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  1. Sobre la Noción de Información Genética: Seméntica Y Excepcionalidad (on the Notion of Genetic Information: Semantics and Exceptionality).Agiriano Arantza Etxeberria & Azkonobieta Tomás Garcia - 2004 - Theoria 19 (2):209-230.
    EI objetivo de este artículo es analizar ciertas críticas a la aplicación de la nocion de informacíon en biología, teniendo en cuenta tanto la historia del concepto como las diferentes posiciones actuales. Creemos que la motivacíon principal de las críticas es negar que los genes sean un factor causal excepcional en el desarrollo, y favorecer la imagen de la vida como un sistema organizado que requiere diferentes recursos. Aunque compartimos el rechazo deI reduccionismo genetico, argumentamos que éste no es atribuible (...)
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  2. Bioinformatics Advances in Saliva Diagnostics.Ji-Ye Ai, Barry Smith & David T. W. Wong - 2012 - International Journal of Oral Science 4 (2):85--87.
    There is a need recognized by the National Institute of Dental & Craniofacial Research and the National Cancer Institute to advance basic, translational and clinical saliva research. The goal of the Salivaomics Knowledge Base (SKB) is to create a data management system and web resource constructed to support human salivaomics research. To maximize the utility of the SKB for retrieval, integration and analysis of data, we have developed the Saliva Ontology and SDxMart. This article reviews the informatics advances in saliva (...)
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  3. Towards a Body Fluids Ontology: A Unified Application Ontology for Basic and Translational Science.Jiye Ai, Mauricio Barcellos Almeida, André Queiroz De Andrade, Alan Ruttenberg, David Tai Wai Wong & Barry Smith - 2011 - Second International Conference on Biomedical Ontology , Buffalo, Ny 833:227-229.
    We describe the rationale for an application ontology covering the domain of human body fluids that is designed to facilitate representation, reuse, sharing and integration of diagnostic, physiological, and biochemical data, We briefly review the Blood Ontology (BLO), Saliva Ontology (SALO) and Kidney and Urinary Pathway Ontology (KUPO) initiatives. We discuss the methods employed in each, and address the project of using them as starting point for a unified body fluids ontology resource. We conclude with a description of how the (...)
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  4. Saliva Ontology: An Ontology-Based Framework for a Salivaomics Knowledge Base.Jiye Ai, Barry Smith & David Wong - 2010 - BMC Bioinformatics 11 (1):302.
    The Salivaomics Knowledge Base (SKB) is designed to serve as a computational infrastructure that can permit global exploration and utilization of data and information relevant to salivaomics. SKB is created by aligning (1) the saliva biomarker discovery and validation resources at UCLA with (2) the ontology resources developed by the OBO (Open Biomedical Ontologies) Foundry, including a new Saliva Ontology (SALO). We define the Saliva Ontology (SALO; http://www.skb.ucla.edu/SALO/) as a consensus-based controlled vocabulary of terms and relations dedicated to the salivaomics (...)
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  5. Ontology Based Annotation of Contextualized Vital Signs.Goldfain Albert, Xu Min, Bona Jonathan & Barry Smith - 2013 - In Proceedings of the Fourth International Conference on Biomedical Ontology (ICBO). Montreal: pp. 28-33.
    Representing the kinetic state of a patient (posture, motion, and activity) during vital sign measurement is an important part of continuous monitoring applications, especially remote monitoring applications. In contextualized vital sign representation, the measurement result is presented in conjunction with salient measurement context metadata. We present an automated annotation system for vital sign measurements that uses ontologies from the Open Biomedical Ontology Foundry (OBO Foundry) to represent the patient’s kinetic state at the time of measurement. The annotation system is applied (...)
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  6. Essential Readings in Biosemiotics: Anthology and Commentary – By Donald Favareau.Victoria N. Alexander - 2011 - Journal of Applied Philosophy 28 (4):412-414.
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  7. Communication and Cognition: Is Information The Connection?C. Allen & M. Hauser - 1992 - Psa 1992:81-91.
