Dear all, Please join us for the CamPoS (Cambridge Philosophy of Science) seminar
Wednesday 12th February 1-2:30pm in HPS Seminar Room 2. Sophia Efstathiou (NTNU Philosophy) will give a talk entitled "How we Manage to Manage 'Knowledge': Contributing transcription factor knowledge to the Gene Ontology Consortium database" Best wishes, Christopher Abstract: Sophia Efstathiou (NTNU Philosophy), Rune Nydal (NTNU Philosophy), Astrid Lægreid (NTNU Molecular Medicine and Cancer Research), Martin Kuiper (NTNU Biology) Working in an interdisciplinary group of philosophers and systems biologists we ask: How can we better construct the scientific approach called systems biology? We focus on work known as "knowledge management", which in the life sciences involves taking care of information published in the biomedical literature through the construction and manipulation of ontologies and knowledge bases. We reflect on our group's submission of knowledge about transcription regulation into the database of the Gene Ontology Consortium and TFcheckpoint.org (Tripathi et al 2013) (see also Leonelli et al. 2011, Leonelli and Ankeny 2011, Leonelli 2012). Domain-specific knowledge of a form and type native to molecular biology is being founded into hybrid epistemological domains infrastructured and conditioned by knowledge and competencies native to the computer sciences and artificial intelligence (AI). Systems biology articulates a vision of biological knowledge that can be managed systematically: collected, assembled, computationally analysed, understood, communicated and built upon systematically. At the same time, the effect of structured controlled vocabularies and computer-reasonable claims can be totalising or oppressive if not tedious and irrelevant for the biologists whose knowledge is to be systematised -and without a clear benefit. Cross-disciplinary buy-in that is crucial for the field to progress is thus limited. In response we flesh out three narratives motivating work in biological knowledge management: first, a *preservation* narrative, a need to ensure that published knowledge is not 'lost' to us when e.g. rates at which new knowledge is published don't match the time we have to read; second a narrative of *democratization* or making common, open and available knowledge that is otherwise kept from us, e.g. in publications that are copyright protected, or journals with specific readerships; third a *mobilization *story, of how available knowledge repackaged and formulated under these new rules is deemed to be fine-tuned or enhanced, transformed in ways that enable new scientific research, such as systems biology. We investigate some conditions under which these three promises could at least hope to be met.
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