Results for 'whole-cell modeling'

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  1. 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 (...)
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  2. Bridging Emotion Theory and Neurobiology Through Dynamic Systems Modeling.Marc D. Lewis - 2005 - Behavioral and Brain Sciences 28 (2):169-194.
    Efforts to bridge emotion theory with neurobiology can be facilitated by dynamic systems (DS) modeling. DS principles stipulate higher-order wholes emerging from lower-order constituents through bidirectional causal processes cognition relations. I then present a psychological model based on this reconceptualization, identifying trigger, self-amplification, and self-stabilization phases of emotion-appraisal states, leading to consolidating traits. The article goes on to describe neural structures and functions involved in appraisal and emotion, as well as DS mechanisms of integration by which they interact. These (...)
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  3.  30
    The Synthetic Cell as a Techno-Scientific Mandala.H. A. E. Zwart - 2018 - International Journal of Jungian Studies 10.
    This paper analyses the technoscientific objective of building a synthetic cell from a Jungian perspective. After decades of fragmentation and specialisation, the synthetic cell symbolises a turn towards restored wholeness, both at the object pole and at the subject pole. From a Jungian perspective, it is no coincidence that visual representations of synthetic cells often reflect an archetypal, mandala-like structure. As a symbol of restored unity, the synthetic cell mandala compensates for technoscientific fragmentation via active imagination, providing (...)
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  4. Destiny or Free Will Decision? A Life Overview From the Perspective of an Informational Modeling of Consciousness Part I: Information, Consciousness and Life Cycle.Florin Gaiseanu - 2019 - Gerontology and Geriatrics Studies 4 (3):1-6.
    We drive our lives permanently by decisions YES/NO, and even we no longer distinguish the elementary intermediary steps of such decisions most often, they form stereotyped chains that once triggered, they run unconsciously, daily facilitating our activities. We lead our lives actually by conscious decisions, each of such decisions establishing our future trajectory. The YES/NO dipole is actually the elemental evaluation and decisional unit in the informational transmission/reception equipment and lines and in computers, respectively. Based on a binary probabilistic system, (...)
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  5. Kuznetsov V. From studying theoretical physics to philosophical modeling scientific theories: Under influence of Pavel Kopnin and his school.Volodymyr Kuznetsov - 2017 - ФІЛОСОФСЬКІ ДІАЛОГИ’2016 ІСТОРІЯ ТА СУЧАСНІСТЬ У НАУКОВИХ РОЗМИСЛАХ ІНСТИТУТУ ФІЛОСОФІЇ 11:62-92.
    The paper explicates the stages of the author’s philosophical evolution in the light of Kopnin’s ideas and heritage. Starting from Kopnin’s understanding of dialectical materialism, the author has stated that category transformations of physics has opened from conceptualization of immutability to mutability and then to interaction, evolvement and emergence. He has connected the problem of physical cognition universals with an elaboration of the specific system of tools and methods of identifying, individuating and distinguishing objects from a scientific theory domain. The (...)
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  6.  63
    Scientific Iconoclasm and Active Imagination: Synthetic Cells as Techo-Schientific Mandalas.Hub Zwart - 2018 - Life Sciences, Society and Policy 14 (1):1-17.
    Metaphors allow us to come to terms with abstract and complex information, by comparing it to something which is structured, familiar and concrete. Although modern science is “iconoclastic”, as Gaston Bachelard phrases it, scientists are at the same time prolific producers of metaphoric images themselves. Synthetic biology is an outstanding example of a technoscientific discourse replete with metaphors, including textual metaphors such as the “Morse code” of life, the “barcode” of life and the “book” of life. This paper focuses on (...)
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  7. What Was Hodgkin and Huxley’s Achievement?Arnon Levy - 2013 - British Journal for the Philosophy of Science 65 (3):469-492.
    The Hodgkin–Huxley (HH) model of the action potential is a theoretical pillar of modern neurobiology. In a number of recent publications, Carl Craver ([2006], [2007], [2008]) has argued that the model is explanatorily deficient because it does not reveal enough about underlying molecular mechanisms. I offer an alternative picture of the HH model, according to which it deliberately abstracts from molecular specifics. By doing so, the model explains whole-cell behaviour as the product of a mass of underlying low-level (...)
