Results for 'Alexei Evsikov'

266 found
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  1.  85
    The Representation of Protein Complexes in the Protein Ontology.Carol Bult, Harold Drabkin, Alexei Evsikov, Darren Natale, Cecilia Arighi, Natalia Roberts, Alan Ruttenberg, Peter D’Eustachio, Barry Smith, Judith Blake & Cathy Wu - 2011 - BMC Bioinformatics 12 (371):1-11.
    Representing species-specific proteins and protein complexes in ontologies that are both human and machine-readable facilitates the retrieval, analysis, and interpretation of genome-scale data sets. Although existing protin-centric informatics resources provide the biomedical research community with well-curated compendia of protein sequence and structure, these resources lack formal ontological representations of the relationships among the proteins themselves. The Protein Ontology (PRO) Consortium is filling this informatics resource gap by developing ontological representations and relationships among proteins and their variants and modified forms. Because (...)
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  2. The Protein Ontology: A Structured Representation of Protein Forms and Complexes.Darren Natale, Cecilia N. Arighi, Winona C. Barker, Judith A. Blake, Carol J. Bult, Michael Caudy, Harold J. Drabkin, Peter D’Eustachio, Alexei V. Evsikov, Hongzhan Huang, Jules Nchoutmboube, Natalia V. Roberts, Barry Smith, Jian Zhang & Cathy H. Wu - 2011 - Nucleic Acids Research 39 (1):D539-D545.
    The Protein Ontology (PRO) provides a formal, logically-based classification of specific protein classes including structured representations of protein isoforms, variants and modified forms. Initially focused on proteins found in human, mouse and Escherichia coli, PRO now includes representations of protein complexes. The PRO Consortium works in concert with the developers of other biomedical ontologies and protein knowledge bases to provide the ability to formally organize and integrate representations of precise protein forms so as to enhance accessibility to results of protein (...)
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  3. Protein-Centric Connection of Biomedical Knowledge: Protein Ontology Research and Annotation Tools.Cecilia N. Arighi, Darren A. Natale, Judith A. Blake, Carol J. Bult, Michael Caudy, Alexander D. Diehl, Harold J. Drabkin, Peter D'Eustachio, Alexei Evsikov, Hongzhan Huang, Barry Smith & Others - 2011 - In Proceedings of the 2nd International Conference on Biomedical Ontology. Buffalo, NY: NCOR. pp. 285-287.
    The Protein Ontology (PRO) web resource provides an integrative framework for protein-centric exploration and enables specific and precise annotation of proteins and protein complexes based on PRO. Functionalities include: browsing, searching and retrieving, terms, displaying selected terms in OBO or OWL format, and supporting URIs. In addition, the PRO website offers multiple ways for the user to request, submit, or modify terms and/or annotation. We will demonstrate the use of these tools for protein research and annotation.
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  4. A Fiduciary Argument Against Stakeholder Theory.Alexei M. Marcoux - 2003 - Business Ethics Quarterly 13 (1):1-24.
    Critics attack normative ethical stakeholder theory for failing to recognize the special moral status of shareholders that justifiesthe fiduciary duties owed to them at law by managers. Stakeholder theorists reply that there is nothing morally significant about shareholders that can underwrite those fiduciary duties. I advance an argument that seeks to demonstrate both the special moral status of shareholders in a firm and the concomitant moral inadequacy of stakeholder theory. I argue that (i) if some relations morally requirefiduciary duties, and (...)
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  5.  21
    Protosemiosis: Agency with Reduced Representation Capacity.Alexei A. Sharov & Tommi Vehkavaara - 2015 - Biosemiotics 8 (1):103-123.
    Life has semiotic nature; and as life forms differ in their complexity, functionality, and adaptability, we assume that forms of semiosis also vary accordingly. Here we propose a criterion to distinguish between the primitive kind of semiosis, which we call “protosemiosis” from the advanced kind of semiosis, or “eusemiosis”. In protosemiosis, agents associate signs directly with actions without considering objects, whereas in eusemiosis, agents associate signs with objects and only then possibly with actions. Protosemiosis started from the origin of life, (...)
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  6.  21
    Evolution of Natural Agents: Preservation, Advance, and Emergence of Functional Information.Alexei A. Sharov - 2016 - Biosemiotics 9 (1):103-120.
