Junk or functional DNA? ENCODE and the function controversy

Pierre Luc Germain, Emanuele Ratti, Federico Boem

Research output: Contribution to journalArticlepeer-review


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.

Original languageEnglish
Pages (from-to)807-831
Number of pages25
JournalBiology and Philosophy
Issue number6
Publication statusPublished - Oct 16 2014


  • Biological function
  • Causal role
  • Junk DNA
  • Selected effect

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • History and Philosophy of Science
  • Philosophy


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