Results for 'protein complexes'

1000+ found
Order:
  1.  73
    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 (...)
    Download  
     
    Export citation  
     
    Bookmark   4 citations  
  2. Toll-Like Receptor Signaling in Vertebrates: Testing the Integration of Protein, Complex, and Pathway Data in the Protein Ontology Framework.Cecilia Arighi, Veronica Shamovsky, Anna Maria Masci, Alan Ruttenberg, Barry Smith, Darren Natale, Cathy Wu & Peter D’Eustachio - 2015 - PLoS ONE 10 (4):e0122978.
    The Protein Ontology (PRO) provides terms for and supports annotation of species-specific protein complexes in an ontology framework that relates them both to their components and to species-independent families of complexes. Comprehensive curation of experimentally known forms and annotations thereof is expected to expose discrepancies, differences, and gaps in our knowledge. We have annotated the early events of innate immune signaling mediated by Toll-Like Receptor 3 and 4 complexes in human, mouse, and chicken. The resulting (...)
    Download  
     
    Export citation  
     
    Bookmark   4 citations  
  3. 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 (...)
    Download  
     
    Export citation  
     
    Bookmark   10 citations  
  4. Framework for a Protein Ontology.Darren A. Natale, Cecilia N. Arighi, Winona Barker, Judith Blake, Ti-Cheng Chang, Zhangzhi Hu, Hongfang Liu, Barry Smith & Cathy H. Wu - 2007 - BMC Bioinformatics 8 (Suppl 9):S1.
    Biomedical ontologies are emerging as critical tools in genomic and proteomic research where complex data in disparate resources need to be integrated. A number of ontologies exist that describe the properties that can be attributed to proteins; for example, protein functions are described by Gene Ontology, while human diseases are described by Disease Ontology. There is, however, a gap in the current set of ontologies—one that describes the protein entities themselves and their relationships. We have designed a (...) Ontology (PRO) to facilitate protein annotation and to guide new experiments. The components of PRO extend from the classification of proteins on the basis of evolutionary relationships to the representation of the multiple protein forms of a gene (products generated by genetic variation, alternative splicing, proteolytic cleavage, and other post-translational modification). PRO will allow the specification of relationships between PRO, GO and other OBO Foundry ontologies. Here we describe the initial development of PRO, illustrated using human proteins from the TGF-beta signaling pathway. (shrink)
    Download  
    Translate
     
     
    Export citation  
     
    Bookmark   11 citations  
  5.  61
    Protein Ontology: Enhancing and Scaling Up the Representation of Protein Entities.Darren A. Natale, Cecilia N. Arighi, Judith A. Blake, Jonathan Bona, Chuming Chen, Sheng-Chih Chen, Karen R. Christie, Julie Cowart, Peter D'Eustachio, Alexander D. Diehl, Harold J. Drabkin, William D. Duncan, Hongzhan Huang, Jia Ren, Karen Ross & Alan Ruttenberg - 2017 - Nucleic Acids Research 45 (D1):D339-D346.
    The Protein Ontology (PRO; http://purl.obolibrary.org/obo/pr) formally defines and describes taxon-specific and taxon-neutral protein-related entities in three major areas: proteins related by evolution; proteins produced from a given gene; and protein-containing complexes. PRO thus serves as a tool for referencing protein entities at any level of specificity. To enhance this ability, and to facilitate the comparison of such entities described in different resources, we developed a standardized representation of proteoforms using UniProtKB as a sequence reference and (...)
    Download  
     
    Export citation  
     
    Bookmark   1 citation  
  6.  93
    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 (...)
    Download  
     
    Export citation  
     
    Bookmark  
  7. Protein Ontology: A Controlled Structured Network of Protein Entities.A. Natale Darren, N. Arighi Cecilia, A. Blake Judith, J. Bult Carol, R. Christie Karen, Cowart Julie, D’Eustachio Peter, D. Diehl Alexander, J. Drabkin Harold, Helfer Olivia, Barry Smith & Others - 2013 - Nucleic Acids Research 42 (1):D415-21..
    The Protein Ontology (PRO; http://proconsortium.org) formally defines protein entities and explicitly represents their major forms and interrelations. Protein entities represented in PRO corresponding to single amino acid chains are categorized by level of specificity into family, gene, sequence and modification metaclasses, and there is a separate metaclass for protein complexes. All metaclasses also have organism-specific derivatives. PRO complements established sequence databases such as UniProtKB, and interoperates with other biomedical and biological ontologies such as the Gene (...)
    Download  
     
