limits of actualism (interpreting the past considering the present).
January, 17 2017
Etienne Coutureau (Decision and Adaptation Team, Aquitaine Institute for Cognitive and Integrative Neuroscience, UMR5287)
Kim Sterelny (Professor of Philosophy, Australian National University)
March 28, 2017
Carl Craver (Professor of Philosophy, Washington University in Saint Louis)
April 11, 2017
Derek Skillings (ERC IDEM, ImmunoConcEpT, CNRS & University of Bordeaux)
May 23, 2017
Leonardo Bich (ERC IDEM, ImmunoConcEpT, CNRS & University of Bordeaux)
June 13, 2017
Marc Daëron (Institut Pasteur, CIML & IHPST) (and Max Kistler?), about the concept of function in biology.
July 2017: TBA
Tim Lewens (Professor of Philosophy, University of Cambridge)
Samir Okasha (Professor of Philosophy, University of Bristol)
Program September 2015-July 2016:
We are used to thinking of cancer as a breakdown in function. Cancer is often defined, in fact, as a “failure” to control cell birth and death, and a disease of “disorganized” growth, due largely to mutations that affect the regulation of the cell cycle, the control of normal cell division, replication, etc.. Yet, we also know that selection can (and sometimes does) operate on more than one level of organization. This can occur both sequentially, and simultaneously.
Some traits are, as a consequence, byproducts of selection at other levels of organization. In this talk, I argue that cancer progression depends, in part, on a cooption of organismic adaptations: cell signaling pathways that play roles in wound healing, & embryogenesis (Schedin, et. al., 2006; Weinberg, 2014). In this sense, cancer progression is a byproduct of natural selection at the organismal level. However, cancer may also be described as a process of natural selection, where selection is acting at the level of individual cells, and potentially also, cell lineages or whole populations (see, e.g., Greaves, et. al., 2010; Crespi and Summers, 2005). Moreover, cancer may be described as a process of niche construction: for, stromal and carcinoma cells cooperate in service of angiogensis, invasion, and metastasis (see, e.g., Egeblad, 2010, Merlo, et. al., 2006). These capacities may be described as traits or characters of the tumor (collective) as a whole, which together contribute to the tumor’s survival. Adopting Queller and Strassman’s (2009) sense of “organismality,” where collectives are more or less “cooperative” and approach the paradigmatic “organism” as a matter of degree, then, one could thus speak of advanced tumors as proto-organisms. This talk will explore the consequences of thinking about cancer’s dynamics from a multi-level evolutionary perspective. The aim is to explore the scope and limitations of this analogy, in the spirit of Campbell (1920), Achinstein (1964), Spector, (1965), and Hesse’s (1966) arguments for the fruitful use of analogy and metaphor in science.
– March 22nd, 2016: Maureen O’Malley (University of Bordeaux; previously: University of Sydney), Why Philosophy of Microbiology?
Attention! Exceptionnellement, la séance commencera à 12h au lieu de 12h30 (The seminar will start at noon, instead of 12:30pm)
- Link to Video of this talk: Video O’Malley
- Link to PDF Presentation of Maureen’s talk: Why Philosophy of Microbiology?
- Short abstract: Microbes have only recently become the objects of sustained philosophical attention. I will discuss some of the reasons why philosophers now find microbes and microbiology interesting, and why philosophy of microbiology might be a worthwhile activity.
- Link to PDF presentation: Chiu, Host-Microbiota Symbiosis
- Video of the talk: Video Chiu
- Abstract: I will distinguish between three types of interactionist reactions to internalist or externalist theories. These theories assign specific theoretical roles to internal and external factors, respectively. A “balanced” interactionist balances the relative weight of internal and external factors without changing their respective roles. An “extension” interactionist reassigns the roles to both factors. A “transformative” interactionist rejects the original theoretical framework, re-organizing internal and external factors under a new alternative. Examples will be drawn from major debates in evolutionary biology, developmental biology, and cognitive science. I then suggest that there could be three alternative interpretations to the “host-microbiota” holobiont/superorganism/metaorganism.
- Slides of the talk: Slides Horvath.
Discovered in 2007, CRISPR-Cas is a bacterial immunity system directed against nucleic acids, notably viral DNA. In this system, the immunological memory is built through the acquisition of short viral DNA sequences into the chromosome of the bacterial host, within peculiar regions called CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats). In the interference stage, these sequences are transcribed into small RNA molecules named crRNAs, that are used by Cas (CRISPR-associated) proteins to recognize and inactivate any foreign DNA showing sequence complementary to the crRNAs. The ability of certain Cas proteins, notably Cas9, to be directed by a short RNA towards a DNA target and to cleave it at a precise position has been diverted and transformed in 2012 into a simple and efficient tool for genome editing. Since then, the Cas9 tool has been applied successfully to genome modification of numerous organisms, including microorganisms, plants, animals, and humans. This presentation will focus on the milestone and fundamental discoveries about CRISPR-Cas systems, and on some of their applications.
- Links to know in more detail Philippe Horvath’s role in the discovery of the CRISPR-Cas system:
- Location: Campus Carreire, Amphi. 12
- Big crowd to listen to Philippe Horvath’s talk:
- Video of the talk: Video Weber
Philosophers of biology have recently been debating to what extent such nucleic acids that are said to carry genetic information (i.e., DNA or mRNA) really play a special role in development. A recent attempt to defend such a special role consists in arguing that nucleic acid is what makes an actual difference (as opposed to potential differences) to the amino acid sequence of proteins. However, this is not sufficient as there are often other actual-difference makers involved in protein synthesis, for example, splicing or post-translational modification mechanisms. For this reasons, it has been suggested that what distinguishes nucleic acid is their causal specificity. Causal specificity has to do with the amount of control that interventions on the cause variable can exert on the effect variable. However, a quantitative measure of causal specificity can be used to show that in many cases the specificity of non-genetic causes is a full match to the genetic causes. In this talk, I will argue that what matters biologically is the causal specificity that inheres in possible interventions that are biologically normal, where biological normality is defined both in terms of what can happen in a population of organisms at a non-negligible probability and what is consistent with normal biological functioning of the rest of the organism. This kind of causal specificity is higher for genetic causes than for the (known) non-genetic causes.
