I got a wonderful surprise a couple of nights ago!

Supersaurus referred scapulocoracoid BYU 12962 back when it was still in the ground. Rough composite assembled from screenshots of the video below, from about 23m17s.

I found myself wondering where the widely quoted (and ludicrous) mass estimate of 180 tons for Ultrasauros came from, and went googling for it. That took me to a blog-post by Brian Switek, which linked to a Google Books scan of what turned out to be my own chapter on the history of sauropod research (Taylor 2010) in the Geological Society’s volume Dinosaurs and Other Extinct Saurians: a Historical Perspective. So it turns out that I once knew the answer to that question. My chapter references McGowan (1991:118), which says:

Jim Jensen’s (1985) Ultrasaurus (“beyond lizard”), found in Colorado in 1979, had an estimated length of more than ninety-eight feet (30 m), compared with seventy-four feet (22.5 m) for the Berlin specimen of Brachiosaurus. This is a length increase of 1.32, so the weight increase would be (1.32)^3 = 2.3, giving an estimated weight of almost 180 tons.

[As I noted in my 2010 chapter, that’s based on Colbert’s (1962) equally silly estimate of 78 tonnes for MB.R.2181 (formerly HMN S II), the Girafatitan brancai paralectotype.]

So that’s a funny story and a mystery solved, but where it gets really good is that as I was grubbing around in the search results that led me to that conclusion, I stumbled on Episode 21 of the I Know Dino podcast, which contains a glorious embedded video: The Great Dinosaur Discovery, a 1976 film by BYU about Jensen’s work at quarries including Dry Mesa, and heavily featuring bones of what would become Supersaurus!

It’s very well worth 25 minutes of your time, despite the horrible 1970s documentary music, and brings actual new information to the table.

Some of the highlights include:

— Right from the start, seeing Jensen himself: someone I’ve been sort of familiar with from the literature, but never really imagined as being an actual human being.

— From about two minutes in, Jensen seems be uncovering bones in dry sand, rather like kids in a palaeo pits at some museums. It takes about one minute to uncover a nice tibia. Is it ever really that easy? Is the Dry Mesa quarry that easy to work?

— Putting faces to the important names of Vivian and Eddie Jones, the uranium prospectors who first led Jensen to several of his important sites, and after whom the species Supersaurus vivianae and Dystylosaurus edwini were named.

Vivian “Supersaurus” Jones and Eddie “Dystylosaurus” Jones in the field [from about 4m41s in the video]

— From about 13m30s onwards, we see what I think must be the Supersaurus pelvis that’s now on display at the North American Museum of Ancient Life. (It doesn’t actually look all that big, in the scheme of things.)

— From 16m50s onwards, things start to get real, with the uncovering (real or re-enacted) of the first Supersaurus scapulocoracoid: that is, the one that Jensen referred to in his 1985 paper as “first specimen”, but which in the end he did not designate as the holtotype. This bone, once accessioned, became BYU 12962 (but Jensen refers to it in his papers as BYU 5501).

The first appearance in the film of the Supersaurus scap BYU 12962 fully unconvered [18m11s]. You can easily recognise it as the bone that Jensen posed with from the lobe-shaped acromion process.

— Within seconds of our seeing the scap, Jensen decides the best thing to do is illustrate how it’s “like a sidewalk” by walking up and down on it. Seriously.

Oh, Jim.

— At about 19m30s, we see what is probably the big Barosaurus vertebra BYU 9024 whose identity Jensen changed his mind about a couple of times. Unfortunately, the film quality is very poor here, and you can’t make much out.

— From 20 minutes in, the video shows comparative skeletal reconstructions of Brontosaurus (clearly from Marsh 1891), “Brachiosaurus” [i.e. Giraffatitan] (clearly from Janensch 1950) and Supersaurus. The fascinating thing is that the latter is restored as a brachiosaurid — in fact, as a scaled-up Janensch-1950 Giraffatitan with some tweaks only to the head and anterior neck. So it seems Jensen thought at this time that he’d found a giant brachiosaur, not a diplodocid. (Note that this film was made three years before the Ultrasaurus scapulocoracoid was discovered in 1979, so the presumed brachiosaurid identity cannot have rested in that.)

