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  1. Wilfried Allaerts (1991). On the Role of Gravity and Positional Information in Embryological Axis Formation and Tissue Compartmentalization. Acta Biotheoretica 39 (1):47-62.
    The idea that gravity affects dorso-ventral polarization in anouran development contrasts with the theories of self-organization through reaction-diffusion processes. As a result of a literature study we discuss the role of gravity in embryological axis formation and speculate on an influence of gravity on tissue compartmentalization. The involvement of compartmentalization in tissue homeostasis is discussed in the light of the recent progress in mammalian cell culture studies.
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  2. Werner Arber (2006). The Evolutionary Strategy of DNA Acquisition as a Possible Reason for a Universal Genetic Code. 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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  3. Lydia Arianova (1996). The Information Processing Organisms. 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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  4. Argyris Arnellos, Luis Emilio Bruni, Charbel Niño El-Hani & John Collier (2012). Anticipatory Functions, Digital-Analog Forms and Biosemiotics: Integrating the Tools to Model Information and Normativity in Autonomous Biological Agents. 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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  5. Gennaro Auletta (2011). Cognitive Biology: Dealing with Information From Bacteria to Minds. 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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  6. Christopher J. Austin (2015). The Dispositional Genome: Primus Inter Pares. 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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  7. Francisco J. Ayala (1989). Thermodynamics, Information, and Evolution: The Problem of Reductionism. [REVIEW] History and Philosophy of the Life Sciences 11 (1):115 - 120.
  8. Marcello Barbieri (forthcoming). From Biosemiotics to Code Biology. Biological Theory.
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  9. Marcello Barbieri (2013). The Paradigms of Biology. 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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  10. Marcello Barbieri (2003). Biology with Information and Meaning. 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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  11. Lluís Barceló-Coblijn (2013). Biology: A Newcomer in Linguistics. [REVIEW] Biological Theory 7 (3):281-284.
  12. J. Bard (2005). Bioinformatics Ain't What It Used to Be By Arthur M. Lesk. Bioessays 27 (9):981.
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  13. J. Bard (2002). An Introduction to BioInformatics By Lesk M. Bioessays 24 (9):867-868.
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  14. Scott Barolo (2012). Shadow Enhancers: Frequently Asked Questions About Distributed Cis‐Regulatory Information and Enhancer Redundancy. Bioessays 34 (2):135-141.
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  15. Carl T. Bergstrom & Martin Rosvall (2011). The Transmission Sense of Information. 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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  16. Carl Bergstrom & Martin Rosvall (2011). Response to Commentaries on “The Transmission Sense of Information”. 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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  17. Jesse M. Bering & Todd K. Shackelford (2004). Supernatural Agents May Have Provided Adaptive Social Information. 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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  18. Philippe M. Binder & Antoine Danchin (2011). Life’s Demons: Information and Order in Biology. 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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  19. Thomas Bittner & Barry Smith (2004). Normalizing Medical Ontologies Using Basic Formal Ontology. In Proceedings of GMDS 2004.
    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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  20. OIivier Bodenreider, Barry Smith & Anita Burgun (2004). The Ontology-Epistemology Divide: A Case Study in Medical Terminology. 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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  21. Olivier Bodenreider, Barry Smith, Anand Kumar & Anita Burgun (2007). Investigating Subsumption in SNOMED CT: An Exploration Into Large Description Logic-Based Biomedical Terminologies”,. Artificial Intelligence in Medicine 39:183-195.
    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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  22. Giovanni Boniolo (2003). Biology Without Information. 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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  23. Joseph Esfandiar Hannon Bozorgmehr (2011). Is Gene Duplication a Viable Explanation for the Origination of Biological Information and Complexity? Complexity 16 (6):17-31.
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  24. Robert N. Brandon & Norbert Hornstein (1986). From Icons to Symbols: Some Speculations on the Origins of Language. [REVIEW] 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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  25. Søren Brier & Cliff Joslyn (2013). What Does It Take to Produce Interpretation? Informational, Peircean and Code-Semiotic Views on Biosemiotics. 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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  26. Luis Emilio Bruni (2002). Does “Quorum Sensing” Imply a New Type of Biological Information? 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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  27. Albert Burger, Duncan Davidson & Richard Baldock (eds.) (2008). Anatomy Ontologies for Bioinformatics: Principles and Practice. Springer.
    16 CARO — The Common Anatomy Reference Ontology Melissa A. Haendel, Fabian Neuhaus, David Osumi-Sutherland, Paula M. Mabee, Jos ́e L.V. Mejino Jr ., Chris J. Mungall, and Barry Smith∗ Summary. The Common Anatomy Reference ...
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  28. Pier Luigi Buttigieg, Norman Morrison, Barry Smith, Christopher J. Mungall & Suzanna E. Lewis (2013). The Environment Ontology: Contextualising Biological and Biomedical Entities. Journal of Biomedical Semantics 4 (43).
    As biological and biomedical research increasingly reference the environmental context of the biological entities under study, the need for formalisation and standardisation of environment descriptors is growing. The Environment Ontology (ENVO; www.environmentontology.org) is a community-led, open project which seeks to provide an ontology for specifying a wide range of environments relevant to multiple life science disciplines and, through an open participation model, to accommodate the terminological requirements of all those needing to annotate data using ontology classes. This paper summarises ENVO’s (...)