    Biological evolution is often viewed narrowly as a change of morphology or allele frequency in a sequence of generations. Here I pursue an alternative informational concept of evolution, as preservation, advance, and emergence of functional information in natural agents. Functional information is a network of signs that are used by agents to preserve and regulate their functions. Functional information is preserved in evolution via complex interplay of copying and construction processes: the digital components are copied, whereas interpreting subagents together with (...)
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  7. Reconstruction of Quantum Theory.Alexei Grinbaum - 2007 - British Journal for the Philosophy of Science 58 (3):387 - 408.
    What belongs to quantum theory is no more than what is needed for its derivation. Keeping to this maxim, we record a paradigmatic shift in the foundations of quantum mechanics, where the focus has recently moved from interpreting to reconstructing quantum theory. Several historic and contemporary reconstructions are analyzed, including the work of Hardy, Rovelli, and Clifton, Bub and Halvorson. We conclude by discussing the importance of a novel concept of intentionally incomplete reconstruction.
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  8.  15
    Evolutionary Biosemiotics and Multilevel Construction Networks.Alexei A. Sharov - 2016 - Biosemiotics 9 (3):399-416.
    In contrast to the traditional relational semiotics, biosemiotics decisively deviates towards dynamical aspects of signs at the evolutionary and developmental time scales. The analysis of sign dynamics requires constructivism to explain how new components such as subagents, sensors, effectors, and interpretation networks are produced by developing and evolving organisms. Semiotic networks that include signs, tools, and subagents are multilevel, and this feature supports the plasticity, robustness, and evolvability of organisms. The origin of life is described here as the emergence of (...)
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  9.  75
    Which Fine-Tuning Arguments Are Fine?Alexei Grinbaum - 2012 - Foundations of Physics 42 (5):615-631.
    Fine-tuning arguments are a frequent find in the literature on quantum field theory. They are based on naturalness—an aesthetic criterion that was given a precise definition in the debates on the Higgs mechanism. We follow the history of such definitions and of their application at the scale of electroweak symmetry breaking. They give rise to a special interpretation of probability, which we call Gedankenfrequency. Finally, we show that the argument from naturalness has been extended to comparing different models of the (...)
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  10.  21
    Comprehending the Semiosis of Evolution.Alexei Sharov, Timo Maran & Morten Tønnessen - 2016 - Biosemiotics 9 (1):1-6.
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  11. Ethics in Robotics Research: CERNA Recommendations.Alexei Grinbaum & Raja Chatila - 2017 - IEEE Robotics and Automation Magazine (99):1-8.
    This article summarizes the recommendations concerning robotics as issued by the Commission for the Ethics of Research in Information Sciences and Technologies (CERNA), the French advisory commission for the ethics of information and communication technology (ICT) research. Robotics has numerous applications in which its role can be overwhelming and may lead to unexpected consequences. In this rapidly evolving technological environment, CERNA does not set novel ethical standards but seeks to make ethical deliberation inseparable from scientific activity. Additionally, it provides tools (...)
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  12.  13
    Towards Synthesis of Biology and Semiotics.Alexei Sharov, Timo Maran & Morten Tønnessen - 2015 - Biosemiotics 8 (1):1-7.
    The journal Biosemiotics was envisioned by its founding editor, Marcello Barbieri, as a major periodical for interdisciplinary papers that integrate biology and semiotics. Since 2008 the journal has published 21 issues, including special issues on crucial problems such as the semiotics of perception, origins of mind, code biology, biohermeneutics, biosemiotic analysis of information and chance. The impact factor of the journal does not fully describe the significance of this journal, because the discipline of biosemiotics is young and remains in its (...)
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  13. Biosemiotics: A Functional-Evolutionary Approach to the Analysis of the Sense of Information.Alexei A. Sharov - forthcoming - Biosemiotics: The Semiotic Web.
     
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  14.  7
    Minimal Mind.Alexei A. Sharov - 2013 - In Liz Swan (ed.), Origins of Mind. pp. 343--360.
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  15.  7
    How Device-Independent Approaches Change the Meaning of Physical Theory.Alexei Grinbaum - 2017 - Studies in History and Philosophy of Science Part B: Studies in History and Philosophy of Modern Physics 58:22-30.
  16.  23
    Umwelt-Theory and Pragmatism.Alexei Sharov - 2001 - Semiotica 2001 (134).
