Last time we looked at the state Elsevier has got itself into, and how it needs to make significant changes to regain the trust of researchers (and librarians for that matter).

By coincidence, literally as I was writing that, Elsevier’s Liz Smith tweeted:

Job opportunity: Executive Editor, Social Media Content at Elsevier Ltd - Oxford, United Kingdom #jobs http://lnkd.in/ZgfusW

I clicked through and looked at the advert:

Can you help us tell our story? We’re looking for someone who is part community manager, part brand manager and part journalist to be in charge of an exciting new website that will help us communicate more effectively and consistently with the research community.

You’ll establish and implement a content strategy for the site, to make sure that we’re talking about the many positive things happening at Elsevier.

This is worth doing — as Richard Poynder pointed out back in January, Elsevier needs to get out more, and hiring someone whose job is just that can’t hurt.  But I hope no-one at Elsevier thinks that it will be enough to “make sure that we’re talking about the many positive things happening at Elsevier”.

The problems run much deeper than that.

So I’m going to discuss some of the things that Elsevier needs to actually do.  By that I mean, not just talking more effectively about what’s happening already, but changes that need to made.

This post will address the easy ones — things that Elsevier should do right now, without even thinking about it.  We’re talking here about things that will have pretty much no cost, and will start to make Elsevier look like people we can do business with.

1. Be explicit about “sponsored article” terms

I’m starting with this one to give Elsevier a head start, since it seems they’ve fixed this now.  As of a few weeks ago, the sponsored article page has a link to a Sponsored Articles – User Rights page which spells out important details about what you are and are not allowed to do with a sponsored article.

(For the moment I am not interested in what those terms are — we’ll discuss how they are and are not satisfactory in the next article.  I am just interested in whether we can find out what the terms are.)

Why am I mentioning this in How Elsevier Can Save Itself when it’s a problem they’ve already fixed?  Two reasons.

First, because it took an incredibly long time to get them to make these terms clear: see previous articles one, two, three, three and a half, four.

Second, the terms are still not completely clear, in that they don’t say who has the copyright in the article.  (It’s Elsevier, by the way, not the author, but we’ll talk about that in the next part.)

This is in contrast to, for example, Springer’s “Open Choice” page, which is crystal clear about both copyright ownership and access conditions in just 55 words of a page that fits on a single sheet of A4.

2. Be explicit about non-sponsored article terms

I have little idea at the moment exactly what I’m allowed to do with regular non-sponsored articles.  I am affiliated with the University of Bristol and have off-campus access via Shibboleth and an intermittently functional VPN, so I assume I am allowed to download ScienceDirect articles.  But I don’t know whether, for example, I’m allowed to email copies to colleagues who should have access but don’t from off-campus; or whether I’m allowed to text-mine the articles that I have access to; or, if so, what I am allowed to do with the results.

To be fair, there is a fairly hefty document on Authors’ Rights & Responsibilities, but that is addressed much more to the authors of articles than to their users.

Immediate Update.  It turns out I was looking in the wrong place: the information doesn’t seem to be on elsevier.com, but it is on sciencedirect.com, where it can be reached by a Terms and Conditions link on almost every page.  Those terms and conditions are very restrictive, but again we’ll discuss that next time.  The important thing is to make sure they are very easy to find.

3. Make it trivially easy to find sponsored articles

When I was first trying to discover the terms of “sponsored articles”, one approach I took was to go to Cretaceous Research, an Elsevier journal, try to find a sample sponsored article, and see what it said about itself.

Well, I couldn’t do it.  The Advanced Search page has fields for subject, date-range and more, but no “limit to sponsored articles” or similar checkbox.

There are lots of reasons people might want to find sponsored articles, and I can’t think of any good reasons why Elsevier might not want them to.  So this should be made very easy.  (Apart from anything else, it’s about the best way to advertise the journal.)

Not providing a searching option makes it look as though Elsevier want to hide sponsored articles — to stop people from getting full value from them.  That perception, whether accurate or not, needs to be dealt with.

4. Stop lying about copyright transfer

This page in the Author’s Rights area discusses a question that comes up a lot:

Why does Elsevier request transfer of copyright?

The research community needs certainty with respect to the validity of scientific papers, which is normally obtained through the editing and peer review processes. The scientific record must be clear and unambiguous. Elsevier believes that, by obtaining copyright transfer, it will always be clear to researchers that when they access an Elsevier site to review a paper, they are reading a final version of the paper which has been edited, peer-reviewed and accepted for publication in an appropriate journal. This eliminates any ambiguity or uncertainty about Elsevier’s ability to distribute, sub-license and protect the article from unauthorized copying, unauthorized distribution, and plagiarism.

This is flagrant nonsense.  No-one — no-one — evaluates the trustworthiness or validity of a paper on the basis of who owns the copyright.  No-one.

So whatever the true reason for copyright transfer, we know it’s not to make it “clear to researchers that when they access an Elsevier site to review a paper, they are reading a final version of the paper.”

When Elsevier tells us things that we know are not true, how can they expect us to believe anything else they say?

5. Root out and destroy and stupid conditions

You sometimes hear stories like this one: an inter-library loan facility where the librarian is sent a PDF, but publisher restrictions do not not allowed it be forwarded to the patron.  Instead, the librarian has to print the PDF out, destroy the original, scan the printout and send the scan to the patron.

