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Published March 2015 | Published
Journal Article Open

Genomics, "Discovery Science," Systems Biology, and Causal Explanation: What Really Works?


Diverse and non-coherent sets of epistemological principles currently inform research in the general area of functional genomics. Here, from the personal point of view of a scientist with over half a century of immersion in hypothesis driven scientific discovery, I compare and deconstruct the ideological bases of prominent recent alternatives, such as "discovery science," some productions of the ENCODE project, and aspects of large data set systems biology. The outputs of these types of scientific enterprise qualitatively reflect their radical definitions of scientific knowledge, and of its logical requirements. Their properties emerge in high relief when contrasted (as an example) to a recent, system-wide, predictive analysis of a developmental regulatory apparatus that was instead based directly on hypothesis-driven experimental tests of mechanism.

Additional Information

© 2016 by Johns Hopkins University Press. The concepts underlying GRN theory and practice have largely been developed in collaboration with Isabelle Peter of Caltech. NICHD has supported our GRN initiatives from their inception, and it is the author's pleasure to acknowledge this invaluable support, in particular grant HD05753, and the program headed by James Coulombe. The author is extremely grateful to Ellen Rothenberg of Caltech and to Isabelle Peter for their own marvelous perspicacity in their comments upon drafts of this essay.

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August 20, 2023
August 20, 2023