Brontosaurus (yellow), Brachiosaurus (blue), and Supersaurus (white) — which is restored as a brachiosaurid.

— During this section, a fascinating section of narration says “The animal found here is so much larger than anything ever dreamed of, the press, for lack of scientific name, called it a Supersaurus.” If this is legit, then it seems Jensen is not guilty of coining this dumb name. It’s the first I’ve heard of it: I wonder if anyone can corroborate?

— As 22m06s we are told: “It was an AP newsman who broke the story to the world. Time and Life followed. Reader’s Digest ran the story. And National Geographic, one of the quarry sponsors, began an article.” I would love to get hold of the AP, Time, Life and National Geographic articles. Can anyone help? It seems that all these organisations have archives online, but they all suffer from problems:

Here’s that scap again, in the process of being excavated. [22:05]

— As 22m40s, Jack McIntosh turns up to give an expert opinion. I don’t know how much film of him there is out there, but it’s nice that we have something here.

Everyone’s favourite avocational sauropod specialist, Jack McIntosh.

— At 23:17, we get our best look at the scap, with a long, slow pan that shows the whole thing. (That’s the sequence that I made the composite from, that we started this whole post with.)

All in all, it’s a facinating insight into a time when the Dry Mesa quarry was new and exciting, when it was thought to contain only a single giant sauropod, when that animal was known only informally as “Supersaurus” having been so nicknamed by the media, and when it was (it seems) thought to be brachiosaurid. Take 25 minutes, treat yourself, and watch it.

Update (the next day)

The Wikipedia entry on Jim Jensen says that “In 1973, Brigham Young University cooperated with producer Steve Linton and director John Linton in order to produce The Great Dinosaur Discovery, a 1-hour-long color documentary showing Jensen’s on-site finds in Dry Mesa. […] the full-length documentary was reduced to a 24-minute-long mini-film which started airing on American television channels throughout the USA as of 1976.”

Can anyone confirm that the original date was 1973, and not 1976 as given on the short version that’s linked above?

And, more important, does anyone have access to the full-hour version?

 

References

 

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I got in a conversation recently with a friend who is about to have his first paper published. It’s been through review and is now accepted at a well-respected old-school journal owned by a legacy publisher. It’s not an open-access journal, and he asked my advice on how he could make the paper open access.

We had a fruitful discussion, and we agreed that I’d write up the conclusions for this blog.

First, you can pay the publisher to open-access your paper. That’s a legitimate option at “hybrid OA” journals, which by this point is pretty much all paywalled journals. But even when the journal invites it, that’s not always possible. In this case, my friend has no institutional funds available, and really isn’t in a position to bung the publisher $3000 out of his own pocket.

The second option is to write to the journal saying that you select the OA option, but that since you have no institutional support you have to ask for a waiver. Will this work? It’s impossible to tell unless you try it. Some journals might have an absolutely-no-waiver policy; heck, some might have a “we always give waivers but don’t advertise the fact” policy. My guess is that most have no policy at all, but that editors (who are nearly all researchers themselves) will tend to be sympathetic, and support your case. Anyway, it can’t hurt to politely ask.

If that fails, the the third approach is to use the SPARC Author Addendum. Using this legal instrument (which is freely available), you do not transfer copyright to the publisher, as they usually request, but instead give them a non-exclusive right to publish — which of course is all they actually need. That leaves you legally free to post the accepted (peer-reviewed) version of the manuscript elsewhere: in an institutional repository, your own web-site or wherever. (I’ve never used this myself, but I hear it’s widely accepted.)

If the publisher is intransigent enough to reject the SPARC Addendum, the fourth approach is to dedicate your manuscript to the public domain (for example by posting it on arXiv with the CC Public Domain Declaration). Then return the copyright transfer form to the publisher, saying truthfully that there is no copyright to transfer. Publishers are used to dealing with submissions that have no copyright: for example, everything authored by U.S. federal employees is in the public domain. Their copyright forms usually already have a section for declaring public domain.

