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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. 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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  6. 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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  7. Making sense of ‘genetic programs’: biomolecular Post–Newell production systems.Mihnea D. I. Capraru - forthcoming - Biology and Philosophy.
    The biomedical literature makes extensive use of the concept of a genetic program. So far, however, the nature of genetic programs has received no satisfactory elucidation from the standpoint of computer science. This unsettling omission has led to doubts about the very existence of genetic programs, on the grounds that gene regulatory networks lack a predetermined schedule of execution, which may seem to contradict the very idea of a program. I show, however, that we can make perfect sense of genetic (...)
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  8. 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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  9. Structure from Data: AI Approaches to Systems Modeling.H. Hyötyniemi - forthcoming - Proc. 8th Finnish Ai Conference Step’98.
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  10. A Complementary Account of Scientific Modelling: Modelling Mechanisms in Cancer Immunology.Martin Zach - forthcoming - British Journal for the Philosophy of Science.
    According to a widely held view, scientific modelling consists in entertaining a set of model descriptions that specify a model. Rather than studying the phenomenon of interest directly, scientists investigate the phenomenon indirectly via a model in the hope of learning about some of the phenomenon’s features. I call this view the description-driven modelling (DDM) account. I argue that although an accurate description of much of scientific research, the DDM account is found wanting as regards the mechanistic modelling found in (...)
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  11. Gain-of-function research and model organisms in biology.Nicholas G. Evans & Charles H. Pence - 2024 - Journal of Medical Ethics 50 (3):201-206.
    So-called ‘gain-of-function’ (GOF) research is virological research that results in a virus substantially more virulent or transmissible than its wild antecedent. GOF research has been subject to ethical analysis in the past, but the methods of GOF research have to date been underexamined by philosophers in these analyses. Here, we examine the typical animal used in influenza GOF experiments, the ferret, and show how despite its longstanding use, it does not easily satisfy the desirable criteria for an _animal model_. We (...)
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  12. From depressed mice to depressed patients: a less “standardized” approach to improving translation.Monika Piotrowska - 2023 - Biology and Philosophy 38 (6):1-19.
    Depression is a widespread and debilitating disorder, but developing effective treatments has proven challenging. Despite success in animal models, many treatments fail in human trials. While various factors contribute to this translational failure, standardization practices in animal research are often overlooked. This paper argues that certain standardization choices in behavioral neuroscience research on depression can limit the generalizability of results from rodents to humans. This raises ethical and scientific concerns, including animal waste and a lack of progress in treating human (...)
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  13. What’s at stake in the debate over naturalizing teleology? An overlooked metatheoretical debate.Carl Sachs & Auguste Nahas - 2023 - Synthese 201 (4):1-22.
    Recent accounts of teleological naturalism hold that organisms are intrinsically goaldirected entities. We argue that supporters and critics of this view have ignored the ways in which it is used to address quite different problems. One problem is about biology and concerns whether an organism-centered account of teleological ascriptions would improve our descriptions and explanations of biological phenomena. This is different from the philosophical problem of how naturalized teleology would affect our conception of nature, and of ourselves as natural beings. (...)
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  14. An account of conserved functions and how biologists use them to integrate cell and evolutionary biology.Jeremy G. Wideman, Steve Elliott & Beckett Sterner - 2023 - Biology and Philosophy 38 (5):1-23.
    We characterize a type of functional explanation that addresses why a homologous trait originating deep in the evolutionary history of a group remains widespread and largely unchanged across the group’s lineages. We argue that biologists regularly provide this type of explanation when they attribute conserved functions to phenotypic and genetic traits. The concept of conserved function applies broadly to many biological domains, and we illustrate its importance using examples of molecular sequence alignments at the intersection of evolution and cell biology. (...)
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  15. Joint representation: Modeling a phenomenon with multiple biological systems.Yoshinari Yoshida - 2023 - Studies in History and Philosophy of Science Part A 99:67-76.
