Results for 'model organism'

977 found
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  1.  4
    Model Organism Databases and Algorithms: A Computing Mechanism for Cross-species Research.Sim-Hui Tee - forthcoming - Foundations of Science:1-26.
    Model organism databases are used extensively for knowledge retrieval and knowledge sharing among biologists. With the invention of genome sequencing and protein profiling technologies, large amount of molecular data provides practical insights into the molecular study of model organisms. The knowledge-intensive characteristic of model organism databases provides a reference point for the comparative study of other species. In this paper, I argue that algorithms could be used to facilitate cross-species research. I emphasize the epistemic significance (...)
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  2.  56
    Stages in the development of a model organism as a platform for mechanistic models in developmental biology: Zebrafish, 1970–2000.Robert Meunier - 2012 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 43 (2):522-531.
    Model organisms became an indispensable part of experimental systems in molecular developmental and cell biology, constructed to investigate physiological and pathological processes. They are thought to play a crucial role for the elucidation of gene function, complementing the sequencing of the genomes of humans and other organisms. Accordingly, historians and philosophers paid considerable attention to various issues concerning this aspect of experimental biology. With respect to the representational features of model organisms, that is, their status as models, the (...)
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  3.  35
    The con man as model organism: the methodological roots of Erving Goffman’s dramaturgical self.Michael Pettit - 2011 - History of the Human Sciences 24 (2):138-154.
    This article offers a historical analysis of the relationship between the practice of participant-observation among American sociologists and Erving Goffman’s dramaturgical model of the self. He was a social scientist who privileged ethnography in the field over the laboratory experiment, the survey questionnaire, or the mental test. His goal was a natural history of communication among humans. Rather than rely upon standardizing technologies for measurement, Goffman tried to obtain accurate recordings of human behavior through secretive observations. During the 1950s, (...)
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  4.  40
    Establishing a model organism: A report from the first annual Nematostella meeting.Adam M. Reitzel, Joseph F. Ryan & Ann M. Tarrant - 2012 - Bioessays 34 (2):158-161.
    Graphical AbstractThe sea anemone Nematostella vectensis has developed into a model organism for studying genome evolution and animal development.
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  5.  94
    The prisoner as model organism: malaria research at Stateville Penitentiary.Nathaniel Comfort - 2009 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 40 (3):190-203.
    In a military-sponsored research project begun during the Second World War, inmates of the Stateville Penitentiary in Illinois were infected with malaria and treated with experimental drugs that sometimes had vicious side effects. They were made into reservoirs for the disease and they provided a food supply for the mosquito cultures. They acted as secretaries and technicians, recording data on one another, administering malarious mosquito bites and experimental drugs to one another, and helping decide who was admitted to the project (...)
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  6.  45
    Mity model: Tetranychus urticae, a candidate for chelicerate model organism.Miodrag Grbic, Abderrahman Khila, Kwang-Zin Lee, Anica Bjelica, Vojislava Grbic, Jay Whistlecraft, Lou Verdon, Maria Navajas & Lisa Nagy - 2007 - Bioessays 29 (5):489-496.
    Chelicerates (scorpions, horseshoe crabs, spiders, mites and ticks) are the second largest group of arthropods and are of immense importance for fundamental and applied science. They occupy a basal phylogenetic position within the phylum Arthropoda, and are of crucial significance for understanding the evolution of various arthropod lineages. Chelicerates are vectors of human diseases, such as ticks, and major agricultural pests, such as spider mites, thus this group is also of importance for both medicine and agriculture. The developmental genetics of (...)
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  7. The Conqueror Worm: An Historical and Philosophical Examination of the Use of the Nematode Caenorhabditis Elegans as a Model Organism.Rachel Allyson Ankeny - 1997 - Dissertation, University of Pittsburgh
    This study focuses on the concept of a 'model organism' in the biomedical sciences through an historical and philosophical examination of research with the nematode Caenorhabditis elegans. I explore the choice of C. elegans in the mid-1960s, showing a rich context existed within which the organism was selected as the focus for a molecular biological research program, including an experimental life prior to Sydney Brenner's work. I argue that this choice can be seen as an obvious outcome (...)
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  8. Re-thinking organisms: The impact of databases on model organism biology.Sabina Leonelli & Rachel A. Ankeny - 2012 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 43 (1):29-36.