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  17.  8
    Alexei F. Losev and the Kant Society.Elena A. Takho-Godi - 2018 - Russian Studies in Philosophy 56 (6):498-503.
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  18.  36
    Freeman and Evan: Stakeholder Theory in the Original Position.Alexei M. Marcoux - 1999 - Business Ethics Quarterly 9 (2):207-224.
    We argue that the Rawlsian social contract argument advanced for stakeholder theory by R. Edward Freeman, writing alone and with William M. Evan, fails in three main ways. First, it is true to Rawls in neither form, nor purpose, nor the level of knowledge (or ignorance) required to motivate the veil of ignorance. Second, it fails to tailor the veil of ignorance to the fairness conditions that are required to solve the moral problem that Freeman and Evan set out to (...)
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  19.  27
    The Effectiveness of Mathematics in Physics of the Unknown.Alexei Grinbaum - 2019 - Synthese 196 (3):973-989.
    If physics is a science that unveils the fundamental laws of nature, then the appearance of mathematical concepts in its language can be surprising or even mysterious. This was Eugene Wigner’s argument in 1960. I show that another approach to physical theory accommodates mathematics in a perfectly reasonable way. To explore unknown processes or phenomena, one builds a theory from fundamental principles, employing them as constraints within a general mathematical framework. The rise of such theories of the unknown, which I (...)
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  20.  56
    Reconstructing Instead of Interpreting Quantum Theory.Alexei Grinbaum - 2007 - Philosophy of Science 74 (5):761-774.
    A paradigmatic shift in the foundations of quantum mechanics is recorded, from interpreting to reconstructing quantum theory. Examples of reconstruction are analyzed, and conceptual foundations of the information-theoretic reconstruction developed. A concept of intentionally incomplete reconstruction is introduced to mark the novel content of research in the foundation of quantum theory. ‡Many thanks to Lucien Hardy, Jeff Bub and Bill Demopoulos for their comments. This research was supported through the ANR grant ANR-06-BLAN-0348-01. Part of this research was held at the (...)
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  21.  74
    Fundamental Principles and Mechanisms of the Conscious Self.Alexei V. Samsonovich & Lynn Nadel - 2005 - Cortex. Special Issue 41 (5):669-689.
  22.  26
    Living with Uncertainty: Toward the Ongoing Normative Assessment of Nanotechnology.Alexei Grinbaum & Jean-Pierre Dupuy - 2004 - Techné: Research in Philosophy and Technology 8 (2):4-25.
  23.  7
    Composite Agency: Semiotics of Modularity and Guiding Interactions.Alexei A. Sharov - 2017 - Biosemiotics 10 (2):157-178.
    Principles of constructivism are used here to explore how organisms develop tools, subagents, scaffolds, signs, and adaptations. Here I discuss reasons why organisms have composite nature and include diverse subagents that interact in partially cooperating and partially conflicting ways. Such modularity is necessary for efficient and robust functionality, including mutual construction and adaptability at various time scales. Subagents interact via material and semiotic relations, some of which force or prescribe actions of partners. Other interactions, which I call “guiding”, do not (...)
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  24.  36
    Business Ethics.Alexei Marcoux - 2008 - Stanford Encyclopedia of Philosophy.
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  25.  8
    The Origin and Evolution of Signs.Alexei A. Sharov - 1999 - Semiotica 127 (1-4):521-536.
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  26.  18
    Toward a Semantic General Theory of Everything.Alexei V. Samsonovich, Rebecca F. Goldin & Giorgio A. Ascoli - 2010 - Complexity 15 (4):NA-NA.
  27.  45
    The Nanotechnological Golem.Alexei Grinbaum - 2010 - NanoEthics 4 (3):191-198.
    We give reasons for the importance of old narratives, including myths, in ethical thinking about science and technology. On the example of a legend about creating artificial men we explore the side effects of having too much success and the problem of intermediate social status of bioengineered artefacts.
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  28.  26
    The Effectiveness of Mathematics in Physics of the Unknown.Alexei Grinbaum - 2017 - Synthese:1-17.
