98 research outputs found

    Size Doesn't Matter: Towards a More Inclusive Philosophy of Biology

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    notes: As the primary author, O’Malley drafted the paper, and gathered and analysed data (scientific papers and talks). Conceptual analysis was conducted by both authors.publication-status: Publishedtypes: ArticlePhilosophers of biology, along with everyone else, generally perceive life to fall into two broad categories, the microbes and macrobes, and then pay most of their attention to the latter. ‘Macrobe’ is the word we propose for larger life forms, and we use it as part of an argument for microbial equality. We suggest that taking more notice of microbes – the dominant life form on the planet, both now and throughout evolutionary history – will transform some of the philosophy of biology’s standard ideas on ontology, evolution, taxonomy and biodiversity. We set out a number of recent developments in microbiology – including biofilm formation, chemotaxis, quorum sensing and gene transfer – that highlight microbial capacities for cooperation and communication and break down conventional thinking that microbes are solely or primarily single-celled organisms. These insights also bring new perspectives to the levels of selection debate, as well as to discussions of the evolution and nature of multicellularity, and to neo-Darwinian understandings of evolutionary mechanisms. We show how these revisions lead to further complications for microbial classification and the philosophies of systematics and biodiversity. Incorporating microbial insights into the philosophy of biology will challenge many of its assumptions, but also give greater scope and depth to its investigations

    SBML Level 3: an extensible format for the exchange and reuse of biological models

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    Systems biology has experienced dramatic growth in the number, size, and complexity of computational models. To reproduce simulation results and reuse models, researchers must exchange unambiguous model descriptions. We review the latest edition of the Systems Biology Markup Language (SBML), a format designed for this purpose. A community of modelers and software authors developed SBML Level 3 over the past decade. Its modular form consists of a core suited to representing reaction-based models and packages that extend the core with features suited to other model types including constraint-based models, reaction-diffusion models, logical network models, and rule-based models. The format leverages two decades of SBML and a rich software ecosystem that transformed how systems biologists build and interact with models. More recently, the rise of multiscale models of whole cells and organs, and new data sources such as single-cell measurements and live imaging, has precipitated new ways of integrating data with models. We provide our perspectives on the challenges presented by these developments and how SBML Level 3 provides the foundation needed to support this evolution

    Recommendations concerning research and model evaluation needs to support breeder reactor environmental radiological assessments

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    Purpose of this report is to present recommendations concerning needs for model evaluations, environmental research, and biomedical research to support breeder reactor environmental radiological assessments. More data are needed to specify dry deposition velocities and to validate plume depletion models. More atmospheric dispersion data are required to characterize flow near buildings, in complex terrain, and for travel distances at 100 km or more. Field data are needed for terrestrial food chain transport models, especially those used to assess the impact of acute radionuclide releases. Efforts are needed to develop models for the estimation of dose from external exposure to photons from a finite, elevated plume resulting from an acute radionuclide release to the atmosphere. Estimates of doses to man from internally deposited radionuclides require scrutiny. Further study of tritium is needed to determine its dependence on dose and dose rate and to specify the relative toxicity of various physiochemical forms of tritium in the environment
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