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  1. On Adjoint and Brain Functors.David Ellerman - 2016 - Axiomathes 26 (1):41-61.
    There is some consensus among orthodox category theorists that the concept of adjoint functors is the most important concept contributed to mathematics by category theory. We give a heterodox treatment of adjoints using heteromorphisms that parses an adjunction into two separate parts. Then these separate parts can be recombined in a new way to define a cognate concept, the brain functor, to abstractly model the functions of perception and action of a brain. The treatment uses relatively simple category theory and (...)
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  2. A Framework for Philosophical Biology.Sepehr Ehsani - manuscript
    Advances in biology, at least over the past two centuries, have mostly relied on theories that were subsequently revised, expanded or eventually refuted using experimental and other means. The field of theoretical biology used to primarily provide a basis, similar to theoretical physics in the physical sciences, to rationally examine the frameworks within which biological experiments were carried out and to shed light on overlooked gaps in understanding. Today, however, theoretical biology has generally become synonymous with computational and mathematical biology. (...)
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  3. Field Equations, Quantum Mechanics and Geotropism.Han J. F. Geurdes - manuscript
    The biochemistry of geotropism in plants and gravisensing in e.g. cyanobacteria or paramacia is still not well understood today [1]. Perhaps there are more ways than one for organisms to sense gravity. The two best known relatively old explanations for gravity sensing are sensing through the redistribution of cellular starch statoliths and sensing through redistribution of auxin. The starch containing statoliths in a gravity field produce pressure on the endoplasmic reticulum of the cell. This enables the cell to sense direction. (...)
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  4. The Literalist Fallacy & the Free Energy Principle: Model Building, Scientific Realism and Instrumentalism.Michael David Kirchhoff, Julian Kiverstein & Ian Robertson - manuscript
    Disagreement about how best to think of the relation between theories and the realities they represent has a longstanding and venerable history. We take up this debate in relation to the free energy principle (FEP) - a contemporary framework in computational neuroscience, theoretical biology and the philosophy of cognitive science. The FEP is very ambitious, extending from the brain sciences to the biology of self-organisation. In this context, some find apparent discrepancies between the map (the FEP) and the territory (target (...)
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  5. Free Energy: A User's Guide.Stephen Francis Mann, Ross Alexander Pain & Michael Kirchhoff - manuscript
    Over the last fifteen years, an ambitious explanatory framework has been proposed to unify explanations across biology and cognitive science. Active inference, whose most famous tenet is the free energy principle, has inspired excitement and confusion in equal measure. Here, we lay the ground for proper critical analysis of active inference, in three ways. First, we give simplified versions of its core mathematical models. Second, we outline the historical development of active inference and its relationship to other theoretical approaches. Third, (...)
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  6. Is It Really so Easy to Model Biological Evolution in Terms of Design-Free Cumulative Selection?Peter Punin - manuscript
    Abstract: Without directly taking sides in the design/anti-design debate, this paper defends the following position: the assertion that biological evolution “is” design-free presupposes the possibility to model biological evolution in a design-free way. Certainly, there are design-free models of evolution based on cumulative selection. But “to model” is a verb denoting “modeling” as the process leading to a model. So any modeling – trivially – needs “previous human design.” Nevertheless, contrary to other scientific activities which legitimately consider models while ignoring (...)
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  7. The Physics and Electronics Meaning of Vivartanam.Varanasi Ramabrahmam - manuscript
    A modern scientific awareness of the famous advaitic expression Brahma sat, jagat mithya, jivo brahmaiva na aparah is presented. The one ness of jiva and Brahman are explained from modern science point of view. The terms dristi, adhyasa, vivartanam, aham and idam are understood in modern scientific terms and a scientific analysis is given. -/- Further, the forward (purodhana) and reverse (tirodhana) transformation of maya as jiva, prapancham, jagat and viswam, undergoing vivartanam is understood and explained using concepts from physics (...)
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  8. Towards an Ecological View of Immunity. [REVIEW]Swiatczak Bartlomiej - forthcoming - Studies in History and Philosophy of Science Part A.