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  29. Werner Callebaut & John Collier (2006). Biological Information. Biological Theory 1 (3):221-223.
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  30. Fernando Castro-Chavez (2012). The Rules of Variation Expanded, Implications for the Research on Compatible Genomics. Biosemiotics 5 (1):121-145.
    The main focus of this article is to present the practical aspect of the code rules of variation and the search for a second set of genomic rules, including comparison of sequences to understand how to preserve compatible organisms in danger of extinction and how to generate biodiversity. Three new rules of variation are introduced: 1) homologous recombination, 2) a healthy fertile offspring, and 3) comparison of compatible genomes. The novel search in the natural world for fully compatible genomes capable (...)
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  31. Werner Ceusters (2009). What Do Identifiers in HL7 Identify? An Essay in the Ontology of Identity. In Mitsu Okada (ed.), Proceedings of InterOntology (Tokyo, Japan, February 27-March 1, 2009). Keio University
    Health Level 7 (HL7) is an organization seeking to provide universal standards for the exchange of healthcare information. In a document entitled ‘HL7 Version 3 Standard: Data Types’, the HL7 organization advances descriptions of data types recommended for use as identifiers. We will argue that the descriptions supplied provide insufficient guidance as to what exactly the entities are which these data types uniquely identify. Are they real things, such as persons or pieces of equipment? Or are they representations of such (...)
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  32. Werner Ceusters & Barry Smith (2010). A Unified Framework for Biomedical Terminologies and Ontologies. Studies in Health Technology and Informatics 160:1050-1054.
    The goal of the OBO (Open Biomedical Ontologies) Foundry initiative is to create and maintain an evolving collection of non-overlapping interoperable ontologies that will offer unambiguous representations of the types of entities in biological and biomedical reality. These ontologies are designed to serve non-redundant annotation of data and scientific text. To achieve these ends, the Foundry imposes strict requirements upon the ontologies eligible for inclusion. While these requirements are not met by most existing biomedical terminologies, the latter may nonetheless support (...)
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  33. Werner Ceusters & Barry Smith (2010). Foundations for a Realist Ontology of Mental Disease. Journal of Biomedical Semantics 1 (10):1-23.
    While classifications of mental disorders have existed for over one hundred years, it still remains unspecified what terms such as 'mental disorder', 'disease' and 'illness' might actually denote. While ontologies have been called in aid to address this shortfall since the GALEN project of the early 1990s, most attempts thus far have sought to provide a formal description of the structure of some pre-existing terminology or classification, rather than of the corresponding structures and processes on the side of the patient. (...)
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  34. Werner Ceusters & Barry Smith (2006). Referent Tracking for Treatment Optimisation in Schizophrenic Patients. Journal of Web Semantics 4 (3):229-236.
    The IPAP Schizophrenia Algorithm was originally designed in the form of a flow chart to help physicians optimise the treatment of schizophrenic patients. We examined the current version from the perspective of recent work on terminologies and ontologies thereby drawing on the resources of Basic Formal Ontology, and this with the objective to make the algorithm appropriate for Semantic Web applications. We found that Basic Formal Ontology is a rich enough theory to represent all the entities involved and that applying (...)
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  35. Werner Ceusters & Barry Smith (2006). A Realism-Based Approach to the Evolution of Biomedical Ontologies. In Proceedings of the Annual AMIA Symposium. AMIA
    We present a novel methodology for calculating the improvements obtained in successive versions of biomedical ontologies. The theory takes into account changes both in reality itself and in our understanding of this reality. The successful application of the theory rests on the willingness of ontology authors to document changes they make by following a number of simple rules. The theory provides a pathway by which ontology authoring can become a science rather than an art, following principles analogous to those that (...)
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  36. Werner Ceusters & Barry Smith (2005). Tracking Referents in Electronic Health Records. Studies in Health Technology and Informatics 116:71–76.
    Electronic Health Records (EHRs) are organized around two kinds of statements: those reporting observations made, and those reporting acts performed. In neither case does the record involve any direct reference to what such statements are actually about. They record not: what is happening on the side of the patient, but rather: what is said about what is happening. While the need for a unique patient identifier is generally recognized, we argue that we should now move to an EHR regime in (...)
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  37. Werner Ceusters, Barry Smith & James Matthew Fielding (2004). LinkSuite™: Software Tools for Formally Robust Ontology-Based Data and Information Integration. In Proceedings of DILS 2004 (Data Integration in the Life Sciences), (Lecture Notes in Bioinformatics, 2994). Springer
    The integration of information resources in the life sciences is one of the most challenging problems facing bioinformatics today. We describe how Language and Computing nv, originally a developer of ontology-based natural language understanding systems for the healthcare domain, is developing a framework for the integration of structured data with unstructured information contained in natural language texts. L&C’s LinkSuite™ combines the flexibility of a modular software architecture with an ontology based on rigorous philosophical and logical principles that is designed to (...)
