Showing posts with label closed access. Show all posts
Showing posts with label closed access. Show all posts

Thursday, November 05, 2015

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

Replaced with Wakelet
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Tuesday, March 03, 2015

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 (http://www.degruyter.com/view/j/micsm).
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 http://creativecommons.org/licenses/by-nc-nd/3.0/., 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 (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
Go Microbiome ...

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Monday, March 26, 2012

Hey Nature Publishing Group - When are you going to live up to your promises about "free" genome papers? #opengate #aaaaaarrgh

This is just ridiculous.  Nature Publishing Group in 2007 announced that they were making all papers in their journals that reported genome sequences would be made freely available and would be given a Creative Commons license: Shared genomes : Article : Nature.

About a year ago I posted to twitter (using the hashtag #opengate) and my blog about how Nature Publishing Group was not following through on their promises.  See for example
and more including some from others
Amazingly, and pleasantly, I note, in my complaining I exacted some responses from people from Nature Publishing Group who swore that these were just oversights and they would fix them.  Well, alas, the money collecting machine of Nature Publishing Group is back.

...... READ MORE .......
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Friday, January 06, 2012

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."

Ridiculous.

Hat tip to Karen Cranston for pointing this out.

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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 ...

UPDATE

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

UPDATE2

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


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Thursday, January 05, 2012

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
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Monday, November 14, 2011

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.

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Saturday, January 29, 2011

Nature's publishing machine really wants you to pay for stuff, even if it is supposed to be free #OA #fb

Well, this is annoying. I recently published a paper in Nature for which I was senior and corresponding author on "A phylogeny driven genomic encyclopedia of bacteria and archaea." Though I did not want to submit it to Nature, the project involved a large large large number of other people and in fairness to their contribution to the project I agreed to submit it to Nature. However, the reason I agreed in the end was that Nature said they would use their Genome Paper open license for it. For papers reporting genome sequence data, Nature claims to make the papers available at no charge and supposedly uses a Creative Commons license for publishing the paper. In addition, I note, that as the work was done my many US Government employees, we did not sign over Copyright to Nature.

On the html version of the paper, this "semi-openness" of the paper is described:
"This article is distributed under the terms of the Creative Commons Attribution-Non-Commercial-Share Alike licence (http://creativecommons.org/licenses/by-nc-sa/3.0/), which permits distribution, and reproduction in any medium, provided the original author and source are credited. This licence does not permit commercial exploitation, and derivative works must be licensed under the same or similar licence."
Other than the strange spelling of license, this seems good. However, Nature's machine seems to not be set up to make the copyright/license issues clear in every place/way. For example: if you go to the Nature site for my paper, it seems Nature is now claiming Copyright for the paper. For example see the PDF here.

And then if you click on the "Rights" link from the paper you get this which makes no mention of the Creative Commons license:

But wait. It gets better. If you go through the rights page and fill out the form asking to use the paper in an academic setting, you find out it will cost hundreds of dollars to use, according to this:


I suppose you could say that this all could be part of the Nature publishing machine just making a mistake here or there.  In fact, I would bet that this is in essence what has happened.  The system is designed for articles for which Nature holds the Copyright and has the rights to sell.  And the papers that do not follow that model get caught up in the machinery.  Nevertheless, it is annoying.  And it  makes me worry a bit about what is going to happen with Nature's new supposedly "open access" journal "Scientific Reports" which actually is not quite as open as it might seem. (The journal uses a somewhat restrictive Creative Commons license which does not fit the standard definition of "Open Access").

This seems to be YARFOA - Yet another reason for (full) open access.  If you set something free, even if someone claimed they had rights to it, it would seem more obvious to everyone out there that such a claim would be inappropriate.

I note - I am not saying Nature is trying to steal rights here.  In fact, in the past Nature has done a decent job at making sure that papers that were supposed to be available at no cost were.  For example, I looked into papers I published in Nature that Nature told us would be freely available for ever more?  This is what we were told for papers reporting genome sequence data years ago.  It was a very nice policy of Nature's that helped spread knowledge about genome papers and also helped convince me publishing in Nature was not so bad in terms of openness while I was starting to become a more openaccess advocate.  So I decided to take a look at some of the papers that I was an author on that were supposedly made freely available forever.  Here is a sampling:
Every once in a while, I had noticed in the past some of these papers were not freely available and Nature quickly corrected this so I do think they are trying not to violate their commitments.  But again, in their system, buying access is a key component and alas if the switch is going to be set wrong, it seems that it is set on "you have to pay for this" as a default.  I hope they use a different default setting for their new semi-open journal ....  