Are these stories true?  I don’t know.  If they are, is Elsevier the publisher concerned?  I don’t know.  But Elsevier needs to make sure of that.  At this point, any such stupidities will be discovered, and trumpeted, and ridiculed.

The same goes for any other equally dumb edge-cases.  If they exist, someone’s going to find them.  Better for Elsevier that it be one of their own people, and that they fix it ASAP.

What do these measures have in common?  None of them will cost Elsevier anything.  These are things that should be done as soon as humanly possible, by which I mean “within the next week” rather than “we’ll set up a group to look into it, and report back at the next six-monthly management meeting”.

These measures are about transparency and sanity.  They are the kinds of changes that will start to put some trust back in place.  Being up-front and clear about what the access situation is will start to chip away at the sense that Elsevier has something to hide.  Getting rid of palpable lies about copyright transfer will be a start towards enabling us to believe Elsevier when they tell us other things.  None of this is enough to make an enemy into a friend; but it will at least help us to feel we’re facing an honourable enemy.  (Of course, there is a lot more that researchers need from Elsevier beyond that baseline.  We’ll look into that next time.)

Please do shout in the comments if I’ve missed any zero-cost transparency or sanity measures that should have been listed here.

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 are seem to be feeling 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.

I’ve been thinking about Barosaurus lately.

<homer>Mmmm … Barosaurus</homer>

The best (and only, really) good recent treatment of Barosaurus is in John McIntosh’s chapter of the 2005 IUP Thunder Lizards volume.  The main weakness of that chapter is that, while a lot of material is illustrated, the figures are rather small and not particularly well reproduced — and, in the case of the two-page spread of dorsal vertebrae, monumentally confusing:

Quick!  find the fourth dorsal in posterior view!  [˙ʇɟǝן ɯoʇʇoq ʇɐ s,ʇı :ɹǝʍsuɐ]

To get a better sense of the variation along the column, I scanned the two pages, loaded them into GIMP, joined them together, cleaned up the “white” of the background while retaining all the contrast I could, then moved each of the 27 illustrations to its own layer.  Then I was able to rearrange them to my liking, align them, and produce this modified version:

So here it is for anyone else who finds it useful.

(One character that varies sequentially is of course the degree of neural spine bifurcation.  But we won’t be flogging that dead horse any more — we’re done blogging, and the paper is in prep.)

References

  • McIntosh, J.S. 2005. The genus Barosaurus Marsh (Sauropoda, Diplodocidae); pp. 38-77 in Virginia Tidwell and Ken Carpenter (eds.), Thunder Lizards: the Sauropodomorph Dinosaurs. Indiana University Press, Bloomington, Indiana, 495 pp.

Item 1: With his new piece at the Guardian,  “Persistent myths about open access scientific publishing”, Mike continues to be a thorn in the side of exploitative commercial publishers, who just can’t seem to keep their facts straight. This time Mike unravels some choice bits of nonsense that keep getting circulated about open access publishing: that OA publishing must necessarily cost as much as barrier-based publishing, that the peer review process is expensive for publishers, and that authors who can’t pay OA publication fees will be left out in the cold. It’s cleanly and compellingly argued–go read for yourself.

Item 2: The Yates et al. prosauropod pneumaticity paper is officially published in the latest issue of Acta Palaeontologica Polonica, and I have updated the citation and links accordingly. This may not seem like big news, in that the accepted manuscript has been available online for 13 months, and the final published version does not differ materially from that version other than being pretty. But it’s an opportunity to talk about something that we haven’t really addressed here before, which is the potential for prompt publication to accelerate research.

A bit of background: standard practice at APP is to post accepted manuscripts as soon as they’re, well, accepted, unless the authors ask otherwise (for example, because the paper contains taxonomic acts and the first public version needs to be the version of record). Not everyone likes this policy–I know Darren objects, and I’m sure there are others. The chief complaint is that it muddies the waters around when the paper is published. Is a paper published when a manuscript is posted to a preprint server like arXiv, or when the accepted manuscript is made freely available by a journal, or when the official, formatted version is published online, or when it arrives in printed hardcopy?

Now, this is an interesting question to ponder, but I think it’s only interesting from the standpoint of rules (e.g., codes governing nomenclature) and how we’re going to decide what counts. From the standpoint of moving science forward, the paper is published as soon as it is available for other researchers to use openly–i.e., not just to use in private in their own research, but also to cite. And since that’s the axis I care most about, I prefer to see accepted manuscripts made widely available as soon as possible, and I support APP’s policy. In the case of Yates et al. (2012), having the accepted manuscript online for the past year meant that it was available for Butler et al. (2012) to use, and cite, in their broad reassessment of pneumaticity in Triassic archosaurs. If our manuscript has not been published, that might not have been the case; Adam gave a talk on our project at the 2009 SVP in Bristol, but Butler et al. might have been loathe to cite an abstract, and some journals explicitly forbid it.

So I say bring it on. Let’s really accelerate research, by letting people see the content as early as possible. Making other researchers wait just so they can see a prettier version of the same information seems to me to be a triumph of style over science.