    Community databases have become crucial to the collection, ordering and retrieval of data gathered on model organisms, as well as to the ways in which these data are interpreted and used across a range of research contexts. This paper analyses the impact of community databases on research practices in model organism biology by focusing on the history and current use of four community databases: FlyBase, Mouse Genome Informatics, WormBase and The Arabidopsis Information Resource. We discuss the standards (...)
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  9. Studying the plasticity of phenotypic integration in a model organism.Massimo Pigliucci - 2004 - In M. Pigliucci K. Preston (ed.), The Evolutionary Biology of Complex Phenotypes. Oxford University Press.
    How to use a model organism to study phenotypic integration and constraints on evolution.
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  10.  35
    Varieties of Data-Centric Science: Regional Climate Modeling and Model Organism Research.Elisabeth Lloyd, Greg Lusk, Stuart Gluck & Seth McGinnis - 2022 - Philosophy of Science 89 (4):802-823.
    Modern science’s ability to produce, store, and analyze big datasets is changing the way that scientific research is practiced. Philosophers have only begun to comprehend the changed nature of scientific reasoning in this age of “big data.” We analyze data-focused practices in biology and climate modeling, identifying distinct species of data-centric science: phenomena-laden in biology and phenomena-agnostic in climate modeling, each better suited for its own domain of application, though each entail trade-offs. We argue that data-centric practices in science are (...)
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  11. Are there Model Behaviours for Model Organism Research? Commentary on Nicole Nelson's Model Behavior.Jacqueline A. Sullivan - 2020 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 82:101266.
    One might be inclined to assume, given the mouse donning its cover, that the behavior of interest in Nicole Nelson's book Model Behavior (2018) is that of organisms like mice that are widely used as “stand-ins” for investigating the causes of human behavior. Instead, Nelson's ethnographic study focuses on the strategies adopted by a community of rodent behavioral researchers to identify and respond to epistemic challenges they face in using mice as models to understand the causes of disordered human (...)
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  12. Mechanism, organism, and society: Some models in natural and social science.Karl W. Deutsch - 1951 - Philosophy of Science 18 (3):230-252.
    Men think in terms of models. Their sense organs abstract the events which touch them; their memories store traces of these events as coded symbols; and they may recall them according to patterns which they learned earlier, or recombine them in patterns that are new. In all this, we may think of our thought as consisting of symbols which are put in relations or sequences according to operating rules. Both symbols and operating rules are acquired, in part directly from interaction (...)
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  13.  43
    The organism as ontological go-between: Hybridity, boundaries and degrees of reality in its conceptual history.Charles T. Wolfe - 2014 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 48:151-161.
    The organism is neither a discovery like the circulation of the blood or the glycogenic function of the liver, nor a particular biological theory like epigenesis or preformationism. It is rather a concept which plays a series of roles, sometimes masked, often normative, throughout the history of biology. Indeed, it has often been presented as a key-concept in life science and its ‘theorization’, but conversely has also been the target of influential rejections: as just an instrument of transmission for (...)
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  14.  66
    Evolution in spatial predator–prey models and the “prudent predator”: The inadequacy of steady‐state organism fitness and the concept of individual and group selection.Charles Goodnight, E. Rauch, Hiroki Sayama, Marcus A. M. De Aguiar, M. Baranger & Yaneer Bar‐yam - 2008 - Complexity 13 (5):23-44.
    Complexity is pleased to announce the installment of Prof Hiroki Sayama as its new Chief Editor. In this Editorial, Prof Sayama describes his feelings about his recent appointment, discusses some of the journal’s journey and relevance to current issues, and shares his vision and aspirations for its future.
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  15. The organism as ontological go-between. Hybridity, boundaries and degrees of reality in its conceptual history.Charles T. Wolfe - 2014 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 1:http://dx.doi.org/10.1016/j.shps.
    The organism is neither a discovery like the circulation of the blood or the glycogenic function of the liver, nor a particular biological theory like epigenesis or preformationism. It is rather a concept which plays a series of roles – sometimes overt, sometimes masked – throughout the history of biology, and frequently in very normative ways, also shifting between the biological and the social. Indeed, it has often been presented as a key-concept in life science and the ‘theorization’ of (...)