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  8.  58
    Wisdom of Crowds, Wisdom of the Few: Expertise Versus Diversity Across Epistemic Landscapes.Patrick Grim, Daniel J. Singer, Aaron Bramson, Bennett Holman, Sean McGeehan & William J. Berger - manuscript
    In a series of formal studies and less formal applications, Hong and Page offer a ‘diversity trumps ability’ result on the basis of a computational experiment accompanied by a mathematical theorem as explanatory background (Hong & Page 2004, 2009; Page 2007, 2011). “[W]e find that a random collection of agents drawn from a large set of limited-ability agents typically outperforms a collection of the very best agents from that same set” (2004, p. 16386). The result has been extremely influential as (...)
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  9. The Mereological Problem of Entanglement.Paul M. Näger - manuscript
    It is well-known that the entangled quantum state of a composite object cannot be reduced to the states of its parts. This quantum holism provides a peculiar challenge to formulate an appropriate mereological model: When a system is in an entangled state, which objects are there on the micro and macro level, and which of the objects carries which properties? This paper chooses a modeling approach to answer these questions: It proceeds from a systematic overview of consistent mereological models (...)
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  10. Heads and Tails: Molecular Imagination and the Lipid Bilayer, 1917–1941.Daniel Liu - 2018 - In Karl Matlin, Jane Maienschein & Manfred Laubichler (eds.), Visions of Cell Biology: Reflections Inspired by Cowdry's General Cytology. Chicago: University of Chicago Press. pp. 209-245.
    Today, the lipid bilayer structure is nearly ubiquitous, taken for granted in even the most rudimentary introductions to cell biology. Yet the image of the lipid bilayer, built out of lipids with heads and tails, went from having obscure origins deep in colloid chemical theory in 1924 to being “obvious to any competent physical chemist” by 1935. This chapter examines how this schematic, strictly heuristic explanation of the idea of molecular orientation was developed within colloid physical chemistry, and how (...)
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  11. What Are Natural Concepts? A Design Perspective.Igor Douven & Peter Gärdenfors - 2019 - Mind and Language (3):313-334.
    Conceptual spaces have become an increasingly popular modeling tool in cognitive psychology. The core idea of the conceptual spaces approach is that concepts can be represented as regions in similarity spaces. While it is generally acknowledged that not every region in such a space represents a natural concept, it is still an open question what distinguishes those regions that represent natural concepts from those that do not. The central claim of this paper is that natural concepts are represented by (...)
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  12. Network Representation and Complex Systems.Charles Rathkopf - 2018 - Synthese (1).
    In this article, network science is discussed from a methodological perspective, and two central theses are defended. The first is that network science exploits the very properties that make a system complex. Rather than using idealization techniques to strip those properties away, as is standard practice in other areas of science, network science brings them to the fore, and uses them to furnish new forms of explanation. The second thesis is that network representations are particularly helpful in explaining the properties (...)
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  13. Trashing Life’s Tree.L. R. Franklin-Hall - 2010 - Biology and Philosophy 25 (4):689-709.
    The Tree of Life has traditionally been understood to represent the history of species lineages. However, recently researchers have suggested that it might be better interpreted as representing the history of cellular lineages, sometimes called the Tree of Cells. This paper examines and evaluates reasons offered against this cellular interpretation of the Tree of Life. It argues that some such reasons are bad reasons, based either on a false attribution of essentialism, on a misunderstanding of the problem of lineage identity, (...)
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  14. Power in Cultural Evolution and the Spread of Prosocial Norms.Nathan Cofnas - 2018 - Quarterly Review of Biology 93 (4):297–318.
    According to cultural evolutionary theory in the tradition of Boyd and Richerson, cultural evolution is driven by individuals' learning biases, natural selection, and random forces. Learning biases lead people to preferentially acquire cultural variants with certain contents or in certain contexts. Natural selection favors individuals or groups with fitness-promoting variants. Durham (1991) argued that Boyd and Richerson's approach is based on a "radical individualism" that fails to recognize that cultural variants are often "imposed" on people regardless of their individual decisions. (...)
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  15. The Origins of Life: The Managed-Metabolism Hypothesis.John E. Stewart - 2018 - Foundations of Science:1-25.
