Eisen Lab Blog

Q & A about Elsevier, my blog retraction, and #OpenAccess

Jop de Vrieze has written an article related to the Elsevier boycott for ScienceInsider:

Thousands of Scientists Vow to Boycott Elsevier to Protest Journal Prices

In the article, one of the things he discusses is my blog post (which I then “retracted) suggesting people ignore any papers published in Elsevier Journals: Boycotting Elsevier is not enough – time to make them invisible (UPDATED/RETRACTED).

In his article he wrote:

One scientist who strongly supports the boycott is Jonathan Eisen, a microbial genomicist at the University of California, Davis, and the Academic Editor-in-Chief of PLoS Biology, an open access journal. On Tuesday, Eisen urged readers of his blog to go one step further, by no longer paying attention to research published by Elsevier. “In essence, ignore them – consider them dead – make them invisible,” he wrote. But after readers protested that no paper should be ignored just because of where it’s published, Eisen quickly retracted the entire post, which he said had been written “at midnight, with a cat on my lap.” “The response to my post helped make me realize that the semi-sarcastic attempted tone was not coming through correctly,” Eisen writes in an e-mail to ScienceInsider.


de Vrieze did a good job of representing my point of view.  But I thought it might be useful to all of the Q&A in the email with him.  Fortunately, he said this was OK to do so … here are my full answers to his questions:

If you would have adjusted your blog, what would have been the main points your would have reconsidered?

Oh – my blog post was really just a thought question written in anger in the middle of the night. I could have written it better but in the end, the idea behind the post was wrong-headed. Any scientific publication or presentation, no matter where it is made, should be considered a contribution to science. The name of the journal or the
publisher does not matter (nor from my point of view does it matter if something is in a journal per se). Thus even though I was being a bit tongue in cheek in the post suggesting we ignore publications in Elsevier journals – clearly my tone was not coming through and I decided to retract the post.

I note – following the recommendation of Ivan Oransky who runs the Retraction Watch site I left up the original post (though I changed it
to strikethrough font) and posted an explanation for the retraction.
I also tried to chase down twitter and blog and Google+ discussions of my post to say I was “retracting” the post and to explain why and what I had been trying to say.

I also note – I had sense knocked into my head on this by people on twitter like @drugmonkey -so the response to my post helped make me realize that the semi-sarcastic attempted tone was not coming through correctly

For your article you might want to check out the discussions happening on Google+ and on Drug Monkey’s blog.

https://plus.google.com/u/0/103101121348859087349/posts/B8f1XyuY7Gk

https://plus.google.com/u/0/106772544387169323774/posts/TszquaTKeoA

What do you think is the value of this petition?

I support the petition. I think scientist’s and others (humanities too …) need to take a stand against some of the publishing policies and political actions (e.g., support of the RWA) of Elsevier. I note – I already do not review for or publish in or edit for any of their journals. And I think if 1000s of scientists really followed through on this Elsevier might be forced to change their policies.

What do you think needs to change in the system?

I should note – I am personally not against for profit companies and not agains the notion that people can make a profit off of publishing.

The problem I have is really two fold.

  1. I think that research and publications that are supported by taxpayer money should be made available broadly to the public. 
  2. I think there is abundant evidence that more openness in science is beneficial to the progress of science – open data (e.g., Genbank) has revolutionized certain fields. True open access publishing frees up the literature so that not only can anyone access it but also allows anyone to remix and utilize the literature in creative ways (and potentially make a profit from doing so). Open release of software is critical for cases where software is used in scientific publications. And so on. Openness aids in the progress of science.

Thus with #1 and #2 above, I think it is imperative that we move towards more openness. The challenge is – how do we get there? And how do we pay for it? (Note – I am not saying above that being open has no cost – I am saying it is beneficial and politically wise). The problem with Elsevier in my mind is they take government subsidies that pay for journal charges, salaries of their reviewers and editors, and subscription fees for libraries – and in return – amazingly – they generally take ownership of the literature. This seems to be an unsound trade.

So – the question is – can we become more open and afford it? Yes, I think it is pretty clear that there is more than enough money being spent currently on publishing broadly that could be reallocated to open publishing. The success of PLoS and Biomed Central and the move of some societies to release publications rapidly (e.g., ASM) indicates that this is possible (though I note – Science still lags in this area).

I think we are still figuring out exactly how to set up a new system – but the old system of signing over the ownership and / or publishing rights for papers is no longer needed and it is not helpful to scientific progress.

Who should take the first, or most important steps? Scientists? Publishers? Libraries? Institutions?