Finally if somehow all of the above tactics fail — if the journal flatly refuses to give an APC waiver, won’t accept the SPARC addendum, and rejects works that are in the public domain though not written by US Government employees — and if despite their evident hostility to science you still want to stick with the journal that accepted your paper — then you have one final option. You can just go ahead and give them the copyright, but then post the final PDF on your own web-site anyway. Of course, you are not technically allowed to do that, but historically it’s never been a problem. It’s very widely done — especially by old-school professors, because it would never even occur to them that sharing their own work could be a problem.

To be clear, I am not advocating the last of these. The four preceding approaches are better because they are fully in compliance with copyright law. But when dealing with a publisher that is simply determined to prevent your work from being read, then you have to weigh for yourself whether you’re more interested in respecting copyright, or doing what’s right.

This is the situation with several of my own old papers, which in my young and stupid days I signed over to publishers without giving it any thought at all. Having got myself into that situation, it seems to me that making those papers available anyway is the least bad of several bad options. But I would never choose that approach now, since I publish exclusively in open-access venues.

Summary

Option zero (not discussed here) is to use an open-access venue to start with: then none of these issues even arise. But failing that:

  1. If you have funds, use them to pay the publisher an APC to make the article open access.
  2. Ask the journal for an APC waiver.
  3. Use the SPARC Author Addendum to retain copyright and give the journal a licence to publish.
  4. Dedicate the manuscript to the public domain and tell the publisher there is no copyright to transfer.
  5. If all else fails, just post the paper publicly anyway.

Walk-in access? Seriously?

November 26, 2013

Reading the Government’s comments on the recent BIS hearing on open access, I see this:

As a result of the Finch Group’s work, a programme devised by publishers, through the Publishers Licensing Society, and without funding from Government, will culminate in a Public Library Initiative. A technical pilot was successfully started on 9 September 2013

Following the link provided, I read:

The Report recommended that the existing proposal to make the majority of journals available for free to walk-in users at public libraries throughout the UK should be supported and pursued vigorously.

I’m completely, completely baffled by this. The idea that people should get in a car and drive to a special magic building in order to read papers that their own computers are perfectly capable of downloading is so utterly wrong-headed I struggle to find words for it. It’s a nineteenth-century solution to a twentieth-century problem. In 2013.

Who thought this was a good idea?

And what were they smoking at the time?

I can tell you now that the take-up for this misbegotten initiative will be zero. Because although it’s a painful waste of time to negotiate the paywalls erected by those corporations we laughably call “publishers”, this “solution” will be more of a waste of time still. (Not to mention a waste of petrol).

I can only assume that was always the intention of the barrier-based publishers on the Finch committee that came up with this initiative: to deliver a stillborn access initiative that they can point to and say “See, no-one wants open access”. Meanwhile, everyone will be over on Twitter using #icanhazpdf and other such 21st-century workarounds.

Sheesh.

As things stand there are two principal types of written communication in science: papers and blog posts. We’ve discussed the relative merits of formally published papers and more informal publications such as blog-posts a couple of times, but perhaps never really dug into what the differences are between them.

Matt and I have been discussing this offline, and at one point Matt suggested that authorial intent is one of the key differences. When we write and submit a paper, we are sending a different message from when we post on a blog.

That’s true — at least in general, although there are edge-cases such as the formal research paper that Zen Faulkes recently posted as an entry on his blog. But even when it’s true, I’m not sure it’s relevant. As Matt pointed out, authorial intent ceases to be a factor once something is published. The audience will read it how they like and do with it what they want. So I think we need to consider the paper-vs.-blog-post question in terms of the artifact itself, and discount what the author intended.

When we do that, what differences do we see? Generalising, we find that:

  • Papers are PDF while blog-posts are HTML. (That’s not quite a trivial distinction: PDFs have less clutter.)
  • Blog-posts allow and invite comments, but papers do not.
  • Blog-posts are part of an ongoing discussion whereas papers are stand-alone.
  • Papers are archived on publisher sites, whereas blog-posts are on blogs, which may be more vulnerable or ephemeral.
  • Papers are immutable once published, whereas blog-posts can be edited after initial publication
  • Papers are peer-reviewed, while blog-posts are not.
  • Blog-posts are fast, but papers are slow.

