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A Kuhnian framework is used to analyze the current controversy over whether two or three fundamental types of life forms exist. Until the 1980s, all life was classified into two primary forms: eukaryotes and prokaryotes. Using molecular sequencing data, Carl Woese suggested the archaebacteria constituted a third domain. In the mid-1990s, Radhey S. Gupta challenged the three-domain hypothesis. While this dispute may seem to be a purely technical debate over the analysis of protein and nucleic acid sequence data, the controversy encompasses broader issues such as the aims of classification and the role of microorganisms in the biosphere. At the heart of this dispute is what kinds of data are relevant to constructing an overall taxonomy. The prestige of molecular biology played a large role in why the three-domain hypothesis was accepted so readily, but supporters of the two-domain hypothesis argue that the fossil record, morphology, and cell physiology should all play a role in taxonomy. This case study provides a good example of a paradigm shift in the making, demonstrating that issues beyond the raw data will be significant factors in deciding whether the three-domain hypothesis will prevail or a new classificatory scheme will emerge.