The ENCODE project is a massive international program to get papers in Nature, and as Larry notes is better described as a publicity campaign than a research project. Every couple of years they pop up with another paper with sensational, but unfounded, claims — in 2012, for instance, they claimed that 80% of the genome was functional, using a wobbly and useless definition of “functional”, and the creationists loved it. They still fling that claim in my eye every time I engage them.
But this time around they’ve dialed the hype-meter down, which is good, I guess. It does mean the paper is dry as dust and not particularly interesting, with nothing but description.
Both of these publicity campaigns, and the published conclusions, were heavily criticized for not understanding the distinction between fortuitous transcription and real genes and for not understanding the difference between fortuitous binding sites and functional binding sites. Hundreds of knowledgeable scientists pointed out that it was ridiculous for ENCODE researchers to claim that most of the human genome is functional based on their data. They also pointed out that ENCODE researchers ignored most of the evidence supporting junk DNA.
ENCODE 3 has just been published and the hype has been toned down considerably. Take a look at the main publicity article just published by Nature (ENCODE 3). The Nature article mentions ENCODE 1 and ENCODE 2 but it conveniently ignores the fact that Nature heavily promoted the demise of junk DNA back in 2007 and 2012. The emphasis now is not on how much of the genome is functional—the main goal of ENCODE—but on how much data has been generated and how many papers have been published. You can read the entire article and not see any mention of previous ENCODE/Nature claims. In fact, they don’t even tell you how many genes ENCODE found or how many functional regulatory sites were detected.
The ENCODE Consortium seems to have learned only two things in 2012. They learned that it’s better to avoid mentioning how much of the genome is functional in order to avoid controversy and criticism and they learned that it’s best to ignore any of their previous claims for the same reason. This is not how science is supposed to work but the ENCODE Consortium has never been good at showing us how science is supposed to work.
What it is is good public relations. Gotta keep the money flowing in and papers flowing out, you know.