“ENCODE Says What?” was Sean Eddy’s first reaction right after ENCODE paper and press releases came out. Here is what he wrote in his blog -
So I read in the newspaper this week that the ENCODE project has disproven the idea of junk DNA. I sure wish Id gotten the memo, because this week a collaboration of labs led by myself, Arian Smit, and Jerzy Jurka just released a new data resource that annotates nearly 50% of the human genome as transposable element-derived, and transposon-derived repetitive sequence is the poster child for what we colloquially call junk DNA.
The newspapers went on to say that ENCODE has revolutionized our understanding of noncoding DNA by showing that far from being junk, noncoding DNA contains lots of genetic regulatory switches. Well, thats also odd, because another part of my lab is (like a lot of other labs in biology these days) studying the regulation of genes in a model animals brain (the fruit fly Drosophila). We and everyone else in biology have known for fifty years that genes are controlled by regulatory elements in noncoding DNA.
Sean Eddy clearly understands that ENCODE’s claims were blatantly false, but is singing a new tune now. Dan Graur thinks that his change of opinion is a financially-motivated decision.
I am so-o-o mad with Sean Eddy. One can see black smoke coming from both of my ears. So let me tall you a true (but possibly paranoid) story.
When the ENCODE Consortium started spreading its revolutionary message of 80% of the genome is active and needed, thus disproving junk DNA and requiring textbooks to be rewritten, Sean Eddy was one of the first to point out the flaws in the ENCODE claims. His paper, however, was so polite, so demure, and so parve, that no one noticed it and the leaders of ENCODE continued to spread their hyped misinformation to the press and the gullible funding agencies. In fact, one of the authors of the misinformation was THE funding agency (see below).
The ENCODE ballon only exploded when my colleagues and I published a critique in Genome Biology and Evolution.
The publication process was not an easy one. The paper was first submitted to Trends in Genetics on 11/11/2013, but three weeks later, the editor, a certain Rhiannon Macrae, told us that he only has one review, but that was irrelevant since he cannot consider the article anyway because it is too long. That was very weird; three weeks to count the words in a text? His letter, moreover, hinted that he would breathe more easily if we withdrew the paper, so we did. We did, however, get the single review by email.
We are not surprised. Right after Dan Graur’s ENCODE criticism paper came out, we sent a note to one of his co-authors saying that it was a courageous decision to write the paper. He was surprised about the ‘courage’ part, and we explained how science in this country gets manipulated by funding con game. You either fall in line, or those controlling funding will cut you off. That means if you are a young scientist and want to express disagreement with ‘big results’, you better keep your opinions limited to your pub buddies. End result? All scientists agree about the big results, and ordinary people see joint press releases from happy scientists hugging each other.
We do not know, whether Sean Eddy’s latest paper is really motivated by funding decisions, but we can safely say the following three things -
(i) Sean Eddy is intellectually dishonest. In his latest paper, he did not provide a single scientific reason for his 180 degrees change in opinion from his first reaction after ENCODE press release came out.
(ii) Sean Eddy is a coward. Instead of backing the courageous decision by Graur et al. to present their scientific arguments (which he happened to agree with), he called Graur’s paper ‘vitriolic’, etc.
(iii) Sean Eddy is the leader of an important computational group, and his opinions can sway the decisions of many major science projects at various institutions.
We do not see how we will be able to trust any science paper from the above institution as long as Sean Eddy continues to stay in his position. For the sake of good science, we recommend that HHMI and Janelia Farm request Sean Eddy to spend more time with his family.