References

Last time, we saw why Haplocanthosaurus couldn’t be a juvenile of Apatosaurus or Diplodocus, based on osteology alone.  But there’s more:

Ontogenetic status of Haplocanthosaurus

Here is where is gets really surreal.  Woodruff and Fowler (2012) blithely assume that Haplocanthosaurus is a juvenile of something, but the type specimen of the type species — H. priscus CM 572 — is an adult.  As Hatcher (1903:3) explains:

The type No. 572 of the present genus consists of the two posterior cervicals, ten dorsals, five sacrals, nineteen caudals, both ilia, ischia and pubes, two chevrons, a femur and a nearly complete series of ribs, all in an excellent state of preservation and pertaining to an individual fully adult as is shown by the coössified neural spines and centra.

So far as I can see, Woodruff and Fowler are confused because the second species that Hatcher describes, H. utterbacki, is based on the subadult specimen CM 879.  Where possible in the previous post, I have used illustrations of the adult H. priscus, so that the comparisons are of adult with adult.  The exceptions are the two anterior cervicals and the first dorsal, which are known only from H. utterbacki.  And sure enough, if you look closely at the illustrations, you can see that in these vertebrae and only these vertebrae, Hatcher had the neurocentral junction illustrated — because it wasn’t yet fused.

As it happens, the difference in ontogenetic status between these two specimens is nicely illustrated by Wedel (2009), although he was only in it for the pneumaticity:

So H. utterbacki CM 879 certainly is an immature form of something; and that something is Haplocanthosaurus, most likely H. priscus.  (The characters which Hatcher used to separate the two species are not particularly convincing.)

With that out the way, we can move on to …

Phylogenetic analysis

A simple way to evaluate the parsimony or otherwise of a synonymy is to use a phylogenetic analysis. In their abstract, Woodruff and Fowler claim that “On the basis of shallow bifurcation of its cervical and dorsal neural spines, the small diplodocid Suuwassea is more parsimoniously interpreted as an immature specimen of an already recognized diplodocid taxon”.  Without getting into the subject of Suuwassea again — Matt pretty much wrapped that up in part 4 — the point here is that the word “parsimony” has a particular meaning in studies of evolution: it refers to minimising the number of character-state changes.  And we have tools for measuring those.

So let’s use parsimony to evaluate the hypothesis that Haplocanthosaurus is one of the previously known diplodocids.  Pretending for the moment that Haplocanthosaurus really was known only from subadults, how many additional steps would we need to account for if ontogeny were to change its position to make it group with one of the diplodocids?

You don’t need to be a cladistics wizard to do this.  (Which is handy, since I am not one.)  Here’s the method:

  • Start with an existing matrix, add constraints, re-run it, and see how the tree-length changes.  Since I am familiar with it, I started with the matrix from my 2009 paper on brachiosaurs.
  • Re-run the matrix to verify that you get the same result as in the published paper based on it.  This gives you confidence that you’re running it right.  In this case, I got a minimum tree length of 791 steps, just as in Taylor (2009).
  • Add extra instructions to the run-script defining and imposing constraints.  Note that you do not have to mess with the characters, taxa or codings to do this.
  • Run the matrix again, with the constraint in place, and see how the tree-length changes.
  • Repeat as needed with other constraints to evaluate other phylogenetric hypotheses.

(This is how we produced the part of the Brontomerus paper (Taylor et al. 2011:89) where we said “One further step is sufficient to place Brontomerus as a brachiosaurid, a basal (non−camarasauromorph) macronarian, a basal (non−diplodocid) diplodocoid or even a non−neosauropod. Three further steps are required for Brontomerus to be recovered as a saltasaurid, specifically an opisthocoelicaudiine”.  And that’s why we weren’t at all dogmatic about its position.)

Anyway, going through this exercise with Haplocanthosaurus constrained in turn to be the sister taxon to Apatosaurus, Diplodocus, etc., yielded the following results:

  • (no constraint) –  791 steps
  • Apatosaurus — 817 (26 extra)
  • Diplodocus — 825 (34 extra)
  • Barosaurus — 815 (24 extra)
  • Camarasaurus — 793 (2 extra)
  • Brachiosaurus — 797 (6 extra)

(I threw in the other well-known Morrisson-Formation sauropods Camarasaurus and Brachiosaurus, even though Woodruff and Fowler don’t mention them, just because it was easy to do and I was interested to see what would happen.  And when I say Brachiosaurus, I mean B. altithorax, not Giraffatitan.)

I hope you’re as shocked as I am to see that for Haplocanthosaurus to emerge as the sister taxon of any diplodocid needs a minimum of 24 additional steps — or an incredible 34 for it to be sister to Diplodocus.  In other words, the hypothesis is grossly unparsimonious.  Of course, that doesn’t in itself mean that it’s false: but it does render it an extraordinary claim, which means that it needs extraordinary evidence.  And while “the simple spines of Haplocanthosaurus might bifurcate when it grows up” is extraordinary evidence, it’s not in the way that Carl Sagan meant it.

In short, running this simple exercise — it took me about a hour, mostly to remember how to do constraints in PAUP* — would have given Woodruff and Fowler pause for thought before dragging Haplocanthosaurus into their paper.

