It doesn't take much imagination to guess what Elizabeth Pennisi is going to write when she heard about the new ENCODE Data. Yep, you guessed it. She says that the ENCODE Project Writes Eulogy for Junk DNA.
Genomes & Junk DNALet's look at the opening paragraph in her "eulogy."
When researchers first sequenced the human genome, they were astonished by how few traditional genes encoding proteins were scattered along those 3 billion DNA bases. Instead of the expected 100,000 or more genes, the initial analyses found about 35,000 and that number has since been whittled down to about 21,000. In between were megabases of “junk,” or so it seemed.This is just a repetition of the Myth Concerning the Historical Estimates of the Number of Genes in the Human Genome. The truth is that knowledgeable scientists knew decades ago that the human genome could only have about 30,000 genes or else the mutation load would be too high. Data collected in the 70s and 80s confirmed that we could only have about 30,000 functional genes because genes were bloated by introns and our genome was full of transposons.
The idea that much of the genome was junk was also a conclusion based on genetic load arguments and on the discovery that most of our genome was littered with defective transposons (pseudogenes). The concept of junk DNA also explained the C-Value "Paradox." None of that evidence has disappeared with the publication of the ENCODE results. The "dark matter" really is junk.
Pennisi continues ...
This week, 30 research papers, including six in Nature and additional papers published by Science, sound the death knell for the idea that our DNA is mostly littered with useless bases. A decadelong project, the Encyclopedia of DNA Elements (ENCODE), has found that 80% of the human genome serves some purpose, biochemically speaking. “I don't think anyone would have anticipated even close to the amount of sequence that ENCODE has uncovered that looks like it has functional importance,” says John A. Stamatoyannopoulos, an ENCODE researcher at the University of Washington, Seattle.There's nothing new in the ENCODE results. Pennisi should remember the controversy when the pilot project results were published in 2007. Many scientists pointed out, correctly, that a transcribed region is not necessarily indicative of a biological function. They also pointed out that DNA binding proteins are EXPECTED to bind to many non-functional loci, especially in a genome full of junk DNA. A binding site does not equate to biological function.
Beyond defining proteins, the DNA bases highlighted by ENCODE specify landing spots for proteins that influence gene activity, strands of RNA with myriad roles, or simply places where chemical modifications serve to silence stretches of our chromosomes. These results are going “to change the way a lot of [genomics] concepts are written about and presented in textbooks,” Stamatoyannopoulos predicts.
There's something seriously wrong when the two leading science journals openly support a radical change in our understanding of genomes based entirely on an incorrect interpretation of the data. Even when that misinterpretation is promoted by the authors of the papers that's no reason for prominent science journalists to stop being skeptical.
This is the time for Nature and Science to ask themselves how they could have been taken in by such hype and how they are going to prevent it in the future. They should also ask themselves whether they should retract the articles they wrote on the death of junk DNA. They would do no less for the science papers they publish if they found that the results were misleading.