ENCODE waves hit the shore…and scientists respond

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: ENCODE Leader Says that 80% of Our Genome Is Functional

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

Michael Eisen: This 100,000 word post on the ENCODE media bonanza will cure cancer

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.

Faye Flam: Did ENCODE Results Get the Junk out of Our Genomic Trunk?

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

Mike White: ENCODE Media FAIL (or, Where’s the Null Hypothesis?)

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

Michael Eisen: Blinded by Big Science: The lesson I learned from ENCODE is that projects like ENCODE are not a good idea

Mark Wanner: ENCODE and the rocky road between data and “so what?”

Will Spooner: ENCODE; a beachcomber’s guide to the genome

Moreno Colaiacovo: Sono stati pubblicati i risultati del progetto ENCODE: da oggi il genoma umano ha meno segreti!

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

Ashutosh Jogalekar: Three reasons why junk DNA makes evolutionary sense

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

Athena Andreadis: Junk DNA, Junky PR



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.

7 thoughts on “ENCODE waves hit the shore…and scientists respond

  1. Pingback: #ENCODE : La revanche du retour du fils du génome humain | Tout se passe comme si

  2. Pingback: more ENCODE publicity « linkstream2 microblog

  3. Pingback: ENCODE; a beachcomber’s guide to the genome | Eagle Genomics

  4. MRR

    “#ENCODE : La revanche du retour du fils du génome humain” is by me, Marc Robinson-Rechavi, alias MRR or @marc_rr

    Thanks for maintaining this list and for all your other great work. I agree, when all this quiets down, the data will remain and be very useful.


  5. Mary Post author

    Merci Mark! I have edited it and you are credited now.

    Funny, I just started the list as a place to keep stuff I needed to read, and then a bunch of other people seemed to find it useful. And I realized today it was unfair to restrict it to English.

    Tomorrow morning I have a “tip of the week” coming up that talks about how bench biologists can get some use of it right away. And I talk about how much I enjoyed the discussion because it was like a world-wide lab meeting on blogs and twitter.

  6. Pingback: Video Tip of the Week: ENCODE enables smaller science | The OpenHelix Blog

  7. Pingback: BioMed Central ENCODE articles: ePubs now available - BioMed Central blog

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