Today, available for the first time, you can read my 2004 paper A survey of dinosaur diversity by clade, age, place of discovery and year of description. It’s freely available (CC By 4.0) as a PeerJ Preprint. It’s one of those papers that does exactly what it says on the tin — you should be able to find some interesting patterns in the diversity of your own favourite dinosaur group.

Fig. 1. Breakdown of dinosaur diversity by phylogeny. The number of genera included in each clade is indicated in parentheses. Non-terminal clades additionally have, in square brackets, the number of included genera that are not also included in one of the figured subclades. For example, there are 63 theropods that are neither carnosaurs nor coelurosaurs. The thickness of the lines is proportional to the number of genera in the clades they represent.

Taylor (2014 for 2004), Figure 1. Breakdown of dinosaur diversity by phylogeny. The number of genera included in each clade is indicated in parentheses. Non-terminal clades additionally have, in square brackets, the number of included genera that are not also included in one of the figured subclades. For example, there are 63 theropods that are neither carnosaurs nor coelurosaurs. The thickness of the lines is proportional to the number of genera in the clades they represent.

“But Mike”, you say, “you wrote this thing ten years ago?”

Yes. It’s actually the first scientific paper I ever wrote (bar some scraps of computer science) beginning in 2003. It’s so old that all the illustrations are grey-scale. I submitted it to Acta Palaeontologica Polonica way back on on 24 October 2004 (three double-spaced hard-copies in the post!) , but it was rejected without review. I was subsequently able to publish a greatly truncated version (Taylor 2006) in the proceedings of the 2006 Symposium on Mesozoic Terrestrial Ecosystems, but that was only one tenth the length of the full manuscript — much potentially valuable information was lost.

My finally posting this comes (as so many things seem to) from a conversation with Matt. Off work sick, he’d been amusing himself by re-reading old SV-POW! posts (yes, we do this). He was struck by my exhortation in Tutorial 14: “do not ever give a conference talk without immediately transcribing your slides into a manuscript”. He bemoaned how bad he’s been at following that advice, and I had to admit I’ve done no better, listing a sequence of old my SVPCA talks that have still never been published as papers.

The oldest of these was my 2004 presentation on dinosaur diversity. Commenting on this, I wrote in email: “OK, I got the MTE four-pager out of this, but the talk was distilled from a 40ish-page manuscript that was never published and never will be.” Quick as a flash, Matt replied:

If I had written this and sent it to you, you’d tell me to put it online and blog about how I went from idea to long paper to talk to short paper, to illuminate the process of science.

And of course he was right — hence this preprint.

Fig. 2. Breakdown of dinosaurian diversity by high-level taxa. "Other sauropodomorphs" are the "prosauropods" sensu lato. "Other theropods" include coelophysoids, neoceratosaurs, torvosaurs (= megalosaurs) and spinosaurs. "Other ornithischians" are basal forms, including heterodontosaurs and those that fall into Marginocephalia or Thyreophora but not into a figured subclade.

Taylor (2014 for 2004), Figure 2. Breakdown of dinosaurian diversity by high-level taxa. “Other sauropodomorphs” are the “prosauropods” sensu lato. “Other theropods” include coelophysoids, neoceratosaurs, torvosaurs (= megalosaurs) and spinosaurs. “Other ornithischians” are basal forms, including heterodontosaurs and those that fall into Marginocephalia or Thyreophora but not into a figured subclade.

I will never update this manuscript, as it’s based on a now wildly outdated database and I have too much else happening. (For one thing, I really ought to get around to finishing up the paper based on my 2005 SVPCA talk!) So in a sense it’s odd to call it a “pre-print” — it’s not pre anything.

Despite the data being well out of date, this manuscript still contains much that is (I think) of interest, and my sense is that the ratios of taxon counts, if not the absolute numbers, are still pretty accurate.

I don’t expect ever to submit a version of this to a journal, so this can be considered the final and definitive version.

References

 

I think it’s fair to say that this “bifurcation heat-map”, from Wedel and Taylor (2013a: figure 9), has been one of the best-received illustrations that we’ve prepared:

Wedel and Taylor 2013 bifurcation Figure 9 - bifurcatogram

(See comments from Jaime and from Mark Robinson.)

