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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 -
    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. 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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  8. 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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  9. 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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  10. 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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  11. 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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  12. 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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  13. 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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  14. 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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  15. 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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  16. 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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  17. 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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  18. 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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  19. 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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  20. 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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  21. 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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  22. 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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  23. 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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  24. Attribution of Information in Animal Interaction.Stephen Francis Mann - 2018 - Biological Theory 13 (3):164–179.
    This article establishes grounds on which attributions of information and encoding in animal signals are warranted. As common interest increases between evolutionary agents, the theoretical approach best suited to describing their interaction shifts from evolutionary game theory to communication theory, which warrants informational language. The take-home positive message is that in cooperative settings, signals can appropriately be described as transmitting encoded information, regardless of the cognitive powers of signalers. The canonical example is the honeybee waggle dance, which is discussed extensively (...)
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  25. Studying Animal Languages without Translation: An Insight from Ants. By Zhanna Reznikova. [REVIEW]Stephen Francis Mann & Jessica Pfeifer - 2018 - Quarterly Review of Biology 93:38.
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  26. 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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  27. 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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  28. Is defining life pointless? Operational definitions at the frontiers of Biology.Leonardo Bich & Sara Green - 2017 - Synthese:1-28.
    Despite numerous and increasing attempts to define what life is, there is no consensus on necessary and sufficient conditions for life. Accordingly, some scholars have questioned the value of definitions of life and encouraged scientists and philosophers alike to discard the project. As an alternative to this pessimistic conclusion, we argue that critically rethinking the nature and uses of definitions can provide new insights into the epistemic roles of definitions of life for different research practices. This paper examines the possible (...)
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  29. ¿Son a priori los modelos explicativos de la selección natural?José Díez & Pablo Lorenzano - 2017 - Metatheoria – Revista de Filosofía E Historia de la Ciencia 8:31--42.
    The epistemic status of Natural Selection has intrigued to biologists and philosophers since the very beginning of the theory to our present times. One prominent contemporary example is Elliott Sober, who claims that Natural Selection, and some other theories in biology, and maybe in economics, are peculiar in including explanatory models/conditionals that are a priori in a sense in which explanatory models/conditionals in Classical Mechanics and most other standard theories are not. In this paper, by analyzing what we take to (...)
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  30. Why one model is never enough: a defense of explanatory holism.Hochstein Eric - 2017 - Biology and Philosophy 32 (6):1105-1125.
    Traditionally, a scientific model is thought to provide a good scientific explanation to the extent that it satisfies certain scientific goals that are thought to be constitutive of explanation. Problems arise when we realize that individual scientific models cannot simultaneously satisfy all the scientific goals typically associated with explanation. A given model’s ability to satisfy some goals must always come at the expense of satisfying others. This has resulted in philosophical disputes regarding which of these goals are in fact necessary (...)
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  31. The Sum of the Parts: Large-Scale Modeling in Systems Biology.Fridolin Gross & Sara Green - 2017 - Philosophy, Theory, and Practice in Biology 9 (10).
    Systems biologists often distance themselves from reductionist approaches and formulate their aim as understanding living systems “as a whole.” Yet, it is often unclear what kind of reductionism they have in mind, and in what sense their methodologies would offer a superior approach. To address these questions, we distinguish between two types of reductionism which we call “modular reductionism” and “bottom-up reductionism.” Much knowledge in molecular biology has been gained by decomposing living systems into functional modules or through detailed studies (...)
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  32. Artificial and Natural Genetic Information Processing.Guenther Witzany - 2017 - In Mark Burgin & Wolfgang Hofkirchner (eds.), Information Studies and the Quest for Transdisciplinarity. Singapore: World Scientific. pp. 523-547.
    Conventional methods of genetic engineering and more recent genome editing techniques focus on identifying genetic target sequences for manipulation. This is a result of historical concept of the gene which was also the main assumption of the ENCODE project designed to identify all functional elements in the human genome sequence. However, the theoretical core concept changed dramatically. The old concept of genetic sequences which can be assembled and manipulated like molecular bricks has problems in explaining the natural genome-editing competences of (...)
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  33. Prefacio.Daniel Blanco, Santiago Ginnobili & Pablo Lorenzano - 2016 - Metatheoria – Revista de Filosofía E Historia de la Ciencia 6:1--2.
    Preface to the Thematic Volume: Models and Theories in Biology.
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  34. Four Ways from Universal to Particular: How Chomsky's Language-Acquisition Faculty is Not Selectionist.David Ellerman - 2016 - Journal of Applied Non-Classical Logics 3 (26):193-207.
    Following the development of the selectionist theory of the immune system, there was an attempt to characterize many biological mechanisms as being "selectionist" as juxtaposed to "instructionist." But this broad definition would group Darwinian evolution, the immune system, embryonic development, and Chomsky's language-acquisition mechanism as all being "selectionist." Yet Chomsky's mechanism (and embryonic development) are significantly different from the selectionist mechanisms of biological evolution or the immune system. Surprisingly, there is a very abstract way using two dual mathematical logics to (...)