Which of these are important? Which count as wins for papers and which as wins for blog-posts? Which of them are tied together with each other? Which are fundamentally properties of the medium, and which are associated with it only by tradition?

Comments, please!

I sent this letter to Wiley today, in response to their announcement of elective open access being available in 81% of their journals. I will blog the response when it comes (or the lack of one if they don’t reply after a reasonable time).

Date: Tue, 3 Jul 2012 11:22:55 +0100
From: Mike Taylor <mike@indexdata.com>
To: cs-onlineopen@wiley.com, info@wileyopenaccesss.com
Cc: sciencenewsroom@wiley.com
Subject: New Open Access option on 81% of journals

Dear Wiley,

I am writing to express my thanks and congratulations on extending your elective open-access policy to 81% of your journals, as announced in yesterday’s press-release.

Wiley is an important publisher and the guardian of many significant journals. Given the increasing inevitability of open access, as noted in recent months by US congressmen, UK government ministers, and numerous academics and publishers, it’s going to be crucial to avoid becoming marginalised during the transition. In concert with your existing all-open-access journals, and your Free Backfiles provision, yesterday’s announcement goes a long way to assuring the community that Wiley will be around to be part of the transformed landscape.

I do have an important reservation, though. When I checked the specific details of what Wiley means by “open access” I saw to my dismay that instead of using the standard Creative Commons Attribution (CC BY) licence, Wiley has rolled its own set of terms and conditions which, in addition to being more restrictive than the standard ones, will not be immediately recognised and comprehended by potential authors.

As you probably know, the CC BY licence unambiguously fulfils all the terms of the original definition of “open access”, as specified in 2001 by the Budapest Open Access Initiative. It is for this reason that it has been overwhelmingly adopted by for-profit and non-profit open-access publishers, including BioMed Central, PLoS and Hindawi. I assume this is also why it was recently adopted by Springer for its own elective open-access programme (“Open Choice”). For a fuller discussion of the merits of fully BOAI-compliant open access, please see the article Why Full Open Access Matters.

The unfortunate upshot is that, as things currently stand, Wiley’s elective open-access programme stands alongside Elsevier’s derided “sponsored article” scheme, rather than having joined the true open-access advocates BMC and PLoS, as Springer’s Open Choice has done. This makes Springer journals currently a much more attractive open-access choice than Wiley’s. At a time when lines are being drawn, and when Elsevier in particular is widely seen in a very negative light, it’s important to establish which side of this divide Wiley is going to position itself on.

So I strongly urge Wiley, with all possible haste, to adopt the Creative Commons Attribute licence for all its open-access activities. In doing so, you will send out a strong statement. I am confident that the commercial benefits will greatly outweigh the loss of whatever minor revenue accrues from the licenced commercial re-use of not-quite-open-access articles under the current scheme.

I hope this is helpful; if desired, I will be more than happy to discuss these issues in more detail with with anyone at Wiley.

Dr. Michael P. Taylor
Research Associate
Department of Earth Sciences
University of Bristol
Bristol BS8 1RJ
ENGLAND
https://svpow.com/

P.S. This is an open letter; I will be posting it on my blog, along with your reply. It’s important that the wider community see and understand what decisions are being made as publishers transition to open access.

Update 1 (Wed  4 Jul 2012 17:38:31 BST)

Received a brief response from Wiley’s Director of OA via LinkedIn:

Dear Mike,

Many thanks for the congratulations and for the helpful comments on your blog. We are well aware of the policies of our competitors and review appropriate licensing arrangements regularly. I’ll be out of the office 6-23 July, but otherwise happy to talk further.

Best wishes,

Rachel

Rachel Burley
Vice President and Director, Open Access
Wiley Blackwell

Quietly promising, I think. Further bulletins as events warrant.