    Export citation  
     
    Bookmark  
  8. On the Limits of Causal Modeling: Spatially-Structurally Complex Biological Phenomena.Marie I. Kaiser - 2016 - Philosophy of Science 83 (5):921-933.
    This paper examines the adequacy of causal graph theory as a tool for modeling biological phenomena and formalizing biological explanations. I point out that the causal graph approach reaches it limits when it comes to modeling biological phenomena that involve complex spatial and structural relations. Using a case study from molecular biology, DNA-binding and -recognition of proteins, I argue that causal graph models fail to adequately represent and explain causal phenomena in this field. The inadequacy of these models is due (...)
    Download  
     
    Export citation  
     
    Bookmark   3 citations  
  9. 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 (...)
    Download  
     
    Export citation  
     
    Bookmark  
  10. Is the Cell Really a Machine?Daniel J. Nicholson - 2019 - Journal of Theoretical Biology 477:108–126.
    It has become customary to conceptualize the living cell as an intricate piece of machinery, different to a man-made machine only in terms of its superior complexity. This familiar understanding grounds the conviction that a cell's organization can be explained reductionistically, as well as the idea that its molecular pathways can be construed as deterministic circuits. The machine conception of the cell owes a great deal of its success to the methods traditionally used in molecular biology. However, the recent introduction (...)
    Download  
     
    Export citation  
     
    Bookmark   2 citations  
  11. That is Life: Communicating RNA Networks From Viruses and Cells in Continuous Interaction.Guenther Witzany - 2019 - Annals of the New York Academy of Sciences:1-16.
    All the conserved detailed results of evolution stored in DNA must be read, transcribed, and translated via an RNAmediated process. This is required for the development and growth of each individual cell. Thus, all known living organisms fundamentally depend on these RNA-mediated processes. In most cases, they are interconnected with other RNAs and their associated protein complexes and function in a strictly coordinated hierarchy of temporal and spatial steps (i.e., an RNA network). Clearly, all cellular life as we (...)
    Download  
     
    Export citation  
     
    Bookmark  
  12.  76
    The Gene as the Unit of Selection: A Case of Evolutive Delusion.Armando Aranda-Anzaldo - 1997 - Ludus Vitalis 5:91-120.
    The unit of selection is the concept of that ‘something’ to which biologists refer when they speak of an adaptation as being ‘for the good of’ something. Darwin identified the organism as the unit of selection because for him the ‘struggle for existence’ was an issue among individuals. Later on it was suggested that, in order to understand the evolution of social behavior, it is necessary to argue that groups, and not individuals, are the units of selection. The last addition (...)
    Download  
     
    Export citation  
     
    Bookmark   1 citation  
  13. Messy Chemical Kinds.Joyce C. Havstad - 2018 - British Journal for the Philosophy of Science 69 (3):719-743.
    Following Kripke and Putnam, the received view of chemical kinds has been a microstructuralist one. To be a microstructuralist about chemical kinds is to think that membership in said kinds is conferred by microstructural properties. Recently, the received microstructuralist view has been elaborated and defended, but it has also been attacked on the basis of complexities, both chemical and ontological. Here, I look at which complexities really challenge the microstructuralist view; at how the view itself might be made more complicated (...)
    Download  
     
    Export citation  
     
    Bookmark   12 citations  
  14. Two Dogmas of Biology.Leonore Fleming - 2017 - Philosophy, Theory, and Practice in Biology 9 (2).
    The problem with reductionism in biology is not the reduction, but the implicit attitude of determinism that usually accompanies it. Methodological reductionism is supported by deterministic beliefs, but making such a connection is problematic when it is based on an idea of determinism as fixed predictability. Conflating determinism with predictability gives rise to inaccurate models that overlook the dynamic complexity of our world, as well as ignore our epistemic limitations when we try to model it. Furthermore, the assumption of a (...)
    Download  
     
    Export citation  
     
    Bookmark  
  15. The Gene as the Unit of Selection: A Case of Evolutive Delusion.Armando Aranda-Anzaldo - 1997 - Ludus Vitalis 5 (9):91-120.
    The unit of selection is the concept of that ‘something’ to which biologists refer when they speak of an adaptation as being ‘for the good of’ something. Darwin identified the organism as the unit of selection because for him the ‘struggle for existence’ was an issue among individuals. Later on it was suggested that, in order to understand the evolution of social behavior, it is necessary to argue that groups, and not individuals, are the units of selection. The last addition (...)
    Download  
     
