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  1.  21
    In Search of the Origins of Consciousness: Simona Ginsburg and Eva Jablonka: The Evolution of the Sensitive Soul: Learning and the Origins of Consciousness. MIT Press, Cambridge, MA, 2019, 646pp, ISBN: 9780262039307. [REVIEW]Jonathan Birch - 2020 - Acta Biotheoretica 68 (2):287-294.
    The Evolution of the Sensitive Soul is a landmark attempt to make progress on the problem of animal consciousness. Ginsburg and Jablonka propose a general cognitive marker of the presence of consciousness: Unlimited Associative Learning. They use this marker to defend a generous view about the distribution of consciousness in the natural world, on which a capacity for conscious experience is common to all vertebrates, many arthropods and some cephalopod molluscs. They use this inferred distribution to defend a view about (...)
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  2. Retraction Note To: Robust Model Selection and Estimation for Censored Survival Data with High Dimensional Genomic Covariates.Guorong Chen, Sijian Wang, Guannan Sun & Huanxue Pan - 2020 - Acta Biotheoretica 68 (2):295-295.
    The authors have retracted this article [1] because they found a fundamental mistake in the methodology that is not correctable at this time. This mistake is found in the methodology and the derivation of the model with Tukey and Huber’s losses. Because of the error, the findings in the article are not reliable. All authors agree to this retraction.
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  3.  10
    The Objectivity of Organizational Functions.Samuel Cusimano & Beckett Sterner - 2020 - Acta Biotheoretica 68 (2):253-269.
    We critique the organizational account of biological functions by showing how its basis in the closure of constraints fails to be objective. While the account treats constraints as objective features of physical systems, the number and relationship of potential constraints are subject to potentially arbitrary redescription by investigators. For example, we show that self-maintaining systems such as candle flames can realize closure on a more thorough analysis of the case, contradicting the claim that these “simple” systems lack functional organization. This (...)
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  4.  6
    A Global-Scale Mid-Domain Effect Cannot Explain the Latitudinal Gradient in Species Richness.Thomas W. Fieldsend - 2020 - Acta Biotheoretica 68 (2):271-274.
    The latitudinal gradient in species richness is perhaps the most fundamental pattern of biodiversity, yet a satisfactory explanation for its existence remains elusive. A geometric “mid-domain effect” is often cited as having potential to help explain the latitudinal gradient in species richness, but the logic underpinning this hypothesis is apparently built on two incorrect assumptions: that a given great circle—usually the Equator—can constitute the geometric “mid-domain” of the Earth’s surface, and that geophysical or bioclimatic boundaries are of geometric relevance in (...)
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  5.  9
    A Host–Parasite System with Multiple Parasite Strains and Superinfection Revisited: The Global Dynamics.Lili Liu, Xinzhi Ren & Xianning Liu - 2020 - Acta Biotheoretica 68 (2):201-225.
    In this paper, we revisit a host–parasite system with multiple parasite strains and superinfection proposed by Nowak and May :81–89, 1994), and study its global dynamics when we relax the two strict conditions assumed therein. As for system with two parasite strains, we derive that the basic reproduction number R0\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$R_0$$\end{document} is the threshold condition for parasite extinction and the invasion reproduction number Rij\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$R_i^j\ (...)
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  6.  8
    Expansion Speed as a Generic Measure of Spread for Alien Species.Hanno Sandvik - 2020 - Acta Biotheoretica 68 (2):227-252.
    The ecological impact of alien species is a function of the area colonised. Impact assessments of alien species are thus incomplete unless they take the spatial component of invasion processes into account. This paper describes a measure, termed expansion speed, that quantifies the speed with which a species increases its spatial presence in an assessment area. It is based on the area of occupancy and can be estimated from grid occupancies. Expansion speed is defined as the yearly increase in the (...)
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  7.  22
    The Cultural Evolution of Human Nature.Mark Stanford - 2020 - Acta Biotheoretica 68 (2):275-285.
    Recent years have seen the growing promise of cultural evolutionary theory as a new approach to bringing human behaviour fully within the broader evolutionary synthesis. This review of two recent seminal works on this topic argues that cultural evolution now holds the potential to bring together fields as disparate as neuroscience and social anthropology within a unified explanatory and ontological framework.
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  8.  4
    On Computing Structural and Behavioral Complexities of Threshold Boolean Networks: Application to Biological Networks.Urvan Christen, Sergiu Ivanov, Rémi Segretain, Laurent Trilling & Nicolas Glade - 2020 - Acta Biotheoretica 68 (1):119-138.
    Various threshold Boolean networks, a formalism used to model different types of biological networks, can produce similar dynamics, i.e. share same behaviors. Among them, some are complex, others not. By computing both structural and behavioral complexities, we show that most TBNs are structurally complex, even those having simple behaviors. For this purpose, we developed a new method to compute the structural complexity of a TBN based on estimates of the sizes of equivalence classes of the threshold Boolean functions composing the (...)
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  9.  3
    A GPU Algorithm for Agent-Based Models to Simulate the Integration of Cell Membrane Signals.Arthur Douillet & Pascal Ballet - 2020 - Acta Biotheoretica 68 (1):61-71.
    Simulation of complex biological systems with agent-based models is becoming more relevant with the increase in Graphics Processing Unit power. In those simulations, up to millions of virtual cells are individually computed, involving daunting processing times. An important part of computational models is the algorithm that manages how agents perceive their surroundings. This can be particularly problematic in three-dimensional environments where agents have deformable virtual membranes. This article presents a GPU algorithm that gives the possibility for agents to integrate the (...)