Everyone. We all need to work together to come up with a system that retains the good things in the old system (e.g., scientific societies, good peer review, paper editing, etc) while being more open. We need to change hiring policies, library subscription systems, peer review, journal search algorithms, and so on.

What, if publishers like Elsevier would disappear, would give scientists a mark of quality or relevance of scientific publications?

Well – the name of a publisher and the name of a journal is a crude mark of quality at best. What should be measured is the ACTUAL quality of publications not a surrogate for quality. Certainly, everyone is busy and surrogates of quality end up being used a lot. But we need to develop systems that measure article quality better and also help people find the right articles for them. There are many examples of things in the works to help do this. The PLoS commenting system was/is an attempt at this. So is Faculty of 1000. I think post-publication peer review is going to be critical. The cream should rise to the top and the more we can do to make sure this happens quickly the better.

Scary and funny: fake researcher Peter Uhnemann on OMICS group Editorial Board #JournalSPAM

OMG.  This is both hilarious and terrifying.

Many out there know there are journals out there that border on SPAM.  I have written about this often before (e.g., see For $&%# sake, Bentham Open Journals, leave me alone and Yet another SPAMMY Science publisher: Scientific and Academic Publishing and The Tree of Life: Really sick of Bentham Open Spam) as have many others (e.g., Open and Shut?: The Open Access Interviews: Matthew Honan and Academic spam and open access publishing – Per Ola Kristensson). UPDATE: forgot to include this link: Science SPAMMER of the month: OMICS publishing group

But this one takes the cake.  There is a journal called “Molecular Biology” from the OMICS Publishing Group (for more on this publisher see Open and Shut?: The Open Access Interviews: OMICS Publishing …).  It seems new – as I cannot find any publications – but you never know – maybe they have been around a while and just have not gotten any submissions.

But I recommend everyone check out their Editorial Board.  In addition to listing Peter Deusberg (the controversial HIV denialist) there is an amazing person on their Board – Peter Uhnemann. He is listed as being from the “Department of Oximology at Daniel-Duesentrieb Institute, Germany”.  Sounds a bit strange right?  Well check out his Bio

And check out his research interests

It is pretty wacky right?  Well it turns out, as some might have guessed – it is made up.  The reason I know this is – is that Burkhard Morgenstern from the University of Goettingen let me know (in fact he is the one who alerted me to the whole story).

He sent me something he wrote on Facebook which I am posting here:

Hi,

I’m delighted to inform you that Peter Uhnemann from the
 Daniel-Duesentrieb Institute in Germany was just appointed
 editor of the OMICS journal “Molecular Biology”:


http://www.omicsgroup.org/journals/editorialboardMBL.php
 

For those of you who don’t know Peter Uhnemann: he is a fake
 person invented by the German satirical magazine Titanic.
 They created an FB account for him to make fun of social
 networks (he soon befriended on FB with various German
 politicians).

 

For those of you who don’t know Daniel Duesentrieb: this is
 the German name of the Walt Disney comic figure Gyro Gearloose.

 

For those of you who don’t know the OMICS journals: these
 are junk journals spamming around invitations to join their
 editorial boards. 

On their web page they say that

 “election of the “right” editor for a journal is one of the
 most important decisions made by OMICS Publishing Group …
 Editors, Executive Editors & Editor-in- Chief of journals
 must be senior researchers, e.g. chaired professors.”

 As it looks, Peter Uhnemann from the Daniel-Duesentrieb
 Institute meets these criteria.

It is both hilarious and a bit terrifying.  Now – mind you – it is possible that this journal could end up with some papers worth looking at.  But clearly, the Editorial process at this journal is probably going to be a bit, well, circumspect.

UPDATE: finally – as of 2/16/12 he is no longer listed on the editorial board …

Lab meeting. Feb, 1st 2012

David Coil is presenting for the Eisenlab meeting this week.  The room 5206 in the genome center has been reserved from 1:30 to 3:30pm.

Boycotting Elsevier is not enough – time to make them invisible (UPDATED/RETRACTED)

Update: The original post here was written at midnight, with a cat on my lap.  I thought this post conveyed some tongue in cheek aspect of this idea to ignore work in Elsevier journals. (one could view it as a midnight middle finger to Elsevier over some of their policies).  But clearly, based on the responses I am seeing that did not come across.  I accept the error of my ways.  Drug Monkey is right – no work should be ignored – no matter where it is published.   I could explain in more detail what I was trying to convey – but in the end that is like explaining a bad joke.  Instead, I am therefore retracting my blog post.  That is one for Ivan Oransky I guess. Now back to your regularly scheduled programs.