    Donald Griffin has suggested that cognitive ethologists can use communication between non-human animals as a "window" into animal minds. Underlying this metaphor seems to be a conception of cognition as information processing and communication as information transfer from signaller to receiver. We examine various analyses of information and discuss how these analyses affect an ongoing debate among ethologists about whether the communicative signals of some animals should be interpreted as referential signals or whether emotional accounts of such signals are adequate. (...)
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  8. The Challenge of Bioinformatics.James G. Anderson & Kenneth W. Goodman - forthcoming - Ethics and Information Technology: A Case-Based Approach to a Health Care System in Transition. New York: Springer.
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  9. Concerning Gaia--Semiosic Production of/in/by/for Our Planet,".Myrdene Anderson - forthcoming - Biosemiotics. The Semiotic Web.
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  10. The Evolutionary Strategy of DNA Acquisition as a Possible Reason for a Universal Genetic Code.Werner Arber - 2006 - History and Philosophy of the Life Sciences 28 (4):525 - 532.
    The evolutionary strategy to generate genetic variants by DNA acquisition involving horizontal gene transfer seems to be widely used by many, if not all, living organisms. A common language between donor and recipient organisms, as provided by the quasi universality of the genetic code, can favor the effectiveness of the DNA acquisition strategy. These considerations are here discussed in the context of our knowledge on the natural strategies of molecular evolution and on the commonly used genetic code.
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  11. The Information Processing Organisms.Lydia Arianova - 1996 - Acta Biotheoretica 44 (2):143-151.
    In spite of the tremendous progress in recent decades of biological science, many aspects of the behaviour of organisms in general and of humans in particular remain still somewhat obscure. A new approach towards the study of the behaviour of man was presented by Heisenberg when he emphasized that a Cartesian view of nature as an object out there is an illusion in so far as the observer is always part of the formula, the man viewing nature must be figured (...)
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  12. 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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  13. Anticipatory Functions, Digital-Analog Forms and Biosemiotics: Integrating the Tools to Model Information and Normativity in Autonomous Biological Agents.Argyris Arnellos, Luis Emilio Bruni, Charbel Niño El-Hani & John Collier - 2012 - Biosemiotics 5 (3):331-367.
    We argue that living systems process information such that functionality emerges in them on a continuous basis. We then provide a framework that can explain and model the normativity of biological functionality. In addition we offer an explanation of the anticipatory nature of functionality within our overall approach. We adopt a Peircean approach to Biosemiotics, and a dynamical approach to Digital-Analog relations and to the interplay between different levels of functionality in autonomous systems, taking an integrative approach. We then apply (...)
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  14. Building Ontologies with Basic Formal Ontology.Robert Arp, Andrew D. Spear & Barry Smith - 2015 - Cambridge, MA: MIT Press.
    In the era of “big data,” science is increasingly information driven, and the potential for computers to store, manage, and integrate massive amounts of data has given rise to such new disciplinary fields as biomedical informatics. Applied ontology offers a strategy for the organization of scientific information in computer-tractable form, drawing on concepts not only from computer and information science but also from linguistics, logic, and philosophy. This book provides an introduction to the field of applied ontology that is of (...)
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  15. Signaling Without Cooperation.Marc Artiga - 2014 - Biology and Philosophy 29 (3):357-378.
    Ethological theories usually attribute semantic content to animal signals. To account for this fact, many biologists and philosophers appeal to some version of teleosemantics. However, this picture has recently came under attack: while mainstream teleosemantics assumes that representational systems must cooperate, some biologists and philosophers argue that in certain cases signaling can evolve within systems lacking common interest. In this paper I defend the standard view from this objection.
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  16. Cognitive Biology: Dealing with Information From Bacteria to Minds.Gennaro Auletta - 2011 - Oxford University Press, Usa.
    Machine generated contents note: -- 1. Quantum Mechanics as a General Framework -- 2. Classical and Quantum Information and Entropy -- 3. The Brain: An Outlook -- 4. Vision -- 5. Dealing with Target's Motion and Our Own Movement -- 6. Complexity: A Necessary Condition -- 7. General Features of Life -- 8. The Organism as a Semiotic and Cybernetic System -- 9. Phylogeny -- 10. Ontogeny -- 11. Epigeny -- 12. Representational Semiotics -- 13. The Brain as an Information-Control (...)