Oh, and it’s ironic that placing Haplo as sister to Brachiosaurus requires only a quarter as many steps as the closest diplodocid, and as sister to Camarasaurus requires only two steps.  If you really want to synonymise Haplocanthosaurus, Camarasaurus is the place to start.  (But don’t get excited, it’s not Camarasaurus either.  It’s Haplocanthosaurus.)

[By the way, anyone who’d like to replicate this experiment for themselves is welcome: all the files are available on my web-site.  You only really need the .nex file, which you can feed to PAUP*, but I threw in the log-file, the generated tree files and the summary file, too.  Extra Credit: run this same exercise to evaluate the parsimony of Suuwassea as a subadult of one of these other genera.  Report back here when you’re done to earn SV-POW! points.]

Conclusion

It’s a truism that we stand on the shoulders of giants.  In the case of sauropod studies, those giants are people like J. B. Hatcher, Charles Gilmore, Osborn and Mook and — bringing it up to date — John McIntosh, Paul Upchurch, Jeff Wilson and Jerry Harris.  When Hatcher described Haplocanthosaurus as a new genus rather than a subadult Diplodocus, he wasn’t naive.  He recognised the effects of ontogeny, and he was aware that one of his two specimens was adult and the other subadult.  He was also probably more familiar with Diplodocus osteology than anyone else has ever been before or since, having written the definitive monograph on that animal just two years previously (Hatcher 1901).

By the same token, people like Upchurch and Wilson have done us all a huge favour by making the hard yards in sauropod phylogenetics.  If we’re going to go challenging the standard consensus phylogeny, it’s just good sense to go back to their work (or the more recent work of others, such as Whitlock 2011), re-run the analyses with our pet hypotheses encoded as constraints, and see what they tell us.

So in the end, my point is this: let’s not waste our giants.  Let’s take the time to get up on their shoulders and survey the landscape from up there, rather than staying down at ground level and seeing how high we can jump from a standing start.

The rest of the series

Links to all of the posts in this series:

and the post that started it all:

 References

  • Hatcher, J.B. 1901. Diplodocus (Marsh): its osteology, taxonomy, and probable habits, with a restoration of the skeleton. Memoirs of the Carnegie Museum 1:1-63.
  • Hatcher, J.B. 1903. Osteology of Haplocanthosaurus with description of a new species, and remarks on the probable habits of the Sauropoda and the age and origin of the Atlantosaurus beds; additional remarks on Diplodocus. Memoirs of the Carnegie Museum 2:1-75.
  • Taylor, M.P. 2009. A re-evaluation of Brachiosaurus altithorax Riggs 1903 (Dinosauria, Sauropoda) and its generic separation from Giraffatitan brancai (Janensch 1914). Journal of Vertebrate Paleontology 29(3):787-806.
  • Taylor, M.P., Wedel, M.J. and Cifelli, R.L. 2011. 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
  • Wedel, M.J. 2009. Evidence for bird-like air sacs in saurischian dinosaurs. Journal of Experimental Zoology 311A:611-628.
  • Whitlock, J.A. 2011. A phylogenetic analysis of Diplodocoidea (Saurischia: Sauropoda). Zoological Journal of the Linnean Society 161(4):872-915. doi: 10.1111/j.1096-3642.2010.00665.x
  • Woodruff, D.C, and Fowler, D.W. 2012. Ontogenetic influence on neural spine bifurcation in Diplodocoidea (Dinosauria: Sauropoda): a critical phylogenetic character. Journal of Morphology, online ahead of print.

Introduction

Last time around, Matt walked through a lot of the detailed cervical morphology of Suuwassea and known diplodocids to show that, contra the suggestion of Woodruff and Fowler (2012), Suuwassea is distinct and can’t be explained away as an ontogenomorph of a previously known genus.

Although Suuwassea is singled out for special treatment in this paper, other genera do not escape unscathed.  From the Conclusions section on page 9:

Just as particularly large diplodocid specimens (e.g., Seismosaurus; Gillette, 1991) have been more recently recognized as large and potentially older individuals of already recognized taxa (Diplodocus; Lucas et al., 2006; Lovelace et al., 2007), taxa defined on small specimens (such as Suuwassea, but also potentially Barosaurus, Haplocanthosaurus, and ‘‘Brontodiplodocus’’), might represent immature forms of Diplodocus or Apatosaurus.

I have to admit I more or less fell out of my chair when I saw the suggestion that poor old Haplocanthosaurus might be Diplodocus or Apatosaurus.  I think this idea comes from a misstatement in the very first sentence of the abstract:

Within Diplodocoidea (Dinosauria: Sauropoda), phylogenetic position of the three subclades Rebbachisauridae, Dicraeosauridae, and Diplodocidae is strongly influenced by a relatively small number of characters.

As a statement of fact, this is simply the opposite of the truth: in all the major phylogenetic analyses, the arrangement of subclades with Diplodocoidea is the most stable part of the tree, supported by more characters than all the other clades.

For example, in the analysis of Upchurch et al. (2004) in The Dinosauria II, fig. 13.18 shows that the nodes with the highest bootstrap percentages are Diplodocinae (96%), Dicraeosauridae (95%) and Diplodocidae (93%).