    The ‘managed-metabolism’ hypothesis suggests that a ‘cooperation barrier’ must be overcome if self-producing chemical organizations are to undergo the transition from non-life to life. This dynamical barrier prevents un-managed autocatalytic networks of molecular species from individuating into complex, cooperative organizations. The barrier arises because molecular species that could otherwise make significant cooperative contributions to the success of an organization will often not be supported within the organization, and because side reactions and other ‘free-riding’ processes will undermine cooperation. As a result, (...)
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  16. Understanding Multicellularity: The Functional Organization of the Intercellular Space.Leonardo Bich, Thomas Pradeu & Jean-Francois Moreau - 2019 - Frontiers in Physiology 10.
    The aim of this paper is to provide a theoretical framework to understand how multicellular systems realize functionally integrated physiological entities by organizing their intercellular space. From a perspective centered on physiology and integration, biological systems are often characterized as organized in such a way that they realize metabolic self-production and self-maintenance. The existence and activity of their components rely on the network they realize and on the continuous management of the exchange of matter and energy with their environment. One (...)
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  17. VO: Vaccine Ontology.Yongqun He, Lindsay Cowell, Alexander D. Diehl, H. L. Mobley, Bjoern Peters, Alan Ruttenberg, Richard H. Scheuermann, Ryan R. Brinkman, Melanie Courtot, Chris Mungall, Barry Smith & Others - 2009 - In ICBO 2009: Proceedings of the First International Conference on Biomedical Ontology. Buffalo:
    Vaccine research, as well as the development, testing, clinical trials, and commercial uses of vaccines involve complex processes with various biological data that include gene and protein expression, analysis of molecular and cellular interactions, study of tissue and whole body responses, and extensive epidemiological modeling. Although many data resources are available to meet different aspects of vaccine needs, it remains a challenge how we are to standardize vaccine annotation, integrate data about varied vaccine types and resources, and support (...)
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  18. Perspectival Logic of Acceptance and Rejection.Alessandro Giordani - 2017 - Logique and Analyse:265-283.
    This paper aims at developing a logical theory of perspectival epistemic attitudes. After presenting a standard framework for modeling acceptance, where the epistemic space of an agent coincides with a unique epistemic cell, more complex systems are introduced, which are characterized by the existence of many connected epistemic cells, and different possible attitudes towards a proposition, both positive and negative, are discussed. In doing that, we also propose some interesting ways in which the systems can be interpreted on (...)
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  19. Formal Biology and Compositional Biology as Two Kinds of Biological Theorizing.Rasmus Grønfeldt Winther - 2003 - Dissertation, Indiana University, HPS
    There are two fundamentally distinct kinds of biological theorizing. "Formal biology" focuses on the relations, captured in formal laws, among mathematically abstracted properties of abstract objects. Population genetics and theoretical mathematical ecology, which are cases of formal biology, thus share methods and goals with theoretical physics. "Compositional biology," on the other hand, is concerned with articulating the concrete structure, mechanisms, and function, through developmental and evolutionary time, of material parts and wholes. Molecular genetics, biochemistry, developmental biology, and physiology, which are (...)
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  20. Covid 19 Pandemic: Impact on Masses and Prevention Knowhow. Namita, Chitra Singh & Vivek Kumar - 2020 - International Journal of Medical and Health Research 6 (9):6-9.
    Today the whole world is facing a very difficult time due to corona virus which initially originated in Wuhan city of China. In China an unusual pneumonia was noticed earlier which later recognized as a pandemic. There have been two events in the past wherein crossover of animal corona viruses to humans has resulted in severe disease, one was SARS-CoV and the other was MERS-CoV. The genetic sequence of the COVID19 showed more than 80% similarities to SARS-CoV and 50% (...)
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  21. Lightning in a Bottle: Complexity, Chaos, and Computation in Climate Science.Jon Lawhead - 2014 - Dissertation, Columbia University
    Climatology is a paradigmatic complex systems science. Understanding the global climate involves tackling problems in physics, chemistry, economics, and many other disciplines. I argue that complex systems like the global climate are characterized by certain dynamical features that explain how those systems change over time. A complex system's dynamics are shaped by the interaction of many different components operating at many different temporal and spatial scales. Examining the multidisciplinary and holistic methods of climatology can help us better understand the nature (...)
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  22. Humanities’ Metaphysical Underpinnings of Late Frontier Scientific Research.Alcibiades Malapi-Nelson - 2014 - Humanities 214 (3):740-765.
