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Which model is best? Let the data decide

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http://pubman.mpdl.mpg.de/cone/persons/resource/persons92185

Bergling,  Sebastian
Department of Cell Physiology, Max Planck Institute for Medical Research, Max Planck Society;

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Citation

Bergling, S. (1999). Which model is best? Let the data decide. The Journal of General Physiology, 114, 591-592. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/10577024.


Cite as: http://hdl.handle.net/11858/00-001M-0000-0024-9B82-C
Abstract
The Perspectives on Ion Permeation center around the question of which approach is the most adequate in describing ion permeation. Obviously, one way to decide is to compare the outcome of the various models with experimental results and to let the range of validity and the model's ability of prediction be the major judge in grading models. An obstacle in doing so has been the lack of standards for electrophysiological recordings. A well−maintained, widely accepted, public database of raw data of current−voltage (IV) recordings and related measurements that, with time, becomes more complete will significantly improve the endeavor of finding realistic descriptions of ion permeation. The idea of a public database is old and databases for protein structures and gene sequences have proven very useful. They act as interfaces in highly multidisciplinary scientific communities. There is a similar need for a database in this case, and there would be many advantages. Modeling of ion permeation can only become better with increasing diversity of a set of data, whereas approaches constrained by a reduced set of data are of limited use since missing experimental data could contain crucial information; a database will help to avoid redundancies and will put grading of different approaches on a firm basis, which, as a result, will spark competition. Public access to a collection of experimental results facilitates cross−talk between experiment and theory. The database, and therefore the scientific community, will profit from additional experimental results that may not be published as parts of peer−reviewed articles because they are spin−offs of bigger experimental projects. Fuzziness of experimental data or its reproducibility might pose a problem that could become manageable by very carefully defining the experiments. Another caveat is that the database has to be maintained by dedicated persons within a bigger organization. How to start to set up a database? After agreeing upon a data format, one could start to ask labs specialized in channel ion permeation to contribute existing raw data to a public database available via the World Wide Web (J.D. Lear: synthetic channels; B. Sakmann: AChR; J.P. Rosenbusch: porins; O.S. Andersen: gramicidin). Hopefully, other labs will join in volunteering to upload data. The first experience will help to formulate standards, or a ranking system for grading raw data based on quality and completeness. A minimal standard for accepting data should then be formulated. At some stage, "wish lists" might be set up. For example a theoretician might wish to get a set of experiments that contains: (a) recordings of IV curves at varying symmetrical and asymmetrical bath concentrations. (b) IV recordings with voltage ranges extending beyond the physiological voltage range of about ±100 mV. Membrane potentials of, say, ±200 mV should be possible to achieve. Some characteristic properties of channels for which electrostatic forces dominate can be observed only at higher potentials. (c) IV recordings of channels subject to bath solutions with varying combinations of ionic species