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Publications of 2017

  1. The Hitchhiker’s Guide to the Cancer Galaxy: How two critics missed their destination

    The Hitchhiker’s Guide to the Cancer Galaxy: How two critics missed their destination

    Organisms. Journal of Biological Sciences


    Two theories aim to understand cancer: the reductionist Somatic Mutation Theory (SMT) and the organicist Tissue Organization Field Theory (TOFT).

    Abstract

    Two main theories aim at understanding carcinogenesis: the reductionist smt locates cancer in cancer cells, while the organicist toft locates cancer at the tissue level. For toft, the ‘cancer cell’ is a phlogiston, smt is an old paradigm which ought to be replaced. Recently two critics have argued that toft and smt, despite their apparent strong incompatibilities, are actually compatible. Here we review their arguments. We show that these arguments are based on interpretation mistakes that become understandable once one grants that criticizing a paradigm from the point of view of another, in which words do not have the same signification, bears the risk of strong misunderstandings. These misunderstandings, in our experience, are common. We hope that this discussion will help clarifying the differences between toft and smt.

    Keywords: TOFT, reductionism, organicism, levels of organization, SMT

  2. From Logic to Biology via Physics: a survey

    From Logic to Biology via Physics: a survey

    Logical Methods in Computer Science


    We summarize the theoretical ideas of our book, Perspectives on Organisms, where we discuss biological time, anti-entropy, randomness, incompleteness, symmetries.

    Abstract

    This short text summarizes the work in biology proposed in our book, Perspectives on Organisms, where we analyse the unity proper to organisms by looking at it from different viewpoints. We discuss the theoretical roles of biological time, complexity, theoretical symmetries, singularities and critical transitions. We explicitly borrow from the conclusions in some key chapters and introduce them by a reflection on "incompleteness", also proposed in the book. We consider that incompleteness is a fundamental notion to understand the way in which we construct knowledge. Then we will introduce an approach to biological dynamics where randomness is central to the theoretical determination: randomness does not oppose biological stability but contributes to it by variability, adaptation, and diversity. Then, evolutionary and ontogenetic trajectories are continual changes of coherence structures involving symmetry changes within an ever-changing global stability.

    Keywords: Incompleteness, symmetries, randomness, critical transitions, biological evolution and ontogenesis

    Citation
    Longo, Giuseppe, and Maël Montévil. 2017. “From Logic to Biology via Physics: A Survey.” Logical Methods in Computer Science 13 (November): Issue 4; 1860-5974. https://doi.org/10.23638/LMCS-13(4:21)2017
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  3. Big Data et connaissance biologique

    Big Data et connaissance biologique

    Sciences de la vie, sciences de l’information


    Que peuvent apporter les approches Big Data en biologie? Peuvent-elle être traitée de manière agnostique. Peuvent-elle remplacer la réflexion théorique?

    Abstract

    Certains auteurs affirment que l’analyse des grandes bases de données pourrait remplacer la méthode scientifique. A contrario, nous argumentons que la bonne manière de faire fructifier ces nouveautés techniques est de les encadrer théoriquement. En biologie, en particulier, il nous semble urgent de développer une théorie des organismes.

    Citation
    Longo, G., and Maël Montévil. 2017. “Big Data et Connaissance Biologique.” In Sciences de La Vie, Sciences de l’information, edited by T. Gaudin, D. Lacroix, M.-C. Maurel, and J.-C. Pomerol, 233–38. Paris: ISTE-Editions. https://www.istegroup.com/fr/produit/sciences-de-la-vie-sciences-de-linformation/
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  4. Philosophical Accounts of Biological Functions

    Philosophical Accounts of Biological Functions

    Science & Education


    Review of "A critical overview of biological functions" by Justin Garson (2016). I focus on the etiological and the organizational accounts of functions.

  5. Une brève discussion sur la science autour d’un verre

    Une brève discussion sur la science autour d’un verre

    Qu’est ce que la science pour vous?


