Storify of Discussions About Shameless Behavior by #AAAS Relating to #Ebola Papers

Another day, another microbiome journal … alas not as "open access" as claimed

Just got this email

Dear Doctor Jonathan Eisen,

I would like to invite you to consider submitting a paper to our recently launched Open Access journal Microbiome Science and Medicine (
As can be seen from the titles of articles published in our first volume, MICSM reflects the full breadth of research in the diverse areas of microbiome-related science, from molecules to ecosystems:
Newton ILG, Sheehan KB, Lee FJ, Horton MA, Hicks RD “Invertebrate systems for hypothesis-driven microbiome research”
Amato KR “Co-evolution in context: The importance of studying gut microbiomes in wild animals”
Nelson DR, Tu ZJ, Lefebvre PA “Heterococcus sp. DN1 draft genome: focus on cold tolerance and lipid production”
Rudlaff RM, Waters CM “What is the role of cyclic di-GMP signaling within the human gut microbiome?”
Fang Y, Chia N, Mazur M, Pettigrew J, Schook LB, White BA “Genetically identical co-housed pigs as models for dietary studies of gut microbiomes”
MICSM is a broad-spectrum platform for the rapid publication of works of broad significance, originality and relevance in all areas related to the study of microbiomes, their components, and their roles in health and disease. We solicit research and review articles, as well as communications and vision papers. The manuscripts submitted in response to this invitation will be processed with the highest priority and all accepted papers will be immediately available on-line.

Authors are offered a variety of benefits:
– transparent, comprehensive and fast peer review;
– language assistance for authors from non-English speaking regions;
– convenient, web-based manuscript submission and tracking system;
– efficient route to fast-track publication and full advantage of De Gruyter Open’s e-technology;
– no publication charge in the first two annual volumes.

I look forward to your manuscript!
Please forward this invitation to any interested colleagues and associates.

Seemed right up my alley – an open access microbiome journal.  Alas, when I clicked on the journal link and then browsed around I found out that articles will be published using some pretty restrictive conditions. Some key parts of the text from this page is below:

1. License
The non-commercial use of the article will be governed by the Creative Commons Attribution-NonCommercial-NoDerivs license as currently displayed on, except that sections 2 through 8 below will apply in this respect and prevail over all conflicting provisions of such license model. Without prejudice to the foregoing, the author hereby grants the Journal Owner the exclusive license for commercial use of the article (for U.S. government employees: to the extent transferable) according to section 2 below, and sections 4 through 9 below, throughout the world, in any form, in any language, for the full term of copyright, effective upon acceptance for publication.

Other than being, well, painfully legalesy, this is just too restrictive for me and does not really seem like “open access”.  The no derivatives part drives me batty.  Also they write:

9. Scope of the Commercial License
The exclusive right and license granted under this agreement to the Journal Owner for commercial use is as follows:
 to prepare, reproduce, manufacture, publish, distribute, exhibit, advertise, promote, license and sub-license printed and electronic copies of the article, through the Internet and other means of data transmission now known or later to be developed; the foregoing will include abstracts, bibliographic information, illustrations, pictures, indexes and subject headings and other proprietary materials contained in the article,
 to exercise, license, and sub-license others to exercise subsidiary and other rights in the article, including the right to photocopy, scan or reproduce copies thereof, to reproduce excerpts from the article in other works, and to reproduce copies of the article as part of compilations with other works, including collections of materials made for use in classes for instructional purposes, customized works, electronic databases, document delivery, and other information services, and publish, distribute, exhibit and license the same.
Where this agreement refers to a license granted to Journal Owner in this agreement as exclusive, the author commits not only to refrain from granting such license to a third party but also to refrain from exercising the right that is the subject of such license otherwise than by performing this agreement.

Well, no thanks.  Too many restrictions and not open access in my view.  If I had to choose a “microbiome” journal to publish in, I would choose “Microbiome” an actually open access journal, where papers have the following info on them:

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver ( applies to the data made available in this article, unless otherwise stated.

Go Microbiome …

YHGTBFKM: Ecological Society of America letter regarding #OpenAccess is disturbing

Wow — I am really disturbed by the letter the Ecological Society of America (ESA) has written to the White House OSTP in regard to Open Access publishing. (For some background see Dear Representatives Issa and Maloney – Are you kidding me? Stop this bill now #ClosedAccess and Calling on Publishers to Resign from The Association of American Publishers Re Anti-Open Access Stance).

In the letter they make many statements that bother me deeply including:

However, it is important to note that there is a significant difference between research results and peer-reviewed publications.

Really – how are they different exactly?

Publishers such as ESA have a long record of reporting, analyzing and interpreting federally funded research.

OMG – seriously?  Apparently ESA is doing the analyzing and reporting and interpreting.  Not the scientists writing the papers.  But the publisher.  Seriously.  This is completely ridiculous.

It is not appropriate for the federal government to expropriate the additional value publishers add to research results.

