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History and Philosophy of the Life Sciences - Vol. 29, no. 3 (2007)
Article

Maureen A. O’Malley, Exploratory Experimentation and Scientifi c Practice: Metagenomics and the Proteorhodopsin Case


Abstract

Exploratory experimentation and high-throughput molecular biology appear to have considerable affi nity 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 fi nding and its detailed investigation illuminates the relationship between exploratory experimentation and metagenomics. Specifi cally, the proteorhodopsin story indicates that a dichotomous interpretation of theory-driven and exploratory experimentation is insuffi cient and that an interactive understanding of these two types of experimentation can be usefully supplemented by another category, “natural history experimentation”. Further refl ection on the context of metagenomics suggests the necessity of thinking more historically about exploratory and other forms of experimentation.


Keywords

Exploratory experimentation, Hypothesis testing, Natural history experimentation, Metagenomics, Proteorhodopsin, Rhodopsins


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