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  17. The Dispositional Genome: Primus Inter Pares.Christopher J. Austin - 2015 - Biology and Philosophy 30 (2):227-246.
    According to the proponents of Developmental Systems Theory and the Causal Parity Thesis, the privileging of the genome as “first among equals” with respect to the development of phenotypic traits is more a reflection of our own heuristic prejudice than of ontology - the underlying causal structures responsible for that specified development no more single out the genome as primary than they do other broadly “environmental” factors. Parting with the methodology of the popular responses to the Thesis, this paper offers (...)
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  18. Thermodynamics, Information, and Evolution: The Problem of Reductionism. [REVIEW]Francisco J. Ayala - 1989 - History and Philosophy of the Life Sciences 11 (1):115 - 120.
  19. The Ontology for Biomedical Investigations.Anita Bandrowski, Ryan Brinkman, Mathias Brochhausen, Matthew H. Brush, Bill Bug, Marcus C. Chibucos, Kevin Clancy, Mélanie Courtot, Dirk Derom, Michel Dumontier, Liju Fan, Jennifer Fostel, Gilberto Fragoso, Frank Gibson, Alejandra Gonzalez-Beltran, Melissa A. Haendel, Yongqun He, Mervi Heiskanen, Tina Hernandez-Boussard, Mark Jensen, Yu Lin, Allyson L. Lister, Phillip Lord, James Malone, Elisabetta Manduchi, Monnie McGee, Norman Morrison, James A. Overton, Helen Parkinson, Bjoern Peters, Philippe Rocca-Serra, Alan Ruttenberg, Susanna-Assunta Sansone, Richard H. Scheuermann, Daniel Schober, Barry Smith, Larisa N. Soldatova, Christian J. Stoeckert, Chris F. Taylor, Carlo Torniai, Jessica A. Turner, Randi Vita, Patricia L. Whetzel & Jie Zheng - 2016 - PLoS ONE 11 (4):e0154556.
    The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to (...)
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  20. From Biosemiotics to Code Biology.Marcello Barbieri - 2014 - Biological Theory 9 (2):239-249.
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  21. The Paradigms of Biology.Marcello Barbieri - 2013 - Biosemiotics 6 (1):33-59.
    Today there are two major theoretical frameworks in biology. One is the ‘chemical paradigm’, the idea that life is an extremely complex form of chemistry. The other is the ‘information paradigm’, the view that life is not just ‘chemistry’ but ‘chemistry-plus-information’. This implies the existence of a fundamental difference between information and chemistry, a conclusion that is strongly supported by the fact that information and information-based-processes like heredity and natural selection simply do not exist in the world of chemistry. Against (...)
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  22. A Short History of Biosemiotics.Marcello Barbieri - 2009 - Biosemiotics 2 (2):221-245.
    Biosemiotics is the synthesis of biology and semiotics, and its main purpose is to show that semiosis is a fundamental component of life, i.e., that signs and meaning exist in all living systems. This idea started circulating in the 1960s and was proposed independently from enquires taking place at both ends of the Scala Naturae. At the molecular end it was expressed by Howard Pattee’s analysis of the genetic code, whereas at the human end it took the form of Thomas (...)
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  23. For a Scientific Biosemiotics.Marcello Barbieri - 2009 - Biosemiotics 2 (2):127-129.
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  24. What is Biosemiotics?Marcello Barbieri - 2008 - Biosemiotics 1 (1):1-3.
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  25. Biology with Information and Meaning.Marcello Barbieri - 2003 - History and Philosophy of the Life Sciences 25 (2):243 - 254.
    It is shown that information and meaning can be defined by operative procedures, and that we need to recognize them as new types of natural entities. They are not quantities (neither fundamental nor derived) because they cannot be measured, and they are not qualities because they are not subjective features. Here it is proposed to call them nominable entities, i.e., entities which can be specified only by naming their components in their natural order.