Meanwhile, if you want to do something non -commercial with our paper, feel free to do so, regardless of what the Nature website says.  
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Saturday, September 23, 2006

Top10 Novel ways to contribute to the Open Access movement

I am pleased to hear from more and more colleagues about how they support the Open Access movement in scientific publishing. Open Access journals are getting stronger and stronger and the tide is clearly turning towards Open Access. However, there are still many things that need to be achieved in order for Open Access to really become the rule. For example, of the colleagues who seem somewhat supportive of Open Access, but who still publish in non Open Access journals, the most common excuse is "I really need this for my resume" or something like that. What they mean is, the non Open Access journal they are trying to publish in is better known to their colleagues (and tenure review committees and job search committees) than a similar Open Access journal. In other words, they support Open Access in their heart, but are worried about the consequences for their careers.

I appreciate the concern of people worried about their jobs or promotions. Therefore, I think it is necessary for supporters of Open Access to turn up the heat even more and try and set up an environment where people to not have to make this choice. How can we do this? Well, I thought I had some good ideas about this but then saw Peter Suber's excellent web site about this here so I will avoid trying to be comprehensive.

Instead, I have made my personal top 10 list of ways to support Open Access that can make your life better and easier too. In italics are things you can do to show you REALLY support Open Access:
  • 1. Review.
    • Do not review for non Open Access journals. Ever. Not only will this save you time, it will ratchet up the cost of business for non Open journals.
    • You can be really insidious about this and not even answer requests for review and gum up their works that way. This is best reserved for Elsevier journals.
  • 2. First timers.
    • Encourage colleagues who are Open Access virgins to submit some (or better yet, all) their papers to Open Access journals. Some will love it and never go back.
  • 3. Promote.
    • For papers you publish in Open Access journals, if you put out a press release, make the open nature a part of the release (e.g., see our release for the Tetrahymena genome paper).
    • Send the press release to your program officer.
  • 4. Legislate.
    • Write to your legislators and librarians and university officials expressing support for Open Access.
    • If you want to be extra supportive, write to local lobbying groups such as medical support groups and tax reduction advocates pointing out the follies of non Open Access.
  • 5. Promote II.
    • Find a good Open Access publication and promote it in some way - by writing about it in a blog or reviewing it for things like Faculty of 1000, submit reviews there only for Open Access articles.
    • To be a true supporter, ONLY write reviews and commentaries about Open Access publications. Pretend like others do not exist.
  • 6. Public.
    • Promote Open Access publications (e.g., your own) to the public. Since the public cannot get access to most non Open Access publications, it is hard to use them to get the public interested in science. But it works well with Open Access publications.
  • 7. Fair use.
    • Take material from Open Access publications and (if allowed) use it to make "Open" educational materials, such as review papers or powerpoint presentations. People should be able to use it (e.g., for teaching) without worrying about copyright issues. Just make sure to cite them correctly.
  • 8. Citations.
    • For citations, when all else is equal, choose to cite Open Access publications. Not only will this increase their Impact Factor, readers will be grateful because they will be able to obtain the papers more easily.
    • Note - I am not advocating not citing others, but just when you have to choose, to choose well.
  • 9. Collaborate.
    • Choose collaborators who support Open Access principles.
    • If you want to really be good, only enter a collaboration is your collaborator is willing to publish the shared findings in Open Access journals.
    • Do not collaborate with those not willing to make such an agreement.
  • 10. Data
    • Find a way to make all your data sets and supplementary material Openly available, regardless of where you publish.
    • My favorite twist on this -a viral license to use your data. If someone wants to make use of unpublished data you have, only share it if they are willing to publish results in an Open Access journal. I am sure some people will say this is against the spirit of Open Access, but it is not. It is simply taking a longer term view of the movement.
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