    The immune system does not just fight pathogens but also engages in interactions with beneficial microbes and non-immune cells of the body to harmonize their behavior by means of cytokines, antibodies and effector cells (Dinarello, 2007; Moticka, 2015, pp. 217e226, 261e267). However, the importance of these “housekeeping” functions has not been fully appreciated (Cohen, 2000). In his new book Immunity: The Evolution of an Idea Alfred I. Tauber traces the history of fundamental ideas in immunology and refers to recent advances (...)
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  9. Discrete Conventional Signalling of a Continuous Variable.Magnus Enquist, Stefano Ghirlanda & Pete L. Hurd - forthcoming - Philosophical Explorations.
    In aggressive interactions, animals often use a discrete set of signals, while the properties being signalled are likely to be continuous, for example fighting ability or value of victory. Here we investigate a particular model of fighting which allows for conventional signalling of subjective resource value to occur. The result shows that neither perfect nor no signalling are evolutionarily stable strategies in the model. Instead, we find ESSs in which partial information is communicated, with discrete displays signalling a range of (...)
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  10. Structure From Data: AI Approaches to Systems Modeling.H. Hyötyniemi - forthcoming - Proc. 8th Finnish Ai Conference Step’98.
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  11. Bayesian Realism and Structural Representation.Alex Kiefer & Jakob Hohwy - forthcoming - Behavioral and Brain Sciences.
    We challenge Bruineberg et al's view that Markov blankets are illicitly reified when used to describe organismic boundaries. We do this both on general methodological grounds, where we appeal to a form of structural realism derived from Bayesian cognitive science to dissolve the problem, and by rebutting specific arguments in the target article.
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  12. Unifying the Essential Concepts of Biological Networks.Daniel Kostic, Claus Hilgetag & Marc Tittgemeyer (eds.) - forthcoming - Royal Society.
  13. Unifying the Essential Concepts of Biological Networks: Biological Insights and Philosophical Foundations.Daniel Kostic, Claus Hilgetag & Marc Tittgemeyer - forthcoming - Oxford, UK: Royal Society.
    Over the last two decades, network-focused approaches have become highly popular in diverse fields of biology, including neuroscience, ecology, molecular biology and genetics. While the network approach continues to grow very rapidly, some of its conceptual and methodological aspects still require a programmatic foundation. This challenge particularly concerns the question of whether a generalized account of explanatory, organisational and descriptive levels of networks can be applied universally across biological sciences. Consequently, the central focus of this theme issue will be on (...)
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  14. Revisiting abstraction and idealization: how not to criticize mechanistic explanation in molecular biology.Martin Zach - 2022 - European Journal for Philosophy of Science 12 (1):1-20.
    Abstraction and idealization are the two notions that are most often discussed in the context of assumptions employed in the process of model building. These notions are also routinely used in philosophical debates such as that on the mechanistic account of explanation. Indeed, an objection to the mechanistic account has recently been formulated precisely on these grounds: mechanists cannot account for the common practice of idealizing difference-making factors in models in molecular biology. In this paper I revisit the debate and (...)
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  15. Combining Causal Bayes Nets and Cellular Automata: A Hybrid Modelling Approach to Mechanisms.Alexander Gebharter & Daniel Koch - 2021 - British Journal for the Philosophy of Science 72 (3):839-864.
    Causal Bayes nets (CBNs) can be used to model causal relationships up to whole mechanisms. Though modelling mechanisms with CBNs comes with many advantages, CBNs might fail to adequately represent some biological mechanisms because—as Kaiser (2016) pointed out—they have problems with capturing relevant spatial and structural information. In this paper we propose a hybrid approach for modelling mechanisms that combines CBNs and cellular automata. Our approach can incorporate spatial and structural information while, at the same time, it comes with all (...)
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  16. Are Scientific Models of Life Testable? A Lesson From Simpson's Paradox.Prasanta S. Bandyopadhyay, Don Dcruz, Nolan Grunska & Mark Greenwood - 2020 - Sci 1 (3).
    We address the need for a model by considering two competing theories regarding the origin of life: (i) the Metabolism First theory, and (ii) the RNA World theory. We discuss two interrelated points, namely: (i) Models are valuable tools for understanding both the processes and intricacies of origin-of-life issues, and (ii) Insights from models also help us to evaluate the core objection to origin-of-life theories, called “the inefficiency objection”, which is commonly raised by proponents of both the Metabolism First theory (...)
