Results for 'proteins'

139 found
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  1. The Protein Ontology: A structured representation of protein forms and complexes.Darren Natale, Cecilia N. Arighi, Winona C. Barker, Judith A. Blake, Carol J. Bult, Michael Caudy, Harold J. Drabkin, Peter D’Eustachio, Alexei V. Evsikov, Hongzhan Huang, Jules Nchoutmboube, Natalia V. Roberts, Barry Smith, Jian Zhang & Cathy H. Wu - 2011 - Nucleic Acids Research 39 (1):D539-D545.
    The Protein Ontology (PRO) provides a formal, logically-based classification of specific protein classes including structured representations of protein isoforms, variants and modified forms. Initially focused on proteins found in human, mouse and Escherichia coli, PRO now includes representations of protein complexes. The PRO Consortium works in concert with the developers of other biomedical ontologies and protein knowledge bases to provide the ability to formally organize and integrate representations of precise protein forms so as to enhance accessibility to results of (...)
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  2. 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 Ontology (GO). PRO relates to (...)
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  3. Protein-centric connection of biomedical knowledge: Protein Ontology research and annotation tools.Cecilia N. Arighi, Darren A. Natale, Judith A. Blake, Carol J. Bult, Michael Caudy, Alexander D. Diehl, Harold J. Drabkin, Peter D'Eustachio, Alexei Evsikov, Hongzhan Huang, Barry Smith & Others - 2011 - In Landgrebe Jobst & Smith Barry (eds.), Proceedings of the 2nd International Conference on Biomedical Ontology. CEUR, vol. 833. pp. 285-287.
    The Protein Ontology (PRO) web resource provides an integrative framework for protein-centric exploration and enables specific and precise annotation of proteins and protein complexes based on PRO. Functionalities include: browsing, searching and retrieving, terms, displaying selected terms in OBO or OWL format, and supporting URIs. In addition, the PRO website offers multiple ways for the user to request, submit, or modify terms and/or annotation. We will demonstrate the use of these tools for protein research and annotation.
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  4. The representation of protein complexes in the Protein Ontology.Carol Bult, Harold Drabkin, Alexei Evsikov, Darren Natale, Cecilia Arighi, Natalia Roberts, Alan Ruttenberg, Peter D’Eustachio, Barry Smith, Judith Blake & Cathy Wu - 2011 - BMC Bioinformatics 12 (371):1-11.
    Representing species-specific proteins and protein complexes in ontologies that are both human and machine-readable facilitates the retrieval, analysis, and interpretation of genome-scale data sets. Although existing protin-centric informatics resources provide the biomedical research community with well-curated compendia of protein sequence and structure, these resources lack formal ontological representations of the relationships among the proteins themselves. The Protein Ontology (PRO) Consortium is filling this informatics resource gap by developing ontological representations and relationships among proteins and their variants and (...)
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  5. 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 PSI-MOD as a (...)
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  6. 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 PRotein Ontology (...)
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  7. 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 (...)
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  8. 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 (...)
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  9. A framework for protein classification.Anand Kumar & Barry Smith - 2003 - In Anand Kumar & Barry Smith (eds.), 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 different purposes and the (...)
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  10. 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. -/- .
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  11. SNARE proteins as molecular masters of interneuronal communication.Danko D. Georgiev & James F. Glazebrook - 2010 - Biomedical Reviews 21:17-23.
    In the beginning of the 20th century the groundbreaking work of Ramon y Cajal firmly established the neuron doctrine, according to which neurons are the basic structural and functional units of the nervous system. Von Weldeyer coined the term “neuron” in 1891, but the huge leap forward in neuroscience was due to Cajal’s meticulous microscopic observations of brain sections stained with an improved version of Golgi’s la reazione nera (black reaction). The latter improvement of Golgi’s technique made it possible to (...)
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  12. Thermal stability of solitons in protein α-helices.Danko D. Georgiev & James F. Glazebrook - 2022 - Chaos, Solitons and Fractals 155:111644.