    The behavior/structure methodological dichotomy as locus of scientific inquiry is closely related to the issue of modeling and theory change in scientific explanation. Given that the traditional tension between structure and behavior in scientific modeling is likely here to stay, considering the relevant precedents in the history of ideas could help us better understand this theoretical struggle. This better understanding might open up unforeseen possibilities and new instantiations, particularly in what concerns the proposed technological modification of the human (...)
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  23. Quantum Resonance & Consciousness.Contzen Pereira - 2015 - Journal of Metaphysics and Connected Consciousness 2.
    Resonance can trigger of a series of quantum events and therefore induce several changes related to consciousness at micro as well as macro level within a living system. Therapeutic effects have been observed in several religious meditative and healing practices, which use resonance in the form of chanting and prayers. A living system may have many resonant frequencies due to their degrees of freedom, where each can vibrate as a harmonic oscillator supporting the progression of vibrations as waves that moves (...)
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  24. In Silico Approaches and the Role of Ontologies in Aging Research.Georg Fuellen, Melanie Börries, Hauke Busch, Aubrey de Grey, Udo Hahn, Thomas Hiller, Andreas Hoeflich, Ludger Jansen, Georges E. Janssens, Christoph Kaleta, Anne C. Meinema, Sascha Schäuble, Paul N. Schofield, Barry Smith & Others - 2013 - Rejuvenation Research 16 (6):540-546.
    The 2013 Rostock Symposium on Systems Biology and Bioinformatics in Aging Research was again dedicated to dissecting the aging process using in silico means. A particular focus was on ontologies, as these are a key technology to systematically integrate heterogeneous information about the aging process. Related topics were databases and data integration. Other talks tackled modeling issues and applications, the latter including talks focussed on marker development and cellular stress as well as on diseases, in particular on diseases of (...)
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  25. Hybridity in Agriculture.Catherine Kendig - 2014 - In Paul B. Thompson & David M. Kaplan (eds.), Encyclopedia of Food and Agricultural Ethics. Springer.
    In a very general sense, hybrid can be understood to be any organism that is the product of two (or more) organisms where each parent belongs to a different kind. For example; the offspring from two or more parent organisms, each belonging to a separate species (or genera), is called a “hybrid”. “Hybridity” refers to the phenomenal character of being a hybrid. And “hybridization ” refers to both natural and artificial processes of generating hybrids. These processes include mechanisms of selective (...)
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  26. Remarks on the Geometry of Complex Systems and Self-Organization.Luciano Boi - 2012 - In Vincenzo Fano, Enrico Giannetto, Giulia Giannini & Pierluigi Graziani (eds.), Complessità e Riduzionismo. © ISONOMIA – Epistemologica, University of Urbino. pp. 28-43.
    Let us start by some general definitions of the concept of complexity. We take a complex system to be one composed by a large number of parts, and whose properties are not fully explained by an understanding of its components parts. Studies of complex systems recognized the importance of “wholeness”, defined as problems of organization (and of regulation), phenomena non resolvable into local events, dynamics interactions in the difference of behaviour of parts when isolated or in higher configuration, etc., in (...)
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  27. Elastic Membrane Based Model of Human Perception.Alexander Egoyan - 2011 - Toward a Science of Consciousness.
    Undoubtedly the Penrose-Hameroff Orch OR model may be considered as a good theory for describing information processing mechanisms and holistic phenomena in the human brain, but it doesn’t give us satisfactory explanation of human perception. In this work a new approach explaining our perception is introduced, which is in good agreement with Orch OR model and other mainstream science theories such as string theory, loop quantum gravity and holographic principle. It is shown that human perception cannot be explained in the (...)
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  28. Assisted Conception and Embryo Research with Reference to the Tenets of Catholic Christianity.Piyali Mitra - 2017 - Online International Interdisciplinary Research Journal 7 (3):165-173.
    Religion has a considerable influence over the public’s attitudes towards science and technologies. The objective of the paper is to understand the ethical and religious problems concerning the use of embryo for research in assisting conception for infertile couples from the perspective of Catholic Christians. This paper seeks to explain our preliminary reflections on how religious communities particularly the Catholic Christian communities respond to and assess the ethics of reproductive technologies and embryo research. Christianity as a whole lacks a (...)