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  17. Glycemia Regulation: From Feedback Loops to Organizational Closure.Leonardo Bich, Matteo Mossio & Ana M. Soto - 2020 - Frontiers in Physiology 11.
    Endocrinologists apply the idea of feedback loops to explain how hormones regulate certain bodily functions such as glucose metabolism. In particular, feedback loops focus on the maintenance of the plasma concentrations of glucose within a narrow range. Here, we put forward a different, organicist perspective on the endocrine regulation of glycaemia, by relying on the pivotal concept of closure of constraints. From this perspective, biological systems are understood as organized ones, which means that they are constituted of a set of (...)
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  18. Analytic Philosophy for Biomedical Research: The Imperative of Applying Yesterday's Timeless Messages to Today's Impasses.Sepehr Ehsani - 2020 - In P. Glauner & P. Plugmann (eds.), Innovative Technologies for Market Leadership - Investing in the Future. Springer. pp. 167-200.
    The mantra that "the best way to predict the future is to invent it" (attributed to the computer scientist Alan Kay) exemplifies some of the expectations from the technical and innovative sides of biomedical research at present. However, for technical advancements to make real impacts both on patient health and genuine scientific understanding, quite a number of lingering challenges facing the entire spectrum from protein biology all the way to randomized controlled trials should start to be overcome. The proposal in (...)
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  19. Information-Matter Bipolarity of the Human Organism and Its Fundamental Circuits: From Philosophy to Physics/Neurosciences-Based Modeling.Florin Gaiseanu - 2020 - Philosophy Study 10 (2):107-118.
    Starting from a philosophical perspective, which states that the living structures are actually a combination between matter and information, this article presents the results on an analysis of the bipolar information-matter structure of the human organism, distinguishing three fundamental circuits for its survival, which demonstrates and supports this statement, as a base for further development of the informational model of consciousness to a general informational model of the human organism. For this, it was examined the Informational System of the Human (...)
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  20. Launching of Davydov Solitons in Protein Α-Helix Spines.Danko D. Georgiev & James F. Glazebrook - 2020 - Physica E: Low-Dimensional Systems and Nanostructures 124:114332.
    Biological order provided by α-helical secondary protein structures is an important resource exploitable by living organisms for increasing the efficiency of energy transport. In particular, self-trapping of amide I energy quanta by the induced phonon deformation of the hydrogen-bonded lattice of peptide groups is capable of generating either pinned or moving solitary waves following the Davydov quasiparticle/soliton model. The effect of applied in-phase Gaussian pulses of amide I energy, however, was found to be strongly dependent on the site of application. (...)
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  21. Quantum Transport and Utilization of Free Energy in Protein Α-Helices.Danko D. Georgiev & James F. Glazebrook - 2020 - Advances in Quantum Chemistry 82:253-300.
    The essential biological processes that sustain life are catalyzed by protein nano-engines, which maintain living systems in far-from-equilibrium ordered states. To investigate energetic processes in proteins, we have analyzed the system of generalized Davydov equations that govern the quantum dynamics of multiple amide I exciton quanta propagating along the hydrogen-bonded peptide groups in α-helices. Computational simulations have confirmed the generation of moving Davydov solitons by applied pulses of amide I energy for protein α-helices of varying length. The stability and mobility (...)
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  22. On Being the Right Size, Revisited: The Problem with Engineering Metaphors in Molecular Biology.Daniel J. Nicholson - 2020 - In Sune Hannibal Holm & Maria Serban (eds.), Philosophical Perspectives on the Engineering Approach in Biology: Living Machines? London, UK: pp. 40-68.
    In 1926, Haldane published an essay titled 'On Being the Right Size' in which he argued that the structure, function, and behavior of an organism are strongly conditioned by the physical forces that exert the greatest impact at the scale at which it exists. This chapter puts Haldane’s insight to work in the context of contemporary cell and molecular biology. Owing to their minuscule size, cells and molecules are subject to very different forces than macroscopic organisms. In a sense, macroscopic (...)
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  23. Mechanist Idealisation in Systems Biology.Dingmar van Eck & Cory Wright - 2020 - Synthese 199 (1-2):1555-1575.