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  16. (1 other version)Model organisms as models: Understanding the 'lingua Franca' of the human genome project.Rachel A. Ankeny - 2001 - Proceedings of the Philosophy of Science Association 2001 (3):S251-.
    Through an examination of the actual research strategies and assumptions underlying the Human Genome Project (HGP), it is argued that the epistemic basis of the initial model organism programs is not best understood as reasoning via causal analog models (CAMs). In order to answer a series of questions about what is being modeled and what claims about the models are warranted, a descriptive epistemological method is employed that uses historical techniques to develop detailed accounts which, in turn, help (...)
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  17.  83
    Organism, community, and the "substitution problem".Eric Katz - 1985 - Environmental Ethics 7 (3):241-256.
    Holistic accounts of the natural environment in environmental ethics fail to stress the distinction between the concepts of comnlunity and organism. Aldo Leopold’s “Land Ethic” adds to this confusion, for it can be interpreted as promoting either a community or an organic model of nature. The difference between the two concepts lies in the degree of autonomy possessed by constituent entities within the holistic system. Members within a community are autonomous, while the parts of an organism are (...)
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  18.  71
    Modelling gene regulation: (De)compositional and template-based strategies.Tarja Knuuttila & Vivette García Deister - 2019 - Studies in History and Philosophy of Science Part A 77:101-111.
    Although the interdisciplinary nature of contemporary biological sciences has been addressed by philosophers, historians, and sociologists of science, the different ways in which engineering concepts and methods have been applied in biology have been somewhat neglected. We examine - using the mechanistic philosophy of science as an analytic springboard - the transfer of network methods from engineering to biology through the cases of two biology laboratories operating at the California Institute of Technology. The two laboratories study gene regulatory networks, but (...)
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  19. Organism and character decomposition: Steps towards an integrative theory of biology.Manfred D. Laubichler & Günter P. Wagner - 2000 - Philosophy of Science 67 (3):300.
    In this paper we argue that an operational organism concept can help to overcome the structural deficiency of mathematical models in biology. In our opinion, the structural deficiency of mathematical models lies mainly in our inability to identify functionally relevant biological characters in biological systems, and not so much in a lack of adequate mathematical representations of biological processes. We argue that the problem of character identification in biological systems is linked to the question of a properly formulated (...) concept. Lastly, we demonstrate how a decomposition of an organism into independent characters in the context of a specific biological process--such as adaptation by means of natural selection--depends on the dynamical properties and invariance conditions of the equations that describe this process. (shrink)
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  20. Entangled Life: Organism and Environment in the Biological and Social Sciences.Gillian Barker, Eric Desjardins & Trevor Pearce (eds.) - 2014 - Dordrecht: Springer.
    Despite the burgeoning interest in new and more complex accounts of the organism-environment dyad by biologists and philosophers, little attention has been paid in the resulting discussions to the history of these ideas and to their deployment in disciplines outside biology—especially in the social sciences. Even in biology and philosophy, there is a lack of detailed conceptual models of the organism-environment relationship. This volume is designed to fill these lacunae by providing the first multidisciplinary discussion of the topic (...)
  21.  36
    Marine invertebrates, model organisms, and the modern synthesis: epistemic values, evo-devo, and exclusion.Alan C. Love - 2009 - Theory in Biosciences 128:19–42.
    A central reason that undergirds the significance of evo-devo is the claim that development was left out of the Modern synthesis. This claim turns out to be quite complicated, both in terms of whether development was genuinely excluded and how to understand the different kinds of embryological research that might have contributed. The present paper reevaluates this central claim by focusing on the practice of model organism choice. Through a survey of examples utilized in the literature of the (...)
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  22.  15
    The Predictors of Consumer Behavior in Relation to Organic Food in the Context of Food Safety Incidents: Advancing Hyper Attention Theory Within an Stimulus-Organism-Response Model.Chunnian Liu & Yan Zheng - 2019 - Frontiers in Psychology 10.
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  23.  27
    Developmental Models for Estimating Ecological Responses to Environmental Variability: Structural, Parametric, and Experimental Issues.Julia L. Moore & Justin V. Remais - 2014 - Acta Biotheoretica 62 (1):69-90.