Or consider the analysis of Wilson (2002).  While it’s getting on a bit, it still scores highly by being the most explicit published sauropod analysis, with comprehensive lists of apomorphies.  Table 12 lists the decay indexes for the 24 nodes in the strict consensus tree.  Apart from the three very basal nodes separating sauropods from their outgroups, the two highest-scoring clades are Diplodocidae and Diplodocinae (DI=7), followed by four clades all with DI=5 of which two are Dicraeosauridae and Flagellicaudata (which Wilson just called “Dicraeosauridae + Diplodocidae” as it had not yet been named).  (It’s well worth reading Wilson’s Appendix 3 to see the synapomorphies supporting these nodes in the MPTs: he lists 14 separating Diplodocimorpha from the node it shares with Haplocanthosaurus, 18 separating Flagellicaudata from the node it shares with Rebbachisauridae, 16 separating Diplodocidae from the node it shares with Dicareosauridae, and seven separating Diplodocinae from the node it shares with Apatosaurus).*

* Why are the lists of apomorphies longer than the decay indexes?  Because they list the apomorphies as they occur in the specific topology of the consensus tree.  Nodes within that tree can be made to collapse without wiping out all the apomorphies by rejuggling other parts of the tree to move character-state transitions around.  So although (for example) 26 characters separate Flagellicaudata from Rebbachisauridae (18 + 8 synapomorphies respectively) you can rejuggle the whole tree to break the monophyly of Flagellicaudata while making the entire tree only five steps longer.

Anyway, for whatever reason, Woodruff and Fowler felt that the stability of the diplodocoid clades was in question, and this presumably influenced their hypothesis that Haplocanthosaurus could be easily moved down into one of the diplodocid genera.

Next time we’ll be considering the implications for the tree.  But today, let’s take a moment to do this the old-fashioned way, by looking at …

Osteology

Pelvis

Hatcher (1903), ever helpful, included a comparative plate in his monograph which should help us to evaluate the idea that Haplo is a known diplodocid:

Pelves of diplodocids and Haplocanthosaurus. 1. Pelvis of Brontosaurus excelsus (No. 568); 2. Pelvis of Diplodocus carnegii (No. 94); 3. Pelvis of Haplocanthosaurus priscus (No. 572).  All seen from left side.  1, 2, 3, 4, 5 indicate neural spines of respective sacral vertebra.  Presumably to scale.  Direct from Hatcher (1903:plate IV).

Based on this, the pelvis of Haplocanthosaurus differs from those of the diplodocids in having a proportionally lower ilium, in the absence of the laterally facing rugosity on the posterodorsal margin of the ilium, in the very small distal expansion of the pubis and in the almost non-existent distal expansion of the ischium.  These are all characters of the limb-girdle elements, which do not change greatly through ontogeny in sauropods.

But the evidence from the sacral vertebrae is just as significant: the neural spines in the sacral area are less than half as tall as in the diplodocids — and this in an animal whose dorsal neural spines are conspicuously tall.  The spines are also more anteroposteriorly elongate and plate-like.  What’s more, sacral spines 1, 2 and 3 have fused into a single plate in Haplocanthosaurus, while the spine of S1 remains well separated from 2 and 3 in the diplodocids.  So the ontogenetic hypothesis would have to say that the spine of S1 unfuses through ontogeny.  Which is not something I’ve heard of happening in any sauropod, or indeed any animal.

So the pelvis and sacrum seem distinct.  But Woodruff and Fowler’s (2012) notion of ontogenetic synonymy is built on the idea that the differences in the cervical and dorsal vertebrae are ontogenetic.  So let’s take a look at them.

Cervical vertebrae

Posterior, mid and anterior cervical vertebrae, in right lateral view, of (top to bottom), Haplocanthosaurus, Apatosaurus louisae CM 3018 (from Gilmore 1936:plate XXIV, reversed for ease of comparison) and Diplodocus carnegii CM 84 (from Hatcher 1901:plate III), scaled to roughly the same size.  For the diplodocids, we illustrate C13, C9 and C4.  For Haplocanthosaurus, we illustrate C14 of H. priscus (from Hatcher 1903:plate I) and C9 and C4 of H. utterbacki (from plate II).

It should be immediately apparent that the Haplocanthosaurus cervicals have less extensive pneumatic features than those of the diplodocids, but that is one feature which we know does vary ontogenetically.  There are other differences: for example, the cervical ribs in Haplocanthosaurus are level with the bottom centrum rather than hanging below.  Still, if you kind of squint a bit, you could probably persuade yourself that the Haplocanthus vertebrae look like possible juveniles of Diplodocus.

Unless you look at them from behind:

Posterior cervical vertebrae C15 and C14, in posterior view, of (top to bottom), Haplocanthosaurus priscus CM 572 (from Hatcher 1903:plate I), Apatosaurus louisae CM 3018 (from Gilmore 1936:plate XXIV) and Diplodocus carnegii CM 84 (from Hatcher 1901:plate III), scaled to the same centrum-to-neural-spine height.

(Unfortunately, these are the only Haplocanthosaurus cervical vertebrae that Hatcher had illustrated in posterior view, so we can’t compare more anterior ones.)