    This paper adds to the philosophical literature on mechanistic explanation by elaborating two related explanatory functions of idealisation in mechanistic models. The first function involves explaining the presence of structural/organizational features of mechanisms by reference to their role as difference-makers for performance requirements. The second involves tracking counterfactual dependency relations between features of mechanisms and features of mechanistic explanandum phenomena. To make these functions salient, we relate our discussion to an exemplar from systems biological research on the mechanism for countering (...)
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  24. How Bioscience Meets Buddhism.Sun Kyeong Yu & Chang-Seong Hong - 2020 - Seoul, South Korea: Unjusa.
    <2020 Buddhist Book Award (2nd place), Korea> <2020 Sejong Book Award, Korea> The book discusses and provides solutions for the philosophical issues of Aristotelian essentialist biology, Darwin’s evolutionary theory, and contemporary molecular biology in light of Buddhist concepts of dependent arising and emptiness. CONTENT 1. Buddhist Teachings from the perspective of Bioscience 2. Bioscience from the Perspective of Buddhist Teachings 3. Enlightenment, Compassion and Bioscientific Phenomena 4. Enlightenment, Revolutionary Change of Worldview 5. The Buddhist Understanding of Development in Biology 1 (...)
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  25. Life/Force: Novelty and New Materialism in Jane Bennett's Vibrant Matter.Jonathan Basile - 2019 - Substance 48 (2):3-22.
    Among those speaking in the name of materialism, whether speculative, dialectical, or "new," it is commonplace to dismiss with a single gesture a vast field of theoretical and philosophical endeavor, indicated as the last 50 or 250 years of theory and philosophy. Self-styled "speculative" writers who would surpass all philosophy since Kant, and various New Materialists who sequester decades of thought under the heading of "constructivism," manufacture the avant-garde status of their own work by claiming to delineate a simple break (...)
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  26. The Aims and Structures of Ecological Research Programs.William Bausman - 2019 - Philosophical Topics 47 (1):1-20.
    Neutral Theory is controversial in ecology. Ecologists and philosophers have diagnosed the source of the controversy as: its false assumption that individuals in different species within the same trophic level are ecologically equivalent, its conflict with Competition Theory and the adaptation of species, its role as a null hypothesis, and as a Lakatosian research programme. In this paper, I show why we should instead understand the conflict at the level of research programs which involve more than theory. The Neutralist and (...)
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  27. Mapping the Continuum of Research Strategies.Matthew Baxendale - 2019 - Synthese 196 (11):4711-4733.
    Contemporary philosophy of science has seen a growing trend towards a focus on scientific practice over the epistemic outputs that such practices produce. This practice-oriented approach has yielded a clearer understanding of how reductive research strategies play a central role in contemporary scientific inquiry. In parallel, a growing body of work has sought to explore the role of non-reductive, or systems-level, research strategies. As a result, the relationship between reductive and non-reductive scientific practices is becoming of increased importance. In this (...)
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  28. Biosemiosis and Causation: Defending Biosemiotics Through Rosen's Theoretical Biology, or, Integrating Biosemiotics and Anticipatory Systems Theory.Arran Gare - 2019 - Cosmos and History 19 (1):31-90.
    The fracture in the emerging discipline of biosemiotics when the code biologist Marcello Barbieri claimed that Peircian biosemiotics is not genuine science raises anew the question: What is science? When it comes to radically new approaches in science, there is no simple answer to this question, because if successful, these new approaches change what is understood to be science. This is what Galileo, Darwin and Einstein did to science, and with quantum theory, opposing interpretations are not merely about what theory (...)
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  29. How to Use Fitness Landscape Models for the Analysis of Collective Decision-Making: A Case of Theory-Transfer and its Limitations.Peter Marks, Lasse Gerrits & Johannes Marx - 2019 - Biology and Philosophy 34 (1):7.
    There is considerable correspondence between theories and models used in biology and the social sciences. One type of model that is in use in both biology and the social sciences is the fitness landscape model. The properties of the fitness landscape model have been applied rather freely in the social domain. This is partly due to the versatility of the model, but it is also due to the difficulties of transferring a model to another domain. We will demonstrate that in (...)
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  30. Possibility Spaces and the Notion of Novelty: From Music to Biology.Maël Montévil - 2019 - Synthese 196 (11):4555-4581.
    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 (...)
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  31. Genetic Relatedness and Its Causal Role in the Evolution of Insect Societies.Tuomas K. Pernu - 2019 - Journal of Biosciences 44:107.
