I have discovered a new nugget of information in my ongoing quest (part 1, part 2, part 3) to discover what the licence terms are for author-pays Gold Open Access articles in Elsevier journals.

You will recall from way back in part 1 that Elsevier’s own “Sponsored Articles” page doesn’t include that information. A while after I posted that, they added a link to this page.  It was initially broken, then briefly mended, and now seems to have been completely removed again — hardly a sequence of actions that conveys a powerful desire for transparency.

However — and thanks to Alf for pointing this out in a comment — Elsevier also at some point after my initial article added a link in the middle of the text of the Sponsored Articles page:

Sponsored Articles have a specific set of user rights – for more information, please External link  follow this link.

I clicked that link, only to find — you couldn’t make this up — that this link is now also broken:

We can only hope it’ll be back soon.

Anyway — since finding out what the terms are from the web-site is such a dead loss, there is another approach to take, and that is talk to an author who has published, or is considering publishing, a Sponsored Article.  I found such an author in David Roberts, and this was his experience:

I emailed Elsevier to ask them what sort of copyright transfer one has to sign when choosing their gold open access option.


Dear sir/madam,

If I pay for my article to be sponsored so that it is ‘available to non-subscribers’ on Elsevier’s ‘electronic platform’, what copyright notice do I sign? Elsevier is giving the article away – that is to say I have paid for the costs associated with the article – does Elsevier still own the copyright, and, more importantly, is the file allowed to be hosted anywhere else? Or, to put it another way, what is the legal status of the published article, and what future-proofing is there to maintain that free access in perpetuity?

David quotes Elsevier’s reply (with permission):

I can advise you to sign your copyright form as normal. Please choose the option that most applies to you.

If you choose to pay for open access, your paper will be freely available to all on Science Direct only for all time.

David quite reasonably comments:

So even if one is paying for the article to be open access, Elsevier still own the copyright to the article. I find this somewhat outrageous.

And finally notes:

In parallel with the above email, I emailed Alicia Wise, Elsevier’s Director of universal access. I received a reply, but I’m still waiting to hear from her if I can make that one public.


So the upshot is that when you publish a Sponsored Article with Elsevier, you give them $3000 and the copyright.  No wonder no-one is choosing this option.

Another picture from the recent ostrich dissection (click for full-size, unlabeled version). Last time we were in the middle of the neck, looking from anterior to posterior. This shot is from closer to the base of the neck, looking from posterior to anterior. A lot of the stuff is the same: the ragged cut from the saw at the meat processing plant where the ostrich was cut up; the spinal cord with the supramedullary airways above it in the neural canal; and the large interspinous ligament with diverticula on either side. We’ll have reason to refer back to some of those things in the not-too-distant future, but right now I want to draw your attention to something else: the tendons of the paired longus colli dorsalis muscles toward the top of the photo.

Here’s a modified version of Wedel and Sander (2002: fig. 2) with the course of the longus colli dorsalis highlighted in red (anterior is to the left). It is a curious aspect of bird necks that the large dorsal muscles do not insert on the neural spines but on the epipophyses (or dorsal tori or dorsal tubercles) above the postzygs. A naive approach based on beam theory would suggest that inserting on the neural spines would give those muscles more leverage, but necks are tricky and often defy such a priori predictions.

Instead of inserting on the neural spines, the longus colli dorsalis muscles originate from them, especially in the posterior part of the neck, and that’s what the photo at the top shows. From the reader’s point of view, the big interspinous ligament runs forward to attach to the posterior side of the neural spine (not visible because it’s buried in gloop, but it’s about a third of the way down from the top). The longus colli dorsalis tendons are running forward from the anterior side of the neural spine.

Fig. 20. An MRI of the mid-cervical series of an ostrich (Struthio camelus). In sagittal section, the interspinous ligaments are lighter than the surrounding muscle because of their high fat content. The neural canal is occupied by the spinal cord and supramedullary pneumatic airways. Also apparent in this image are the tendons of the longus colli dorsalis muscle originating from the neural spine. Scale bar is 4 cm.