    Export citation  
     
    Bookmark  
  16. Genome Informatics: The Role of DNA in Cellular Computations.James A. Shapiro - 2006 - Biological Theory 1 (3):288-301.
    Cells are cognitive entities possessing great computational power. DNA serves as a multivalent information storage medium for these computations at various time scales. Information is stored in sequences, epigenetic modifications, and rapidly changing nucleoprotein complexes. Because DNA must operate through complexes formed with other molecules in the cell, genome functions are inherently interactive and involve two-way communication with various cellular compartments. Both coding sequences and repetitive sequences contribute to the hierarchical systemic organization of the genome. By virtue of (...)
    Download  
     
    Export citation  
     
    Bookmark   7 citations  
  17. Macromolecular Pluralism.Matthew H. Slater - 2009 - Philosophy of Science 76 (5):851-863.
    Different chemical species are often cited as paradigm examples of structurally delimited natural kinds. While classificatory monism may thus seem plausible for simple molecules, it looks less attractive for complex biological macromolecules. I focus on the case of proteins that are most plausibly individuated by their functions. Is there a single, objective count of proteins? I argue that the vagaries of function individuation infect protein classification. We should be pluralists about macromolecular classification.
    Download  
     
    Export citation  
     
    Bookmark   9 citations  
  18. Biometaphysics.Barry Smith - 2009 - In Robin Le Poidevin, Peter Simons, Andrew McGonigal & Ross Cameron (eds.), The Routledge Companion to Metaphysics. Routledge. pp. 537-544.
    While Darwin is commonly supposed to have demonstrated the inapplicability of the Aristotelian ontology of species to biological science, recent developments, especially in the wake of the Human Genome Project, have given rise to a new golden age of classification in which ontological ideas -- as for example in the Gene Ontology, the Cell Ontology, the Protein Ontology, and so forth -- are once again playing an important role. In regard to species, on the other hand, matters are more (...)
    Download  
     
    Export citation  
     
    Bookmark   3 citations  
  19.  94
    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 advanced (...)
    Download  
     
    Export citation  
     
    Bookmark   2 citations  
  20. A New Method for Analysis of Biomolecules Using the BSM-SG Atomic Models.Stoyan Sarg Sargoytchev - 2017 - J. Biom Biostat 8 (2):1000339.
    Biomolecules and particularly proteins and DNA exhibit some mysterious features that cannot find satisfactory explanation by quantum mechanical modes of atoms. One of them, known as a Levinthal’s paradox, is the ability to preserve their complex three-dimensional structure in appropriate environments. Another one is that they possess some unknown energy mechanism. The Basic Structures of Matter Supergravitation Unified Theory (BSM-SG) allows uncovering the real physical structures of the elementary particles and their spatial arrangement in atomic nuclei. The resulting physical models (...)
    Download  
     
    Export citation  
     
    Bookmark  
  21. MAPK Cascades and Major Abiotic Stresses.Khaled Moustafa - 2014 - Plant Cell Reports 33.
    Plants have evolved with complex signaling circuits that operate under multiple conditions and govern numerous cellular functions. Stress signaling in plant cells is a sophisticated network composed of interacting proteins organized into tiered cascades where the function of a molecule is dependent on the interaction and the activation of another. In a linear scheme, the receptors of cell surface sense the stimuli and convey stress signals through specific pathways and downstream phosphorylation events controlled by mitogen-activated protein (MAP) kinases and (...)
    Download  
    Translate
     
     
    Export citation  
     
    Bookmark  
  22.  80
    A Framework for Philosophical Biology.Sepehr Ehsani - manuscript
    Advances in biology, at least over the past two centuries, have mostly relied on theories that were subsequently revised, expanded or eventually refuted using experimental and other means. The field of theoretical biology used to primarily provide a basis, similar to theoretical physics in the physical sciences, to rationally examine the frameworks within which biological experiments were carried out and to shed light on overlooked gaps in understanding. Today, however, theoretical biology has generally become synonymous with computational and mathematical biology. (...)
    Download  
     
