A farewell to Nature Precedings

April 2, 2012

The story so far …

Nature Precedings is, or was, a preprint server, somewhat in the spirit of an arXiv for biology.  It describes, or described, itself as “a permanent, citable archive for pre-publication research and preliminary findings”.

This is a very useful thing.  In our recentish paper on how sauropod necks were not sexually selected (Taylor et al. 2011), we wanted to mention in passing (as part of a much more involved argument about sauropod feeding ecology) that the DinoMorph results should not be taken as face value because “assumptions about the mobility of intervertebral joints are probably incorrect”.  The obvious thing to cite for this is an old SV-POW! post (Taylor 2009) and so we did.  (It’s gratifying to see an SV-POW! post sitting cheerfully in the bibliography of a conventionally published paper.  There have been a few of these now.)

But what happens if SV-POW! goes away?  What if Matt, Darren and I are all simultaneously run over by buses, and WordPress cancel the blog after a period of inactivity?  For that matter, what if WordPress goes bust and shuts down its servers, or starts charging for hosting so that we decided to go elsewhere?  Anyone trying to follow the reference in our necks-for-sex paper would by stymied.  It seemed to me that the professional thing to do was to post a copy somewhere more permanent.

The answer is, or was, Nature Precedings.  So a couple of months ago I made up an PDF containing the same text and images as the blog post, and submitted it to Precedings, where it can be found now (Taylor 2012).  Matt and I were talking about doing the same for all the SV-POW! posts we know of that have been cited in formal literature, and perhaps getting into the habit of repositing PDFs of all such articles whenever we want to cite them, and then citing the Precedings version instead.

Not so fast!

I got an email three days ago from Precedings:

Subject: Nature Precedings change in service

Dear registrant:

As you are an active user of Nature Precedings, we want to let you know about some upcoming changes to this service. As of April 3rd 2012, we will cease to accept submissions to Nature Precedings. Submitted documents will be processed as usual and hosted provided they are uploaded by midnight on April 3rd. Nature Precedings will then be archived, and the archive will be maintained by NPG, while all hosted content will remain freely accessible to all.

Be assured that Nature and the Nature research journals continue to permit the posting of preprints and there is no change to this policy, which is detailed here.

Nature Precedings was launched in 2007 as NPG’s preprint server, primarily for the Life Science community. Since that date, we have learned a great deal from you about what types of content are valued as preprints, and which segments of the research community most embrace this form of publication. While a great experiment, technological advances and the needs of the research community have evolved since 2007 to the extent that the Nature Precedings site is unsustainable as it was originally conceived.

Looking forward, NPG remains committed to exploring ways to help researchers, funders, and institutions manage data and best practices in data management, and we plan to introduce new services in this area. We have truly valued your contributions as authors and users to Nature Precedings and hope that you will actively participate in this research and development with us.

Nature Publishing Group

Well, let’s pick this apart.

  • “Change in service” means “end of service”.  A really pointless and insulting euphemism.  Come on, NPG, give it to us straight!  We can take it!
  • We have a promise that “the archive will be maintained by NPG, while all hosted content will remain freely accessible to all”.
  • The reason given for shutting down is that “technological advances and the needs of the research community have evolved since 2007 to the extent that the Nature Precedings site is unsustainable as it was originally conceived”.  I can’t start to understand what, if anything, that means.
  • What to make of “we plan to introduce new services in this area”?  What kind of new service can there be in this area that isn’t a preprint server?

Now I don’t want to be too harsh here, just because NPG have withdrawn a service that was free in the first place.  They were under no obligation to keep providing it, of course.  And the most important thing is that the papers already reposited there will live on.

But it’s just sad that this is going away.  We need it, or something like it.

Now what?

The number one question is, will the archived documents really stay around?  I want to trust that they will, but it’s harder to keep trusting a no-longer-live system than one that has blood circulating.  It would be ironic indeed if the original SV-POW! post turns out to be more durable than the Precedings version!

But going forward, the question is where to reposit future citation-worthy SV-POW! posts?  What are the alternative services to Precedings?

It’s at times like these that we biologists suffer from Physics envy.  They have arXiv, which does this right and has been doing it right since forever.  We really need an arXiv for biology.  Or better still, we need arXiv to expand to cover our field.

References

Taylor, Michael P.  2009. Range of motion in intervertebral joints: why we don’t trust DinoMorph. Sauropod Vertebra Picture of the Week, 30 May 2009. Available at http://svpow.wordpress.com/2009/05/30/range-of-motion-in-intervertebral-joints-why-we-dont-trust-dinomorph/

Taylor, Michael P.  2012.  Range of motion in intervertebral joints: why we don’t trust DinoMorph.  Nature Precedings.  doi:10.1038/npre.2012.6878.1

Taylor, Michael P., David W. E. Hone, Mathew J. Wedel and Darren Naish. 2011. The long necks of sauropods did not evolve primarily through sexual selection. Journal of Zoology 285:150-161. doi:10.1111/j.1469-7998.2011.00824.x

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14 Responses to “A farewell to Nature Precedings

  1. beccrew Says:

    Please don’t all get run over by a bus.