    If physics is a science that unveils the fundamental laws of nature, then the appearance of mathematical concepts in its language can be surprising or even mysterious. This was Eugene Wigner’s argument in 1960. I show that another approach to physical theory accommodates mathematics in a perfectly reasonable way. To explore unknown processes or phenomena, one builds a theory from fundamental principles, employing them as constraints within a general mathematical framework. The rise of such theories of the unknown, which I (...)
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  29.  8
    Alexei Ratmansky’s Serenade After Plato’s Symposium.Julie C. Van Camp - 2017 - The Philosophers' Magazine 76:105-107.
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  30.  34
    The Mental State Formalism of Gmu-Bica.Alexei V. Samsonovich, Kenneth A. de Jong & Anastasia Kitsantas - 2009 - International Journal of Machine Consciousness 1 (1):111-130.
  31.  52
    A Counterintuitive Argument for Résumé Embellishment.Alexei M. Marcoux - 2006 - Journal of Business Ethics 63 (2):183-194.
    Applied ethicists say little about résumé embellishment. Presumably, this is so because résumé embellishment seems obviously wrong; an instance of ordinary lying, familiar moral prohibitions against which cover the case completely. Analysis of résumé embellishment merely as ordinary lying overlooks its collective action aspects. Taking account of those aspects and their implications, I argue on consequentialist grounds that, given some plausible background conditions, a limited form of résumé embellishment is morally permissible. This outcome is a particular instantiation of a more (...)
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  32.  9
    Kant and the Problem of Optimism: The Origin of the Debate.Alexei N. Krouglov - 2018 - Kantian Journal 37 (1):9-24.
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  33.  8
    Role of Utility and Inference in the Evolution of Functional Information.Alexei A. Sharov - 2009 - Biosemiotics 2 (1):101-115.
    Functional information means an encoded network of functions in living organisms from molecular signaling pathways to an organism’s behavior. It is represented by two components: code and an interpretation system, which together form a self-sustaining semantic closure. Semantic closure allows some freedom between components because small variations of the code are still interpretable. The interpretation system consists of inference rules that control the correspondence between the code and the function (phenotype) and determines the shape of the fitness landscape. The utility (...)
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  34.  19
    Manifest Reason: Walter Benjamin on Violence and Collective Agency.Alexei Procyshyn - 2014 - Constellations 21 (3):390-400.
  35.  14
    Organisms Reshape Sign Relations.Alexei Sharov, Timo Maran & Morten Tønnessen - 2015 - Biosemiotics 8 (3):361-365.
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  36.  32
    Quantum Theory as a Critical Regime of Language Dynamics.Alexei Grinbaum - 2015 - Foundations of Physics 45 (10):1341-1350.
    Some mathematical theories in physics justify their explanatory superiority over earlier formalisms by the clarity of their postulates. In particular, axiomatic reconstructions drive home the importance of the composition rule and the continuity assumption as two pillars of quantum theory. Our approach sits on these pillars and combines new mathematics with a testable prediction. If the observer is defined by a limit on string complexity, information dynamics leads to an emergent continuous model in the critical regime. Restricting it to a (...)
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  37.  23
    Evolution of Sex Differences in Lifespan and Aging: Causes and Constraints.Alexei A. Maklakov & Virpi Lummaa - 2013 - Bioessays 35 (8):717-724.
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  38.  15
    Can Social Systems Theory Be Used for Immanent Critique?Alexei Procyshyn - 2017 - Thesis Eleven 143 (1):97-114.
    Two trends have emerged in recent work from the Frankfurt School: the first involves a reconsideration of immanent critique’s basic commitments and viability for critical social theory, while the second involves an effort to introduce temporal considerations for social interaction into critical theorizing to help make sense of the phenomenon of social acceleration. This article contributes to these ongoing discussions by investigating whether social systems theory, in which temporal relations play a primary role, can be integrated with immanent critique. If (...)
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  39.  77
    Carnap’s 1934 Objections to Wittgenstein’s Say/Show Distinction.Alexei Angelides - 2012 - Erkenntnis 76 (2):147-169.
    In sections 18 and 73 of Carnap’s Logical Syntax of Language , Carnap famously presents what he understands to be decisive objections to Wittgenstein’s Tractarian distinction between saying and showing. However, Carnap has been criticized in recent literature for severely misinterpreting that distinction. Against this criticism it is argued that Carnap reads that distinction as applying to two distinct classes of expressions ( Unsinn and sinnlos ) that he holds to emerge from his reading of Tractatus 4.1212 and related Tractarian (...)