Back when the paper came out, Matt rashly said “Stand by for a post by Mike explaining how it came it be” — a post which has not materialised. Until now!

This illustration was (apart from some minor tweaking) produced by a program that I wrote for that purpose, snappily named “vcd2svg“. That name is because it converts a vertebral column description (VCD) into a scalable vector graphics (SVG) file, which you can look at with a web-browser or load into an image editor for further processing.

The vertebral column description is in a format designed for this purpose, and I think it’s fairly intuitive. Here, for example, is the fragment describing the first three lines of the figure above:

Taxon: Apatosaurus louisae
Specimen: CM 3018
Data: —–YVVVVVVVVV|VVVuuunnn-

Taxon: Apatosaurus parvus
Specimen: UWGM 155556/CM 563
Data: –nnn-VVV—V-V|VVVu——

Taxon: Apatosaurus ajax
Specimen: NMST-PV 20375
Data: –n–VVVVVVVVVV|VVVVYunnnn

Basically, you draw little ASCII pictures of the vertebral column. Other directives in the file explain how to draw the various glyphs represented by (in this case) “Y”, “V”, “u”, and “n”.

It’s pretty flexible. We used the same program to generate the right-hand side (though not the phylogenetic tree) of Wedel and Taylor (2013b: figure 2):

Wedel and Taylor (2013b: Figure 2).

Wedel and Taylor (2013b: Figure 2).

The reason I mention this is because I released the software today under the GNU General Public Licence v3.0, which is kind of like CC By-SA. It’s free for anyone to download, use, modify and redistribute either verbatim or in modified form, subject only to attribution and the requirement that the same licence be used for modified versions.

vcd2svg is written in Perl, and implemented in part by the SVG::VCD module, which is included in the package. It’s available as a CPAN module and on GitHub. There’s documentation of the command-line vcd2svg program, and of the VCD file format. Also included in the distribution are two documented examples: the bifurcation heat-map and the caudal pneumaticity diagram.

Folks, please use it! And feel free to contribute, too: as the change-log notes, there’s work still to be done, and I’ll be happy to take pull requests from those of you who are programmers. And whether you’re a programmer or not, if you find a bug, or want a new feature, feel free to file an issue.

A final thought: in academia, you don’t really get credit for writing software. So to convert the work that went into this release into some kind of coin, I’ll probably have to write a short paper describing it, and let that stand as a proxy for the actual program. Hopefully people will cite that paper when they generate a figure using the software, the way we all reflexively cite Swofford every time we use PAUP*.

Update (12 April 2014)

On Vertebrat’s suggestion, I have renamed the program VertFigure.

References

“Look at all the things you’ve done for me
Opened up my eyes,
Taught me how to see,
Notice every tree.”

So sings Dot in Move On, the climactic number of Stephen Sondheim’s Pulitzer Prize-winning music Sunday in the Park with George, which on the surface is about the post-impressionist painter Georges Seurat, but turns out to be a study of obsession and creativity.

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Un dimanche après-midi à l’Île de la Grande Jatte – 1884 [A Sunday Afternoon on the Island of La Grande Jatte – 1884]

“Taught me how to see”? What kind of talk is that? One the surface, it seems silly — we all know how to see. We do it constantly, without thinking. Yet it’s something that artists talk about all the time. And anyone who’s sat down and seriously tried to paint or draw something will have some understanding of what the phrase means. We have such strong implicit ideas of what things look like that we tend to reproduce what we “know” is there rather than what’s actually there. Like I said, we see without thinking.

In fact, the psychology of perception is complicated and sophisticated, and the brain does an extraordinary amount of filtering of the visual signals we get, to save us the bother of having to consciously process way too much data. This is a whole scientific field of its own, and I’m going to avoid saying very much about it for fear of making a fool of myself — as scientists so often do when wandering outside their own field. But I think it’s fair to say that we all have a tendency to see what we expect to see.

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Phylogeny of Sauropoda, strict consensus of most parsimonious trees according to Wilson (2002:fig. 13a)

In the case of sauropods, this tendency has meant that we’ve all been startlingly bad at seeing pneumaticity in the caudal vertebrae of sauropods. Because the literature has trained us to assume it’s not there. For example, in the two competing sauropod phylogenies that dominated the 2000s, both Wilson (2002) and Upchurch et al. (2004) scored caudal pneumaticity as very rare: Wilson’s character 119, “Anterior caudal centra, pneumatopores (pleurocoels)”, was scored 1 only for Diplodocus and Barosaurus; and  Upchurch et al. (2004:286) wrote that “A few taxa (Barosaurus, Diplodocus, and Neuquensaurus) have pleurocoel-like openings in the lateral surfaces of the cranial [caudal] centra that lead into complex internal chambers”. That’s all.

