1. Quelques opacités computationnelles: de la biologie aux décisions humaines

    En biologie expérimentale et théorique, les approches computationnelles prennent une place croissante. Sur la base d’un exemple, j’aborderai les différentes étapes computationnelles entre l’échantillon et la discussion biologique. L’analyse morphométrique est traditionnellement effectuée directement par un observateur, mais cette méthode est de plus en plus remplacée par l’utilisation d’algorithmes. Il est alors impératif de proposer une critique de ces approches computationnelle que j’esquisserait sur la base d’une comparaison entre ces deux méthodes. Enfin, je montrerai que la notion de symétrie permet, au moins dans certains cas, d’aborder parallèlement ces questions épistémologiques et des problèmes politiques dans l’utilisation des intelligences artificielles.

  2. 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

    Citation
    Montévil, Maël, and Arnaud Pocheville. 2017. “The Hitchhiker’s Guide to the Cancer Galaxy: How Two Critics Missed Their Destination.” Organisms. Journal of Biological Sciences 1 (2): 37–48. https://doi.org/10.13133/2532-5876_2.9
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  5. 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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  7. Enjeux de l’historicité du vivant pour la modélisation mathématique en biologie

    En physique, les objets sont définis théoriquement par les relations qu'il entretiennent les uns avec les autres. Ce sont ces relations qui sont instanciées dans les modèles mathématiques et qui expliquent le lien profond entre physique et mathématiques. Les modèles mathématique en biologie héritent de cet épistémologie. Nous montrerons pourtant que l'historicité des objets biologiques a des conséquences profondes sur la manière dont on peut envisager ces modèles. Ces conséquences portent d'abord sur l'étude d'organismes actuels qui ne peuvent être envisagée sans leurs histoires évolutives. Elles interviennent ensuite dans la modélisation de la variation phénotypique elle même, laquelle semble bien nécessiter des changements d'espace des possibles et une théorie des contraintes biologiques.

  8. 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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  9. 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.

    Citation
    Montévil, Maël. 2017. “Philosophical Accounts of Biological Functions.” Science & Education 26 (7–9): 1071–73. https://doi.org/10.1007/s11191-017-9917-z
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  10. Modeling mammary organogenesis from biological first principles: The default state of cells and its physical constraints.

    The typical approach for mathematical modeling in biology is to apply mathematical tools and concepts which originated from theoretical principles in physics and computer sciences. Instead, the authors propose to construct a mathematical model based on proper biological principles. Specifically, they use principles identified as fundamental for the elaboration of a theory of organisms, namely i) the default state of cells and ii) the principle of organization. Cells display agency, move and proliferate unless constrained. They exert mechanical forces that i) act on collagen fibers and ii) on other cells. When fibers organize, they constrain the cells on their ability to move and to proliferate. The model exhibits a circularity that can be interpreted in terms of a closure of constraints. Implementing the mathematical model shows that constraints to the default state are sufficient to explain ductal and acinar formation, and points to a target of future research.

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