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  26. The Blood Ontology: An Ontology in the Domain of Hematology.Almeida Mauricio Barcellos, Proietti Anna Barbara de Freitas Carneiro, Ai Jiye & Barry Smith - 2011 - In Proceedings of the Second International Conference on Biomedical Ontology, Buffalo, NY, July 28-30, 2011 (CEUR 883). pp. (CEUR Workshop Proceedings, 833).
    Despite the importance of human blood to clinical practice and research, hematology and blood transfusion data remain scattered throughout a range of disparate sources. This lack of systematization concerning the use and definition of terms poses problems for physicians and biomedical professionals. We are introducing here the Blood Ontology, an ongoing initiative designed to serve as a controlled vocabulary for use in organizing information about blood. The paper describes the scope of the Blood Ontology, its stage of development and some (...)
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  27. Biology: A Newcomer in Linguistics. [REVIEW]Lluís Barceló-Coblijn - 2013 - Biological Theory 7 (3):281-284.
  28. Bioinformatics Ain't What It Used to Be By Arthur M. Lesk.J. Bard - 2005 - Bioessays 27 (9):981.
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  29. An Introduction to BioInformatics By Lesk M.J. Bard - 2002 - Bioessays 24 (9):867-868.
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  30. Shadow Enhancers: Frequently Asked Questions About Distributed Cis‐Regulatory Information and Enhancer Redundancy.Scott Barolo - 2012 - Bioessays 34 (2):135-141.
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  31. Biology Needs Information Theory.Gérard Battail - 2013 - Biosemiotics 6 (1):77-103.
    Communication is an important feature of the living world that mainstream biology fails to adequately deal with. Applying two main disciplines can be contemplated to fill in this gap: semiotics and information theory. Semiotics is a philosophical discipline mainly concerned with meaning; applying it to life already originated in biosemiotics. Information theory is a mathematical discipline coming from engineering which has literal communication as purpose. Biosemiotics and information theory are thus concerned with distinct and complementary possible meanings of the word (...)
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  32. The Transition to Civilization and Symbolically Stored Genomes.J. Beach - 2003 - Studies in History and Philosophy of Science Part C 34 (1):109-141.
    The study of culture and cultural selection from a biological perspective has been hampered by the lack of any firm theoretical basis for how the information for cultural traits is stored and transmitted. In addition, the study of any living system with a decentralized or multi-level information structure has been somewhat restricted due to the focus in genetics on the gene and the particular hereditary structure of multicellular organisms. Here a different perspective is used, one which regards living systems as (...)
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  33. The Transmission Sense of Information.Carl T. Bergstrom & Martin Rosvall - 2011 - Biology and Philosophy 26 (2):159-176.
    Biologists rely heavily on the language of information, coding, and transmission that is commonplace in the field of information theory developed by Claude Shannon, but there is open debate about whether such language is anything more than facile metaphor. Philosophers of biology have argued that when biologists talk about information in genes and in evolution, they are not talking about the sort of information that Shannon’s theory addresses. First, philosophers have suggested that Shannon’s theory is only useful for developing a (...)
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  34. Response to Commentaries on “The Transmission Sense of Information”.Carl Bergstrom & Martin Rosvall - 2011 - Biology and Philosophy 26 (2):195-200.
    Response to commentaries on “The Transmission Sense of Information” Content Type Journal Article Pages 195-200 DOI 10.1007/s10539-011-9257-3 Authors Carl T. Bergstrom, Department of Biology, University of Washington, Seattle, WA 98195-1800, USA Martin Rosvall, Integrated Science Lab, Department of Physics, Umeå University, 901 87 Umeå, Sweden Journal Biology and Philosophy Online ISSN 1572-8404 Print ISSN 0169-3867 Journal Volume Volume 26 Journal Issue Volume 26, Number 2.
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  35. Supernatural Agents May Have Provided Adaptive Social Information.Jesse M. Bering & Todd K. Shackelford - 2004 - Behavioral and Brain Sciences 27 (6):732-733.