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  35. Categorizing the Mental.Eric Hochstein - 2016 - Philosophical Quarterly 66 (265):745-759.
    A common view in the philosophy of mind and philosophy of psychology is that there is an ideally correct way of categorizing the structures and operations of the mind, and that the goal of neuroscience and psychology is to find this correct categorizational scheme. Categories which cannot find a place within this correct framework ought to be eliminated from scientific practice. In this paper, I argue that this general idea runs counter to productive scientific practices. Such a view ignores the (...)
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  36. On the Limits of Causal Modeling: Spatially-Structurally Complex Biological Phenomena.Marie I. Kaiser - 2016 - Philosophy of Science 83 (5):921-933.
    This paper examines the adequacy of causal graph theory as a tool for modeling biological phenomena and formalizing biological explanations. I point out that the causal graph approach reaches it limits when it comes to modeling biological phenomena that involve complex spatial and structural relations. Using a case study from molecular biology, DNA-binding and -recognition of proteins, I argue that causal graph models fail to adequately represent and explain causal phenomena in this field. The inadequacy of these models is due (...)
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  37. Contrasting Cases: The Lotka-Volterra Model Times Three.Tarja Knuuttila & Andrea Loettgers - 2016 - Boston Studies in the Philosophy of Science 319:151-178.
    How do philosophers of science make use of historical case studies? Are their accounts of historical cases purpose-built and lacking in evidential strength as a result of putting forth and discussing philosophical positions? We will study these questions through the examination of three different philosophical case studies. All of them focus on modeling and on Vito Volterra, contrasting his work to that of other theoreticians. We argue that the worries concerning the evidential role of historical case studies in philosophy are (...)
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  38. Introducción: Modelos y teorías en biología.Pablo Lorenzano - 2016 - Metatheoria – Revista de Filosofía E Historia de la Ciencia 6:5--46.
    Two metascientific concepts that have been ― and still are ― object of philosophical analysis are the concepts of model and theory. But while the concept of scientific theory was one of the concepts to which philosophers of science devoted most attention during the 20th century, it is only in recent decades that the concept of scientific model has come to occupy a central position in philosophical reflection. However, it has done so in such a way that, at present, as (...)
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  39. On the Incompatibility of Dynamical Biological Mechanisms and Causal Graphs.Marcel Weber - 2016 - Philosophy of Science 83 (5):959-971.
    I examine to what extent accounts of mechanisms based on formal interventionist theories of causality can adequately represent biological mechanisms with complex dynamics. Using a differential equation model for a circadian clock mechanism as an example, I first show that there exists an iterative solution that can be interpreted as a structural causal model. Thus, in principle, it is possible to integrate causal difference-making information with dynamical information. However, the differential equation model itself lacks the right modularity properties for a (...)
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  40. Practice oriented controversies and borrowed epistemic support in current evolutionary biology. The case of phylogeography.Alfonso Arroyo-Santos, Mark E. Olson & Francisco Vergara-Silva - 2015 - Perspectives on Science 23 (3):310-334.
    Although there is increasing recognition that theory and practice in science are often inseparably intertwined, discussions of scientific controversies often continue to focus on theory, and not practice or methodologies. As a contribution to constructing a framework towards understanding controversies linked to scientific practices, we introduce the notion of borrowed epistemic credibility, to describe the situation in which scientists exploit fallacious similarities between accepted tenets in other fields to garner support for a given position in their own field. Our proposal (...)
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  41. Programming the Emergence in Morphogenetically Architected Complex Systems.Franck Varenne, Pierre Chaigneau, Jean Petitot & René Doursat - 2015 - Acta Biotheoretica 63 (3):295-308.
    Large sets of elements interacting locally and producing specific architectures reliably form a category that transcends the usual dividing line between biological and engineered systems. We propose to call them morphogenetically architected complex systems (MACS). While taking the emergence of properties seriously, the notion of MACS enables at the same time the design (or “meta-design”) of operational means that allow controlling and even, paradoxically, programming this emergence. To demonstrate our claim, we first show that among all the self-organized systems studied (...)
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  42. Gene Mobility and the Concept of Relatedness.Jonathan Birch - 2014 - Biology and Philosophy 29 (4):445-476.
    Cooperation is rife in the microbial world, yet our best current theories of the evolution of cooperation were developed with multicellular animals in mind. Hamilton’s theory of inclusive fitness is an important case in point: applying the theory in a microbial setting is far from straightforward, as social evolution in microbes has a number of distinctive features that the theory was never intended to capture. In this article, I focus on the conceptual challenges posed by the project of extending Hamilton’s (...)
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  43. Causal graphs and biological mechanisms.Alexander Gebharter & Marie I. Kaiser - 2014 - In Marie I. Kaiser, Oliver Scholz, Daniel Plenge & Andreas Hüttemann (eds.), Explanation in the special sciences: The case of biology and history. Dordrecht: Springer. pp. 55-86.