    The role of genetic relatedness in social evolution has recently come under critical attention. These arguments are here critically analyzed, both theoretically and empirically. It is argued that when the conceptual structure of the theory of natural selection is carefully taken into account, genetic relatedness can be seen to play an indispensable role in the evolution of both facultative and advanced eusociality. Although reviewing the empirical evidence concerning the evolution of eusociality reveals that relatedness does not play a role in (...)
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  32. Mathematical Modeling of Substrates Fluxes and Tumor Growth in the Brain.Angélique Perrillat-Mercerot, Nicolas Bourmeyster, Carole Guillevin, Alain Miranville & Rémy Guillevin - 2019 - Acta Biotheoretica 67 (2):149-175.
    The aim of this article is to show how a tumor can modify energy substrates fluxes in the brain to support its own growth. To address this question we use a modeling approach to explain brain nutrient kinetics. In particular we set up a system of 17 equations for oxygen, lactate, glucose concentrations and cells number in the brain. We prove the existence and uniqueness of nonnegative solutions and give bounds on the solutions. We also provide numerical simulations.
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  33. Cancer Modeling: The Advantages and Limitations of Multiple Perspectives.A. Plutynski - 2019 - In Michela Massimi & Casey McCoy (eds.), Understanding Perspectivism: Scientific Challenges and Methodological Prospects. New York: Routledge.
    Cancer is a paradigmatic case of a complex causal process; causes of cancer operate at a variety of temporal and spatial scales, and the respects in which these causes act and interact are diverse. There are, for instance, temporal order effects, organizational effects, structural effects, and dynamic relationships between causes operating at different temporal and spatial scales. Because of this complexity, models of cancer initiation and progression often involve deliberate choices to focus on one time scale, one causal pathway, or (...)
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  34. Control by Viability in a Chemotherapy Cancer Model.M. Serhani, H. Essaadi, K. Kassara & A. Boutoulout - 2019 - Acta Biotheoretica 67 (3):177-200.
    The aim of this study is to provide a feedback control, called the Chemotherapy Protocol Law, with the purpose to keep the density of tumor cells that are treated by chemotherapy below a “tolerance level” L_c, while retaining the density of normal cells above a “healthy level” N_c. The mathematical model is a controlled dynamical system involving three nonlinear differential equations, based on a Gompertzian law of cell growth. By evoking viability and set-valued theories, we derive sufficient conditions for the (...)
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  35. Constructing Reality with Models.Tee Sim-Hui - 2019 - Synthese 196 (11):4605-4622.
    Scientific models are used to predict and understand the target phenomena in the reality. The kind of epistemic relationship between the model and the reality is always regarded by most of the philosophers as a representational one. I argue that, complementary to this representational role, some of the scientific models have a constructive role to play in altering and reconstructing the reality in a physical way. I hold that the idealized model assumptions and elements bestow the constructive force of a (...)
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  36. Some Concerns Regarding Explanatory Pluralism: The Explanatory Role of Optimality Models.Gabriel Târziu - 2019 - Filozofia Nauki 28 (4):95-113.
    Optimality models are widely used in different parts of biology. Two important questions that have been asked about such models are: are they explanatory and, if so, what type of explanations do they offer? My concern in this paper is with the approach of Rice (2012, 2015) and Irvine (2015), who claim that these models provide non-causal explanations. I argue that there are serious problems with this approach and with the accounts of explanation it is intended to justify. The idea (...)
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  37. A 3D Individual-Based Model to Study Effects of Chemotaxis, Competition and Diffusion on the Motile-Phytoplankton Aggregation.Ilhem Bouderbala, Nadjia El Saadi, Alassane Bah & Pierre Auger - 2018 - Acta Biotheoretica 66 (4):257-278.
    In this paper, we develop a 3D-individual-based model to understand effect of various small-scale mechanisms in phytoplankton cells, on the cellular aggregation process. These mechanisms are: spatial interactions between cells due to their chemosensory abilities, a molecular diffusion and a demographical process. The latter is considered as a branching process with a density-dependent death rate to take into account the local competition on resources. We implement the IBM and simulate various scenarios under real parameter values for phytoplankton cells. To quantify (...)