    Atran & Norenzayan's (A&N's) target article effectively combines the insights of evolutionary biology and interdisciplinary cognitive science, neither of which alone yields sufficient explanatory power to help us fully understand the complexities of supernatural belief. Although the authors' ideas echo those of other researchers, they are perhaps the most squarely grounded in neo-Darwinian terms to date. Nevertheless, A&N overlook the possibility that the tendency to infer supernatural agents' communicative intent behind natural events served an ancestrally adaptive function.
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  36. Life’s Demons: Information and Order in Biology.Philippe M. Binder & Antoine Danchin - 2011 - EMBO Reports 12 (6):495-499.
    Two decades ago, Rolf Landauer (1991) argued that “information is physical” and ought to have a role in the scientific analysis of reality comparable to that of matter, energy, space and time. This would also help to bridge the gap between biology and mathematics and physics. Although it can be argued that we are living in the ‘golden age’ of biology, both because of the great challenges posed by medicine and the environment and the significant advances that have been made—especially (...)
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  37. Normalizing Medical Ontologies Using Basic Formal Ontology.Thomas Bittner & Barry Smith - 2004 - In K. Versorgung & V. Forschung (eds.), Ubiquitäre Information (Proceedings of GMDS 2004). Videel OHG. pp. 199-201.
    Description Logics are nowadays widely accepted as formalisms which provide reasoning facilities which allow us to discover inconsistencies in ontologies in an automatic fashion. Where ontologies are developed in modular fashion, they allow changes in one module to propogated through the system of ontologies automatically in a way which helps to maintain consistency and stability. For this feature to be utilized effectively, however, requires that domain ontologies be represented in a normalized form.
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  38. The Ontology-Epistemology Divide: A Case Study in Medical Terminology.OIivier Bodenreider, Barry Smith & Anita Burgun - 2004 - In Achille Varzi & Laure Vieu (eds.), Formal Ontology in Information Systems. Proceedings of the Third International Conference (FOIS 2004). IOS Press.
    Medical terminology collects and organizes the many different kinds of terms employed in the biomedical domain both by practitioners and also in the course of biomedical research. In addition to serving as labels for biomedical classes, these names reflect the organizational principles of biomedical vocabularies and ontologies. Some names represent invariant features (classes, universals) of biomedical reality (i.e., they are a matter for ontology). Other names, however, convey also how this reality is perceived, measured, and understood by health professionals (i.e., (...)
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  39. Special Issue: Biomedical Ontology in Action.Olivier Bodenreider - 2009 - Applied Ontology 4 (1):1-4.
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  40. Investigating Subsumption in SNOMED CT: An Exploration Into Large Description Logic-Based Biomedical Terminologies.Olivier Bodenreider, Barry Smith, Anand Kumar & Anita Burgun - 2007 - Artificial Intelligence in Medicine 39 (3):183-195.
    Formalisms based on one or other flavor of Description Logic (DL) are sometimes put forward as helping to ensure that terminologies and controlled vocabularies comply with sound ontological principles. The objective of this paper is to study the degree to which one DL-based biomedical terminology (SNOMED CT) does indeed comply with such principles. We defined seven ontological principles (for example: each class must have at least one parent, each class must differ from its parent) and examined the properties of SNOMED (...)
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  41. Investigating Subsumption in DL-Based Terminologies: A Case Study in SNOMED CT.Olivier Bodenreider, Barry Smith, Anand Kumar & Anita Burgun - 2004 - In Proceedings of the First International Workshop on Formal Biomedical Knowledge Representation (KR-MED 2004). pp. 12-20.
    Formalisms such as description logics (DL) are sometimes expected to help terminologies ensure compliance with sound ontological principles. The objective of this paper is to study the degree to which one DL-based biomedical terminology (SNOMED CT) complies with such principles. We defined seven ontological principles (for example: each class must have at least one parent, each class must differ from its parent) and examined the properties of SNOMED CT classes with respect to these principles. Our major results are: 31% of (...)
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  42. Biology Without Information.Giovanni Boniolo - 2003 - History and Philosophy of the Life Sciences 25 (2):255-273.