Here’s the same thing again, also in an ostrich, but in an MRI this time (and with anterior to the right; Wedel et al. 2000: fig. 20). The dark streaks running forward from the neural spines are those longus colli dorsalis tendons. The interspinous ligament also shows up nicely as a series of white bands connecting adjacent neural spines.


I was searching for some information — what proportion of Elsevier’s revenue is from journal subscriptions.  So far, I’ve been unsuccessful with that (can anyone help?), but along the way I stumbled across Elsevier’s Annual Reports and Financial Statements for 2011.

And it makes happy reading.  In these times when people are constantly moaning and whining and complaining about shrinking library budgets, it’s good to see that if you just pull your socks up and work hard, you can still do well for yourself!  Check it out:

As you can see, whereas in 2010 Elsevier were only able to generate an operating profit of £724M/£2026M = 35.7%, by sheer hard work and gumption they were able in 2011 to bring this up to £768M/£2058M = 37.3%.  This continues a fine trend of five successive years of increasing profits — not just increasing in absolute amount (although that’s true, too), but increasing as a proportion of all revenue.

So hats off to Elsevier, and to the valiant shareholders whose self-sacrifice allows us all to obtain more than adequate typesetting for our papers!  Pay no attention to the moaning Minnies — this is an all-American success story!

Those ostrich necks I went to Oro Grande to get last Thursday? Vanessa and I started dissecting them last Friday. The necks came to us pre-cut into segments with two to three vertebrae per segment. The transverse cuts were made without regard for joints so we got a bunch of cross sections at varying points through the vertebrae. This was fortuitous; we got to see a bunch of cool stuff at the cut faces, and those cut faces gave us convenient avenues for picking up structures and dissecting them out further.

In particular, the pneumatic diverticula in the neck of this ostrich were really prominent and not hard at all to see and to follow. The photo above shows most of the external diverticula; click through for the full-resolution, unlabeled version. The only ones that aren’t shown or labeled are the diverticula around the esophagus and trachea (which had already been stripped off the neck segments, so those diverticula were simply gone), those around carotid arteries, which are probably buried in the gloop toward the bottom of the photo, and the intermuscular diverticula, of which we found a few in parting out the dorsal and lateral neck muscles.

There is one final group of diverticula that are shown in the photo but not labeled: the interosseous diverticula that fill the air spaces inside the bone.

We have tons of cool photos from this dissection, so expect more posts on this stuff in the future.

For previous posts showing diverticula in bird neck dissections, see:

Things to Make and Do, part 7: fun with rhea necks

Things to Make and Do, part 7b: more fun with rhea necks (admittedly, not the most creative title ever)

In the middle of February, Times Higher Education ran a piece by Elsevier boycott originator Tim Gowers, entitled Occupy publishing.  A week ago, they published a letter in response, written by Elsevier Senior VP David Clark, under the title If it ain’t broke, don’t bin it, in which he argued that “there is little merit in throwing away a system that works in favour of one that has not even been developed yet”.

Seeing the current journal system, with its arbitrary barriers, economic inefficiencies and distorted perspective on impact, described as “a system that works” was more than I could bear.  So I sent a letter in response, and it’s published in today’s issue as Open, moral and pragmatic.

Space limitations of THE letters meant that I was only able to address one aspect — the economics.  Based on numbers in their own annual report, I show that the cost of each article that Elsevier makes available to subscribers is twelve times the cost of each article that PLoS makes available to the world.  And since Elsevier’s 200,000 articles per year are about a seventh of the total global output, the money paid to Elsevier alone would easily pay for every single paper to be published as open access.  Easily.