    Protein α-helices provide an ordered biological environment that is conducive to soliton-assisted energy transport. The nonlinear interaction between amide I excitons and phonon deformations induced in the hydrogen-bonded lattice of peptide groups leads to self-trapping of the amide I energy, thereby creating a localized quasiparticle (soliton) that persists at zero temperature. The presence of thermal noise, however, could destabilize the protein soliton and dissipate its energy within a finite lifetime. In this work, we have computationally solved the system of stochastic (...)
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  13. 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 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 ontology and annotation data set has (...)
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  14. Launching of Davydov solitons in protein α-helix spines.Danko D. Georgiev & James F. Glazebrook - 2020 - Physica E: Low-Dimensional Systems and Nanostructures 124:114332.
    Biological order provided by α-helical secondary protein structures is an important resource exploitable by living organisms for increasing the efficiency of energy transport. In particular, self-trapping of amide I energy quanta by the induced phonon deformation of the hydrogen-bonded lattice of peptide groups is capable of generating either pinned or moving solitary waves following the Davydov quasiparticle/soliton model. The effect of applied in-phase Gaussian pulses of amide I energy, however, was found to be strongly dependent on the site of application. (...)
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  15. Quantum transport and utilization of free energy in protein α-helices.Danko D. Georgiev & James F. Glazebrook - 2020 - Advances in Quantum Chemistry 82:253-300.
    The essential biological processes that sustain life are catalyzed by protein nano-engines, which maintain living systems in far-from-equilibrium ordered states. To investigate energetic processes in proteins, we have analyzed the system of generalized Davydov equations that govern the quantum dynamics of multiple amide I exciton quanta propagating along the hydrogen-bonded peptide groups in α-helices. Computational simulations have confirmed the generation of moving Davydov solitons by applied pulses of amide I energy for protein α-helices of varying length. The stability and (...)
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  16. (1 other version)A Monist Proposal: Against Integrative Pluralism About Protein Structure.Agnes Bolinska - 2022 - Erkenntnis 1 (4).
    Mitchell & Gronenborn propose that we account for the presence of multiple models of protein structure, each produced in different contexts, through the framework of integrative pluralism. I argue that two interpretations of this framework are available, neither of which captures the relationship between a model and the protein structure it represents or between multiple models of protein structure. Further, it inclines us toward concluding prematurely that models of protein structure are right in their contexts and makes extrapolation of findings (...)
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  17. Function of aggregated reticulocyte ribosomes in protein synthesis.Alfred Gierer - 1963 - J. Mol. Biol 6:148-157.
    Applying mild methods of preparation, part of the ribosomes of rabbit reticulocytes are found in aggregates (later called polyribosomes) of up to six ribosomal units. Upon treatment with RNA-ase, they desintegrate into single ribosomes. The fast-sedimenting aggregates are found to be more active in protein synthesis in terms of incorporation of radioactive amino acids, whereas the single ribosomes are more receptive to stimulation by the artificial messenger RNA poly-U. The findings indicate that the linkage of ribosomes into aggregates is due (...)
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  18. Estimation of C-Reactive Protein, Immunoglobulin’s and Complements in SCD Patients.Maha Khalaf Al-Mishry, Nadhim K. Mahdi & Sadeq K. Ali AlSalait - 2018 - International Journal of Academic Health and Medical Research (IJAHMR) 2 (6):1-4.
    Abstract: Sickle cell disease (SCD) comprises an inherited blood disorder that is life long and affects many people globally. Despite progress in therapy, SCA is a considerable cause of mortality and morbidity. This study was designed to measure the immunological and inflammatory parameters of patients with sickle cell disease (SCD) and to found if there is any role of it in the pathogenicity of the disease. This study included A total of 32 patients, their ages ranged from 16 to 55 (...)
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  19. Quantum tunneling of three-spine solitons through excentric barriers.Danko D. Georgiev & James F. Glazebrook - 2022 - Physics Letters A 448:128319.
    Macromolecular protein complexes catalyze essential physiological processes that sustain life. Various interactions between protein subunits could increase the effective mass of certain peptide groups, thereby compartmentalizing protein α-helices. Here, we study the differential effects of applied massive barriers upon the soliton-assisted energy transport within proteins. We demonstrate that excentric barriers, localized onto a single spine in the protein α-helix, reflect or trap three-spine solitons as effectively as concentric barriers with comparable total mass. Furthermore, wider protein solitons, whose energy is (...)
