My post about the ENCODE news bonanza yesterday focused on the news and general public sort of outreach stories. But soon after the flood of actual information + hype was hitting the shore, scientists and science writers began to push back on some of the related issues. Some are about the media, some about the process of consortium-style publishing and embargoes, some about other aspects. I’ll collect those sorts of posts here and update them as they come along. I’m going to add a personal anecdote about ENCODE data at the end.
Casey Bergman: The Cost to Science of the ENCODE Publication Embargo
Daniel MacArthur: The ENCODE project: lessons for scientific publication
Larry Moran (further, and threatening more): The ENCODE Data Dump and the Responsibility of Science Journalists
But Larry, what do you really think? The ENCODE Data Dump and the Responsibility of Scientists
Alan Dove: Decoding ENCODE
Steven Salzberg comments at Nature: ENCODE was an interesting experiment back in 2003… and now
an interview on this in more detail: Interview with Steven Salzberg about the ENCODE Project.
TR Gregory: Michael Eisen’s take on ENCODE — there’s no junk? (and several other items over there)
Nature News Blog summarizes the drama: Fighting about ENCODE and junk
Manuel Corpas: The Problem With ENCODE
Sean Eddy: ENCODE says what?
Eli Rodgers-Melnick: The genome as Detroit – my reaction to ENCODE
Steve Mount: ENCODE: Data, Junk and Hype
NEW–>read this: Response on ENCODE reaction
From Ewan’s Response, I quote this–which will be the emphasis of the piece I’m about to write on this whole thing:
I am tremendously proud of the way that the consortium worked together and created the resources that it did. The real measure of a foundational resource such as ENCODE is not the press reaction, nor the papers, but the use of its data by many scientists in the future.
Casey Bergman: On The Neutral Sequence Fallacy
Will Spooner: ENCODE; a beachcomber’s guide to the genome
Marc Robinson-Rechavi: #ENCODE : La revanche du retour du fils du génome humain
Martín Bonfil Olivera: Más allá del genoma
Dan Koboldt: A new guide to human genome content and function
Mike White: I swore I wouldn’t link to HuffPo ever, but this is an actual piece of quality information: A Genome-Sized Media Failure
Greg Williams: Genomic marathon is worth it
Personal comment on ENCODE:
We’ve been doing training and outreach on ENCODE for years. But our role was paid for by the UCSC DCC team, not directly as part of the ENCODE project. So our focus was about how the data can be found and used in the context of the UCSC Genome Browser, and we were downstream of the actual ENCODE consortium.
This has been very rewarding work. In nearly every workshop we did someone used the ENCODE tracks we showed them to learn new details about their favorite region of the genome. Sometimes they would write to us later for more help, so we know they were persisting and looking further. The best moment, though, was one workshop at NIH. I had showed how to turn on the Transcription Factor Binding Site data. The woman in the front row had me come over and look upstream of her favorite gene and confirm that we saw binding evidence for a certain TF there. And then she began to giggle like crazy. She was so pleased to see this, and it was going to change a lot of things for her work.
So we know that this is going to really help bench biologists as the word gets out.
I wish we could have done more workshops–we loved doing them. We know they worked, and they got the data in the hands of researchers well before the publications. But our funds were limited. Our training materials are online, and we try to get that word out too, but not everyone has made the transition to online learning yet, and they like hands-on workshops.
But basically, after the waves of drama and hype recede, there’s going to be very good stuff for the bench-biologists and biomedical researchers. I assure you. I’ve seen it. And I can’t wait for folks with a specific topic area to start looking through the data and bringing their insights and questions on the regions they are interested in to the tools that are available to them.