    Modeling mechanisms is central to the biological sciences – for purposes of explanation, prediction, extrapolation, and manipulation. A closer look at the philosophical literature reveals that mechanisms are predominantly modeled in a purely qualitative way. That is, mechanistic models are conceived of as representing how certain entities and activities are spatially and temporally organized so that they bring about the behavior of the mechanism in question. Although this adequately characterizes how mechanisms are represented in biology textbooks, contemporary biological research practice (...)
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  44. From Silico to Vitro: Computational Models of Complex Biological Systems Reveal Real-World Emergent Phenomena.Orly Stettiner - 2014 - In Vincent C. Muller (ed.), Computing and Philosophy, Selected Papaers from IACAP 2014. Springer. pp. 133-147.
    Computer simulations constitute a significant scientific tool for promoting scientific understanding of natural phenomena and dynamic processes. Substantial leaps in computational force and software engineering methodologies now allow the design and development of large-scale biological models, which – when combined with advanced graphics tools – may produce realistic biological scenarios, that reveal new scientific explanations and knowledge about real life phenomena. A state-of-the-art simulation system termed Reactive Animation (RA) will serve as a study case to examine the contemporary philosophical debate (...)
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  45. Representing disease courses: An application of the Neurological Disease Ontology to Multiple Sclerosis Typology.Mark Jensen, Alexander P. Cox, Barry Smith & Alexander Diehl - 2013 - In Proceedings of the Fourth International Conference on Biomedical Ontology (ICBO), CEUR, vol. 1060.
    The Neurological Disease Ontology (ND) is being developed to provide a comprehensive framework for the representation of neurological diseases (Diehl et al., 2013). ND utilizes the model established by the Ontology for General Medical Science (OGMS) for the representation of entities in medicine and disease (Scheuermann et al., 2009). The goal of ND is to include information for each disease concerning its molecular, genetic, and environmental origins, the processes involved in its etiology and realization, as well as its clinical presentation (...)
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  46. Defusing Ideological Defenses in Biology.Angela Potochnik - 2013 - BioScience 63 (2):118-123.
    Ideological language is widespread in theoretical biology. Evolutionary game theory has been defended as a worldview and a leap of faith, and sexual selection theory has been criticized for what it posits as basic to biological nature. Views such as these encourage the impression of ideological rifts in the field. I advocate an alternative interpretation, whereby many disagreements between different camps of biologists merely reflect methodological differences. This interpretation provides a more accurate and more optimistic account of the state of (...)
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  47. The Altruism Paradox: A Consequence of Mistaken Genetic Modeling.Yussif Yakubu - 2013 - Biological Theory 8 (1):103-113.
    The theoretical heuristic of assuming distinct alleles (or genotypes) for alternative phenotypes is the foundation of the paradigm of evolutionary explanation we call the Modern Synthesis. In modeling the evolution of sociality, the heuristic has been to set altruism and selfishness as alternative phenotypes under distinct genotypes, which has been dubbed the “phenotypic gambit.” The prevalence of the altruistic genotype that is of lower evolutionary fitness relative to the alternative genotype for non-altruistic behavior in populations is the basis of the (...)
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  48. Reduktionismus und Rückübertragung.Patrick Grüneberg - 2012 - In Das modellierte Individuum. Biologische Modelle und ihre ethischen Implikationen. Transcript. pp. 227-244.
    »Welche [Zugangsweise] man wählt, hängt weitgehend von der Fragestellung ab und davon, was man eigentlich erreichen möchte. Jede Betrachtung, die sich nur auf den einen Zugang beschränkt, ist einseitig. Es gibt hier ein Spannungsfeld, das es auszuhalten gilt«, so Ulrich Freund in einer Diskussion über das Verhältnis reduktionistischer und holistischer Verfahrensweisen in der Medizin. Während seine Äußerung durchaus von einem gewissen Optimismus geprägt ist, dass die Gegensätze zwischen Reduktionismus und Holismus nicht überbetont werden sollten, verdeckt sie doch ein grundlegendes Problem. (...)
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  49. Philosophy of Experimental Biology.Jacob Stegenga - 2009 - Erkenntnis 71 (3):431-436.
    Philosophers have committed sins while studying science, it is said – philosophy of science focused on physics to the detriment of biology, reconstructed idealizations of scientific episodes rather than attending to historical details, and focused on theories and concepts to the detriment of experiments. Recent generations of philosophers of science have tried to atone for these sins, and by the 1980s the exculpation was in full swing. Marcel Weber’s Philosophy of Experimental Biology is a zenith mea culpa for philosophy of (...)
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  50. Object spaces: An organizing strategy for biological theorizing.Beckett Sterner - 2009 - Biological Theory 4 (3):280-286.
    A classic analytic approach to biological phenomena seeks to refine definitions until classes are sufficiently homogenous to support prediction and explanation, but this approach founders on cases where a single process produces objects with similar forms but heterogeneous behaviors. I introduce object spaces as a tool to tackle this challenging diversity of biological objects in terms of causal processes with well-defined formal properties. Object spaces have three primary components: (1) a combinatorial biological process such as protein synthesis that generates objects (...)
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