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  20. Towards a proteomics meta-classification.Anand Kumar & Barry Smith - 2004 - In Kumar Anand & Smith Barry (eds.), IEEE Fourth Symposium on Bioinformatics and Bioengineering, Taichung, Taiwan. IEEE Press. pp. 419–427.
    that can serve as a foundation for more refined ontologies in the field of proteomics. Standard data sources classify proteins in terms of just one or two specific aspects. Thus SCOP (Structural Classification of Proteins) is described as classifying proteins on the basis of structural features; SWISSPROT annotates proteins on the basis of their structure and of parameters like post-translational modifications. Such data sources are connected to each other by pairwise term-to-term mappings. However, there are obstacles (...)
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  21. Biochemical Kinds.Jordan Bartol - 2014 - British Journal for the Philosophy of Science (2):axu046.
    Chemical kinds (e.g. gold) are generally treated as having timelessly fixed identities. Biological kinds (e.g. goldfinches) are generally treated as evolved and/or evolving entities. So what kind of kind is a biochemical kind? This paper defends the thesis that biochemical molecules are clustered chemical kinds, some of which–namely, evolutionarily conserved units–are also biological kinds.On this thesis, a number of difficulties that have recently occupied philosophers concerned with proteins and kinds are shown to be resolved or dissolved.
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  22. Crick's Adaptor Hypothesis and the Discovery of Transfer RNA: Experiment Surpassing Theoretical Prediction.Michael Fry - 2022 - Philosophy, Theory, and Practice in Biology 14 (11):1-31.
    Historically, hypotheses failed in most cases to correctly forecast the workings of complex biological systems. Francis Crick’s adaptor hypothesis, however, stands out as an exceptional case of a confirmed abstract prediction. This hypothesis presciently anticipated the existence of RNA adaptors that function as bridges between amino acids and the chemically different nucleic acid template for proteins. Crick conjectured that the adaptors are enzymatically charged with cognate amino acids, they bind to complementary protein-coding nucleic acid, and their liberated amino acids (...)
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  23. Medicinal Uses of Cashew (Anacardium occidentale): Review.Akram Muhammad & Talha Muhammad - 2021 - Journal of Science Technology and Research (JSTAR) 2 (1):1-10.
    The cashew nut is essential for physical and emotional well-being. It is an energetic diet and the best food medication for many illnesses. Nuts protects from malignant growth, coronary illness, circulatory strain, and various degenerative infirmities connected to aging. It can be used for several medicinal purposes. Every part of cashew has some important medicinal properties. Cashew kernel contains proteins, carbohydrates, vitamins, and fats which help gain energy. Cashew nuts are used for many purposes like blood sugar, weight loss, (...)
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  24. 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 (...)
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  25. Infectivity of ribonucleic acid from Tobacco Mosaic Virus.Alfred Gierer & Gerhard Schramm - 1956 - Nature 177:702-703.
    Upon separation of the protein from the nucleic acid component of tobacco mosaic virus by phenol, using a fast and gentle procedure, the nucleic acid is infective in assays on tobacco leaves. A series of qualitative and quantitative control experiments demonstrates that the biological activity cannot depend on residual proteins in the preparation, but is a property of isolated nucleic acid which is thus the genetic material of the virus.
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  26. 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 (...)
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  27. Save the Meat for Cats: Why It’s Wrong to Eat Roadkill.Cheryl Abbate & C. E. Abbate - 2019 - Journal of Agricultural and Environmental Ethics 32 (1):165-182.
    Because factory-farmed meat production inflicts gratuitous suffering upon animals and wreaks havoc on the environment, there are morally compelling reasons to become vegetarian. Yet industrial plant agriculture causes the death of many field animals, and this leads some to question whether consumers ought to get some of their protein from certain kinds of non factory-farmed meat. Donald Bruckner, for instance, boldly argues that the harm principle implies an obligation to collect and consume roadkill and that strict vegetarianism is thus immoral. (...)
