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Articles of 2020

  1. From physics to biology by extending criticality and symmetry breakings: An update

    From physics to biology by extending criticality and symmetry breakings: An update

    Acta Europeana Systemica


    We introduce our theoretical analysis in biology and show that symmetries play a radically different role in this discipline, by comparison with physics.

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    Abstract:

    Symmetries play a major role in physics, in particular since the work by E. Noether and H. Weyl in the first half of last century. Herein, we briefly review their role by recalling how symmetry changes allow to conceptually move from classical to relativistic and quantum physics. We then introduce our ongoing theoretical analysis in biology and show that symmetries play a radically different role in this discipline, when compared to those in current physics. By this comparison, we stress that symmetries must be understood in relation to conservation and stability properties, as represented in the theories. We posit that the dynamics of biological organisms, in their various levels of organization, are not “just” processes, but permanent (extended, in our terminology) critical transitions and, thus, symmetry changes. Within the limits of a relative structural stability (or interval of viability), qualitative variability is at the core of these transitions.

    Keywords: Coherent structures, Critical transitions, downward causation, Hidden variables, Levels of organization, Symmetries, Systems biology

    Citation:

    Longo, Giuseppe, and Maël Montévil. 2020. “From Physics to Biology by Extending Criticality and Symmetry Breakings: An Update.” Acta Europeana Systemica 9 (1): 77–92. https://doi.org/10.14428/aes.v9i1.56043

  2. Historicity at the heart of biology

    Historicity at the heart of biology

    Theory in Biosciences


    Most mathematical modeling in biology rely on the epistemology of physics. By contrast, we argue that historicity comes first in biology.

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    Abstract:

    Most mathematical modeling in biology relies either implicitly or explicitly on the epistemology of physics. The underlying conception is that the historicity of biological objects would not matter to understand a situation here and now, or, at least, historicity would not impact the method of modeling. We analyze that it is not the case with concrete examples. Historicity forces a conceptual reconfiguration where equations no longer play a central role. We argue that all observations depend on objects defined by their historical origin instead of their relations as in physics. Therefore, we propose that biological variations and historicity come first, and regularities are constraints with limited validity in biology. Their proper theoretical and empirical use requires specific rationales.

    Keywords: Historicity, Organization, Epistemology, Mathematical modeling, Constraints

    Citation:

    Montévil, Maël. 2020. “Historicity at the Heart of Biology.” Theory in Biosciences, July. https://doi.org/10.1007/s12064-020-00320-8

  3. The Identity of Organisms in Scientific Practice: Integrating Historical and Relational Conceptions

    The Identity of Organisms in Scientific Practice: Integrating Historical and Relational Conceptions

    Frontiers in Physiology


    We address the identity of biological organisms in scientific practices by combining historical and relational, organizational conceptions.

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    Abstract:

    We address the identity of biological organisms at play in experimental and modeling practices. We first examine the central tenets of two general conceptions, and we assess their respective strengths and weaknesses. The historical conception, on the one hand, characterizes organisms’ identity by looking at their past, and specifically at their genealogical connection with a common ancestor. The relational conception, on the other hand, interprets organisms’ identity by referring to a set of distinctive relations between their parts, and between the organism and its environment. While the historical and relational conceptions are understood as opposed and conflicting, we submit that they are also fundamentally complementary. Accordingly, we put forward a hybrid conception, in which historical and relational (and more specifically, organizational) aspects of organisms’ identity sustain and justify each other. Moreover, we argue that organisms’ identity is not only hybrid but also bounded, insofar as the compliance with specific identity criteria tends to vanish as time passes, especially across generations. We spell out the core conceptual framework of this conception, and we outline an original formal representation. We contend that the hybrid and bounded conception of organisms’ identity suits the epistemological needs of biological practices, particularly with regards to the generalization and reproducibility of experimental results, and the integration of mathematical models with experiments.

    Citation:
  4. De l’œuvre de Turing aux défis contemporains pour la compréhension mathématique du vivant

    De l’œuvre de Turing aux défis contemporains pour la compréhension mathématique du vivant

    Intellectica


    Turing distingue soigneusement l’imitation d’un phénomène de sa modélisation. En biologie, il n'y a cependant pas de cadre théorique bien établi pour encadrer la pratique de modélisation.

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    Abstract:

    Turing distingue soigneusement l’imitation de la modélisation d’un phénomène. Cette dernière vise à saisir la structure causale du phénomène étudié. En biologie, il n’y a cependant pas de cadre théorique bien établi pour encadrer la pratique de modélisation. Nous partons de l’articulation entre la compréhension du vivant et la thermodynamique, en particulier le second principe. Ceci nous conduira à expliciter les défis théoriques et épistémologiques pour la compréhension mathématique du vivant. En particulier, l’historicité du vivant est un défi rarement abordé explicitement dans ce domaine. Nous pensons que ce défi nécessite un renversement complet de l’épistémologie de la physique afin d’aborder de manière théoriquement précise les organismes vivants. Ce changement épistémologique est pertinent tant pour la pratique théorique que pour l’interprétation des protocoles et résultats expérimentaux.

    Keywords: anti-entropie, entropie, épistémologie, historicité, morphogenèse, Turing

    Citation:
  5. A combined morphometric and statistical approach to assess non-monotonicity in the developing mammary gland of rats in the CLARITY-BPA study

    A combined morphometric and statistical approach to assess non-monotonicity in the developing mammary gland of rats in the CLARITY-BPA study

    Environmental Health Perspectives


    We can and should take advantage of nonmonotonic properties to perform statistical analysis rigorously by new statistical and morphometric methods.

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    Abstract:

    We aimed to a) determine whether BPA showed effects on the developing rat mammary gland using new quantitative and established semiquantitative methods in two laboratories, b) develop a software tool for automatic evaluation of quantifiable aspects of the mammary ductal tree, and c) compare those methods. Conclusions: Both the semiquantitative and the quantitative methods revealed nonmonotonic effects of BPA. The quantitative unsupervised analysis used 91 measurements and produced the most striking nonmonotonic dose–response curves. At all time points, lower doses resulted in larger effects, consistent with the core study, which revealed a significant increase of mammary adenocarcinoma incidence in the stop-dose animals at the lowest BPA dose tested.

    Citation:

    Montévil, Maël, Nicole Acevedo, Cheryl M. Schaeberle, Manushree Bharadwaj, Suzanne E. Fenton, and Ana M. Soto. 2020. “A Combined Morphometric and Statistical Approach to Assess Non-Monotonicity in the Developing Mammary Gland of Rats in the CLARITY-BPA Study.” Environmental Health Perspectives 128 (5): 057001. https://doi.org/10.1289/EHP6301