  2. Mickey Mortimer Says:

    Didn’t you contact arXiv recently to ask about it hosting biology papers? Has there been no reply?

  3. Mike Taylor Says:

    Mickey, there was indeed been a reply, but I’ve been writing about so many other things recently that I’ve not got around to writing it up yet. I will do: this post on Precedings was in part to set that up.

  4. robintw Says:

    I’d be very interested in the reply from arXiv too – I wish they would expand to cover my field, and all fields really, too.

  5. Michael Richmond Says:

    ArXiv ran for a number of years on a small desktop computer under Ginsberg’s desk, without any real financial support. I suspect that the arXiv people would provide copies of their software to someone who wanted to set up a similar system for biology papers.

  6. Matt BK Says:

    How about plain old Archive.org? I imagine you could submit PDF versions to them, although I’ve never been impressed with their search functions.

  7. Mike Taylor Says:

    Do you really mean archive.org? Do they accept submissions at all? Or did you mean arxiv.org? That would be an obvious route to take, but at present they do not accept papers in palaeontology, or any area of biology other than “computational biology”. One more thing that I must get around to blogging about.

  8. Matt BK Says:

    I really mean http://archive.org. As they say on their upload page “We would love to host your digital artifacts.” They are the group behind the Internet Wayback Machine, but they also archive generally anything people submit.

  9. Mike Taylor Says:

    Interesting! I didn’t know that about them.

  10. philliplord Says:

    We’ve been building http://greycite.knowledgeblog.org for this reason. It mines and stores bibliographic metadata from blog posts, and links through to various archive servers, when it can.

    In terms of permance, I would contact the British library who run archive.org.uk. I believe that they are after more science content. Archive.org will get to your website anyway just by crawling.

    Nature Preceedings was fine, but a lot of what we need as scientists is out there anyway. We don’t need entirely bespoke solutions; they are already out there. We probably do need a bit of glue to make the process easier.

  11. Mike Taylor Says:

    archive.org.uk seems to be a squatted domain.

    Nature Precedings gave biologists a nice combination of things that’s a pretty close match to what physicists get from arXiv: permanence and citability. It’s true that “a lot of what we need as scientists is out there” but is this particular combination available?

  12. Sean Ekins Says:

    Mike – I too mourn the loss of Nature Precedings (NP). I submitted one paper far too late in the day. I have started to put my posters and things on FigShare. Perhaps they could take over the former and revive it. I think a free place to publish data is what is needed in Science in general. Did anyone calculate an impact factor for NP? Would be interesting to see this.

  13. Matt BK Says:

    I can’t recall if you guys have touched on this before, but maybe it doesn’t matter if we have “one repository to rule them all” if it were easier to apply DOIs to things like blog posts. As long as the blog post existed somewhere public (be it on a site specifically for scientific blog archiving or through a web crawler like Google’s cache or Archive.org), couldn’t a unique ID make it accessible by way of our current search technology?

    Taking it one step further, if a strict (official) DOI weren’t applied, the original URL should act as a unique identifier for a blog post, as long as it was included in the text of the post. If this were the case, maybe someone could set up an opt-in “science blogging” repository that would archive (via RSS?) posts automatically.

    Just thinking out loud.


  14. I hate to be a Gloomy Gus — as it were — here, but I’d like to reiterate my comments from previous discussion on this matter:

    1. So far, only SV-POW! authors are citing blog posts as if they were equivalent to the literature normally cited. I asked if anyone else was doing this, and there was no response BUT the SV-POW! group.
    2. The permanence of the archive and its ability to be a future repository was part of the argument for archiving blog posts in the future, thus it could not only be sustained, but was useful to do with incidental work. While future “permanence” (such as it is) is being assured, future submission is not, and thus no future ability to “archive” occurs. One wonders if WordPress’s “permanence” might be sufficient, edited or not.

    Let me be bold enough to point out that some of the SV-POW! authors has argued that they have some personal bias about the issue of publication, not just the form of peer-review but the ownership and such of publishers, and rights of access in regards to authors and taxpayer-funded research. These are valid issues in and of themselves, but compounded they spell out not just a disillusionment with the current form of publishing, but also an aversion to “paper publishing.”

    Institutions want their authors to “publish around,” not focus on a few journals. This is a step back from the mid and early 1900s when there were authors who ONLY published primary works in their own institutional journals, or where they were editors, past presidents, etc., could and did abuse this privilege and savage their opponents or use this “prestige” for political advancement. Marsh is only one of these persons. This practice continues today, especially with groups like the AMNH crew, albeit in smaller doses. But we have now much greater oversight and visibility for smaller, “house” journals — with some exceptions, which we’ve agreed not to talk about.

    Extrapolating the accessibility with the visibility and generalization of the editors (and that peer-review is occurring as intended) from these issues to now suggests we are headed to a largely digital publisher period, and I think rather than make issue of archiving for smaller “fluff” pieces that these pieces instead be submitted as actual papers.

    That’s right. You submit your comments you think are “good” for papers to journals, polished up. Digital ones. Like PLoS ONE or PLoS Biology. So that commentary that “becomes papers” are actually that. They have already agreed to cover the issue of archiving, submission is free, etc.


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