Is It Time to Get the ENCODE Paper Retracted?

Dan Graur’s ENCODE bombshell - “On the immortality of television sets: function in the human genome according to the evolution-free gospel of ENCODE” came out in February 2013. For several months, he was treated like pariah, and well-connected researchers with vested interests (e.g. Daniel Macarthur and BioMickWatson) called him a troll in public. Others quickly distanced themselves from him, except for one fringe blog.

These days, we sense seeping anger against ENCODE among almost all biologists not connected with the project. They realize by now that Dan Graur stated the obvious - ENCODE was pulling the wool over everyone’s eyes. All those press releases and simultaneous publication of 30 or so papers had only one purpose

• to hide the fact that the mega-project achieved nothing. The other part of the equation has also become clear. The $300 million ENCODE wasted to fool them was supposed to go for their research under normal circumstances.

Science magazine possibly sensed that change in mood, when they decided to publish a full profile and interview of Dan Graur last month. One may find the abstract written by Yudhijit Bhattacharjee titled toward ENCODE (“others have taken issue with his style”). However, everyone should recognize that by publishing the interview, Science made a major shift from where they stood last year and before (check Pennisi’s “ENCODE Project Writes Eulogy for Junk DNA”). Full abstract of Yudhijit Bhattacharjee’s interview of Dan Graur is posted below.

When the ENCODE Project claimed that there is no such thing as junk DNA, Dan Graur counterattacked. The heart of his critique is that ENCODE researchers have made an unwarranted leap in the interpretation of their data. He alleges that the motivation of ENCODE leaders was to create a media splash that would justify the project’s cost. Some agree with the substance of his criticisms; others have taken issue with his style.

It is absolutely clear that ENCODE claims and methods have done incalculable damage to science. For example, check this coverage of “Evolution News and Views” (an Intelligent Design website) of Dan Graur’s interview in Science. They argue that Dan Graur is refusing to accept the facts published in a major scientific journal and is holding on to his old dogma of evolution.

Bhattacharjee leaves the situation at a standoff. The ENCODE leaders consider Graur’s provocations rude; Graur considers them guilty of self- promotion and self-delusion. Graur asks, “How do you know it’s functional?” ENCODE responds, “How do you know it’s not?” Graur’s null hypothesis is “assume no function”; ENCODE thinks the opposite: “specific biological activity” indicates that something interesting is happening.

By assuming that “everything is shaped by evolution,” Graur begs the question of evolution. Not only that, he mixes metaphors: intelligent agents shape things. His argument is contradictory: he says that evolution is “weeding out” junk, but he knows that the cell continues to expend wasted energy by transcribing all that alleged junk. He discounts the “tremendous amount of activity” ENCODE found in non-coding DNA. Finally, his choice of null hypothesis is dependent on his worldview: “assume no function” fits his belief that the genome is filled with junk.

Why not “assume function” as the null hypothesis? We see from history that the evolutionary teaching about “vestigial organs” held science back for a century or more. More recently, we have seen the “junk DNA” myth to be a science stopper. And now, the modENCODE project is showing the same pattern of pervasive biological activity in the fruit fly genome that was found in the human genome.

Sadly, their line of reasoning is absolutely correct, if scientific methods and records are to be trusted. ENCODE published a very high-profile and peer- reviewed paper claiming functionality of 80% of human genome and then refused to address Graur’s objections. How can we now tell the public to believe in peer-reviewed research on vaccination and other issues, yet ask them not to trust ENCODE’s findings?

Clearly, the only way to remedy this incalculable harm is through retraction of the main ENCODE paper. Given the visibility ENCODE obtained through their press releases and other PR methods, we do not see how else the problem can be fixed. In addition to the main ENCODE paper, Lior Pachter will likely argue about also retracting the Ward-Kellis paper as well.

Edit. He says he will be happy to see a correction of Ward/Kellis.