    Developmental models that account for the metabolic effect of temperature variability on poikilotherms, such as degree-day models, have been widely used to study organism emergence, range and development, particularly in agricultural and vector-borne disease contexts. Though simple and easy to use, structural and parametric issues can influence the outputs of such models, often substantially. Because the underlying assumptions and limitations of these models have rarely been considered, this paper reviews the structural, parametric, and experimental issues that arise when using (...)
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  24.  47
    Model Organisms as Simulators: The Context of Cross-Species Research and Emergence.Sim-Hui Tee - 2019 - Axiomathes 29 (4):363-382.
    Model organisms are a living form of scientific models. Despite the widespread use of model organisms in scientific research, the actual representational relationship between model organisms and their target species is often poorly characterized in the context of cross-species research. Many model organisms do not represent the target species adequately, let alone accurately. This is partly due to the complex and emergent life phenomena in the organism, and partly due to the fact that a (...) organism is always taken to represent a broad range of diverse organisms. More often than not, model organisms are taken as a reference point for an extrapolation to be made to the unknown characteristics of other species. I propose to view model organisms as analogue simulators which represent the emergent phenomenon in the context of cross-species research. A model organism represents a wide range of species by simulating their molecular microstates which underlie various emergent phenomena. I show that although model organisms represent the target species inadequately at many levels of complexity, they have epistemic values as a simulator in virtue of which the emergent phenomenon can be modeled dynamically, a virtue that is hardly attainable by non-dynamic models. (shrink)
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  25.  12
    Organism versus Mechanism?Gerard de Zeeuw - 2021 - Constructivist Foundations 16 (3):341-342.
    While there is often good reason to study our world by abstracting properties from its parts to the point where the result can be modelled as mechanisms, there is no need to do so when humans are ….
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  26.  34
    A Conceptual Model of Morphogenesis and Regeneration.Angélique Stéphanou & Nicolas Glade - 2015 - Acta Biotheoretica 63 (3):283-294.
    This paper is devoted to computer modelling of the development and regeneration of multicellular biological structures. Some species are able to regenerate parts of their body after amputation damage, but the global rules governing cooperative cell behaviour during morphogenesis are not known. Here, we consider a simplified model organism, which consists of tissues formed around special cells that can be interpreted as stem cells. We assume that stem cells communicate with each other by a set of signals, and (...)
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  27.  52
    Model Organisms.Rachel Ankeny & Sabina Leonelli - 2020 - Cambridge University Press.
    This Element presents a philosophical exploration of the concept of the 'model organism' in contemporary biology. Thinking about model organisms enables us to examine how living organisms have been brought into the laboratory and used to gain a better understanding of biology, and to explore the research practices, commitments, and norms underlying this understanding. We contend that model organisms are key components of a distinctive way of doing research. We focus on what makes model organisms (...)
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  28.  22
    A Conceptual Model of Morphogenesis and Regeneration.A. Tosenberger, N. Bessonov, M. Levin, N. Reinberg, V. Volpert & N. Morozova - 2015 - Acta Biotheoretica 63 (3):283-294.
    This paper is devoted to computer modelling of the development and regeneration of multicellular biological structures. Some species are able to regenerate parts of their body after amputation damage, but the global rules governing cooperative cell behaviour during morphogenesis are not known. Here, we consider a simplified model organism, which consists of tissues formed around special cells that can be interpreted as stem cells. We assume that stem cells communicate with each other by a set of signals, and (...)
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  29.  21
    Seeking a new biomedical model. How evolutionary biology may contribute.Stephen Lewis - 2009 - Journal of Evaluation in Clinical Practice 15 (4):745-748.
    The medical profession is not to blame for the limitations of the biomedical model with which it is often associated; the biology upon which that model is built is incomplete and bears some of the responsibility. Some of the more fundamental aspects of biological theory which are currently missing from the biomedical model need to be introduced in order to help provide a better description of the integrated biology involved. AIMS AND OBJECTIVES: By considering the biological nature (...)
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  30.  49
    Spirits and Clocks: Machine & Organism in Descartes (review).Cees Leijenhorst - 2002 - Journal of the History of Philosophy 40 (1):122-123.