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  38. Quaternion-Based Texture Analysis of Multiband Satellite Images: Application to the Estimation of Aboveground Biomass in the East Region of Cameroon.Cedrigue Boris Djiongo Kenfack, Olivier Monga, Serge Moto Mpong & René Ndoundam - 2018 - Acta Biotheoretica 66 (1):17-60.
    Within the last decade, several approaches using quaternion numbers to handle and model multiband images in a holistic manner were introduced. The quaternion Fourier transform can be efficiently used to model texture in multidimensional data such as color images. For practical application, multispectral satellite data appear as a primary source for measuring past trends and monitoring changes in forest carbon stocks. In this work, we propose a texture-color descriptor based on the quaternion Fourier transform to extract relevant information from multiband (...)
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  39. Landscapes of Collectivity in the Life Sciences.Snait B. Gissis, Ehud Lamm & Ayelet Shavit (eds.) - 2018 - MIT Press.
    The aim of the book is to explore common concerns regarding methodological individualism in different fields of the life sciences broadly construed. It will address conceptual problems regarding individuals and their relation and dependence on the collectivities they are part of and consider innovative new viewpoints, grounded in specific scientific projects that question the present descriptions and understanding and raise challenges. A wide variety of recent, influential contributions in the life sciences utilize notions of collectivity, sociality, rich interactions and emergent (...)
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  40. Design Under Randomness: How Variation Affects the Engineering of Biological Systems.Tero Ijäs - 2018 - Biological Theory 13 (3):153-163.
    Synthetic biology offers a powerful method to design and construct biological devices for human purposes. Two prominent design methodologies are currently used. Rational design adapts the design methodology of traditional engineering sciences, such as mechanical engineering. Directed evolution, in contrast, models its design principles after natural evolution, as it attempts to design and improve systems by guiding them to evolve in a certain direction. Previous work has argued that the primary difference between these two is the way they treat variation: (...)
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  41. Inference to the More Robust Explanation.Nicholaos Jones - 2018 - British Journal for the Philosophy of Science 69 (1):75-102.
    ABSTRACT There is a new argument form within theoretical biology. This form takes as input competing explanatory models; it yields as output the conclusion that one of these models is more plausible than the others. The driving force for this argument form is an analysis showing that one model exhibits more parametric robustness than its competitors. This article examines these inferences to the more robust explanation, analysing them as variants of inference to the best explanation. The article defines parametric robustness (...)
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  42. Theoretical Assessment of the Impact of Climatic Factors in a Vibrio Cholerae Model.G. Kolaye, I. Damakoa, S. Bowong, R. Houe & D. Békollè - 2018 - Acta Biotheoretica 66 (4):279-291.
    A mathematical model for Vibrio Cholerae (V. Cholerae) in a closed environment is considered, with the aim of investigating the impact of climatic factors which exerts a direct influence on the bacterial metabolism and on the bacterial reservoir capacity. We first propose a V. Cholerae mathematical model in a closed environment. A sensitivity analysis using the eFast method was performed to show the most important parameters of the model. After, we extend this V. cholerae model by taking account climatic factors (...)
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  43. Mathematical Basis of Predicting Dominant Function in Protein Sequences by a Generic HMM–ANN Algorithm.Siddhartha Kundu - 2018 - Acta Biotheoretica 66 (2):135-148.
    The accurate annotation of an unknown protein sequence depends on extant data of template sequences. This could be empirical or sets of reference sequences, and provides an exhaustive pool of probable functions. Individual methods of predicting dominant function possess shortcomings such as varying degrees of inter-sequence redundancy, arbitrary domain inclusion thresholds, heterogeneous parameterization protocols, and ill-conditioned input channels. Here, I present a rigorous theoretical derivation of various steps of a generic algorithm that integrates and utilizes several statistical methods to predict (...)
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  44. Multiple Regression Is Not Multiple Regressions: The Meaning of Multiple Regression and the Non-Problem of Collinearity.Michael B. Morrissey & Graeme D. Ruxton - 2018 - Philosophy, Theory, and Practice in Biology 10 (3).
    Simple regression (regression analysis with a single explanatory variable), and multiple regression (regression models with multiple explanatory variables), typically correspond to very different biological questions. The former use regression lines to describe univariate associations. The latter describe the partial, or direct, effects of multiple variables, conditioned on one another. We suspect that the superficial similarity of simple and multiple regression leads to confusion in their interpretation. A clear understanding of these methods is essential, as they underlie a large range of (...)