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  40.  32
    Tetens und die Deduktion der Kategorien bei Kant.Alexei N. Krouglov - 2013 - Kant-Studien 104 (4):466-489.
  41.  51
    On the Eve of the LHC: Conceptual Questions in High-Energy Physics.Alexei Grinbaum - unknown
    We start by remarks on the scientific and societal context of today's theoretical physics. Major classes of models for physics to be explored at the LHC are then reviewed. This leads us to propose an LHC timeline and a list of potential effects on theoretical physics and the society. We then explore three conceptual questions connected with the LHC physics: symmetry (and symmetry breaking), effective field theory, and fine tuning.
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  42.  25
    Kant and the Crusians in the Debate on Optimism.Alexei N. Krouglov - 2018 - Kantian Journal 37 (2):7-31.
  43.  8
    The Hanf Number for Amalgamation of Coloring Classes.Alexei Kolesnikov & Chris Lambie-Hanson - 2016 - Journal of Symbolic Logic 81 (2):570-583.
  44.  16
    The Great War, the Russian Civil War, and the Invention of Big Science.Alexei Kojevnikov - 2002 - Science in Context 15 (2):239-275.
  45.  14
    N-Simple Theories.Alexei S. Kolesnikov - 2005 - Annals of Pure and Applied Logic 131 (1-3):227-261.
    The main topic of this paper is the investigation of generalized amalgamation properties for simple theories. That is, we are trying to answer the question of when a simple theory has the property of n-dimensional amalgamation, where two-dimensional amalgamation is the Independence Theorem for simple theories. We develop the notions of strong n-simplicity and n-simplicity for 1≤n≤ω, where both “1-simple” and “strongly 1-simple” are the same as “simple”. For strong n-simplicity, we present examples of simple unstable theories in each subclass (...)
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  46.  20
    Beyond Rasiowan Systems: Unital Deductive Systems.Alexei Y. Muravitsky - 2014 - Logica Universalis 8 (1):83-102.
    We deal with monotone structural deductive systems in an unspecified propositional language \ . These systems fall into several overlapping classes, forming a hierarchy. Along with well-known classes of deductive systems such as those of implicative, Fregean and equivalential systems, we consider new classes of unital and weakly implicative systems. The latter class is auxiliary, while the former is central in our discussion. Our analysis of unital systems leads to the concept of Lindenbaum–Tarski algebra which, under some natural conditions, is (...)
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  47.  1
    Kants Raum-Zeit-Lehre und die Freiheit in der russischen Lyrik.Alexei N. Krouglov - 2018 - In Violetta L. Waibel, Margit Ruffing & David Wagner (eds.), Natur Und Freiheit. Akten des Xii. Internationalen Kant-Kongresses. De Gruyter. pp. 327-352.
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  48.  90
    The Geometrical Aspects of the Bell Inequalities.Alexei A. Tyapkin & Milan Vindushka - 1991 - Foundations of Physics 21 (2):185-195.
    The Bell inequalities of the metric form are introduced. The quantum-mechanical correlations of the particles with s=1/2 and photons are described using the relative measure of probability on the concave surfaces. The relation of the proposed scheme with the Bayes theorem about conditional information entropy and J. von Neumann's postulates is discussed.
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  49. Islam in Russia.Alexei V. Malashenko - 2009 - Social Research: An International Quarterly 76 (1):321-358.
    According to the 2002 census, the Muslim population of Russia was 14.5 million people. During the past decade, the idea of a Muslim demographic "threat" has spread, discussed most often by politicians with nationalist views, along with journalists and some writers. Islam remains a factor that regulates relations in society. The current revival of Islam is contradictory and diverse in terms of its consequences. Its main result is that we are dealing with a new Islam and new Muslims.
     
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  50. The Ethics of Business: A Concise Introduction.Al Gini & Alexei Marcoux - 2011 - Rowman & Littlefield Publishers.
    In a field dominated by books that focus exclusively on the perspective of business in large corporations or that assume that business has a moral deficiency in need of reform, Al Gini and Alexei Marcoux offers students and business people alike a concise guide to what everyone ought to do when doing business. Where other books are organized topically, Gini and Marcoux look at the moral features of business that recur across topical areas, stressing the considerations that bear on (...)
     
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