No doubt there are errors in some of the numbers, which are necessarily estimates; and the calculation is overly simplistic.  But even allowing for that, there is plenty enough slop in the figures that the conclusion stands.  If we stopped paying Elsevier subscriptions alone — we can keep Wiley, Springer and the rest — the money we save would pay for all our work to be available to the whole world, with hundreds of millions of pounds left over to fund more research.

Worried about the lack of jobs in palaeontology?  Concerned that universities are reducing the number of tenure-track positions?  Disturbed by the elimination of curators and preparators from museums?  We need to cut the inefficient, profiteering publishers out of the loop.

It came from my desk

March 8, 2012

I was putting a new card in my camera and needed some test photos, so I shot what was on my desk: some random doodles from discussions with various folks, and an ostrich cervical.

I love my job.

Bonus SV-POW!bucks to the first person to decipher the diagram on the lower left.

David Roberts just commented on the last-but-one post, Winkling licence information out of Elsevier, bit bit bit:

David Roberts Says:
March 6, 2012 at 11:41 pm e

The extra rights for sponsored articles page is now linked to from http://www.elsevier.com/wps/find/authorsview.authors/sponsoredarticles

And he’s right: here’s a screenshot of the Sponsored Articles page:


So this is a step in the right direction, isn’t it?  Movement in the direction of openness. (Not openness of the actual articles, of course; just openness about the non-open status of the articles. But still.)

Except …  What do you get if you click on the new link?


So in the spirit of collegiality and just generally being a helpful kind of chap, I suggest the following modification to Elsevier’s “building insights, breaking boundaries” motto:


“Oh, har har har”, you might say, in your best sarcastic voice.  “What is the purpose of this pointless snarking at Elsevier?”

Simple.  It shows that they just don’t care.

It takes ten seconds, max, to check that a link works.  All you have to do is click on it.  That they didn’t even take that ten seconds shows just how much they don’t get it.  I wanted to believe that adding the “User Rights” link showed that Elsevier recognised the importance of being explicit about such things, that they see that authors deserve at the very least to be actually told what rights they are giving away along with their $3000.

But if they had learned to care about this stuff, they would have done it right.  They they just shoved up a link and moved on without even clicking on it says to me that it’s just a cynical get-people-to-shut-up move.

So, no, it’s not pointless snarking.  In Elsevier, we are dealing with a corporation that has learned, through years of market dominance, author passivity and unchallenged exploitation, that it can do whatever the hell it wants and it doesn’t matter.  Which is why it routinely treats authors with contempt.

You’d hope the Cost of Knowledge boycott (now closing in on 8000 signatories) would have taught them better.  Apparently not.

Building Insights.  Breaking Links.

My new favourite blog

March 6, 2012

Folks, you should all stop reading this blog right now, and get yourselves across to What’s In John’s Freezer?, the awesome new blog of biomechanics wizard and brachiosaur-cervical scan facilitator John Hutchinson.

Oh, and if you wonder about the blog title, and can’t see how the contents of someone’s freezer could be very interesting, here’s a photo of two of John’s many freezers that I took when I was visiting:

This post is part three in what, astonishingly, seems now to be an ongoing series about trying to discover what Elsevier’s licenses are.  For parts one and two, see:

Today I read an article that I think was meant to be encouraging, but which instead I found disturbing.  Talking text mining with Elsevier recounts Heather Piwowar’s recent experiences in trying to use Elsevier articles in her text-mining project.

The happy ending for Heather is that she’s managed to get Elsevier’s permission to do at least part of her project, although the process involved a monumental waste of everyone’s time, including a conference call between Heather, her librarian, and six Elsevier staff, plus consulatations with lawyers.

The sad part is that, as Heather acknowledges in her post, all of this manouevering has done absolutely nothing to help the many other authors who might have awesome text-mining project ideas: all of them will have to go through the same ludicrously inefficient process.  (That’s assuming that they, like Heather, are fortunate enough to catch a senior Elsevier executive’s attention on Twitter.  Because otherwise, Elsevier are actively discouraging researchers from approaching them directly.  Why?  Because the Elsevier Director of Universal Access’s “only hesitation was that she might be overwhelmed by requests from others who also want text mining access”.  Heaven forfend that people should waste her time trying to obtain access!)

