Saturday, February 18, 2023

Chapter 9: The ENCODE Publicity Campaign

On Sept. 5, 2012 Nature published a number of papers by the ENCODE Consortium. (The papers were rejected by Science.) The main summary paper announced that 80% of the human genome has a function and many of the ENCODE leaders pronounced the death of junk DNA. (pp. 238-141)
[The 10th anniversary of the ENCODE publicity campaign fiasco]
ENCODE results
The main results were that the human genome has 20,687 protein-coding genes and 18,451 noncoding genes. About 62% of the genome is transcribed. There are 636,336 binding sites for the 120 transcription factors they examined and these cover 231 million bp or 8.1% of the genome. The researchers identified more than 5 million open chromatin domains accounting for about 40% of the genome. If you add up all the biochemcally active DNA it somes to 80.4% of the genome. (pp. 241-244)
The ENCODE publicity campaign
The papers that appeared in the Sept. 5th edition of Nature were accompanied by a massive publicity campaign orgnanized by the editors at Nature. There were press releases from the univesities and government research centers that were involved in the project. The main message was that 80% of the genome is functional and the idea of junk DNA has been refuted. The de facto ENCODE leader, Ewan Birney, was hailed as a "Big Talker." (pp. 244-246)
[The ENCODE publicity campaign of 2007]
Criticisms of ENCODE
The blogosphere, Twitter, and Facebook erupted immediately with posts criticising ENCODE for misleading the public about the meaning of function and pointing out that junk DNA is alive and well. Brendan Maher, the feature editor for Nature realized the next day (Sept. 6) that they had a problem and he announced that the main purpose of the publicity capmaign was to create "the biggest splash possible" to promote results that usually don't get much attention in the popular press. He conceded that the claim of 80% functional might have been an exaggeration. Over the next couple of years a number of papers critical of the ENCODE claim have been published in the scientific literature. I have never seen such a strong and rapid criticism of papers published by leading scientists in a well-respected journal like Nature (pp. 247-254)
Science journal doubles down
In December 2012 Science listed the ENCODE results as one of the breakthroughs of the year. Although it ackonwledged the controversy, it still reported that 80% of the human genome is functional. (pp. 254-255)
ENCODE backpedals
In 2014, the ENCODE researchers partially retracted their claims about function and announced that the main purpose of ENCODE is to map all the spurious transcripts and spurious transcription factor biding sites in order to provide a resource for the community of scientists. (pp. 255-260)
[ENCODE and their current definition of "function"] [The Function Wars Part XII: Revising history and defending ENCODE] [Manolis Kellis dismisses junk DNA] [What did ENCODE researchers say on Reddit?] [Tim Minchin's "Storm," the animated movie, and another no-so-good Minchin cartoon]
ENCODE III said in 2020 that there are 20,225 protein-coding genes and 37,595 noncoding genes. There are now 2,157,387 open chromatin domains and 1,224,154 transcription factor binding sites. ENCODE III made no claims about function. (pp. 260-261)
What went wrong?
ENCODE failed to consider the null hypothesis of no function. The researchers failed to acknolwedge the critisisms of their claims back in 2007 and they failed to take into account alternative explanations of their data. This is not how science is supposed to work. (pp. 261-263)
[The 20th anniversary of the human genome sequence: 6. Nature doubles down on ENCODE results] [Style vs substance in science communication: The role of science writers in major science journals]

Notes for Chapter 9 (pp. 330-331)

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