Biology & Philosophy

, Volume 29, Issue 6, pp 807–831

Junk or functional DNA? ENCODE and the function controversy

  • Pierre-Luc Germain
  • Emanuele Ratti
  • Federico Boem
Article

Abstract

In its last round of publications in September 2012, the Encyclopedia Of DNA Elements (ENCODE) assigned a biochemical function to most of the human genome, which was taken up by the media as meaning the end of ‘Junk DNA’. This provoked a heated reaction from evolutionary biologists, who among other things claimed that ENCODE adopted a wrong and much too inclusive notion of function, making its dismissal of junk DNA merely rhetorical. We argue that this criticism rests on misunderstandings concerning the nature of the ENCODE project, the relevant notion of function and the claim that most of our genome is junk. We argue that evolutionary accounts of function presuppose functions as ‘causal roles’, and that selection is but a useful proxy for relevant functions, which might well be unsuitable to biomedical research. Taking a closer look at the discovery process in which ENCODE participates, we argue that ENCODE’s strategy of biochemical signatures successfully identified activities of DNA elements with an eye towards causal roles of interest to biomedical research. We argue that ENCODE’s controversial claim of functionality should be interpreted as saying that 80 % of the genome is engaging in relevant biochemical activities and is very likely to have a causal role in phenomena deemed relevant to biomedical research. Finally, we discuss ambiguities in the meaning of junk DNA and in one of the main arguments raised for its prevalence, and we evaluate the impact of ENCODE’s results on the claim that most of our genome is junk.

Keywords

Biological function Causal role Selected effect ENCODE Junk DNA 

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Copyright information

© Springer Science+Business Media Dordrecht 2014

Authors and Affiliations

  • Pierre-Luc Germain
    • 1
    • 2
  • Emanuele Ratti
    • 1
    • 2
  • Federico Boem
    • 1
    • 2
  1. 1.Department of Experimental OncologyEuropean Institute of Oncology (IEO)MilanItaly
  2. 2.Dipartimento di Scienze Della SaluteUniversità degli Studi di MilanoMilanItaly

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