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

• Calling for Nature Publishing Group to return all money charged for articles that were supposed to be free #OpenAccess
• Today is a day to be annoyed with Nature (Publishing Group that is) #NatureFail
• The Tree of Life: Nature's publishing machine really wants you to pay for stuff even if it is supposed to be free.
• The Tree of Life: Please help keep the pressure on Nature ...

and more including some from others

• On science blogs this week: Evolution | ScienceWriters (www.nasw.org)
• The price for Nature Open Access: $32 | Mario's Entangled Bank

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.

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:

• The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria. Still free. Yay. Anyone can get anthrax.
• Genome sequence of the human malaria parasite Plasmodium falciparum. Still free.
• Genome sequencing: Brouhaha over the other yeast. Still free. 
• Microbiology: Gastrogenomics. Still free. 

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.  

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.