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  28. Rule Based System for Diagnosing Bean Diseases and Treatment.Mohammed H. S. Abueleiwa, Fadi E. S. Harara, Mustafa M. K. Al-Ghoul, Sami M. Okasha & Samy S. Abu-Naser - 2022 - International Journal of Engineering and Information Systems (IJEAIS) 6 (5):67-74.
    Background: A bean is the seed of one of several genera of the flowering plant family Fabaceae, which are used as vegetables for human or animal food. They can be cooked in many different ways, including boiling, frying, and baking, and are used in many traditional dishes throughout the world. Beans are one of the longest-cultivated plants. Broad beans, also called fava beans, in their wild state the size of a small fingernail, were gathered in Afghanistan and the Himalayan foothills. (...)
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  29. The Evolution of Consciousness & Subjectivity in a Biological Framework for The Universe.Ronald Williams - manuscript
    This paper explores the evolution of consciousness and subjectivity through a biological framework for understanding the universe. It posits that functional patterns in biological systems mirror cosmic mathematical principles, defining our objective reality. Similar to wave and Fibonacci patterns in different physical phenomena, biological patterns are intrinsic to all things and can be quantified using Dedre Gentner’s approach to analogy. For example, Earth’s ocean currents and the melting and freezing of Antarctica resemble the circulatory system and heart, while the production (...)
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  30. Differential Activation of ER Stress Signal Pathway s Contributes to Palmitate-Induced Hepatocyte Lipoapoptosis.Xiaofang Zhao - 2016 - Cell Biology 4 (1):128.
    Saturated free fatty acids-induced hepatocyte lipoapoptosis plays a pivotal role in non-alcoholic steatohepatitis. Theactivation of endoplasmic reticulum (ER) stress isinvolved in hepatocyte lipoapoptosis induced by thesaturated free fatty acidpalmitate (PA). However, the underlying mechanismsof the role of ER stress in hepatocyte lipoapoptosis remain largely unclear.In this study, we showed that PA and tunicamycin (Tun), a classic ER stress inducer, resulted in differential activation of ERstress pathways. Our data revealed that PA inducedchronic and persistent ER stress response, but Tuninduced acute and (...)
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  31. 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 (...)
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  32. 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 (...)
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  33. 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 know it (...)
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  34. 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.
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  35. Bacteria are small but not stupid: cognition, natural genetic engineering and socio-bacteriology.J. A. Shapiro - 2007 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 38 (4):807-819.
    Forty years’ experience as a bacterial geneticist has taught me that bacteria possess many cognitive, computational and evolutionary capabilities unimaginable in the first six decades of the twentieth century. Analysis of cellular processes such as metabolism, regulation of protein synthesis, and DNA repair established that bacteria continually monitor their external and internal environments and compute functional outputs based on information provided by their sensory apparatus. Studies of genetic recombination, lysogeny, antibiotic resistance and my own work on transposable elements revealed multiple (...)
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  36. 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 (...)
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  37. A critical review of the ethical and legal issues in human germline gene editing: Considering human rights and a call for an African perspective.B. Shozi - 2020 - South African Journal of Bioethics and Law 13 (1):62.
    In the wake of the advent of genome editing technology CRISPR-Cas9 (clustered regularly interspaced palindromic repeat (CRISPR)-associated protein 9), there has been a global debate around the implications of manipulating the human genome. While CRISPR-based germline gene editing is new, the debate about the ethics of gene editing is not – for several decades now, scholars have debated the ethics of making heritable changes to the human genome. The arguments that have been raised both for and against the use of (...)
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  38. Integrative pluralism for biological function.Beckett Sterner & Samuel Cusimano - 2019 - Biology and Philosophy 34 (6):1-21.
    We introduce a new type of pluralism about biological function that, in contrast to existing, demonstrates a practical integration among the term’s different meanings. In particular, we show how to generalize Sandra Mitchell’s notion of integrative pluralism to circumstances where multiple epistemic tools of the same type are jointly necessary to solve scientific problems. We argue that the multiple definitions of biological function operate jointly in this way based on how biologists explain the evolution of protein function. To clarify how (...)