    Export citation  
     
    Bookmark   1 citation  
  23. Analytic Philosophy for Biomedical Research: The Imperative of Applying Yesterday's Timeless Messages to Today's Impasses.Sepehr Ehsani - 2020 - In P. Glauner & P. Plugmann (eds.), Innovative Technologies for Market Leadership - Investing in the Future. Springer. pp. 167-200.
    The mantra that "the best way to predict the future is to invent it" (attributed to the computer scientist Alan Kay) exemplifies some of the expectations from the technical and innovative sides of biomedical research at present. However, for technical advancements to make real impacts both on patient health and genuine scientific understanding, quite a number of lingering challenges facing the entire spectrum from protein biology all the way to randomized controlled trials should start to be overcome. The proposal (...)
    Download  
     
    Export citation  
     
    Bookmark  
  24. Energy in the Universe and its Syntropic Forms of Existence According to the BSM - Superg Ravitation Unified Theory.Stoyan Sarg Sargoytchev - 2013 - Syntropy 2013 (2).
    According to the BSM- Supergravitation Unified Theory (BSM-SG), the energy is indispensable feature of matter, while the matter possesses hierarchical levels of organization from a simple to complex forms, with appearance of fields at some levels. Therefore, the energy also follows these levels. At the fundamental level, where the primary energy source exists, the matter is in its primordial form, where two super-dense fundamental particles (FP) exist in a classical pure empty space (not a physical vacuum). They are associated with (...)
    Download  
     
    Export citation  
     
    Bookmark  
  25.  27
    Probable Role of Ablation of Cerebral Ganglia and Injection of its Extracts on O:N Ratio of Lamellidens Corrianis During Summer Season.N. G. Shinde - 2020 - Internat Ional Journal of Applied Research 6 (6):391-394.
    Amongst invertebrates, molluscs show great variability in their nervous system ranging from primitive arrangement in Chitons to the complex mass of fused ganglia forming the ‘brain’ of cephalopods. Most of the effector organs used for pharmacological or physiological experiments. The neurosecretory cells (NSCs) with their combination of neuronal and glandular capabilities are perfectly suited to translate a neuronal input into the hormonal output best suited to long-term process. In this capacity, the NSCs may produce hormones, which act directly upon the (...)
    Download  
     
    Export citation  
     
    Bookmark  
  26. Two Genetic Codes: Repetitive Syntax for Active Non-Coding RNAs; Non-Repetitive Syntax for the DNA Archives.Witzany Guenther - 2017 - Communicative and Integrative Biology 10 (2):e1297352-1 - e1297352-12.
    Current knowledge of the RNA world indicates 2 different genetic codes being present throughout the living world. In contrast to non-coding RNAs that are built of repetitive nucleotide syntax, the sequences that serve as templates for proteins share—as main characteristics—a non-repetitive syntax. Whereas non-coding RNAs build groups that serve as regulatory tools in nearly all genetic processes, the coding sections represent the evolutionarily successful function of the genetic information storage medium. This indicates that the differences in their syntax structure are (...)
    Download  
     
    Export citation  
     
    Bookmark  
  27. The Origin of Cellular Life and Biosemiotics.Attila Grandpierre - 2013 - Biosemiotics (3):1-15.
    Recent successes of systems biology clarified that biological functionality is multilevel. We point out that this fact makes it necessary to revise popular views about macromolecular functions and distinguish between local, physico-chemical and global, biological functions. Our analysis shows that physico-chemical functions are merely tools of biological functionality. This result sheds new light on the origin of cellular life, indicating that in evolutionary history, assignment of biological functions to cellular ingredients plays a crucial role. In this wider picture, even if (...)
    Download  
     
    Export citation  
     
    Bookmark  
  28.  71
    ANN Model for Predicting Protein Localization Sites in Cells.Mohammed Nafez Abu Samra, Bilal Ezz El-Din Abed, Hossam Abdel Nasser Zaqout & Samy S. Abu-Naser - 2020 - International Journal of Academic and Applied Research (IJAAR) 4 (9):43-50.
    To automate examination of massive amounts of sequence data for biological function, it is important to computerize interpretation based on empirical knowledge of sequence-function relationships. For this purpose, we have been constructing an Artificial Neural Network (ANN) by organizing various experimental and computational observations as a collection ANN models. Here we propose an ANN model which utilizes the Dataset for UCI Machine Learning Repository, for predicting localization sites of proteins. We collected data for 336 proteins with known localization sites and (...)
    Download  
     