From this perspective, we can immediately significant differences:

  • First, that unsplit spine.  Yes, we know that Woodruff and Fowler (2012) have argued that it could be ontogenetic, but these are vertebrae from the most deeply bifurcated region of a diplodocid neck, in a decent sized animal, and there is nothing that so much as hints at bifurcation.
  • That whacking great ligament scar running right down the back (and also the front, not pictured) of the neural spine.  There is nothing like this in any diplodocid — neither on the metapophyses nor running though the trough.  And remember, scars like these tend to become more prominent through ontogeny.
  • The neural arch (i.e. the region between the postzygapophyses and the centrum) is taller in Haplocanthosaurusmuch taller in the case of C15.
  • The plates running out to the diapophyses are less dorsoventrally expanded in Haplocanthosaurus.
  • The centrum is smaller as a proportion of total height — especially, much smaller than in Diplodocus.
  • The parapophyses extend directly laterally rather than ventrolaterally (hence the position of the cervical ribs level with the bottom of the centrum).

So it doesn’t look good for the juvenile-diplodocid hypothesis.  But let’s take a look at the …

Dorsal vertebrae

Posterior, mid and anterior dorsal vertebrae, in right lateral view, of (top to bottom), Haplocanthosaurus, Apatosaurus louisae CM 3018 (from Gilmore 1936:plate XXV, reversed for ease of comparison) and Diplodocus carnegii CM 84 (from Hatcher 1901:plate VII), scaled to roughly the same size.  For the diplodocids, we illustrate D9, D5 and D2.  For Haplocanthosaurus, which has four more dorsals, we illustrate D13 and D7 of H. priscus (from Hatcher 1903:plate I) and D2 of H. utterbacki (from plate II).

Here we see that Haplocanthosaurus has dorsolaterally inclined diapophyses (which we’ll see more clearly in a minute), a prominent spinodiapohyseal lamina in posterior dorsals, and no infraparapophyseal lamination.  Also, the dorsal vertebrae have reached their full height by the middle of the series (in fact the last nine dorsals are startlingly similar in proportions), whereas in diplodocids, total height continues to increase posteriorly.

Now let’s see those vertebrae in posterior view:

Posterior, mid and anterior dorsal vertebrae, in posterior view, of (top to bottom), Haplocanthosaurus priscus CM 572 (From Hatcher 1903:plate I), Apatosaurus louisae CM 3018 (from Gilmore 1936:plate XXV) and Diplodocus carnegii CM 84 (from Hatcher 1901:plate VII), scaled to the same height of the mid dorsal.  For the diplodocids, we illustrate D9, D5 and D1.  For Haplocanthosaurus, which has four more dorsals, we illustrate D13, D6 and D1.

Here is where it all falls apart.  The Haplocanthosaurus dorsals differ from those of the diplodocids in almost every respect:

  • Of course we have the non-bifid spine in again, in the anterior dorsal, but let’s not keep flogging that dead horse.
  • In the mid and posterior dorsals, the neurapophysis is rounded in posterior view rather than square.
  • In the posterior dorsal, the neural spine has laterally directed triangular processes near the top.
  • All three Haplocanthosaurus neural spines have broad, rugose ligament scars, whereas those of the diplodocids have narrow postspinal laminae.
  • The neural spines (measured from the diapophyses upwards) are much shorter than in the diplodocids; but
  • The neural arches (measured from the centrum up to the diapophyses) are much taller.
  • The diapophyses have distinct club-like rugosities at their tips.
  • the diapophyses of the mid and posterior dorsals are inclined strongly upwards
  • The hyposphenes of mid and posterior dorsals have very long centropostzygapophyseal laminae curving up in a gentle arch.
  • The centra are smaller than those of Apatosaurus, and much smaller than those of Diplodocus.

(By the way, it’s interesting how very different the D5s of Apatosaurus and Diplodocus are.  Since both are from uncontroversially adult specimens, bifurcation was evidently very different between these genera.)

So based on the vertebrae alone, the case of Haplocanthosaurus as an immature form of Diplodocus or Apatosaurus is blown right out of the water.  And this is without even looking at the appendicular material — for example, the scapula and coracoid illustrated by Hatcher (1903:figs 17-19), which are so completely different from those of diplodocids.

But there’s more.  Tune in next time for the rest.

The rest of the series

Links to all of the posts in this series:

and the post that started it all:

