Nature’s access absurdity: Human Genome Paper free but access to corrections will costs $64

Ahh – the saga continues.  Though I peripherally noted this in a previous post this deserves a post of it’s own.  Nature Publishing Group has a policy of making genome sequencing papers freely available.  Alas, not all such papers have in fact been made freely available (see Hey Nature Publishing Group – When are you going to live up to your promises about “free” genome papers?  and A Solution to Nature Publishing Group’s Inability to Keep Free Papers Free: Deposit them in Pubmed Central for more on this).

But I have discovered a just painful though funny absurdity with NPG’s money making machine.  They have in fact made the Lander et al. Human genome paper from 2001 freely available.  But there is an Erratum to this paper.  And if you want to get it (and without getting it there is no way to know what is being corrected), you have to pay $32: Access : erratum: Initial sequencing and analysis of the human genome : Nature.  Oh, and in addition a Correction “We have identified several items requiring correction or clarification in our paper on the sequencing of the human genome” for this paper also costs $32.  So the incorrect version of the paper is free but the corrections will cost you $64.

I wonder, for papers for which people pay $$, if there are corrections do they get them for free?

A Solution to Nature Publishing Group’s Inability to Keep Free Papers Free: Deposit them in Pubmed Central

Well, tick tock tick tock.  I am still awaiting some explanation for Nature Publishing Group once again charging for access to genome papers that they promised would be available for free.  See my last post for more details: The Tree of Life: Hey Nature Publishing Group – When are you going to live up to your promises about “free” genome papers? #opengate #aaaaaarrgh

In the meantime I have come up with a solution even if NPG folks cannot figure one out.  It is very simple.  How about Nature Publishing just deposit’s all genome papers in Pubmed Central and thus even when the money making machine of Nature switches some setting and makes the papers not freely available at the Nature web site(s) for some time, the papers will  still be officially free in Pubmed Central.  I think this is probably the only solution I would trust given that this is at least the third time this has happened.

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.
For example, currently the following papers are not freely available even though at one point they were or they clearly fit in the “Shared genomes” definition Nature Publishing Group so happily promotes:
These above are all papers of mine, so I noticed them first (I noticed this when trying to create a Pintarest Baord for all my papers and not being able to get to a free page for these papers meant I couldn’t add them to the Board.  Could it be that Nature Publishing Group is just trying to get my goat?  Let’s see.  A brief search found these papers by others – all also not freely available even though all clearly fit Nature’s own definition of genome sequencing papers:
Here are some others

I think the funniest (and scariest) part may be the corrections and errata that are not freely available. And these are just the articles I found in a 15 minute search. I am sure there are more.  Yes, Nature Publishing Group has made many genome papers freely available.  That is great.  Much better than many other publishers.  But the cracks in your system are large and suggest that nobody there is actually dedicated to seeing through on the promises.  Promises are meaningless.  Follow through is the key.  Come on Nature Publishing Group – how about assigning a “Free access ombudsman” or something like that who will make sure that free means free.  I am sick of writing these posts.  You should do your own QC …

UPDATE: see some more recent blog posts of mine about this topic:

UPDATE 3-28-12 1 PM PST:
Well, if you look at the comments, Nature is apparently trying to fix this and most of the articles I listed above are now freely available (the corrections are still not free but they claim to be working on it).  But a simple search of Nature finds there are still some papers that are closed off that shouldn’t be:

It’s not that hard to find these.  It baffles me a bit how people at Nature don’t seem to be able to find them.  But maybe I am just really good at searching …

Strange things at #PLoS; a public call to get rid of the constraints of describing author contributions

Well, am working with some others to submit a paper from a DARPA project to PLoS Computational Biology. And yet again, we have to fill out this form regarding author contributions. And yet again, I am baffled by this. PLoS can be so wise in some areas of publishing. But yet remarkably non creative in others. They ask for you to say which authors “Conceived and designed the experiments” which “Performed the experiments” which “Contributed reagents/materials/analysis tools” and which “Analyzed the data” which “Wrote the paper.” This has always seemed completely inane to me. First of all, this just does not work for some types of scientific research. Plus it seems so forced and arbitrary.

Why not actually let the authors say who did what in their own words? You can, I note, sort of get around this by badgering the copy editors a bit (e..g, see in my PLoS ONE: Stalking the Fourth Domain in Metagenomic Data: Searching for, Discovering, and Interpreting Novel, Deep Branches in Marker Gene Phylogenetic Trees where we added some additional categories of “Ideas and discussion” “Built microbial genome database” “Analyzed sequences linked to RecA and RpoB clusters” and “Analysis of distributions of sequences in GOS data.”