But that’s not the really stupid part.  Here’s the really stupid part.  Heather writes:

I asked for the text of the standard reuse agreement. It was sent to me but I was asked not to share it publicly because “it is a legal element”.

What this means that no-one is allowed to know what the text-mining terms are.  Extending this, it means that no-one who publishes in an Elsevier journal knows what rights they have conferred on, or withheld from, future text-miners.  And that includes those authors who have elected to take Elsevier’s “sponsored article” option — this is just one more aspect of the agreement they sign that is completely unspecified.  So when I pay $3000 to make my article “open access”, I do not know and have no way to find out whether that means it will be available for text-mining, and if so what the text-mining project is allowed to do with its results.

Come on, Elsevier.  We all understand that, rightly or wrongly, we’ve signed our copyright over to you when we published in your journals, and that you therefore have the legal (if not moral) right to impose whatever restrictions you choose.

But would it kill you just to tell us what those restrictions are?

BTW., for those who have wondered why it’s Elsevier in particular that is the subject of the Cost Of Knowledge boycott, this kind of opacity is a contributing factor.  By contrast, if you look at another exploitative profiteering barrier-based publisher, Springer, you can clearly see from their “Open Choice” page what the terms of publication are: Creative Commons Attribution (CC BY).

I can’t see what’s stopping Elsevier from doing the same.

In among all the open-access discussion and ostrich-herding, we at SV-POW! Towers do still try to get some actual science done.  As we all know all too well, the unit of scientific communication is the published paper, and getting a submission ready involves a lot more than just the research itself.  One of the most important aspects is preparing the illustrations — indeed Matt once told me that he thinks one of the best ways to put a paper together is to start with the illustrations, then write the text around them.

[Illustrations are often referred to as “figures”.  I don’t know how the tradition got started, but since that term also means numbers, I will try to avoid it.  If I tell you “I am working on the figures for my diversity paper”, you don’t know if I am accumulating statistics or preparing illustrations.]

Done well, illustrations can be things of beauty as well as scientifically informative.

Taylor et al. 2011b:fig. 1 -- Sauropod neck gallery

Taylor et al. (2011b: figure 1). Sauropod necks, showing relationships for a selection of species, and the range of necks lengths and morphologies that they encompass. Phylogeny based on that of Upchurch et al. (2004: fig. 13.18). Mamenchisaurus hochuanensis (neck 9.5 m long) modified from Young & Zhao (1972: fig. 4); Dicraeosaurus hansemanni (2.7 m) modified from Janensch (1936: plate XVI); Diplodocus carnegii (6.5 m) modified from Hatcher (1903: plate VI); Apatosaurus louisae (6 m) modified from Lovelace, Hartman & Wahl (2008: fig. 7); Camarasaurus supremus (5.25 m) modified from Osborn & Mook (1921: plate 84); Giraffatitan brancai (8.75 m) modified from Janensch (1950: plate VIII); giraffe (1.8 m) modified from Lydekker (1894:332). Alternating grey and white vertical bars mark 1 m increments.

There are a few things to be said about preparing good illustrations, so we’re kicking off a short series on the subject.  This is the first.

But the zeroth was published here a couple of years ago.  Since the most important illustrations in many palaeontology papers are those of the specimens, the base you’re working from is your specimen photographs.  So you might want to refresh your memory by reading Tutorial 8: how to photograph big bones before we proceed.

There are various steps in getting from a photo to a finished, publishable figure, and we’ll look at those along the way.  But somewhere along the line, if you’re publishing in a conventional journal such as the Journal of Vertebrate Paleontology, you’re going to flatten your colour images down to greyscale. Postpone that step till the last possible moment.