 References

  • Gillette, D.D. 1991. Seismosaurus halli, gen. et sp. nov., a new sauropod dinosaur from the Morrison Formation (Upper Jurassic/Lower Cretaceous) of New Mexico, USA. Journal of Vertebrate Paleontology 11(4):417-433.
  • Gilmore, C.W. 1936. Osteology of Apatosaurus with special reference to specimens in the Carnegie Museum. Memoirs of the Carnegie Museum 11:175-300.
  • Hatcher, J.B. 1901. Diplodocus (Marsh): its osteology, taxonomy, and probable habits, with a restoration of the skeleton. Memoirs of the Carnegie Museum 1:1-63.
  • Hatcher, J.B. 1903. Osteology of Haplocanthosaurus with description of a new species, and remarks on the probable habits of the Sauropoda and the age and origin of the Atlantosaurus beds; additional remarks on Diplodocus. Memoirs of the Carnegie Museum 2:1-75.
  • Lovelace, D.M., Hartman, S.A., Wahl, W.R. 2008. Morphology of a specimen of Supersaurus (Dinosauria, Sauropoda) from the Morrison Formation of Wyoming, and a re-evaluation of diplodocid phylogeny. Arquivos do Museu Nacional, Rio de Janeiro 65(4):527-544.
  • Lucas, S.G., Spielmann, J.A., Rinehart, L.F., Heckert, A.B., Herne, M.C., Hunt, A.P., Foster, J.R., Sullivan, R.M. 2006, Taxonomic status of Seismosaurus hallorum, a Late Jurassic sauropod dinosaur from New Mexico. New Mexico Museum of Natural History and Science Bulletin 36:149-162.
  • Upchurch, P. Barrett, P.M., Dodson, P. 2004. Sauropoda. pp. 259-322 in D.B. Weishampel, P. Dodson and H. Osmólska (eds.), The Dinosauria, 2nd edition. University of California Press, Berkeley and Los Angeles. 861 pp.
  • Wilson, J.A. 2002. Sauropod dinosaur phylogeny: critique and cladistic analysis. Zoological Journal of the Linnean Society 136:217-276.
  • Woodruff, D.C, and Fowler, D.W. 2012. Ontogenetic influence on neural spine bifurcation in Diplodocoidea (Dinosauria: Sauropoda): a critical phylogenetic character. Journal of Morphology, online ahead of print.

Special bonus illustrations

I composited the cervical and dorsal series above into the following compound illustrations.  As always, click through for full resolution.

Lateral view:

Posterior, mid and anterior dorsal vertebrae and cervical vertebrae, in right lateral view, of (top to bottom), Haplocanthosaurus, Apatosaurus louisae CM 3018 (from Gilmore 1936:plates XXIV and XXV, reversed for ease of comparison) and Diplodocus carnegii CM 84 (from Hatcher 1901:plates III and VII), scaled to roughly the same size. For the diplodocids, we illustrate D9, D5, D2, C13, C9 and C4. For Haplocanthosaurus, which has four more dorsals, we illustrate D13, D7 and C14 of H. priscus (from Hatcher 1903:plate I) and D2, C9 and C4 of H. utterbacki (from plate II).

Posterior view:

Posterior, mid and anterior dorsal vertebrae and posterior cervical vertebrae C15 and C14, in posterior view, of (top to bottom), Haplocanthosaurus priscus CM 572 (From Hatcher 1903:plate I), Apatosaurus louisae CM 3018 (from Gilmore 1936:plates XXIV and XXV) and Diplodocus carnegii CM 84 (from Hatcher 1901:plates III and VII), scaled to the same height of the mid dorsal. For the diplodocids, we illustrate D9, D5 and D1. For Haplocanthosaurus, which has four more dorsals, we illustrate D13, D6 and D1.

As everyone now knows, last week the respected and trusted Today programme on BBC Radio 4 ran an absurd nonscience piece on Brian Ford’s wild, ignorant, uninformed speculation that all dinosaurs lived in shallow lakes because that was the only way they could support their weight.  Plenty of people have shown what utter, contemptible nonsense this is, and I won’t waste everyone’s time by reiterating it.

Inspired by a comment by Stephen Curry, I put together a request for a formal retraction, and solicited signatories from the VRTPALEO list and Dinosaur Mailing List during a 24-hour window.  During that time 20 palaontologists contacted me to sign, and so this is what I submitted at 3pm on Thursday 5th April:

Dear Radio 4,

The Today Programme for Tuesday 3rd April 2012 contained a science piece by Tom Feilden:

http://news.bbc.co.uk/today/hi/today/newsid_9710000/9710630.stm

regarding Professor Brian J. Ford’s “theory” that dinosaurs did not live on land but in shallow lakes which supported their weight.

Professor Ford’s theory was published in a magazine rather than a peer-reviewed journal, and is wholly unsupported by any evidence whatsoever. It contradicts all evidence from dinosaur anatomy, biomechanics, sedimentology and palaeoenvironments, and does not even qualify as fringe science. It is unsupported and uninformed speculation which Ford could have disproved had he taken just ten minutes to look at the readily available literature representing a century of consensus.

By giving air-time to this speculation, even comparing Ford with Galileo, Radio 4 has unfortunately lent it a credibility that it has not earned, introduced a time-wasting controversy where there is not a controversy, misled the public, and maybe most importantly compromised its own credibility as a trusted source of science reporting. No listener with any knowledge of palaeontology will have been able to take this report seriously; will they believe the next science report you broadcast?

To mitigate this damage, we recommend and request that you broadcast a formal retraction.