Even Nature lets the authors use their own words. For example, in my Genomic Encyclopedia paper published with Nature’s Creative Commons license for genome papers we wrote:
“D.W. (rRNA analysis, gene families, actin tree, manuscript preparation), P.H. (selection of strains, analysis, manuscript preparation, project coordination), L.G. and D.B. (project management), R.P., B.J.T., E.L., S.G., S.S. (strain curation and growth), K.M., N.N.I., I.J.A., S.D.H., A.P., A.Ly. (annotation, genome analysis), V.K. (CRISPRs, actin), M.W. (whole genome tree), P.D., C.K., A.Z. and M.S. (actin studies), M.N., S.L., J.-F.C., F.C. and E.D. (sequencing), C.H., A.La., M.N. and A.C. (finishing), P.C. (analysis), E.M.R. (manuscript preparation), N.C.K. (selection of strains, annotation, analysis), H.-P.K. (strain selection and growth, DNA preparation, manuscript preparation), J.A.E. (project lead and coordination, analysis, manuscript preparation).”
Which is more useful? I think without a doubt, the constraints by the PLoS system obfuscate what people did. And it is so unnecessary. Here’s a public call for PLoS to get rid of this constraint. (I am sure some at PLoS will give me grief for a public call like this, but hey it is the Public Library of Science right?). It seems completely inconsistent with many other aspects of PLoS publishing. Let the author’s describe what they did in their own words.

Please help keep the pressure on Nature Publishing Group to restore free access to genome papers #opengate

Well, I realize of course some things take time, but I cannot imagine it is that hard to restore free access to all papers reporting genome sequence data.  Nature had promised to do this when many papers were published but recently I noticed that this was not being done.  For some background see:

So today I browsed around to see if access had been restored to these genome papers.  And alas they had not for many. For example, the Plasmodium genome paper is not available

The Shewanella genome paper is also not available.  I know things take time.  But I note, I have pointed out failings in the free access previously to Nature and it was seemingly fixed but not permanently.  They really need to fix their system so that this stops happening.  So I am going to keep at them.  A bit tongue in cheek I have called this #opengate but perhaps I should call it Openomics?  

Calling for Nature Publishing Group to return all money charged for articles that were supposed to be free #OpenAccess

Well, in case you did not see, yesterday I got really pissed off at Nature Publishing Group.  Short summary – many articles of mine that were supposed to be freely available on their journal sites were not.  For more information see

People from Nature Publishing Group have responded quite quickly saying they will look into this and try to fix it and indeed they have fixed many if not all of the mistakes in accessibility I found yesterday.  Glad they responded so quickly.  However, their response raises quite a few questions.  Like “what happened?” – as in – why did access get closed off?  And why were they charging to for article use when they should not have been?
It would be good for Nature to publish / post a full description of what went wrong.  And perhaps they will.  Apparently, it was just a glitch in the system.  Whatever the cause however, almost certainly some people paid for access for articles that were supposed to be freely available.  I am calling on Nature here to audit their systems and return all money that was paid for such access.

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.  

Crawdads from Wildhorse Creek, Davis, CA

Just a quick one here. Went for a walk last night on the Wildhorse Agricultural Buffer trail near Wildhorse and bumped into a few families “fishing” for crawdads on the bridge over the little creek there. They were catching them just for the kids to look at them and then let them go on the bridge, which entertained my kids quite a bit … here is a slide show of the crawdads:

http://picasaweb.google.com/s/c/bin/slideshow.swf

Nature Endorses Obama for President

Nature has an editorial (America’s choice : Article : Nature) on the US Presidential Election that is worth looking at. For those interested in the Cliff Notes Version they end the piece with

“This journal does not have a vote, and does not claim any particular standing from which to instruct those who do. But if it did, it would cast its vote for Barack Obama.”

For more detail, I think the key point is here:

On a range of topics, science included, Obama has surrounded himself with a wider and more able cadre of advisers than McCain. This is not a panacea. Some of the policies Obama supports — continued subsidies for corn ethanol, for example — seem misguided. The advice of experts is all the more valuable when it is diverse: ‘groupthink’ is a problem in any job. Obama seems to understands this. He tends to seek a range of opinions and analyses to ensure that his own opinion, when reached, has been well considered and exposed to alternatives. He also exhibits pragmatism — for example in his proposals for health-care reform — that suggests a keen sense for the tests reality can bring to bear on policy.

They basically reiterate my concern for the McCain-Palin platform regarding science but they do not really go far enough. McCain and Palin have expressed decidedly anti-science positions recently (well, Palin has expressed them previously too). And thus it is not simply what advisors they surround themselves with but whether they would listen to any of them. Sadly the hints are that McCain and Palin will not listen to scientific advisors on many issues. Obama has made it clear that he will. Not that he puts science above all else (nor should he) But at least he will listen and make rational decisions that include science as a component. McCain and Palin seem dead set against “evidence” of any kind much of the time (note – McCain still exhibits occasional glimpses of the reasonable person he used to be on some issues like Global Warming – but these are few and far between).

Hat tip to Oliver M. for sending this around …