    Qu'est ce que la science pour vous? Dialogue entre Candido et Cinico sur la nature de la science. Humilité, méthode, institutions, psychologie.

    Abstract

    Deux collègues chercheurs terminent une longue réunion de travail. Ils décident de boire un verre ensemble dans un café voisin. Le bon vin y étant sans doute pour quelque chose, ils se retrouvent à confronter leurs points de vue sur un sujet ô combien difficile...

    Citation
    Montévil, Maël, and Matteo Mossio. 2017. “Une Brève Discussion Sur La Science Autour d’un Verre.” In Qu’est Ce Que La Science Pour Vous?, edited by M. Silberstein. Editions Matériologiques. https://materiologiques.com/fr/sciences-philosophie/244-qu-est-ce-que-la-science-pour-vous--9782373611076.html
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  6. Du siècle du gène à celui de l’organisme : introduction à de nouvelles perspectives théoriques

    Du siècle du gène à celui de l’organisme : introduction à de nouvelles perspectives théoriques

    Sciences de la vie, sciences de l’information


    Nous décrivons trois principes proposés pour une théorie des organismes : l'état par défaut des cellules et les principes de variation et d'organisation.

    Abstract

    Les organismes, qu’ils soient uni ou multi-cellulaires, sont des agents capables de créer leurs propres normes ; ils articulent continuellement leur capacité à créer de la nouveauté et de la stabilité, c’est-à-dire qu’ils combinent plasticité et robustesse. Ici, nous présentons et articulons brièvement les trois principes proposés récemment pour une théorie des organismes, à savoir : l’état par défaut, prolifération avec variation et motilité, le principe de variation et le principe d’organisation. Ces principes modifient profondément les observables biologiques et leur nature théorique par rapport aux cadres des théories physiques. Ce changement radical ouvre la possibilité d’ancrer la modélisation mathématique à des principes proprement biologiques.

    Citation
    Montévil, Maël, G. Longo, and Ana M. Soto. 2017. “Du Siècle Du Gène à Celui de l’organisme : Introduction à de Nouvelles Perspectives Théoriques.” In Sciences de La Vie, Sciences de l’information, edited by T. Gaudin, D. Lacroix, M.-C. Maurel, and J.-C. Pomerol, 76–90. Paris: ISTE-Editions. https://www.istegroup.com/fr/produit/sciences-de-la-vie-sciences-de-linformation/
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  7. Repetition and Reversibility in Evolution: Theoretical Population Genetics

    Repetition and Reversibility in Evolution: Theoretical Population Genetics

    Time of Nature and the Nature of Time: Philosophical Perspectives of Time in Natural Sciences


    We analyze repetitiveness, reversibility and irreversibility in theoretical population genetics and disentangle concepts that are often confused.

    Abstract

    Repetitiveness and reversibility have long been considered as characteristic features of scientific knowledge. In theoretical population genetics, repetitiveness is illustrated by a number of genetic equilibria realized under specific conditions. Since these equilibria are maintained despite a continual flux of changes in the course of generations (reshuffling of genes, reproduction…), it can legitimately be said that population genetics reveals important properties of invariance through transformation. Time-reversibility is a more controversial subject. Here, the parallel with classical mechanics is much weaker. Time-reversibility is unquestionable in some stochastic models, but at the cost of a special, probabilistic concept of reversibility. But it does not seem to be a property of the most basic deterministic models describing the dynamics of evolutionary change at the level of populations and genes. Furthermore, various meanings of “reversibility” are distinguished. In particular, time-reversibility should not be confused with retrodictability.

    Keywords: population genetics, repetition, retrodiction, reversibility

    Citation
    Gayon, Jean, and Maël Montévil. 2017. “Repetition and Reversibility in Evolution: Theoretical Population Genetics.” In Time of Nature and the Nature of Time: Philosophical Perspectives of Time in Natural Sciences, edited by Christophe Bouton and Philippe Huneman, 275–314. Cham: Springer International Publishing. https://doi.org/10.1007/978-3-319-53725-2_13
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