  • Dr. Mike Taylor, Department of Earth Sciences, University of Bristol, UK
  • Dr. David Marjanović, Museum für Naturkunde, Berlin, Germany
  • Silvio C. Renesto, Associate Professor of Palaeontology, Department of Theoretical and Applied Sciences, Università degli Studi dell’Insubria, Italy
  • Dr. Grant Hurlburt, Department of Natural History, Royal Ontario Museum, Canada
  • Dr. Michael Balsai, Department of Biology, Temple University, Philadelphia, USA
  • Dr. Bill Sanders, Museum of Paleontology, University of Michigan, USA
  • Dr. Stephen Poropat, Department of Earth Sciences, Uppsala University, Sweden
  • Dr. Oliver Wings, Curator of Vertebrate Palaeontology, Museum für Naturkunde, Berlin, Germany
  • Jon Tennant, Independent Researcher, UK
  • Prof. John R. Hutchinson, Department of Veterinary Basic Sciences, The Royal Veterinary College, UK.
  • Prof. Lorin R. King, Dept. of Science, Math and Physical Education, Western Nebraska Community College
  • Scott Hartman, paleontologist and scientific illustrator, SkeletalDrawing.com
  • Neil Kelley, Department of Geology, University of California at Davis, USA
  • Dr. Matteo Belvedere, Department of Geosciences, University of Padova, Italy
  • Andrew R. C. Milner, Paleontologist and Curator, St. George Dinosaur Discovery Site, Utah, USA
  • Dr. James I. Kirkland, State Paleontologist, Utah Geological Survey, USA
  • Dr. Jerry D. Harris, Director of Paleontology, Dixie State College, Utah, USA
  • Dr. Andrew A. Farke, Curator, Raymond M. Alf Museum of Paleontology, Claremont, California, USA
  • Dr. Daniel Marty, Editor (Palaeontology) of the Swiss Journal of Geosciences
  • Dr. Manabu Sakamoto, School of Earth Sciences, University of Bristol, UK

(My thanks to all who signed.)

To give it the best chance of being seen by the relevant people, I submitted this three times on the BBC’s rather confusing web-site: on the Today feedback page, on the BBC complaints page, and on the Contact Today page.

Today at 2pm, I got the following reply:

Dear Dr Taylor

Reference CAS-1387310-3W6PSD

Thanks for contacting us regarding ‘Today’ broadcast on BBC Radio 4 on 3 April.

I understand that you were unhappy with the inclusion of a report by Tom Feilden on a theory proposed by Professor Brian Ford regarding how dinosaurs’ lived. I note you believe the report gave credibility to this theory, and compared the professor with Galileo.

Your concerns were forwarded to the programme who explained in response that the item in question was a light-hearted feature looking at an outlandish new idea about the dinosaurs and which was clearly signposted as such.

They added that the item even included one of the world’s leading experts on dinosaurs, Paul Barrett, exposing it’s flaws and ridiculing it and that it was very clear where Brian Ford’s article was published since Laboratory News was clearly mentioned.

They also added that the reference to Galileo was simply an aside about the importance of dissent in science, with Brian Ford was unlikely to be put off by the condemnation of the established experts, and not, as you suggest, a comparison between Brian Ford and one of the greatest scientists of all time.

In closing they explained:

“Today does a lot of good, serious science, indeed that same morning we had items on carbon capture and storage and the controversy over the publication of flu research, but that doesn’t mean it all has to be serious and we must be free to include light-hearted items, reported in a more humorous way.”

Nevertheless, we’re guided by the feedback we receive and I can assure you I’ve registered your complaint on our audience log. This is a daily report of audience feedback that’s made available to all BBC staff, including members of the BBC Executive Board, channel controllers and other senior managers.

The audience logs are seen as important documents that can help shape decisions about future programming and content.

Thanks for taking the time to contact us.

Kind Regards

Mark Roberts

BBC Complaints

I guess I don’t need to say that I find this completely unsatisfactory.  Trying to pass the segment off as “a light-hearted feature looking at an outlandish new idea about the dinosaurs and which was clearly signposted as such” just won’t fly: its page on the BBC site is entitled “Aquatic dinosaur theory debated”, and there is nothing about it that signposts it as any less serious than, say, the piece they did with me on Brontomerus, or on sauropod neck posture.

As it happens, my mum called me for a chat a couple of days ago, asking me whether I’d heard “the new theory” on the Today show.  It was pretty painful having to let her down.  She obviously didn’t hear it as “a light-hearted feature”.  It’s going to be harder now for her to accept other science reporting on Today.

The response claims that “the reference to Galileo was simply an aside about the importance of dissent in science [...] and not, as you suggest, a comparison between Brian Ford and one of the greatest scientists of all time”.  Well, let’s take a listen and see what exactly was said:

Somehow, I don’t think that [Paul Barrett's gentle disagreement] is going to be enough to persuade Professor Brian Ford. As another famous scientific dissenter, Galileo, was reported to have to have muttered under his breath when forced to deny that the Earth revolves around the Sun, “Eppur si muove” — “And yet, it moves“.

Yikes.

This is just so disappointing.  It would have taken Today‘s Tom Feilden five, maybe ten minutes of high-school-level research to discover that Ford has no grounding in palaeontology, sedimentology, biomechanics or palaeoenvironments; that his “theory” is as emphatically contradicted by the evidence as geocentricism; and that its publication was in a trade newsletter.  By skipping that basic due diligence, and blindly reporting Ford’s fantasy as serious science, Today has dramatically undermined its own credibility; by refusing to retract or even apologise, they’ve missed a chance to regain some of that lost credibility.

Why does it matter?  Scott Hartman said it best:

We live in a world where huge swaths of people don’t understand basic scientific concepts, and this sort of nonsense just makes it harder to teach. Worse, listeners that were sympathetic to the reporting will become disillusioned when they find out the reality of the situation, possibly making them view all science more cynically (or simply avoiding science altogether).

We deserve better science reporting than this. The BBC and everyone else who carried this story should be ashamed.

Yes.

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