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  39. A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology.Yongqun He, Hong Yu, Anthony Huffman, Asiyah Yu Lin, Darren A. Natale, John Beverley, Ling Zheng, Yehoshua Perl, Zhigang Wang, Yingtong Liu, Edison Ong, Yang Wang, Philip Huang, Long Tran, Jinyang Du, Zalan Shah, Easheta Shah, Roshan Desai, Hsin-hui Huang, Yujia Tian, Eric Merrell, William D. Duncan, Sivaram Arabandi, Lynn M. Schriml, Jie Zheng, Anna Maria Masci, Liwei Wang, Hongfang Liu, Fatima Zohra Smaili, Robert Hoehndorf, Zoë May Pendlington, Paola Roncaglia, Xianwei Ye, Jiangan Xie, Yi-Wei Tang, Xiaolin Yang, Suyuan Peng, Luxia Zhang, Luonan Chen, Junguk Hur, Gilbert S. Omenn, Brian Athey & Barry Smith - 2022 - Journal of Biomedical Semantics 13 (1):25.
    The current COVID-19 pandemic and the previous SARS/MERS outbreaks of 2003 and 2012 have resulted in a series of major global public health crises. We argue that in the interest of developing effective and safe vaccines and drugs and to better understand coronaviruses and associated disease mechenisms it is necessary to integrate the large and exponentially growing body of heterogeneous coronavirus data. Ontologies play an important role in standard-based knowledge and data representation, integration, sharing, and analysis. Accordingly, we initiated the (...)
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  40. The Central Dogma as a Thesis of Causal Specificity.Marcel Weber - 2006 - History and Philosophy of the Life Sciences 28 (4):595-610.
    I present a reconstruction of F.H.C. Crick's two 1957 hypotheses "Sequence Hypothesis" and "Central Dogma" in terms of a contemporary philosophical theory of causation. Analyzing in particular the experimental evidence that Crick cited, I argue that these hypotheses can be understood as claims about the actual difference-making cause in protein synthesis. As these hypotheses are only true if restricted to certain nucleic acids in certain organisms, I then examine the concept of causal specificity and its potential to counter claims about (...)
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  41. Genotype–phenotype mapping and the end of the ‘genes as blueprint’ metaphor.Massimo Pigliucci - 2010 - Philosophical Transactions Royal Society B 365:557–566.
    In a now classic paper published in 1991, Alberch introduced the concept of genotype–phenotype (G!P) mapping to provide a framework for a more sophisticated discussion of the integration between genetics and developmental biology that was then available. The advent of evo-devo first and of the genomic era later would seem to have superseded talk of transitions in phenotypic space and the like, central to Alberch’s approach. On the contrary, this paper shows that recent empirical and theoretical advances have only sharpened (...)
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  42. The Origin of Consciousness.Ronald Williams - forthcoming - Biologicaluniverse.Org.
    This paper explores the evolution of consciousness and subjectivity through a biological framework for understanding the universe. It posits that functional patterns in biological systems mirror cosmic mathematical principles, defining our objective reality. Similar to wave and Fibonacci patterns in different physical phenomena, biological patterns are intrinsic to all things and can be quantified using Dedre Gentner’s approach to analogy. For example, Earth’s ocean currents and the melting and freezing of Antarctica resemble the circulatory system and heart, while the production (...)
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  43. A new framework for host-pathogen interaction research.Hong Yu, Li Li, Anthony Huffman, John Beverley, Junguk Hur, Eric Merrell, Hsin-hui Huang, Yang Wang, Yingtong Liu, Edison Ong, Liang Cheng, Tao Zeng, Jingsong Zhang, Pengpai Li, Zhiping Liu, Zhigang Wang, Xiangyan Zhang, Xianwei Ye, Samuel K. Handelman, Jonathan Sexton, Kathryn Eaton, Gerry Higgins, Gilbert S. Omenn, Brian Athey, Barry Smith, Luonan Chen & Yongqun He - 2022 - Frontiers in Immunology 13.