There has been much written in the last few days about multiple calls to boycott journals published by Elsevier due to Elsevier’s generally problematic publishing policies and support of SOPA/ RWA, etc.  People have called for people to not only boycott publishing in Elsevier journals but to also stop reviewing for them, editing for them, and also to try to get libraries to stop subscribing to them.  Some good reading in this area includes:
I think these are good steps.  But I also think they are not enough.  I am therefore calling for people to go one step further – to stop helping promote articles published in Elsevier journals.  Don’t blog about papers in Elsevier journals.  Don’t tweet about them.  Don’t use Elsevier papers for journal clubs.  In essence, ignore them – consider them dead – make them invisible.  Not completely of course.  Any work should be considered a contribution to science or math or whatever your field is.  But there are LOTS and LOTS of things to do with your time.  And if you like to share – to communicate – to discuss – it is easy to find non Elsevier articles articles for those purposes (even better – pick open access articles ..)

This may be a minor thing in the fight for more openness in publishing, but it should help.  After all, for many scientists, the worst thing that can happen is to be ignored.

How are these @kejames re: #PLoSOne cc: @boraz @edyong209 @danielaphd

How are these @kejames re: #PLoSOne cc: @boraz @edyong209 @danielaphd

Having lots of fun with my @Olloclip macro lens for my iPhone

Having lots of fun with my @Olloclip macro lens for my iPhone

First "Guardians of microbial diversity" award to Rob Dunn #microbiology #GMDs

For this I am awarding him the first of what will be many “Guardians of Microbial Diversity” awards here (we can just call these the GMDs). Not only will he get an award – I am going to send him a GMD gift from the various GMD doodads I am putting together.
Congratulations Rob.  Now off to design some more diverse GMD doodads. 

Dear #AAAS, I am NOT embargoing my own talk & I plan to record it and post afterwards #embargowatch

Just got another email from AAAS regarding their big meeting in February in Vancouver where I am scheduled to talk:

—————————————-
This request for materials is from the AAAS media relations team and is separate from any you may receive from your symposium organizer or the AAAS Annual Meeting office.
—————————————-
Dear AAAS Annual Meeting Participant:


Thanks to all of you who uploaded materials to the AAAS Virtual Newsroom by Jan. 16. For those of you who have not submitted materials or want to submit additional materials, you may do so right up through the meeting. The materials will be available online to reporters, although we can no longer guarantee that we’ll be able to copy new
submissions at our expense for placement in the on-site library of speaker materials. We will try to include materials received in the next several days in our copy order, however.



You also can make printed copies (10-15 copies) yourself and ship them to Vancouver so that we can place them in the on-site papers library for reporters. Ideally, press materials should be on-site prior to your presentation. Please see below for appended mailing instructions.


Speakers and organizers can submit materials by going to:
http://www.eurekalert.org/aaasnewsroom/mcm/speakers


Your individual username and password for the site:


Please provide the following:


— A one-paragraph biographical sketch (not a C.V.)


— A short lay-language summary of your talk, beyond the abstract.


— The text of your talk, if available, or a related (ideally recent) technical paper, either as a Word file or a PDF. PowerPoint presentations are acceptable, but a full text will better serve reporters’ needs.


— Any additional supporting materials, including multimedia files such as JPEG or TIFF photos in high resolution (300 dpi) and/or digitized video clips.


IMPORTANT: Please note that all AAAS meeting presentations are strictly embargoed and your speaker materials should not be released publicly until the time of your presentation.


If you upload your materials by 16 January, we will copy them at our expense for placement in the on-site library of speaker materials, available only to newsroom registrants.


Please notify your institution’s press office of your AAAS Annual Meeting presentation as soon as possible. Your press office can help you submit speaker materials to us and can begin to generate media interest.
….

The thing is – I did not agree to “Embargo” my talk and as I wrote about before, I do not even know what that means.  I figured, in the interest of being “open” about my feelings about this, I should write to AAAS to let them know I was not going to embargo my own talk, and I plan to record my talk and post it afterwards:

To whom it may concern


I am scheduled to speak at the AAAS meeting and I am writing this in regard to the email attached below.  I do not support the notion of an Embargo for my talk and I am unwilling to participate in the embargo. I plan to post information about my talk to the web and to my blog and am writing to specifically let you know I fundamentally do not support the embargo nor did I agree to it when I agreed to give a talk at AAAS.


I also plan to record my own talk and to post the recording and the slides to various websites.  I am not sure if AAAS has a policy about that but wanted to let you know of my plans in the interest of not having any surprises.


Sincerely


Jonathan Eisen

Will report back if I get a reply … and maybe I can get Ivan Oransky to help make sense out of what a talk embargo means.