    Over these last few years once again the relationship between biology and information has been debated with great liveliness. The crucial points concern the meaning of the term ‘information’ and whether the so-called “information talk” is really necessary inside biology.I will proceed by first commenting on some points of the debate (§ 2), then showing that a biophysical account of the process from the nucleotide sequences to the correlated amino acid sequences is possible (§ 3). In this way, I will (...)
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  43. Is Gene Duplication a Viable Explanation for the Origination of Biological Information and Complexity?Joseph Esfandiar Hannon Bozorgmehr - 2011 - Complexity 16 (6):17-31.
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  44. William F. Harms, Information and Meaning in Evolutionary Processes.M. Bradie - 2006 - Biological Theory 1 (4):431.
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  45. From Icons to Symbols: Some Speculations on the Origins of Language. [REVIEW]Robert N. Brandon & Norbert Hornstein - 1986 - Biology and Philosophy 1 (2):169-189.
    This paper is divided into three sections. In the first section we offer a retooling of some traditional concepts, namely icons and symbols, which allows us to describe an evolutionary continuum of communication systems. The second section consists of an argument from theoretical biology. In it we explore the advantages and disadvantages of phenotypic plasticity. We argue that a range of the conditions that selectively favor phenotypic plasticity also favor a nongenetic transmission system that would allow for the inheritance of (...)
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  46. Cybersemiotics and the Question of Semiotic and Informational Thresholds.S. ren Brier - 2003 - World Futures 59 (5):361 – 380.
    The present article discusses various suggestions for a philosophical framework for a transdisciplinary information science or a semiotic doctrine. These are: the mechanical materialistic, the pan-informational, the Luhmanian second order cybernetic approach, Peircian biosemiotics and finally the pan-semiotic approach. The limitations of each are analyzed. The conclusion is that we will not have to choose between either a cybernetic-informational or a semiotic approach. A combination of a Peircian-based biosemiotics with autopoiesis theory, second order cybernetics and information science is suggested in (...)
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  47. What Does It Take to Produce Interpretation? Informational, Peircean and Code-Semiotic Views on Biosemiotics.Søren Brier & Cliff Joslyn - 2013 - Biosemiotics 6 (1):143-159.
    This paper presents a critical analysis of code-semiotics, which we see as the latest attempt to create paradigmatic foundation for solving the question of the emergence of life and consciousness. We view code semiotics as a an attempt to revise the empirical scientific Darwinian paradigm, and to go beyond the complex systems, emergence, self-organization, and informational paradigms, and also the selfish gene theory of Dawkins and the Peircean pragmaticist semiotic theory built on the simultaneous types of evolution. As such it (...)
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  48. Biomedizinische Ontologien für die Praxis.M. Brochhausen & Barry Smith - 2009 - European Journal for Biomedical Informatics 1.
    Hintergrund: Biomedizinische Ontologien existieren unter anderem zur Integration von klinischen und experimentellen Daten. Um dies zu erreichen ist es erforderlich, dass die fraglichen Ontologien von einer großen Zahl von Benutzern zur Annotation von Daten verwendet werden. Wie können Ontologien das erforderliche Maß an Benutzerfreundlichkeit, Zuverlässigkeit, Kosteneffektivität und Domänenabdeckung erreichen, um weitreichende Akzeptanz herbeizuführen? -/- Material und Methoden: Wir konzentrieren uns auf zwei unterschiedliche Strategien, die zurzeit hierbei verfolgt werden. Eine davon wird von SNOMED CT im Bereich der Medizin vertreten, die (...)
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  49. Biomolecular Information Analysis in Neurotransmitter Systems.Sidney C. Brooks - 1984 - Acta Biotheoretica 33 (1):3-33.
  50. Does “Quorum Sensing” Imply a New Type of Biological Information?Luis Emilio Bruni - 2002 - Sign Systems Studies 30 (1):221-242.
    When dealing with biological communication and information, unifying concepts are necessary in order to couple the different “codes” that are being inductively “cracked” and defined at different emergent and “deemergent” levels of the biological hierarchy. In this paper I compare the type of biological information implied by genetic information with that implied in the concept of “quorum sensing” (which refers to a prokaryotic cell-to-cell communication system) in order to explore if such integration is being achieved. I use the Lux operon (...)
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