- Location: salle TP – Visio 2. Plan d’accès à cette salle : Plan-acces-visio-CARREIRE
Stem cell models: cell identity, development, and levels of organization
- Slides of the talk: Slides Fagan
The concept of a stem cell is a peculiar one, uniting two very different
ideas. A cell is a well-characterized biological entity, observable via
relatively simple technology and clearly distinguished from its
environment and other cells by a bounding membrane. A stem is the
beginning of a process, the point of origin for something that is to be.
A stem cell, then, is both entity and process; a cell defined by what it
gives rise to rather than its observable traits. In this talk, I present
a minimal abstract model of the stem cell concept, and explore its
implications for key questions in philosophy of biology. The model
explicates the general definition of ³stem cell² as a cell that has both
the capacity to self-renew and the capacity to differentiate. After
presenting the model, I discuss three of its implications. (1) Stem cells
can be individuated only relative to particular experimental methods and
hypotheses, such that the concept in practice is diverse and
context-dependent. (2) Stem cell concepts involve substantive assumptions
about biological development, at organismal, cellular, and molecular
levels. The modeling approach offers a systematic framework for
representing and comparing these concepts, via the topology of lineage
trees. (3) The aforementioned assumptions about development have
implications for theories of cancer, in particular the idea of ³cancer
- Location: 1pm, salle de conférences de l’IBGC (directions)
Kith selection: simple theory, complicated amoebas and bacteria
Commentator: Johannes Martens (IHPST, CNRS & Paris 1 Panthéon Sorbonne)
The evolution of cooperation is well understood when the cooperators are relatives but perhaps less so when they are unrelated. We will explore two aspects of evolutionary interactions among non-relatives, which we call kith selection. On the theoretical side, we show how these interactions can be expressed in form exactly parallel Hamilton’s rule. On the empirical side, we describe a complex “farming” symbiosis between Burkholderia bacteria and Dictyostelid amoebas.
Location: Salle des conférences du Bâtiment Espace Santé (Map_Espace santé)
– June 6th 10am-12pm: Denis Walsh (University of Toronto, Canada)
Bibliothèque du service de Rhumatologie, 12e étage du Tripode, groupe hospitalier Pellegrin.
Rencontre avec l’auteur à propos de son livre : Organisms, Agency, and Evolution (2016)
La séminaire se tiendra en anglais.
What does a ‘global history’ of biology bring to us?
- Video of the talk: Video Morange
To write a global history of life sciences from Antiquity to extant research, from molecular biology to ecology and ethology is an impossible task, the promise to be inaccurate and wrong in many issues.
Nevertheless, the result is not without interest. It casts a new light on continuities and discontinuities in biological thought, and on the relations between biology and other scientific disciplines. It reveals the circulation of concepts and methods between biological subdisciplines, and between Society and biology. It shows the complex dynamics of biological transformations that gives biology its specific nature.
- Location: salle TP – Visio 2. Plan d’accès à cette salle : Plan-acces-visio-CARREIRE
Philosophical lessons learned from Galton’s statistical innovations about the nature of scientific explanation.
Salle de réunion FR TransBioMed (Université Bordeaux Segalen, Bât 1A, 2ème étage – Zone Nord – Case 53, 146, rue Léo Saignat, 33076 Bordeaux cedex France)
– Date TBA: workshop dedicated to plants. Speakers: Quentin Hiernaux (Bruxelles) Sophie Gerber (INRA Bordeaux), Marie-Laure Loustau (INRA Bordeaux).
Past program (January-July 2015):
Mardi 13 Janvier, 12h30 à 14h (Site de Carreire, Amphi 6) :
Andreas Bikfalvi – ‘Variations, évolutions et métamorphoses de l’arbre vasculaire’ (discutant: Thomas Pradeu)
Mardi 10 Février, 12h30 à 14h (Site de Carreire, Amphi 6) :
Cédric Brun – ‘L’explication en neurosciences, mécanisme et réductionnisme?’ (discutant: Thomas Boraud)
Vendredi 20 Mars, de 14h à 15h30 (Salle de conférences du Centre de génomique fonctionnelle) :
Philippe Kourilsky – ‘Le jeu du hasard et de la complexité’
(discutant: Thomas Pradeu)
Lundi 20 Avril, de 12h30 à 14h (Site de Carreire, Amphi 6) :
Maël Lemoine – Comment définir la maladie?
(discutant à préciser)
Lundi 18 Mai, de 12h20 à 14h (Site de Carreire, Amphi 6) :
Nora Abrous (Titre à préciser)
(discutant: A.M. Ferner)
Lundi 8 juin, de 12h à 14h (Site de Carreire, Amphi 7) :
Thomas Boraud, Les neurosciences peuvent-elle étudier les processus de prise de décision sans tomber dans la néo-phrénologie?
(discutant: Cédric Brun)
Mardi 23 juin de 12h30 à 14h, (Salle de conférences du Centre de génomique fonctionnelle (site Carreire)) :
Jan Pieter Konsman, Titre à préciser
(discutant à préciser)
Jeudi 16 Juillet, de 12h30 à 14h (Site de Carreire, Amphi 6) :
Adam Ferner – Organic individuals