They can’t be serious.  This is not expropriation in any way.  This is the trying to guarantee that research taxpayers have paid for – that is done by scientists that taxpayers pay the salaries of – is not then published in a way that forces the taxpayers to pay for it again.

Furthermore, subscription revenue helps to support other Society services, including scientific conferences, education programs, and the distribution of science information resources to policymakers and the public.

So now what they are saying is that the government should hand them money via subscription fees so that they can then carry out some services they think are important.  How about this – how about the ESA applies for peer reviewed grants to fund their activities so that these can be reviewed by others.  As it is ESA can do whatever it wants with that money – being fed to it without any peer review – via indirect costs and grant money.

Papers published in ESA journals may therefore be just as relevant in several years as they are today, which means that any potential embargo period will do little to mitigate the financial losses that would result from full open access.

So – the justification here for not making ecological articles available is that they are MORE important over time?  So the taxpayers pays for research that is valuable and because it is valuable over time we should make it less freely available?  Seriously?

And here is the best one:

One way to make taxpayer funded research more visible and accessible to interested members of the public would be to require federally-funded grantees to provide a second version of the research summaries they already prepare, specifically for the lay reader. To aid in online searches, these summaries could also include the source of federal funding institutions and grant numbers. Publishers could also include grant information in paper abstracts which are usually available without a subscription.

That is right, they are suggesting that scientists write a second paper to go with their science papers that would be for the lay reader.  And that these summaries could include grant IDs to help in online searches.  WTF?  So now rather than making the actual scientific papers available they are proposing that scientists write a second paper because lay people would not be able to understand the first paper?  And what about scientists who want to read the papers but are at small institutions?  And never mind that “open access” is not just about money – it is also about “freedom” in the usage of published material.

The ESA has really gone off the deep end on this.  I note – I am in full support of companies and publishers making money.  I am also generally against government regulations.  But this issue is about taxpayers rights, government waste, and the progress of science.  It is simply inexcusable for the government to not use taxpayer money judiciously.

If the government pays for the research, pays for the research supplies, pays the salaries of researchers and peer reviewers, then it is unacceptable that publishers would then limit access to papers and force taxpayers to pay for them again.

The ESA basically is saying “taxpayers should be required to subsidize us“.

Or – another way to look at this – ESA is saying: “Taxpayers – we want your money -but you are too stupid to understand what we are doing with it.


Hat tip to Karen Cranston for pointing this out.

Some responses to this post:













Calling on Publishers to Resign from The Association of American Publishers Re Anti-Open Access Stance

Well, much has been said recently about the ickyness of a new bill in Congress that is targeting open access publishing.
For more about how this new “Research Works Act” is a bad idea see
And many more.  
I think a key aspect of this bill is the disturbing support for it from the The Association of American Publishers.  Now, this association includes many you might expect to be in favor of an anti open access bill, like Elsevier and Disney and Wiley and Macmillan.  But it also includes many publishers I would not have expected to see supporting this bill such as the University of California Press and MIT Press and there National Science Teachers Association   The full list of members of AAP is here.  I think it is clearly time for the Academic community to pressure groups to abandon AAP as suggested by John Dupais: Scholarly Societies: It’s time to abandon the AAP over The Research Works Act
I therefore am calling on the academic and scientific communities to look at the list of members of AAP and if one of them is an institution with which you have any affiliation please call on them to drop themselves from the membership list.  I will be doing this for the UC Press ASAP …


Just discovered a similar but much more detailed call from Cameron Neylon.


See my post from 2007 calling for a boycott of AAP over their inane “PRISM” effort

Dear Representatives Issa and Maloney – Are you kidding me? Stop this bill now #ClosedAccess

Should the results of research funded by taxpayer money be freely available? Apparently two in Congress think no – Darrell Issa and Carolyn Maloney have cosponsored a bill that would reverse the NIH open access policies.

Why would they do this? Well, if you follow the money, you can see that they are well supported by Elsevier – one of the publishers vehemently against open access to scientific research results.

For more on this see

Seriously annoyed with Nucleic Acids Research and Oxford University Press right now

Well, I was working on adding some paper links for an online version of my CV and I discovered something very annoying.

I went to get a link for my 1994 paper in Nucleic Acids Research.  I wrote this paper with my then girlfriend, now wife, and her advisor Ginny Walbot.  The paper was on finding a “transpose” motif in one of the proteins that was part of the autonomous element for the Mutator transposon in maize “Sequence similarity of putative transposases links the maize Mutator autonomous element and a group of bacterial insertion sequences.”

So I went to Pubmed and searched for Eisen JA and Mutator and got the Pubmed entry here.  And then I looked at the links in the upper right and there were two.  One to NAR and one to Pubmed Central.  I note – the paper has been freely available online for years.  I vaguely remembered noticing some issue with the NAR version in the past so I went to that site.  And there it was

Wow.  Even though the paper is freely available in Pubmed Central, NAR is trying to charge for it.

What the f**#?

Same thing for my other NAR articles:

Not sure what the deal with this is.  Could be a glitch.  COuld be a feature.