    In lieu of an abstract, here is a brief excerpt of the content:Journal of the History of Philosophy 40.1 (2002) 122-123 [Access article in PDF] Book Review Spirits and Clocks: Machine & Organism in Descartes Dennis Des Chene. Spirits and Clocks: Machine & Organism in Descartes. Ithaca, NY and London: Cornell University Press, 2001. Pp. xiii + 181. Cloth, $39.95. Confronted with the thousandth "entirely new" interpretation of the Cartesian mind-body union, one sometimes wonders whether anything new can (...)
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  31.  32
    Quantitative assessment of organism–environment couplings.J.-L. Torres, O. Pérez-Maqueo, M. Equihua & L. Torres - 2009 - Biology and Philosophy 24 (1):107-117.
    The evolutionary implications of environmental change due to organismic action remain a controversial issue, after a decades—long debate on the subject. Much of this debate has been conducted in qualitative fashion, despite the availability of mathematical models for organism–environment interactions, and for gene frequencies when allele fitness can be related to exploitation of a particular environmental resource. In this article we focus on representative models dealing with niche construction, ecosystem engineering, the Gaia Hypothesis and community interactions of Lotka–Volterra type, (...)
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  32.  22
    Stalk‐eyed flies (Diopsidae): Modelling the evolution and development of an exaggerated sexual trait.Ian Warren & Hazel Smith - 2007 - Bioessays 29 (3):300-307.
    Stalk‐eyed flies of the family Diopsidae exhibit a unique form of hypercephaly, which has evolved under both natural and sexual selection. Male hypercephaly is used by female diopsids as an indicator of male quality. By choosing to mate with males expressing the most‐exaggerated hypercephaly, females can benefit both from the enhanced fertility of these males and the transmission of other heritable advantages to their offspring. Stalk‐eyed flies are close relatives of the model organism, Drosophila melanogaster. We have shown (...)
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  33. What’s so special about model organisms?Rachel A. Ankeny & Sabina Leonelli - 2011 - Studies in History and Philosophy of Science Part A 42 (2):313-323.
    This paper aims to identify the key characteristics of model organisms that make them a specific type of model within the contemporary life sciences: in particular, we argue that the term “model organism” does not apply to all organisms used for the purposes of experimental research. We explore the differences between experimental and model organisms in terms of their material and epistemic features, and argue that it is essential to distinguish between their representational scope and (...)
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  34.  31
    Invertebrate models of spinal muscular atrophy: Insights into mechanisms and potential therapeutics.Stuart J. Grice, James N. Sleigh, Ji-Long Liu & David B. Sattelle - 2011 - Bioessays 33 (12):956-965.
    Invertebrate genetic models with their tractable neuromuscular systems are effective vehicles for the study of human nerve and muscle disorders. This is exemplified by insights made into spinal muscular atrophy (SMA) using the fruit fly Drosophila melanogaster and the nematode worm Caenorhabditis elegans. For speed and economy, these invertebrates offer convenient, whole‐organism platforms for genetic screening as well as RNA interference (RNAi) and chemical library screens, permitting the rapid testing of hypotheses related to disease mechanisms and the exploration of (...)
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  35.  21
    Between Laws and Norms. Genesis of the Concept of Organism in Leibniz and in the Early Modern Western Philosophy.Antonio M. Nunziante - 2020 - In Andrea Altobrando & Pierfrancesco Biasetti (eds.), Natural Born Monads: On the Metaphysics of Organisms and Human Individuals. De Gruyter. pp. 11-32.
    The word “organism” represents an original keyword of the early-modern philosophical world. As it was first developed by Leibniz, it seems to blend together two different conceptual paradigms: the Cartesian model of the “machines” and the Aristotelian legacy of the “individual natures”. According to the first, nature represents itself the prototype of any good mechanical functioning, but at the same time its inner development is explained by the occurrence of a normative dimension that rules the world of primitive (...)
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  36.  29
    Are Model Organisms Theoretical Models?Veli-Pekka Parkkinen - 2017 - Disputatio 9 (47):471-498.
    This article compares the epistemic roles of theoretical models and model organisms in science, and specifically the role of non-human animal models in biomedicine. Much of the previous literature on this topic shares an assumption that animal models and theoretical models have a broadly similar epistemic role—that of indirect representation of a target through the study of a surrogate system. Recently, Levy and Currie have argued that model organism research and theoretical modelling differ in the justification of (...)
