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  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).


    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.


    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

    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
    Manuscript Citation Publisher Full text
  3. 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.

  4. 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.

  5. What counterpart to the principle of inertia in Population Genetics ?

    In this paper, we will discuss the notion of inertia in Classical Mechanics and its possible counterparts in Theoretical Population Genetics. We will show that, in Population Genetics, changes take place in a mathematical space whose structure is not compatible with notions such as the conservation of momentum or of angular momentum. In spite of this difference, we will argue that there is a fundamental analogy holds between the two fields. The principle of inertia describes the behavior of a system when nothing acts upon it. In Mechanics, this behavior is described by the conservation of momentum. We will show that different situations may be analogous to inertia in evolution. In particular, Theoretical Population Genetics uses a similar line of reasoning in at least two cases: random genetic drift, and geometric growth. However, we will argue that genetic drift is mathematically very different from mechanical inertia as it is far richer in contingent events having lasting consequences.

  6. 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.


    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

    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
    Manuscript Citation Publisher Full text