The scientific community has recently been abuzz with news of the completed ENCODE (Encyclopedia of DNA Elements) project — a collaborative consortium-driven endeavour to comprehensively identify functional DNA elements in the human genome.


ENCODE’s implications are numerous, from insight into the function of individual genes, to the interactions responsible for genetic diseases. As understanding of the human genome increases, advances in research, health care, and personalized medicine could follow. “It is going to impact every single molecular scientist in the world,” claimed University of Toronto professor Aled Edwards in a Toronto Star article shortly after the news of the project’s completion broke.

While the initial reaction to ENCODE’s achievement was extremely favourable, the project’s founders have recently had to weather a significant amount of criticism. Some members of the scientific community objected to the significant claims it made, while others took arms with the method in which the news was released.

One controversial issue lies with the project’s most significant conclusion. According to over 30 articles and news releases published in reputable journals such as Science, Nature and Genome Research, as well as major public media outlets such as The Washington Post and The New York Times, the team at ENCODE claimed they had identified 80 per cent of the human genome as having “functional” value. This was a staggering statement, since only one per cent of the human genome was previously thought to code for protein and the majority is colloquially referred to as “junk DNA.”

The claim has led to a debate about the reasonable definition of “functional.” Ewan Birney, ENCODE’s lead analysis coordinator, stated on his personal blog that the team interpreted “functional” as having biochemical action, whether that was DNA being transcribed into RNA, protein-encoding regions,  regulation elements associated with proteins, or other RNAs.

Though this definition may sound reasonable, there are many sequences of DNA transcribed into RNA that have no physiological role in the cell or human body. Michael Eisen, a biologist at UC Berkeley, tweeted that ENCODE’s definition was a “Meaningless measure of functional significance.”

The project’s broad definition of “functional” explains ENCODE’s reportedly high percentage of functional DNA elements, which led to a second issue. ENCODE’s statements frequently referred to the high functional statistic in conjunction with the term junk DNA. Initial news articles implied that the project’s results were debunking the old concept that the human genome consisting of mainly insignificant data. To a layperson with no background in genetics, the association threatens to promote an incorrect narrative of the current understanding of genomics.

A third item of criticism was the publishing embargo placed on the final results. ENCODE’s intent was to maximize the impact of their findings, so the publication of individual articles was prevented until all works could be published simultaneously. The danger with this approach, some have noted, is that all the hype surrounding the project led to a disproportionate reaction to the results relative to the actual significance and impact of the data.

Much like the Human Genome Project a decade ago, projects like ENCODE can create idealized expectations of medical breakthroughs and giant leaps forward in science research that are not realistic. The publications embargo only facilitated this mentality, as scientists were not given access to the data gradually, but all at once in overwhelming amounts.

Regardless of the criticism due to misleading semantics and the politics of peer-review, the data presented by ENCODE could fuel fields of science research from molecular biology to genetics and personalized medicine.

Despite its public missteps, one of ENCODE’s major achievements is that the data resulting from the project is online and freely available. Over time, should the controversy subside, ENCODE could set an example and spur the creation of more open access, collaborative science research projects for the future.

Sources: Sandwalk, In the Pipeline 

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