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  37. The Machine Conception of the Organism in Development and Evolution: A Critical Analysis.Daniel J. Nicholson - 2014 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 48:162-174.
    This article critically examines one of the most prevalent metaphors in modern biology, namely the machine conception of the organism (MCO). Although the fundamental differences between organisms and machines make the MCO an inadequate metaphor for conceptualizing living systems, many biologists and philosophers continue to draw upon the MCO or tacitly accept it as the standard model of the organism. This paper analyses the specific difficulties that arise when the MCO is invoked in the study of development (...)
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  38.  18
    Gene silencing in non‐model insects: Overcoming hurdles using symbiotic bacteria for trauma‐free sustainable delivery of RNA interference.Miranda Whitten & Paul Dyson - 2017 - Bioessays 39 (3).
    Insight into animal biology and development provided by classical genetic analysis of the model organism Drosophila melanogaster was an incentive to develop advanced genetic tools for this insect. But genetic systems for the over one million other known insect species are largely undeveloped. With increasing information about insect genomes resulting from next generation sequencing, RNA interference is now the method of choice for reverse genetics, although it is constrained by the means of delivery of interfering RNA. A recent (...)
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  39.  5
    Three‐dimensional stem cell models of mammalian gastrulation.David A. Turner & Alfonso Martinez Arias - 2024 - Bioessays 46 (12):2400123.
    Gastrulation is a key milestone in the development of an organism. It is a period of cell proliferation and coordinated cellular rearrangement, that creates an outline of the body plan. Our current understanding of mammalian gastrulation has been improved by embryo culture, but there are still many open questions that are difficult to address because of the intrauterine development of the embryos and the low number of specimens. In the case of humans, there are additional difficulties associated with technical (...)
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  40.  18
    The chicken, and the egg. The Avian Model in Developmental Biology: from Organism to Genes(1990). Edited by N. Le Douarin, F. Dieterlen‐Lievre and J. Smith. Editions du CNRS, Paris. 319pp. 250 FFr. [REVIEW]Peter G. H. Clarke - 1991 - Bioessays 13 (12):693-694.
  41.  82
    Unknotting reciprocal causation between organism and environment.Jan Baedke, Alejandro Fábregas-Tejeda & Guido I. Prieto - 2021 - Biology and Philosophy 36 (5):1-29.
    In recent years, biologists and philosophers of science have argued that evolutionary theory should incorporate more seriously the idea of ‘reciprocal causation.’ This notion refers to feedback loops whereby organisms change their experiences of the environment or alter the physical properties of their surroundings. In these loops, in particular niche constructing activities are central, since they may alter selection pressures acting on organisms, and thus affect their evolutionary trajectories. This paper discusses long-standing problems that emerge when studying such reciprocal causal (...)
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  42. The self model and the conception of biological identity in immunology.Thomas Pradeu & Edgardo D. Carosella - 2006 - Biology and Philosophy 21 (2):235-252.
    The self/non-self model, first proposed by F.M. Burnet, has dominated immunology for 60 years now. According to this model, any foreign element will trigger an immune reaction in an organism, whereas endogenous elements will not, in normal circumstances, induce an immune reaction. In this paper we show that the self/non-self model is no longer an appropriate explanation of experimental data in immunology, and that this inadequacy may be rooted in an excessively strong metaphysical conception of biological (...)
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  43.  85
    (1 other version)Models in Search of Targets: Exploratory Modelling and the Case of Turing Patterns.Axel Gelfert - 2018 - In Alexander Christian, David Hommen, Gerhard Schurz & N. Retzlaff (eds.), Philosophy of Science. European Studies in Philosophy of Science, vol 9. Springer. pp. 245-269.
    Traditional frameworks for evaluating scientific models have tended to downplay their exploratory function; instead they emphasize how models are inherently intended for specific phenomena and are to be judged by their ability to predict, reproduce, or explain empirical observations. By contrast, this paper argues that exploration should stand alongside explanation, prediction, and representation as a core function of scientific models. Thus, models often serve as starting points for future inquiry, as proofs of principle, as sources of potential explanations, and as (...)
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  44. Efficiency in Organism-Environment Information Exchanges: A Semantic Hierarchy of Logical Types Based on the Trial-and-Error Strategy Behind the Emergence of Knowledge.Mattia Berera - 2024 - Biosemiotics 17 (1):131-160.