    Biologists often study particular biological systems as models of a phenomenon of interest even if they already know that the phenomenon is produced by diverse mechanisms and hence none of those systems alone can sufficiently represent it. To understand this modeling practice, the present paper provides an account of how multiple model systems can be used to study a phenomenon that is produced by diverse mechanisms. Even if generalizability of results from a single model system is significantly limited, generalizations concerning (...)
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  16. Quantum tunneling of three-spine solitons through excentric barriers.Danko D. Georgiev & James F. Glazebrook - 2022 - Physics Letters A 448:128319.
    Macromolecular protein complexes catalyze essential physiological processes that sustain life. Various interactions between protein subunits could increase the effective mass of certain peptide groups, thereby compartmentalizing protein α-helices. Here, we study the differential effects of applied massive barriers upon the soliton-assisted energy transport within proteins. We demonstrate that excentric barriers, localized onto a single spine in the protein α-helix, reflect or trap three-spine solitons as effectively as concentric barriers with comparable total mass. Furthermore, wider protein solitons, whose energy is lower, (...)
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  17. Thermal stability of solitons in protein α-helices.Danko D. Georgiev & James F. Glazebrook - 2022 - Chaos, Solitons and Fractals 155:111644.
    Protein α-helices provide an ordered biological environment that is conducive to soliton-assisted energy transport. The nonlinear interaction between amide I excitons and phonon deformations induced in the hydrogen-bonded lattice of peptide groups leads to self-trapping of the amide I energy, thereby creating a localized quasiparticle (soliton) that persists at zero temperature. The presence of thermal noise, however, could destabilize the protein soliton and dissipate its energy within a finite lifetime. In this work, we have computationally solved the system of stochastic (...)
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  18. Bayesian realism and structural representation.Alex Kiefer & Jakob Hohwy - 2022 - Behavioral and Brain Sciences 45:e199.
    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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  19. Free energy: a user’s guide.Stephen Francis Mann, Ross Pain & Michael D. Kirchhoff - 2022 - Biology and Philosophy 37 (4):1-35.
    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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  20. Immunoglobulins and Antibodies: Conceptual Projections All the Way Down.Bartlomiej Swiatczak - 2022 - Constructivist Foundations 18 (1):85-86.
    Central to vaccination-induced responses, antibodies are suggested by Vaz to operate as observer-dependent entities that owe their status to categorization schemes of immunologists. Inspired by color research by Maturana, he argues that antibodies should be distinguished from immunoglobulins, which unlike the former can be considered as constituents of structural dynamics of an organism, products of millions of years of evolution. However, a deeper understanding of the historical roots of the concept of immunoglobulin and associated “languaging” and naming processes reveals that (...)
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  21. 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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  22. 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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  23. 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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  24. 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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  25. 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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  26. 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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  27. 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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  28. 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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  29. Unifying the essential concepts of biological networks: biological insights and philosophical foundations.Daniel Kostic, Claus Hilgetag & Marc Tittgemeyer (eds.) - 2020 - 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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  30. Unifying the essential concepts of biological networks.Daniel Kostic, Claus Hilgetag & Marc Tittgemeyer (eds.) - 2020 - Royal Society.
    Over the last decades, network-based approaches have become highly popular in diverse areas of biology. While these approaches continue to grow very rapidly, some of their conceptual and methodological aspects still require a programmatic foundation. In order to unify and systematize network approaches across biological sciences, this theme issue brings together scientists working in many diverse areas of biological sciences as well as philosophers working on foundational issues of network explanations and modelling, who together aim to develop universally applicable norms (...)
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  31. On Being the Right Size, Revisited: The Problem with Engineering Metaphors in Molecular Biology.Daniel J. Nicholson - 2020 - In Sune Holm & Maria Serban (eds.), Philosophical Perspectives on the Engineering Approach in Biology: Living Machines? London, UK: Routledge. 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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  32. 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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  33. 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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  34. 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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  35. 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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  36. 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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  37. 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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  38. 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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  39. 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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  40. 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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  41. 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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  42. 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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  43. 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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  44. 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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  45. 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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  46. 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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  47. 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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  48. 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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  49. 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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  50. 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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