Exploratory Experimentation and Scientific Practice: Metagenomics and the Proteorhodopsin Case

Abstract
Exploratory experimentation and high-throughput molecular biology appear to have considerable affinity for each other. Included in the latter category is metagenomics, which is the DNA-based study of diverse microbial communities from a vast range of non-laboratory environments. Metagenomics has already made numerous discoveries and these have led to reinterpretations of fundamental concepts of microbial organization, evolution, and ecology. The most outstanding success story of metagenomics to date involves the discovery of a rhodopsin gene, named proteorhodopsin, in marine bacteria that were never suspected to have any photobiological capacities. A discussion of this finding and its detailed investigation illuminates the relationship between exploratory experimentation and metagenomics. Specifically, the proteorhodopsin story indicates that a dichotomous interpretation of theory-driven and exploratory experimentation is insufficient and that an interactive understanding of these two types of experimentation can be usefully supplemented by another category, "natural history experimentation". Further reflection on the context of metagenomics suggests the necessity of thinking more historically about exploratory and other forms of experimentation
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What's so Special About Model Organisms?Rachel A. Ankeny & Sabina Leonelli - 2011 - Studies in History and Philosophy of Science Part A 42 (2):313-323.
When One Model is Not Enough: Combining Epistemic Tools in Systems Biology.Sara Green - 2013 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 44 (2):170-180.
Re-Thinking Organisms: The Impact of Databases on Model Organism Biology.Sabina Leonelli & Rachel A. Ankeny - 2012 - Studies in History and Philosophy of Science Part C 43 (1):29-36.
From Genetic to Genomic Regulation: Iterativity in microRNA Research.Maureen A. O'Malley, Kevin C. Elliott & Richard M. Burian - 2010 - Studies in History and Philosophy of Science Part C 41 (4):407-417.
Why Do Funding Agencies Favor Hypothesis Testing?Chris Haufe - 2013 - Studies in History and Philosophy of Science Part A 44 (3):363-374.

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