Update 2 (Thu Jul 5 09:57:01 BST 2012)

Another, independent response, from Wiley’s STM publicity manager:

Dear Mike,

Thank you for your timely note. We are considering our options for open access licensing arrangements at the moment, so it’s useful to hear the views of the wider community.

Best wishes
Jen

Jennifer Beal
Global Publicity Manager
Scientific, Technical, Medical, and Scholarly
Wiley

Again, noncommittally encouraging. We’ll see what comes of this.

Background

Today has seen the release of a Bernstein Research investment report by Claudio Aspesi, entitled Reed Elsevier: Is Elsevier Heading for a Political Train-Wreck?  It contains some stark warnings to potential investors:

Elsevier’s original support for the RWA has triggered a rising level of support for open mandates, in turn escalating an obscure bill into both a public policy debate on dissemination of publicly-funded research as well as an unwelcome scrutiny into the finances of Elsevier.

And:

Another controversy, this time around text mining, is brewing in the background, and could possibly further escalate the issues triggered by the RWA debacle.

And most importantly, this conclusion:

Adding acrimonious relationships with the research community to the difficult ones it already has with academic librarians looks self-defeating. We believe that Elsevier needs to rethink altogether how it thinks of researchers as customers, or it could end up, in a few years, facing the same hostility it encounters with much of the academic librarian community.

I’m not here to gloat.  I mention this report only as the timely backdrop to a short series of posts that I’ve been planning to write for a few weeks now.

State of the nation

It should now be clear to everyone who’s been paying attention that Elsevier has got itself into a rotten position.  No-one trusts it or likes it.  Even people who act as associate editors for its journals seem to be feeling that that’s something to be a bit apologetic about rather than something to declare proudly.  The feeling has grown stronger and more widespread — the Cost of Knowledge boycott is now closing in on 10,000 signatories — and all but the most head-in-the-sand types are now being forced to recognise that the distrust, dislike and resolution is real and significant, and that it’s not going away.

Every time I’ve got into conversation with an actual Elsevier employee (Liz Smith, Tom Reller) they’ve been friendly, reasonable and polite — and I should add, rather forbearing, when you think of how much I’ve had to say against their employer.  But there’s often an undertone of hurt.  I don’t know if I’m over-interpreting, but it seems to me that Elsevier employees feel mystified and a bit put out that all this hostility has arisen suddenly.  But of course, it hasn’t really been sudden at all.  It’s been building for many years.  Elsevier has been shielded from having to take the anger seriously because its power in the marketplace has let them bulldoze right over the dissatisfaction.  Now that the dam is finally breaking it’s catastophic.

Matt has explained in detail why no-one trusts Elsevier any more in an outstanding post that I urge all scholarly publisher employees to read if they don’t understand how things have got so bad.  To (over-)summarise Matt’s analysis, scientists are trained to see dishonesty as a permanent stain, whereas in business a certain amount of dishonesty is expected.  So things like the fake journals are a huge deal to scientists, while the career businessmen at the helm of Elsevier can’t necessarily see what all the fuss is about.  Because of half a dozen big things and a thousand small things, Elsevier has lost the trust of both librarians and researchers.

These posts are about how Elsevier can win back the trust it’s lost.  I think that’s the only way it can survive in the medium and long term.

Why do I care whether Elsevier survives?

Elsevier as it is today?  I don’t.  But there has be a core of something worth saving in a company with that much experience, with so many skilled people.  It can be done.  Same goes for Springer, Wiley, Blackwell and the rest.  In the end it’s up to each publisher whether it’s prepared to embrace the necessary changes (both cosmetic and radical), or whether it’ll keep chasing short-term megaprofits at the cost of sliding into irrelevance.

And the world needs a flourishing ecosystem of different publishers.  Much as I admire PLoS, a PLoS monoculture in publishing wouldn’t be in anyone’s best interests.  We need competition between multiple publishers to drive prices down and services up, to keep everyone on their toes.

So if Elsevier can make themselves a part of that, so much the better for them.

What Elsevier needs to do

I’m planning to post five articles in this series — most of them pretty short.

Stay tuned!  And, Elsevier folks: please do chip in with comments.

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 https://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