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  29. Some Resonances Between Eastern Thought and Integral Biomathics in the Framework of the WLIMES Formalism for Modelling Living Systems.Plamen L. Simeonov & Andree C. Ehresmann - forthcoming - Progress in Biophysics and Molecular Biology 131 (Special).
    Forty-two years ago, Capra published “The Tao of Physics” (Capra, 1975). In this book (page 17) he writes: “The exploration of the atomic and subatomic world in the twentieth century has …. necessitated a radical revision of many of our basic concepts” and that, unlike ‘classical’ physics, the sub-atomic and quantum “modern physics” shows resonances with Eastern thoughts and “leads us to a view of the world which is very similar to the views held by mystics of all ages and (...)
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  30.  69
    "Life" Shaped by Genes That Depend on Their Surrounds.Paul Gottlob Layer - 2011 - Annals of the History and Philosophy of Biology 16:153-170.
    Never was dogmatic reductionism helpful in conceiving the phenomenon of life. The post-genomic era has made it clear that genes alone cannot explain the functioning of whole organisms. Already each cell represents a unique, non-recurring individual. Recent progress in developmental biology has conveyed new perspectives both on the makings of individual organisms (ontogeny), as on evolutionary change (Evo-Devo). The genome (the entirety of all genes) of an animal remains constant from fertilization onwards in each cell. The realization (...)
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  31.  47
    Life, Local Constraints and Meaning Generation. An Evolutionary Approach to Cognition (2015).Christophe Menant - manuscript
    The relations between life and cogntion have been addressed through different perspectives [Stewart 1996, Boden 2001, Bourgine and Stewart 2004, van Duijn & all 2006, Di Paolo 2009]. We would like here to address that subject by relating life to cognition through a process of meaning generation. Life emerged on earth as a far from thermodynamic equilibrium performance that had to maintain herself. Life is charactertized by a ‘stay alive’ constraint that has to be satisfied (such constraint can be included (...)
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  32.  78
    A Wormhole of Light by Using Electronic Materials.Areena Bhatti - 2020 - Physics Tomorrow Letters 2:9.
    Wormhole is a popular tool for interstellar travel in science fiction. It connects two different space-time points directly although such an astrophysical object is not yet observed, but in 2015, researchers in Spain created a tiny magnetic wormhole for the first time ever. They used it to connect two regions of space so that a magnetic field could travel 'invisibly' between them. This article presents a model of making a wormhole of light on the principle of conversion of energy so (...)
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  33.  38
    Improving Regional Regulatory Platform Tools for the Development of Small and Medium Businesses.A. V. Zakharkina & O. A. Kuznetsova - 2019 - Bulletin of Omsk University. Series Andquot;Law" 16 (4):94-103.
    Introduction. Taking into account the priorities of the state policy in the field of economic and innovative development of the Perm region, assessment of the regional potential of the digital economy, the strategic importance of economic activities implemented by SMEs for the economy of the region and the country as a whole, the actual impact of the norms on the instruments of development of small and medium-sized enterprises in the Perm region is assessed. The purpose of this study is (...)
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  34. COVID-19 Pandemic – Philosophical Approaches.Sfetcu Nicolae (ed.) - 2020 - Drobeta Turnu Severin: MultiMedia Publishing.
    The paper begins with a retrospective of the debates on the origin of life: the virus or the cell? The virus needs a cell for replication, instead the cell is a more evolved form on the evolutionary scale of life. In addition, the study of viruses raises pressing conceptual and philosophical questions about their nature, their classification, and their place in the biological world. The subject of pandemics is approached starting from the existentialism of Albert Camus and (...)
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  35. Modeling Practical Thinking.Matthew Mosdell - 2019 - Mind and Language 34 (4):445-464.
    Intellectualists about knowledge how argue that knowing how to do something is knowing the content of a proposition (i.e, a fact). An important component of this view is the idea that propositional knowledge is translated into behavior when it is presented to the mind in a peculiarly practical way. Until recently, however, intellectualists have not said much about what it means for propositional knowledge to be entertained under thought's practical guise. Carlotta Pavese fills this gap in the intellectualist view by (...)
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  36. Experimental Modeling in Biology: In Vivo Representation and Stand-Ins As Modeling Strategies.Marcel Weber - 2014 - Philosophy of Science 81 (5):756-769.
