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  1. Entropies and the Anthropocene crisis

    Entropies and the Anthropocene crisis

    AI and society


    Entropy is a transversal notion to understand the Anthropocene, from physics to biology and social organizations. For the living, it requires a counterpart: anti-entropy.

    Abstract

    The Anthropocene crisis is frequently described as the rarefaction of resources or resources per capita. However, both energy and minerals correspond to fundamentally conserved quantities from the perspective of physics. A specific concept is required to understand the rarefaction of available resources. This concept, entropy, pertains to energy and matter configurations and not just to their sheer amount.
    However, the physics concept of entropy is insufficient to understand biological and social organizations. Biological phenomena display both historicity and systemic properties. A biological organization, the ability of a specific living being to last over time, results from history, expresses itself by systemic properties, and may require generating novelties The concept of anti-entropy stems from the combination of these features. We propose that Anthropocene changes disrupt biological organizations by randomizing them, that is, decreasing anti-entropy. Moreover, second-order disruptions correspond to the decline of the ability to produce functional novelties, that is, to produce anti-entropy.

    Keywords: entropy, anti-entropy, resources, organization, disruption, Anthropocene

  2. Disruption of biological processes in the Anthropocene: the case of phenological mismatch


    Biologists increasingly report anthropogenic disruptions of both organisms and ecosystems, suggesting that these processes are a fundamental, qualitative component of the Anthropocene crisis, seemingly generating disorder. Nonetheless, the notion of disruption has not yet been theorized as such in...

    Abstract

    Biologists increasingly report anthropogenic disruptions of both organisms and ecosystems, suggesting that these processes are a fundamental, qualitative component of the Anthropocene crisis, seemingly generating disorder. Nonetheless, the notion of disruption has not yet been theorized as such in biology. To progress on this matter, we build on a specific case. Relatively minor temperature changes disrupt plant-pollinator synchrony, tearing apart the web of life. Understanding this phenomenon requires a specific rationale since models describing them use both historical and systemic reasoning. Specifically, history justifies that the system is initially in a narrow part of the possibility space where it is viable, and the disruption randomizes this configuration. Building on this rationale, we develop a formal framework inspired by Boltzmann’s entropy. This framework defines the randomization of the system and leads to analyze its consequences systematically. Notably, maximum randomization does not lead to the complete collapse of the ecosystem. Moreover, pollinators’ robustness mostly increases viability for low randomizations, while resilience enhances viability after high randomizations. Applying this framework to empirical networks, we show historical trends depending on latitude, providing further evidence of climate change’s impact on ecosystems via phenology changes. These results lead to an initial definition of disruption in ecology. When a specific historical outcome contributes to a system’s viability, disruption is the randomization of this outcome, decreasing this viability.

  3. Vaccines, Germs, and Knowledge

    Vaccines, Germs, and Knowledge

    Philosophy World Democracy


    To provide a rational assessment of COVID-19 vaccines, we take a step back on both the history of this practice and the current theories in immunology.

    Abstract

    Vaccines for COVID-19 have led to questions, debates, and polemics on both their safety and the political and geopolitical dimension of their use. We propose to take a step back on both the history of this practice and how current theories in immunology understand it. Both can contribute to providing a rational assessment of COVID-19 vaccines. This assessment cannot consider vaccine as an isolated procedure, and we discuss its intergradation with the broader question of knowledge and politics in the COVID-19 pandemic.

    Keywords: epistemology, immunology, politics

  4. 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 show that symmetries play a radically different role in biology by comparison with physics. This article is an updated version of the 2011 paper.

    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

  5. 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.

    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

  6. 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 relational and historical conceptions, and introduce a new symbol for that.

    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.

  7. 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.

    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
    Manuscript Supplementary Citation Publisher Full text
  8. Possibility spaces and the notion of novelty: from music to biology

    Possibility spaces and the notion of novelty: from music to biology

    Synthese


    What is a biological novelty? Is it possible to coin a sound concept of new possibility? What articulation between the concepts of novelty and function?

    Abstract

    We provide a new perspective on the relation between the space of description of an object and the appearance of novelties. One of the aims of this perspective is to facilitate the interaction between mathematics and historical sciences. The definition of novelties is paradoxical: if one can define in advance the possibles, then they are not genuinely new. By analyzing the situation in set theory, we show that defining generic (i.e., shared) and specific (i.e., individual) properties of elements of a set are radically different notions. As a result, generic and specific definitions of possibilities cannot be conflated. We argue that genuinely stating possibilities requires that their meaning has to be made explicit. For example, in physics, properties playing theoretical roles are generic; then, generic reasoning is sufficient to define possibilities. By contrast, in music, we argue that specific properties matter, and generic definitions become insufficient. Then, the notion of new possibilities becomes relevant and irreducible. In biology, among other examples, the generic definition of the space of DNA sequences is insufficient to state phenotypic possibilities even if we assume complete genetic determinism. The generic properties of this space are relevant for sequencing or DNA duplication, but they are inadequate to understand phenotypes. We develop a strong concept of biological novelties which justifies the notion of new possibilities and is more robust than the notion of changing description spaces. These biological novelties are not generic outcomes from an initial situation. They are specific and this specificity is associated with biological functions, that is to say, with a specific causal structure. Thus, we think that in contrast with physics, the concept of new possibilities is necessary for biology.

    Keywords: Novelty, Possibility space, Biological functions, Organization, Emergence

  9. Measurement in biology is methodized by theory

    Measurement in biology is methodized by theory

    Biology & Philosophy


    We characterize measurement in biology from a theoretical perspective with a focus on historicity. We analyze experimental strategies and reproducibility.

    Abstract

    We characterize access to empirical objects in biology from a theoretical perspective. Unlike objects in current physical theories, biological objects are the result of a history and their variations continue to generate a history. This property is the starting point of our concept of measurement. We argue that biological measurement is relative to a natural history which is shared by the different objects subjected to the measurement and is more or less constrained by biologists. We call symmetrization the theoretical and often concrete operation which leads to considering biological objects as equivalent in a measurement. Last, we use our notion of measurement to analyze research strategies. Some strategies aim to bring biology closer to the epistemology of physical theories, by studying objects as similar as possible, while others build on biological diversity.

    Keywords: Biological measurement, evolution, experiments, strains, symmetry, systematics

  10. Which first principles for mathematical modelling in biology?

    Which first principles for mathematical modelling in biology?

    Rendiconti di Matematica e delle sue Applicazioni


    Like theoretical physics, theoretical biology is not just mathematical modeling. Instead, it should strive to find principles to frame experiments and models.

    Abstract

    Like theoretical physics, theoretical biology is not just mathematical modeling. Instead, theoretical biology should strive to find suitable first principles to ground the understanding of biological phenomena and ultimately frame biological experiments and mathematical models. First principles in physics are expressed in terms of symmetries and the associated conservations, on the one side, and optimization on the other side. In biology, we argue instead that a strong notion of variation is fundamental. This notion encompasses new possibilities and the historicity of biological phenomena. By contrast, the relative regularity of some aspects of biological organisms, which we call constraints, should be regarded as the consequence of a mutual stabilization of the parts of organisms. We exemplify several aspects of this framework with the modeling of allometric relationships. Our change of perspective leads to reconsider the meaning of measurements and the structure of the space of description.

    Keywords: Allometry, first principles, Historicity, invariants, theoretical biology, Variability

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