    Export citation  
     
    Bookmark   2 citations  
  29. Where Do You Get Your Protein? Or: Biochemical Realization.Tuomas E. Tahko - 2020 - British Journal for the Philosophy of Science 71 (3):799-825.
    Biochemical kinds such as proteins pose interesting problems for philosophers of science, as they can be studied from the points of view of both biology and chemistry. The relationship between the biological functions of biochemical kinds and the microstructures that they are related to is the key question. This leads us to a more general discussion about ontological reductionism, microstructuralism, and multiple realization at the biology-chemistry interface. On the face of it, biochemical kinds seem to pose a challenge for ontological (...)
    Download  
     
    Export citation  
     
    Bookmark   2 citations  
  30. TGF-Beta Signaling Proteins and the Protein Ontology.Arighi Cecilia, Liu Hongfang, Natale Darren, Barker Winona, Drabkin Harold, Blake Judith, Barry Smith & Wu Cathy - 2009 - BMC Bioinformatics 10 (Suppl 5):S3.
    The Protein Ontology (PRO) is designed as a formal and principled Open Biomedical Ontologies (OBO) Foundry ontology for proteins. The components of PRO extend from a classification of proteins on the basis of evolutionary relationships at the homeomorphic level to the representation of the multiple protein forms of a gene, including those resulting from alternative splicing, cleavage and/or posttranslational modifications. Focusing specifically on the TGF-beta signaling proteins, we describe the building, curation, usage and dissemination of PRO. PRO provides (...)
    Download  
     
    Export citation  
     
    Bookmark   2 citations  
  31. Complex Demonstratives, Hidden Arguments, and Presupposition.Ethan Nowak - 2019 - Synthese (4):1-36.
    Standard semantic theories predict that non-deictic readings for complex demonstratives should be much more widely available than they in fact are. If such readings are the result of a lexical ambiguity, as Kaplan (1977) and others suggest, we should expect them to be available wherever a definite description can be used. The same prediction follows from ‘hidden argument’ theories like the ones described by King (2001) and Elbourne (2005). Wolter (2006), however, has shown that complex demonstratives admit non-deictic interpretations only (...)
    Download  
     
    Export citation  
     
    Bookmark   3 citations  
  32.  41
    Complexics as a Meta-Transdisciplinary Field.Albert Bastardas-Boada - 2019 - Congrès Mondial Pour la Pensée Complexe. Les Défis D’Un Monde Globalisé. (Paris, 8-9 Décembre. UNESCO).
    ‘Complexics’ denotes the meta-transdisciplinary field specifically concerned with giving us suitable cognitive tools to understand the world’s complexity. Additionally, the use of the adjective ‘complexical’ would avoid the common confusion caused by the adjective ‘complex’, which belongs to everyday usage and already has its own connotations of complication and confusion. Thus, ‘complexical’ thinking and ‘complexical’ perspective would provide clearer terms, be freer of confusion, and refer more precisely to epistemic elements in contrast to the ‘complexity’ typical of many phenomena of (...)
    Download  
     
    Export citation  
     
    Bookmark   1 citation  
  33. The Complex Act of Projecting Oneself Into the Future.Stan Klein - 2013 - WIREs Cognitive Science 4:63-79.
    Research on future-oriented mental time travel (FMTT) is highly active yet somewhat unruly. I believe this is due, in large part, to the complexity of both the tasks used to test FMTT and the concepts involved. Extraordinary care is a necessity when grappling with such complex and perplexing metaphysical constructs as self and time and their co-instantiation in memory. In this review, I first discuss the relation between future mental time travel and types of memory (episodic and semantic). I then (...)
    Download  
    Translate
     
     
    Export citation  
     
    Bookmark   21 citations  
  34.  61
    Really Complex Demonstratives: A Dilemma.Ethan Nowak - forthcoming - Erkenntnis:1-24.
    I have two aims for the present paper, one narrow and one broad. The narrow aim is to show that a class of data originally described by Lynsey Wolter empirically undermine the leading treatments of complex demonstratives that have been described in the literature. The broader aim of the paper is to show that Wolter demonstratives, as I will call the constructions I focus on, are a threat not just to existing treatments, but to any possible theory that retains the (...)
    Download  
    Translate
     