    Experimental modeling in biology involves the use of living organisms (not necessarily so-called "model organisms") in order to model or simulate biological processes. I argue here that experimental modeling is a bona fide form of scientific modeling that plays an epistemic role that is distinct from that of ordinary biological experiments. What distinguishes them from ordinary experiments is that they use what I call "in vivo representations" where one kind of causal process is used to stand in (...)
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  37. Optimality Modeling in a Suboptimal World.Angela Potochnik - 2009 - Biology and Philosophy 24 (2):183-197.
    The fate of optimality modeling is typically linked to that of adaptationism: the two are thought to stand or fall together (Gould and Lewontin, Proc Relig Soc Lond 205:581–598, 1979; Orzack and Sober, Am Nat 143(3):361–380, 1994). I argue here that this is mistaken. The debate over adaptationism has tended to focus on one particular use of optimality models, which I refer to here as their strong use. The strong use of an optimality model involves the claim that selection (...)
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  38. Stem Cell Research and Same Sex Reproduction.Thomas Douglas, Catherine Harding, Hannah Bourne & Julian Savulescu - 2012 - In Muireann Quigley, Sarah Chan & John Harris (eds.), Stem Cells: New Frontiers in Science and Ethics. World Scientific.
    Recent advances in stem cell research suggest that in the future it may be possible to create eggs and sperm from human stem cells through a process that we term in vitro gametogenesis (IVG). IVG would allow treatment of some currently untreatable forms of infertility. It may also allow same-sex couples to have genetically-related children. For example, cells taken from one man could potentially be used to create an egg, which could then be fertilised using naturally produced sperm from (...)
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  39. Optimality Modeling and Explanatory Generality.Angela Potochnik - 2007 - Philosophy of Science 74 (5):680-691.
    The optimality approach to modeling natural selection has been criticized by many biologists and philosophers of biology. For instance, Lewontin (1979) argues that the optimality approach is a shortcut that will be replaced by models incorporating genetic information, if and when such models become available. In contrast, I think that optimality models have a permanent role in evolutionary study. I base my argument for this claim on what I think it takes to best explain an event. In certain contexts, (...)
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  40. Teleosemantic Modeling of Cognitive Representations.Marc Artiga - 2016 - Biology and Philosophy 31 (4):483-505.
    Naturalistic theories of representation seek to specify the conditions that must be met for an entity to represent another entity. Although these approaches have been relatively successful in certain areas, such as communication theory or genetics, many doubt that they can be employed to naturalize complex cognitive representations. In this essay I identify some of the difficulties for developing a teleosemantic theory of cognitive representations and provide a strategy for accommodating them: to look into models of signaling in evolutionary game (...)
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  41. Modeling Truth.Paul Teller - manuscript
    Many in philosophy understand truth in terms of precise semantic values, true propositions. Following Braun and Sider, I say that in this sense almost nothing we say is, literally, true. I take the stand that this account of truth nonetheless constitutes a vitally useful idealization in understanding many features of the structure of language. The Fregean problem discussed by Braun and Sider concerns issues about application of language to the world. In understanding these issues I propose an alternative modeling (...)
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  42. Cell Types as Natural Kinds.Matthew H. Slater - 2013 - Biological Theory 7 (2):170-179.
    Talk of different types of cells is commonplace in the biological sciences. We know a great deal, for example, about human muscle cells by studying the same type of cells in mice. Information about cell type is apparently largely projectible across species boundaries. But what defines cell type? Do cells come pre-packaged into different natural kinds? Philosophical attention to these questions has been extremely limited [see e.g., Wilson (Species: New Interdisciplinary Essays, pp 187–207, 1999; Genes and the Agents (...)
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  43.  9
    Modeling Morality.Walter Veit - 2019 - In Matthieu Fontaine, Cristina Barés-Gómez, Francisco Salguero-Lamillar, Lorenzo Magnani & Ángel Nepomuceno-Fernández (eds.), Model-Based Reasoning in Science and Technology. Springer Verlag. pp. 83–102.
    Unlike any other field, the science of morality has drawn attention from an extraordinarily diverse set of disciplines. An interdisciplinary research program has formed in which economists, biologists, neuroscientists, psychologists, and even philosophers have been eager to provide answers to puzzling questions raised by the existence of human morality. Models and simulations, for a variety of reasons, have played various important roles in this endeavor. Their use, however, has sometimes been deemed as useless, trivial and inadequate. The role of models (...)