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  10. Proceedings of the XXXVIIIth Seminar of the French-Speaking Society for Theoretical Biology; Saint-Flour (Cantal), France, 11–13 June, 2018. [REVIEW]Sergiu Ivanov, Ibrahim Cheddadi & Nicolas Glade - 2020 - Acta Biotheoretica 68 (1):1-3.
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  11.  4
    Sensitivity Analysis of a Left Ventricle Model in the Context of Intraventricular Dyssynchrony.Virginie Le Rolle, Elena Galli, David Danan, Karim El Houari, Arnaud Hubert, Erwan Donal & Alfredo I. Hernández - 2020 - Acta Biotheoretica 68 (1):45-59.
    The objective of the current study was to propose a sensitivity analysis of a 3D left ventricle model in order to assess the influence of parameters on myocardial mechanical dispersion. A finite element model of LV electro-mechanical activity was proposed and a screening method was used to evaluate the sensitivity of model parameters on the standard deviation of time to peak strain. Results highlight the importance of propagation parameters associated with septal and lateral segments activation. Simulated curves were compared to (...)
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  12.  4
    Phylogeny and Sequence Space: A Combined Approach to Analyze the Evolutionary Trajectories of Homologous Proteins. The Case Study of Aminodeoxychorismate Synthase.Sylvain Lespinats, Olivier De Clerck, Benoît Colange, Vera Gorelova, Delphine Grando, Eric Maréchal, Dominique Van Der Straeten, Fabrice Rébeillé & Olivier Bastien - 2020 - Acta Biotheoretica 68 (1):139-156.
    During the course of evolution, variations of a protein sequence is an ongoing phenomenon however limited by the need to maintain its structural and functional integrity. Deciphering the evolutionary path of a protein is thus of fundamental interest. With the development of new methods to visualize high dimension spaces and the improvement of phylogenetic analysis tools, it is possible to study the evolutionary trajectories of proteins in the sequence space. Using the data-driven high-dimensional scaling method, we show that it is (...)
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  13.  18
    Formalizing Metabolic-Regulatory Networks by Hybrid Automata.Lin Liu & Alexander Bockmayr - 2020 - Acta Biotheoretica 68 (1):73-85.
    Computational approaches in systems biology have become a powerful tool for understanding the fundamental mechanisms of cellular metabolism and regulation. However, the interplay between the regulatory and the metabolic system is still poorly understood. In particular, there is a need for formal mathematical frameworks that allow analyzing metabolism together with dynamic enzyme resources and regulatory events. Here, we introduce a metabolic-regulatory network model that allows integrating metabolism with transcriptional regulation, macromolecule production and enzyme resources. Using this model, we show that (...)
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  14.  3
    A Combinatorial Exploration of Boolean Dynamics Generated by Isolated and Chorded Circuits.B. Mossé & É Remy - 2020 - Acta Biotheoretica 68 (1):87-117.
    Most studies of motifs of biological regulatory networks focus on the analysis of asymptotical behaviours, but transient properties are rarely addressed. In the line of our previous study devoted to isolated circuits 19:172–178, 2003), we consider chorded circuits, that are motifs made of an elementary positive or negative circuit with a chord, possibly a self-loop. We provide detailed descriptions of the boolean dynamics of chorded circuits versus isolated circuits, under the synchronous and asynchronous updating schemes within the logical formalism. To (...)
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  15.  6
    On the Effect of Age-Dependent Mortality on the Stability of a System of Delay-Differential Equations Modeling Erythropoiesis.Frédéric Paquin-Lefebvre & Jacques Bélair - 2020 - Acta Biotheoretica 68 (1):5-19.
    We present an age-structured model for erythropoiesis in which the mortality of mature cells is described empirically by a physiologically realistic probability distribution of survival times. Under some assumptions, the model can be transformed into a system of delay differential equations with both constant and distributed delays. The stability of the equilibrium of this system and possible Hopf bifurcations are described for a number of probability distributions. Physiological motivation and interpretation of our results are provided.
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  16.  2
    Clustering of Thrombin Generation Test Data Using a Reduced Mathematical Model of Blood Coagulation.N. Ratto, A. Tokarev, P. Chelle, B. Tardy-Poncet & V. Volpert - 2020 - Acta Biotheoretica 68 (1):21-43.
    Correct interpretation of the data from integral laboratory tests, including Thrombin Generation Test, requires biochemistry-based mathematical models of blood coagulation. The purpose of this study is to describe the experimental TGT data from healthy donors and hemophilia A and B patients. We derive a simplified ODE model and apply it to analyze the TGT data from healthy donors and HA/hb patients with in vitro added tissue factor pathway inhibitor antibody. This model allows the characterization of hemophilia patients in the space (...)
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  17.  8
    New Schemes of Dynamic Preservation of Diversity: Remarks on Stability and Topology.Evariste Sanchez-Palencia & Jean-Pierre Françoise - 2020 - Acta Biotheoretica 68 (1):157-169.
    We address the biological dynamics problem of the persistence of several species in conditions of non-existence of an equilibrium, including an example of stabilization by predation and the very controversial “competitive exclusion”. We give normal forms for various examples of such persistence and comments on the involved topology, which implies the presence of exceptional heteroclinic connections binding equilibria on the boundary.
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  18.  10
    Individuation and the Organization in Complex Living Ecosystem: Recursive Integration and Self-Assertion by Holon-Lymphocytes.Véronique Thomas-Vaslin - 2020 - Acta Biotheoretica 68 (1):171-199.
    Individuation and organization in complex living multi-level ecosystem occurs as dynamical processes from early ontogeny. The notion of living “holon” displaying dynamic self-assertion and integration is used here to explain the ecosystems dynamic processes. The update of the living holon state according to the continuous change of the dynamic system allows for its viability. This is interpreted as adaptation, selection and organization by the human that observes the system a posteriori from its level. Our model concerns the complex dynamics of (...)
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