     
    Export citation  
     
    Bookmark   1 citation  
  35.  44
    Complexity Perspectives on Language, Communication and Society.Albert Bastardas-Boada & Àngels Massip-Bonet (eds.) - 2013 - Berlin: Springer.
    The “language-communication-society” triangle defies traditional scientific approaches. Rather, it is a phenomenon that calls for an integration of complex, transdisciplinary perspectives, if we are to make any progress in understanding how it works. The highly diverse agents in play are not merely cognitive and/or cultural, but also emotional and behavioural in their specificity. Indeed, the effort may require building a theoretical and methodological body of knowledge that can effectively convey the characteristic properties of phenomena in human terms. New complexity approaches (...)
    Download  
     
    Export citation  
     
    Bookmark   5 citations  
  36.  27
    Complexity and Language Contact: A Socio-Cognitive Framework.Albert Bastardas-Boada - 2017 - In Salikoko Mufwene, F. Pellegrino & C. Coupé (eds.), Complexity in language. Developmental and evolutionary perspectives. Cambridge, UK: Cambridge University Press. pp. 218-243.
    Throughout most of the 20th century, analytical and reductionist approaches have dominated in biological, social, and humanistic sciences, including linguistics and communication. We generally believed we could account for fundamental phenomena in invoking basic elemental units. Although the amount of knowledge generated was certainly impressive, we have also seen limitations of this approach. Discovering the sound formants of human languages, for example, has allowed us to know vital aspects of the ‘material’ plane of verbal codes, but it tells us little (...)
    Download  
     
    Export citation  
     
    Bookmark   1 citation  
  37. Model for DNA and Protein Interactions and the Function of the Operator.Alfred Gierer - 1966 - Nature 212:1480-1481.
    The short paper introduces the concept of possible branches of double-stranded DNA (later sometimes called palindromes): Certain sequences of nucleotides may be followed, after a short unpaired stretch, by a complementary sequence in reversed order, such that each DNA strand can fold back on itself, and the DNA assumes a cruciform or tree-like structure. This is postulated to interact with regulatory proteins. -/- .
    Download  
     
    Export citation  
     
    Bookmark   1 citation  
  38. Complexity of Judgment Aggregation.Ulle Endriss, Umberto Grandi & Daniele Porello - 2012 - Journal of Artificial Intelligence Research 45:481--514.
    We analyse the computational complexity of three problems in judgment aggregation: (1) computing a collective judgment from a profile of individual judgments (the winner determination problem); (2) deciding whether a given agent can influence the outcome of a judgment aggregation procedure in her favour by reporting insincere judgments (the strategic manipulation problem); and (3) deciding whether a given judgment aggregation scenario is guaranteed to result in a logically consistent outcome, independently from what the judgments supplied by the individuals are (the (...)
    Download  
     
    Export citation  
     
    Bookmark   4 citations  
  39.  54
    A Framework for Protein Classification.Anand Kumar & Barry Smith - 2003 - In Proceedings of the 2003 German Conference on Bioinformatics, Vol. II. pp. 55-57.
    It is widely understood that protein functions can be exhaustively described in terms of no single parameter, whether this be amino acid sequence or the three-dimensional structure of the underlying protein molecule. This means that a number of different attributes must be used to create an ontology of protein functions. Certainly much of the required information is already stored in databases such as Swiss-Prot, Protein Data Bank, SCOP and MIPS. But the latter have been developed for (...)
    Download  
     
    Export citation  
     
    Bookmark   1 citation  
  40. Complexity Biology-Based Information Structures Can Explain Subjectivity, Objective Reduction of Wave Packets, and Non-Computability.Alex Hankey - 2014 - Cosmos and History 10 (1):237-250.
    Background: how mind functions is subject to continuing scientific discussion. A simplistic approach says that, since no convincing way has been found to model subjective experience, mind cannot exist. A second holds that, since mind cannot be described by classical physics, it must be described by quantum physics. Another perspective concerns mind's hypothesized ability to interact with the world of quanta: it should be responsible for reduction of quantum wave packets; physics producing 'Objective Reduction' is postulated to form the basis (...)
    Download  
     
    Export citation  
     
    Bookmark   3 citations  
  41. Complexity Science: A "Gray" Science for the "Stuff in Between".Kurt A. Richardson, Paul Cilliers & Michael Lissack - 2001 - Emergence: Complexity and Organization 3 (2):6-18.
    Download  
     
