The 10th anniversary of the ENCODE publicity campaign fiasco

On Sept. 5, 2012 ENCODE researchers, in collaboration with the science journal Nature, launched a massive publicity campaign to convince the world that junk DNA was dead. We are still dealing with the fallout from that disaster.

The Encyclopedia of DNA Elements (ENCODE) was originally set up to discover all of the functional elements in the human genome. They carried out a massive number of experiments involving a huge group of researchers from many different countries. The results of this work were published in a series of papers in the September 6th, 2012 issue of Nature. (The papers appeared on Sept. 5th.)

Most of the papers are quite technical, and several of them are almost unreadable, so the consortium leaders published a summary article in order to explain the results to the average reader (Birney et al., 2012). The summary article contained these sentences in the abstract [my emphasis, LAM].

The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions.

The idea that 80% of the genome is functional was taken to mean that there's almost no junk DNA in our genome and this was the main theme of the publicity campaign launched by Nature and promoted in videos, press releases, and guest editorials [What did the ENCODE Consortium say in 2012?]. The death of junk DNA was announced on the same day in newspapers and science websites all over the world. (Science journalists were provided with advanced notice under embargo until Sept. 5th.)

There was immediate criticism on blogs and other websites and this prompted an explanation from a senior Nature editor, Brendan Maher [Brendan Maher Writes About the ENCODE/Junk DNA Publicity Fiasco]. Here's how he explained the reason for the publicity campaign on the very next day (Sept. 6).

ENCODE was conceived of and practised as a resource-building exercise. In general, such projects have a huge potential impact on the scientific community, but they don’t get much attention in the media. The journal editors and authors at ENCODE collaborated over many months to make the biggest splash possible and capture the attention of not only the research community but also of the public at large. Similar efforts went into the coordinated publication of the first drafts of the human genome, another resource-building project, more than a decade ago. Although complaints and quibbles will probably linger for some time, the real test is whether scientists will use the data and prove ENCODE’s worth.

The important point here is that the publicity campaign was deliberate. It was planned over several months in order to make "the biggest splash possible." Apparently the "real test" will be whether researchers use the date but another, fairly important, "real test" is whether they will agree with the conclusions reached by ENCODE researchers.

As the nature of the fiasco became known in the scientific community, there was some attempt to make excuses by claiming that the ENCODE researchers and Nature editors were misunderstood. The revisionist story is that there were using a very particular definition of function and they didn't mean to imply that this refuted junk DNA [How does Nature deal with the ENCODE publicity hype that it created?]. That's nonsense and everybody knows it. There's abundant evidence that the ENCODE researchers really did mean to sound the death knell for junk DNA and Nature supported them [The truth about ENCODE]. One of the best examples is a press release from the Sanger Institute (UK) on Sept. 5, 2012.

The ENCODE Project, today, announces that most of what was previously considered as ‘junk DNA’ in the human genome is actually functional. The ENCODE Project has found that 80 per cent of the human genome sequence is linked to biological function.

One of the best analyses of the ENCODE publicity campaign fiasco is a paper by Casane et al. (2015). Unfortunately, it is written in french but the english abstract tells you all you need to know [The apophenia of ENCODE or Pangloss looks at the human genome].

In September 2012, a batch of more than 30 articles presenting the results of the ENCODE (Encyclopaedia of DNA Elements) project was released. Many of these articles appeared in Nature and Science, the two most prestigious interdisciplinary scientific journals. Since that time, hundreds of other articles dedicated to the further analyses of the Encode data have been published. The time of hundreds of scientists and hundreds of millions of dollars were not invested in vain since this project had led to an apparent paradigm shift: contrary to the classical view, 80% of the human genome is not junk DNA, but is functional. This hypothesis has been criticized by evolutionary biologists, sometimes eagerly, and detailed refutations have been published in specialized journals with impact factors far below those that published the main contribution of the Encode project to our understanding of genome architecture. In 2014, the Encode consortium released a new batch of articles that neither suggested that 80% of the genome is functional nor commented on the disappearance of their 2012 scientific breakthrough. Unfortunately, by that time many biologists had accepted the idea that 80% of the genome is functional, or at least, that this idea is a valid alternative to the long held evolutionary genetic view that it is not. In order to understand the dynamics of the genome, it is necessary to re-examine the basics of evolutionary genetics because, not only are they well established, they also will allow us to avoid the pitfall of a panglossian interpretation of Encode. Actually, the architecture of the genome and its dynamics are the product of trade-offs between various evolutionary forces, and many structural features are not related to functional properties. In other words, evolution does not produce the best of all worlds, not even the best of all possible worlds, but only one possible world.

It's now been ten years since publication of the original paper and ENCODE has never again mentioned their 80% functional claim or claimed that most of the genome is functional.

We still have to deal with fallout from the huge success of a massive publicity campaign that spread false information about junk DNA. Ten years later, the majority of scientists and most of the general public still believe that ENCODE refuted junk DNA. It tells us that propaganda is much more effective than scientific evidence.

---

Birney et al. (The ENCODE Consortium) 2012) An integrated encyclopedia of DNA elements in the human genome. Nature 489:57–74. [doi: 10.1038/nature11247]

Casane, D., Fumey, J., et Laurenti, P. (2015) L’apophénie d’ENCODE ou Pangloss examine le génome humain. Med. Sci. (Paris) 31: 680-686. [doi: 10.1051/medsci/20153106023]