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  44. The Cell and Protoplasm as Container, Object, and Substance, 1835–1861.Daniel Liu - 2017 - Journal of the History of Biology 50 (4):889-925.
    (Recipient of the 2020 Everett Mendelsohn Prize.) This article revisits the development of the protoplasm concept as it originally arose from critiques of the cell theory, and examines how the term “protoplasm” transformed from a botanical term of art in the 1840s to the so-called “living substance” and “the physical basis of life” two decades later. I show that there were two major shifts in biological materialism that needed to occur before protoplasm theory could be elevated to have equal (...)
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  45. Modeling Measurement: Error and Uncertainty.Alessandro Giordani & Luca Mari - 2014 - In Marcel Boumans, Giora Hon & Arthur Petersen (eds.), Error and Uncertainty in Scientific Practice. Pickering & Chatto. pp. 79-96.
    In the last few decades the role played by models and modeling activities has become a central topic in the scientific enterprise. In particular, it has been highlighted both that the development of models constitutes a crucial step for understanding the world and that the developed models operate as mediators between theories and the world. Such perspective is exploited here to cope with the issue as to whether error-based and uncertainty-based modeling of measurement are incompatible, and thus alternative (...)
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  46. Stem Cell Lineages: Between Cell and Organism.Melinda Bonnie Fagan - 2017 - Philosophy, Theory, and Practice in Biology 9 (6).
    Ontologies of living things are increasingly grounded on the concepts and practices of current life science. Biological development is a process, undergone by living things, which begins with a single cell and (in an important class of cases) ends with formation of a multicellular organism. The process of development is thus prima facie central for ideas about biological individuality and organismality. However, recent accounts of these concepts do not engage developmental biology. This paper aims to fill the gap, proposing (...)
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  47. Modeling Epistemology: Examples and Analysis in Computational Philosophy of Science.Patrick Grim - 2019 - In A. Del Barrio, C. J. Lynch, F. J. Barros & X. Hu (eds.), IEEE SpringSim Proceedings 2019. IEEE. pp. 1-12.
    What structure of scientific communication and cooperation, between what kinds of investigators, is best positioned to lead us to the truth? Against an outline of standard philosophical characteristics and a recent turn to social epistemology, this paper surveys highlights within two strands of computational philosophy of science that attempt to work toward an answer to this question. Both strands emerge from abstract rational choice theory and the analytic tradition in philosophy of science rather than postmodern sociology of science. The first (...)
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  48. Cancer Cells and Adaptive Explanations.Pierre-Luc Germain - 2012 - Biology and Philosophy 27 (6):785-810.
    The aim of this paper is to assess the relevance of somatic evolution by natural selection to our understanding of cancer development. I do so in two steps. In the first part of the paper, I ask to what extent cancer cells meet the formal requirements for evolution by natural selection, relying on Godfrey-Smith’s (2009) framework of Darwinian populations. I argue that although they meet the minimal requirements for natural selection, cancer cells are not paradigmatic Darwinian populations. In the second (...)
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  49. Modeling and Experimenting.Isabelle Peschard - 2009 - In Paul Humphreys & Cyrille Imbert (eds.), Models, Simulations, and Representations. Routledge.
    Experimental activity is traditionally identified with testing the empirical implications or numerical simulations of models against data. In critical reaction to the ‘tribunal view’ on experiments, this essay will show the constructive contribution of experimental activity to the processes of modeling and simulating. Based on the analysis of a case in fluid mechanics, it will focus specifically on two aspects. The first is the controversial specification of the conditions in which the data are to be obtained. The second is (...)
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  50. Modeling Economic Systems as Locally-Constructive Sequential Games.Leigh Tesfatsion - 2017 - Journal of Economic Methodology 24 (4):1-26.
    Real-world economies are open-ended dynamic systems consisting of heterogeneous interacting participants. Human participants are decision-makers who strategically take into account the past actions and potential future actions of other participants. All participants are forced to be locally constructive, meaning their actions at any given time must be based on their local states; and participant actions at any given time affect future local states. Taken together, these essential properties imply real-world economies are locally-constructive sequential games. This paper discusses a modeling (...)
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