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  38. Werner Ceusters, Barry Smith & Louis Goldberg (2005). A Terminological and Ontological Analysis of the NCI Thesaurus. Methods of Information in Medicine 44:498-507.
    We performed a qualitative analysis of the Thesaurus in order to assess its conformity with principles of good practice in terminology and ontology design. We used both the on-line browsable version of the Thesaurus and its OWL-representation (version 04.08b, released on August 2, 2004), measuring each in light of the requirements put forward in relevant ISO terminology standards and in light of ontological principles advanced in the recent literature. Version 04.08b of the NCI Thesaurus suffers from the same broad range (...)
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  39. Laurel Cooper, Ramona Walls, Justin Elser, Maria A. Gandolfo, Dennis W. Stevenson & Barry Smith (2013). The Plant Ontology as a Tool for Comparative Plant Anatomy and Genomic Analyses. Plant and Cell Physiology 54:1-23..
    The Plant Ontology (PO; http://www.plantontology.org/) is a publicly-available, collaborative effort to develop and maintain a controlled, structured vocabulary (“ontology”) of terms to describe plant anatomy, morphology and the stages of plant development. The goals of the PO are to link (annotate) gene expression and phenotype data to plant structures and stages of plant development, using the data model adopted by the Gene Ontology. From its original design covering only rice, maize and Arabidopsis, the scope of the PO has been expanded (...)
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  40. Antoine Danchin (2009). Information of the Chassis and Information of the Program in Synthetic Cells. Systems and Synthetic Biology 3:125-134.
    Synthetic biology aims at reconstructing life to put to the test the limits of our understanding. It is based on premises similar to those which permitted invention of computers, where a machine, which reproduces over time, runs a program, which replicates. The underlying heuristics explored here is that an authentic category of reality, information, must be coupled with the standard categories, matter, energy, space and time to account for what life is. The use of this still elusive category permits us (...)
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  41. Soraya De Chadarevian (1996). Sequences, Conformation, Information: Biochemists and Molecular Biologists in the 1950s. [REVIEW] Journal of the History of Biology 29 (3):361-386.
  42. Andrew R. Deans, Barry Smith & Others (2015). Finding Our Way Through Phenotypes. PLoS Biology 13 (1).
    Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that (...)
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  43. William Dembski, Evolution of Biological Information.
    National Cancer Institute, Frederick Cancer Research and Development Center, Laboratory of Experimental and Computational Biology, PO Box B, Frederick, MD 21702-1201, USA..
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  44. William Dembski, If Only Darwinists Scrutinized Their Own Work as Closely: A Response to "Erik".
    An Internet persona known as "Erik" reviewed those aspects of my book No Free Lunch dealing with the Law of Conservation of Information and specificational resources. Erik's review is titled "On Dembski's Law of Conservation of Information" and is available at http://www.talkreason.org/articles/dembski_LCI.pdf. I respond to the review here.
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  45. Stephen M. Downes, Biological Information.
    This paper discussses various concepts of biological information with particular attention being paid to genetic information.
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  46. Alfred Driessen (forthcoming). Life and Quantum Biology, an Interdisciplinary Approach. Acta Philosophica.
    The rapidly increasing interest in the quantum properties of living matter stimulates a discussion of the fundamental properties of life as well as quantum mechanics. In this discussion often concepts are used that originate in philosophy and ask for a philosophical analysis. In the present work the classic philosophical tradition based on Aristotle and Aquinas is employed which surprisingly is able to shed light on important aspects. Especially one could mention the high degree of unity in living objects and the (...)
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  47. Manfred Eigen (1973). The Origin of Biological Information. In Jagdish Mehra (ed.), The Physicist's Conception of Nature. Boston,Reidel 594--632.
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  48. Arantza Etxeberria Agiriano & Tomás Garcia Azkonobieta (2004). Sobre la noción de información genética: seméntica y excepcionalidad (On the notion of genetic information: semantics and exceptionality). 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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  49. Keith Farnsworth, John Nelson & Carlos Gershenson (2013). Living is Information Processing: From Molecules to Global Systems. Acta Biotheoretica 61 (2):203-222.
    We extend the concept that life is an informational phenomenon, at every level of organisation, from molecules to the global ecological system. According to this thesis: living is information processing, in which memory is maintained by both molecular states and ecological states as well as the more obvious nucleic acid coding; this information processing has one overall function—to perpetuate itself; and the processing method is filtration of, and synthesis of, information at lower levels to appear at higher levels in complex (...)
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  50. James M. Fielding, Jonathan Simon, Werner Ceusters & Barry Smith (2004). Ontological Theory for Ontological Engineering: Biomedical Systems Information Integration. In Proceedings of the Ninth International Conference on the Principles of Knowledge Representation and Reasoning. AMIA
    Software application ontologies have the potential to become the keystone in state-of-the-art information management techniques. It is expected that these ontologies will support the sort of reasoning power required to navigate large and complex terminologies correctly and efficiently. Yet, there is one problem in particular that continues to stand in our way. As these terminological structures increase in size and complexity, and the drive to integrate them inevitably swells, it is clear that the level of consistency required for such navigation (...)
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