    Export citation  
     
    Bookmark   14 citations  
  42. Unextended Complexes.Martin Pickup - 2016 - Thought: A Journal of Philosophy 5 (3):257-264.
    Extended simples are fruitfully discussed in metaphysics. They are entities which are located in a complex region of space but do not themselves have parts. In this paper, I will discuss unextended complexes: entities which are not located at a complex region of space but do themselves have parts. In particular, I focus on one type of unextended complex: pointy complexes. Four areas are indicated where pointy complexes might prove philosophically useful. Unextended complexes are therefore philosophically (...)
    Download  
     
    Export citation  
     
    Bookmark   4 citations  
  43. Complexity, Existence and Infinite Analysis.Giovanni Merlo - 2012 - The Leibniz Review 22:9-36.
    According to Leibniz’s infinite-analysis account of contingency, any derivative truth is contingent if and only if it does not admit of a finite proof. Following a tradition that goes back at least as far as Bertrand Russell, several interpreters have been tempted to explain this biconditional in terms of two other principles: first, that a derivative truth is contingent if and only if it contains infinitely complex concepts and, second, that a derivative truth contains infinitely complex concepts if and only (...)
    Download  
     
    Export citation  
     
    Bookmark   5 citations  
  44. Complexity.Marie I. Kaiser - 2013 - In W. Dubitzky, O. Wolkenhauser, K.-H. Cho & H. Yokota (eds.), Encyclopedia of Systems Biology. New York, USA: Springer. pp. 456-460.
    Download  
     
    Export citation  
     
    Bookmark   2 citations  
  45. The Complex Nonlinear Thinking: Edgar Morin's Demand of a Reform of Thinking and the Contribution of Synergetics.Helena Knyazeva - 2004 - World Futures 60 (5 & 6):389 – 405.
    Main principles of the complex nonlinear thinking which are based on the notions of the modern theory of evolution and self-organization of complex systems called also synergetics are under discussion in this article. The principles are transdisciplinary, holistic, and oriented to a human being. The notions of system complexity, nonlinearity of evolution, creative chaos, space-time definiteness of structure-attractors of evolution, resonant influences, nonlinear and soft management are here of great importance. In this connection, a prominent contribution made to system analysis (...)
    Download  
     
    Export citation  
     
    Bookmark   2 citations  
  46. Complex Individuals and Multigrade Relations.Adam Morton - 1975 - Noûs 9 (3):309-318.
    I relate plural quantification, and predicate logic where predicates do not need a fixed number of argument places, to the part-whole relation. For more on these themes see later work by Boolos, Lewis, and Oliver & Smiley.
    Download  
     
    Export citation  
     
    Bookmark   38 citations  
  47. Transparency in Complex Computational Systems.Kathleen A. Creel - 2020 - Philosophy of Science 87 (4):568-589.
    Scientists depend on complex computational systems that are often ineliminably opaque, to the detriment of our ability to give scientific explanations and detect artifacts. Some philosophers have s...
    Download  
     
    Export citation  
     
    Bookmark   6 citations  
  48. 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 (...)
    Download  
     
    Export citation  
     
    Bookmark   12 citations  
  49. Bergson, Complexity and Creative Emergence.David Kreps - 2015 - Palgrave-Macmillan.
    This is a book about evolution from a post-Darwinian perspective. It recounts the core ideas of French philosopher Henri Bergson and his rediscovery and legacy in the poststructuralist critical philosophies of the 1960s, and explores the confluences of these ideas with those of complexity theory in environmental biology. The failings in the development of systems theory, many of which complex systems theory overcomes, are retold; with Bergson, this book proposes, some of the rest may be overcome too. It asserts that (...)
    Download  
     
    Export citation  
     
    Bookmark   1 citation  
  50. Assertion, Complexity, and Sincerity.Robin McKenna - 2015 - Australasian Journal of Philosophy 93 (4):782-798.
    The target of this paper is the ‘simple’ knowledge account of assertion, according to which assertion is constituted by a single epistemic rule of the form ‘One must: assert p only if one knows p’. My aim is to argue that those who are attracted to a knowledge account of assertion should prefer what I call the ‘complex’ knowledge account, according to which assertion is constituted by a system of rules all of which are, taken together, constitutive of assertion. One (...)
    Download  
     
    Export citation  
     
    Bookmark   2 citations  
1 — 50 / 1000