    Based on Kolchinsky and Wolpert’s work on the semantics of autonomous agents, I propose an application of Mathematical Logic and Probability to model cognitive processes. In this work, I will follow Bateson’s insights on the hierarchy of learning in complex organisms and formalize his idea of applying Russell’s Type Theory. Following Weaver’s three levels for the communication problem, I link the Kolchinsky–Wolpert model to Bateson’s insights, and I reach a semantic and conceptual hierarchy in living systems as an (...)
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  45.  14
    Model Operations: Morphogenesis and the Design Process.Carolin Höfler - 2021 - Perspectives on Science 29 (5):602-626.
    Since the emergence of digital design techniques in combination with so-called responsive materials, the concept of organic forms in architecture seems to be gaining a new quality. The resemblance to an organism should no longer apply only superficially but be inscribed in the materiality as well as in the history of origin and functioning. This article addresses these new transformative effects between architecture and biology. They are presented primarily in relation to the structural architecture of the 1960s and the (...)
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  46. Embryological models in ancient philosophy.Devin Henry - 2005 - Phronesis 50 (1):1 - 42.
    Historically embryogenesis has been among the most philosophically intriguing phenomena. In this paper I focus on one aspect of biological development that was particularly perplexing to the ancients: self-organisation. For many ancients, the fact that an organism determines the important features of its own development required a special model for understanding how this was possible. This was especially true for Aristotle, Alexander, and Simplicius, who all looked to contemporary technology to supply that model. However, they did not (...)
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  47.  3
    Ontologies in Evolutionary Biology: The Role of the Organism in the Two Syntheses.David Cortés-García & Arantza Etxeberria - 2023 - In José Manuel Viejo & Mariano Sanjuán (eds.), Life and Mind - New Directions in the Philosophy of Biology and Cognitive Sciences. Springer. pp. 185–205.
    This paper examines evolutionary ontologies from Darwin’s work to the genesis and maturation of the Modern Evolutionary Synthesis, followed by the onset of the more inclusive framework of the Extended Evolutionary Synthesis. We show how, in an attempt to unify different biological fields under evolutionary principles, the first synthetic theory of evolution progressively disregarded the relevance of organismic-level properties and processes. Yet, failure to reduce the systemic nature and ecological dynamics of the organism (including properties of agency and organization) (...)
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  48.  38
    Reconstructing an incomparable organism: the Chalicothere in nineteenth and early-twentieth century palaeontology.Chris Manias - 2018 - History and Philosophy of the Life Sciences 40 (1):22.
    Palaeontology developed as a field dependent upon comparison. Not only did reconstructing the fragmentary records of fossil organisms and placing them within taxonomic systems and evolutionary lineages require detailed anatomical comparisons with living and fossil animals, but the field also required thinking in terms of behavioural, biological and ecological analogies with modern organisms to understand how prehistoric animals lived and behaved. Yet palaeontological material often worked against making easy linkages, bringing a sense of mystery and doubt. This paper will look (...)
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    Hydrodynamic modelling of stress.J. Viret, L. Grimaud & J. Jimenez - 1999 - Acta Biotheoretica 47 (3-4):173-190.
    This work is a qualitative study of an organism''s physiological adaptative response to stress. The experimental data were selected from a previous study leading to the conclusion that stress may be considered as a topological retraction within a vital space that must be more precisely defined. The experimental methodology uses rat poisoning by neurotoxins. The control parameter is the intensity of the toxic doses. Measured parameters are the animals'' survival rate and the kinetics of cerebral acetylcholinesterase activity. The results, (...)
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  50.  22
    Opening the genetic toolbox of niche model organisms with high throughput techniques: Novel proteins in regeneration as a case study.Mario Looso - 2014 - Bioessays 36 (4):407-418.
    Understanding in vivo regeneration of complex structures offers a fascinating perspective for translation into medical applications. Unfortunately, mammals in general lack large‐scale regenerative capacity, whereas planarians, newts or Hydra can regenerate complete body parts. Such organisms are, however, poorly annotated because of the lack of sequence information. This leads to limited access for molecular biological investigations. In the last decade, high throughput technologies and new methods enabling the effective generation of transgenic animals have rapidly evolved. These developments have allowed the (...)
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