    COVID-19 often manifests with different outcomes in different patients, highlighting the complexity of the host-pathogen interactions involved in manifestations of the disease at the molecular and cellular levels. In this paper, we propose a set of postulates and a framework for systematically understanding complex molecular host-pathogen interaction networks. Specifically, we first propose four host-pathogen interaction (HPI) postulates as the basis for understanding molecular and cellular host-pathogen interactions and their relations to disease outcomes. These four postulates cover the evolutionary dispositions involved (...)
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  44. Antifragility and Tinkering in Biology (and in Business) Flexibility Provides an Efficient Epigenetic Way to Manage Risk.Antoine Danchin, Philippe M. Binder & Stanislas Noria - 2011 - Genes 2 (4):998-1016.
    The notion of antifragility, an attribute of systems that makes them thrive under variable conditions, has recently been proposed by Nassim Taleb in a business context. This idea requires the ability of such systems to ‘tinker’, i.e., to creatively respond to changes in their environment. A fairly obvious example of this is natural selection-driven evolution. In this ubiquitous process, an original entity, challenged by an ever-changing environment, creates variants that evolve into novel entities. Analyzing functions that are essential during stationary-state (...)
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  45. 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 (...)
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  46. SynBio 2.0, a new era for synthetic life: Neglected essential functions for resilience.Antoine Danchin & Jian Dong Huang - 2022 - Environmental Microbiology 25 (1):64-78.
    Synthetic biology (SynBio) covers two main areas: application engineering, exemplified by metabolic engi- neering, and the design of life from artificial building blocks. As the general public is often reluctant to embrace synthetic approaches, preferring nature to artifice, its immediate future will depend very much on the public’s reaction to the unmet needs created by the pervasive demands of sustainability. On the other hand, this reluctance should not have a negative impact on research that will now take into account the (...)
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  47. A semiotic analysis of the genetic information.Charbel El-Hani, Joao Queiroz & Claus Emmeche - 2006 - Semiotica - Journal of the International Association for Semiotic Studies / Revue de l'Association Internationale de Sémiotique 160 (1/4):1-68.
    Terms loaded with informational connotations are often employed to refer to genes and their dynamics. Indeed, genes are usually perceived by biologists as basically ‘the carriers of hereditary information.’ Nevertheless, a number of researchers consider such talk as inadequate and ‘just metaphorical,’ thus expressing a skepticism about the use of the term ‘information’ and its derivatives in biology as a natural science. First, because the meaning of that term in biology is not as precise as it is, for instance, in (...)
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  48. On the Possible Transformation and Vanishment of Epistemic Objects.Hans-Jörg Rheinberger - 2016 - Teorie Vědy / Theory of Science 38 (3):269-278.
    When considering the question of possible transformation and disappearance of scientific objects, it is useful to distinguish between epistemic and technical objects. This paper presents preliminary observations and offers a typology of obsolescence. It is based on several case studies drawn from the history of life sciences. The paper proceeds as follows: first, the dynamics of epistemic objects is considered through the examples of Carl Correns’ study of “xenia”, Alfred Kühn’s work on physiological developmental genetics, and Paul Zamecnik’s research on (...)
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  49. Blood Products and the Commodification Debate: The Blurry Concept of Altruism and the ‘Implicit Price’ of Readily Available Body Parts.Annette Dufner - 2015 - HEC Forum 27 (4):347-359.
    There is a widespread consensus that a commodification of body parts is to be prevented. Numerous policy papers by international organizations extend this view to the blood supply and recommend a system of uncompensated volunteers in this area—often, however, without making the arguments for this view explicit. This situation seems to indicate that a relevant source of justified worry or unease about the blood supply system has to do with the issue of commodification. As a result, the current health minister (...)
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  50. Making sense of ‘genetic programs’: biomolecular Post–Newell production systems.Mihnea Capraru - 2024 - Biology and Philosophy 39 (2):1-12.
    The biomedical literature makes extensive use of the concept of a genetic program. So far, however, the nature of genetic programs has received no satisfactory elucidation from the standpoint of computer science. This unsettling omission has led to doubts about the very existence of genetic programs, on the grounds that gene regulatory networks lack a predetermined schedule of execution, which may seem to contradict the very idea of a program. I show, however, that we can make perfect sense of genetic (...)
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