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Exploratory experimentation and scientific practice: Metagenomics and the proteorhodopsin case

O'Malley, Maureen (2008) Exploratory experimentation and scientific practice: Metagenomics and the proteorhodopsin case. [Preprint]

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    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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    Item Type: Preprint
    Additional Information: This is one of a group of three papers (plus an introduction by C. Kenneth Waters) on exploratory experimentation in recent molecular life sciences. The other papers are by Richard Burian and Kevin Elliott; preprints of the articles are available on the PhilSci Archive:
    Keywords: Exploratory experimentation, hypothesis testing, natural history experimentation, metagenomics, proteorhodopsin, rhodopsins
    Subjects: Specific Sciences > Biology > Molecular Biology/Genetics
    General Issues > Theory/Observation
    General Issues > Experimentation
    General Issues > History of Science Case Studies
    Depositing User: Maureen O'Malley
    Date Deposited: 13 Apr 2008
    Last Modified: 07 Oct 2010 11:16
    Item ID: 3985

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