That should be too obvious to need saying, but I’ve got it wrong myself.  When I was preparing the specimen photographs for the Xenoposeidon paper, destined for Palaeontology, I flattened the images too early in the process, with the result that the greyscale versions of the figures that were included in the paper are the only versions in existence.  The upshot is that if you look at the full-resolution illustrations in the unofficial supplementary information, you’ll see that the version of Figure 3 available there is greyscale, just like the one in the paper.

By the time the three of us did our neck-posture paper in Acta Palaeontologica Polonica, we weren’t quite so dumb.  So although the illustrations in the published paper are all greyscale, the two that are based on specimen photographs, rather than assembled from previously published greyscale components, were prepared in full colour, then flattened as the very last process before submission.  As a result, the full-resolution illustrations in the unofficial supplementary information have figures 1 and 2 in colour:

Taylor et al. (2009: Figure 1). Cape hare Lepus capensis RAM R2 in right lateral view, illustrating maximally extended pose and ONP: skull, cervical vertebrae 1-7 and dorsal vertebrae 1-2. Note the very weak dorsal deflection of the base of the neck in ONP, contrasting with the much stronger deflection illustrated in a live rabbit by Vidal et al. (1986: fig. 4). Scale bar 5 cm.

So we were pretty happy with that.  But by the time we came to submit the Brontomerus description a couple of years later, we’d had a rather obvious (in retrospect) thought: just because we can’t have colour in the printed journal, does that mean we can’t have it in the PDF?  We asked the good people at Acta Pal. Pol., and they agreed that we could submit colour illustrations, they’d use them in the PDF, and then flatten them to greyscale themselves for the printed edition.

Since about fifty times as many people see the PDF as see the printed journal [yes, I just made than number up out of my head], that solution suited us very well.  The outcome was the the PDF has gorgeous figures like this one:

Taylor er al. 2011a: fig. 4 -- Brontomerus caudal vertebra

Taylor et al. (2011a: figure 4). Mid-caudal vertebra of the camarasauromorph sauropod Brontomerus mcintoshi from the Lower Cretaceous Cedar Mountain Formation of Utah, OMNH 61248 in dorsal (A), anterior (B), left lateral (C), posterior (D) and ventral (E) views.

(I’m slightly sorry to be displaying all our own illustrations here, but they do make the point and frankly I like looking at them.  Especially that beautiful caudal vertebra.)

Why am I making such a big deal about colour?  Because colour is information, and as scientists we love information.  When you flatten a colour image to greyscale, you lose information, and that should never be done without regret.  It’s perfectly possible that adjacent regions of a fossil will be a different hue but the same brightness: flatten the image and the two colours look the same, but in the original you can see a distinction.  That’s valuable.

So in this day and age, The Right Thing is:

  • Prepare your figures in colour
  • Submit them in colour
  • If the journal has a printed edition (and charges extra for colour printing, as most do), tell them to flatten to greyscale.

On the other hand, if you’re submitting to an open-access journal — and you should be, if you want to be widely read — there’s a good chance that it’s online-only (as with PLoS ONE and Palaeontologia Electronica), in which case the use of colour is a complete non-issue.  The only reason to prepare monochrome figures then is (as with the Taylor et al. 2011b sauropod-neck bestiary above) when you’re constructing them from pre-existing greyscale images.


Taylor, Michael P., Mathew J. Wedel and Darren Naish. 2009. Head and neck posture in sauropod dinosaurs inferred from extant animals. Acta Palaeontologica Polonica 54(2):213-230.

Taylor, Michael P., Mathew J. Wedel and Richard L. Cifelli. 2011a. A new sauropod dinosaur from the Lower Cretaceous Cedar Mountain Formation, Utah, USA. Acta Palaeontologica Polonica 56(1):75-98. doi: 10.4202/app.2010.0073

Taylor, Michael P., David W. E. Hone, Mathew J. Wedel and Darren Naish. 2011b. 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