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  45. Study of the Population Dynamics of Busseola Fusca, Maize Pest.Janvier Pesser Ntahomvukiye, Anatole Temgoua & Samuel Bowong - 2018 - Acta Biotheoretica 66 (4):379-397.
    Busseola fusca is a maize and sorghum pest that can cause significant damage to both crops. Given that maize is one of the main cereals grown in the worldwide, this pest is a major challenge for maize production and therefore for the economies of several countries . In this paper , based on the life cycle of B. fusca, we propose a mathematical model to study the population dynamics of this insect pest . A sensitivity analysis using the eFast method (...)
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  46. ‘Models of’ and ‘Models For’: On the Relation Between Mechanistic Models and Experimental Strategies in Molecular Biology.Emanuele Ratti - 2018 - British Journal for the Philosophy of Science (2):773-797.
    Molecular biologists exploit information conveyed by mechanistic models for experimental purposes. In this article, I make sense of this aspect of biological practice by developing Keller’s idea of the distinction between ‘models of’ and ‘models for’. ‘Models of (phenomena)’ should be understood as models representing phenomena and are valuable if they explain phenomena. ‘Models for (manipulating phenomena)’ are new types of material manipulations and are important not because of their explanatory force, but because of the interventionist strategies they afford. This (...)
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  47. Holobionts as Units of Selection and a Model of Their Population Dynamics and Evolution.Joan Roughgarden, Scott F. Gilbert, Eugene Rosenberg, Ilana Zilber-Rosenberg & Elisabeth A. Lloyd - 2018 - Biological Theory 13 (1):44-65.
    Holobionts, consisting of a host and diverse microbial symbionts, function as distinct biological entities anatomically, metabolically, immunologically, and developmentally. Symbionts can be transmitted from parent to offspring by a variety of vertical and horizontal methods. Holobionts can be considered levels of selection in evolution because they are well-defined interactors, replicators/reproducers, and manifestors of adaptation. An initial mathematical model is presented to help understand how holobionts evolve. The model offered combines the processes of horizontal symbiont transfer, within-host symbiont proliferation, vertical symbiont (...)
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  48. Thought Experiments in Biology.Guillaume Schlaepfer & Marcel Weber - 2018 - In Michael T. Stuart, Yiftach J. H. Fehige & James Robert Brown (eds.), The Routledge Companion to Thought Experiments. London: Routledge. pp. 243-256.
    Unlike in physics, the category of thought experiment is not very common in biology. At least there are no classic examples that are as important and as well-known as the most famous thought experiments in physics, such as Galileo’s, Maxwell’s or Einstein’s. The reasons for this are far from obvious; maybe it has to do with the fact that modern biology for the most part sees itself as a thoroughly empirical discipline that engages either in real natural history or in (...)
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  49. Adaptive Control Based Harvesting Strategy for a Predator–Prey Dynamical System.Moitri Sen, Ashutosh Simha & Soumyendu Raha - 2018 - Acta Biotheoretica 66 (4):293-313.
    This paper deals with designing a harvesting control strategy for a predator–prey dynamical system, with parametric uncertainties and exogenous disturbances. A feedback control law for the harvesting rate of the predator is formulated such that the population dynamics is asymptotically stabilized at a positive operating point, while maintaining a positive, steady state harvesting rate. The hierarchical block strict feedback structure of the dynamics is exploited in designing a backstepping control law, based on Lyapunov theory. In order to account for unknown (...)
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  50. Importance of Initial Concentration of Factor VIII in a Mechanistic Model of In Vitro Coagulation.M. Susree & M. Anand - 2018 - Acta Biotheoretica 66 (3):201-212.
    This computational study generates a hypothesis for the coagulation protein whose initial concentration greatly influences the course of coagulation. Many clinical malignancies of blood coagulation arise due to abnormal initial concentrations of coagulation factors. Sensitivity analysis of mechanistic models of blood coagulation is a convenient method to assess the effect of such abnormalities. Accordingly, the study presents sensitivity analysis, with respect to initial concentrations, of a recently developed mechanistic model of blood coagulation. Both the model and parameters to which model (...)
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