And that’s part of the reason that every year since World War II, a million people have walked right past the awesome mounted brachiosaur in the Museum Für Naturkunde Berlin without noticing that it has pneumatic caudals. After all, we all knew that brachiosaur caudals were apneumatic.

But in my 2005 Progressive Palaeontology talk about upper limits on the mass of land animals estimated through the articular area of limb-bone cartilage, I included this slide that shows how much bigger the acetabulum of Giraffatitan is than the femoral head that it houses:

Screenshot from 2014-01-24 17:30:30

And looking at that picture made me wonder: those dark areas on the sides of the first few caudals (other than the first, which is a very obvious plaster model) certainly look pneumatic.

Then a few years later, I was invited to give a talk at the Museum Für Naturkunde Berlin itself, on the subject “Brachiosaurus brancai is not Brachiosaurus“. (This of course was drawn from the work that became my subsequent paper on that subject, Taylor 2009) And as I was going through my photos to prepare the slides of that talk, I thought to myself: darn it, yes, it does have pneumatic caudals!

So I threw this slide into the talk, just in passing:

Screenshot from 2014-01-24 17:32:06

Those photos were pretty persuasive; and a closer examination of the specimen on that same trip was to prove conclusive.

Meanwhile …

Earlier in 2009, I’d been in Providence, Rhode Island, with my Index Data colleagues. I’d managed to carve a day out of the schedule to hope along the coast to the Yale Peabody Museum in New Haven, Connecticut. My main goal was to examine the cervicals of the mounted Apatosaurus (= “Brontosaurus“) excelsus holotype (although it was also on that same trip that I first saw the Barosaurus holotype material that we’ve subsequently published a preprint on).

The Brontosaurus cervicals turned out to be useless, being completely encased in plaster “improvements” so that you can’t tell what’s real and what’s not. hopefully one day they’ll get the funding they want to take that baby down off its scaffold and re-prep the material.

But since I had the privilege of spending quality time with such an iconic specimen, it would have been churlish not to look at the rest of it. And lo and behold, what did I see when I looked at the tail but more pneumaticity that we thought we knew wasn’t there!

Wedel and Taylor (2013b: Figure 10).

An isolated pneumatic fossa is present on the right side of caudal vertebra 13 in Apatosaurus excelsus holotype YPM 1980. The front of the vertebra and the fossa are reconstructed, but enough of the original fossil is visible to show that the feature is genuine. (Wedel and Taylor 2013b: Figure 10).

What does this mean? Do other Giraffatitan and Apatosaurus specimens have pneumatic tails? How pervasive is the pneumaticity? What are the palaeobiological implications?

Stay tuned! All will be revealed in Matt’s next post (or, if you can’t wait, in our recent PLOS ONE paper, Wedel and Taylor 2013b)!

References

It’s now widely understood among researchers that the impact factor (IF) is a statistically illiterate measure of the quality of a paper. Unfortunately, it’s not yet universally understood among administrators, who in many places continue to judge authors on the impact factors of the journals they publish in. They presumably do this on the assumption that impact factor is a proxy for, or predictor of, citation count, which is turn is assumed to correlate with influence.

As shown by Lozano et al. (2012), the correlation between IF and citations is in fact very weak — r2 is about 0.2 — and has been progressively weakening since the dawn of the Internet era and the consequent decoupling of papers from the physical journal that they appear in. This is a counter-intuitive finding: given that the impact factor is calculated from citation counts you’d expect it to correlate much more strongly. But the enormous skew of citation rates towards a few big winners renders the average used by the IF meaningless.

To bring this home, I plotted my own personal impact-factor/citation-count graph. I used Google Scholar’s citation counts of my articles, which recognises 17 of my papers; then I looked up the impact factors of the venues they appeared in, plotted citation count against impact factor, and calculated a best-fit line through my data-points. Here’s the result (taken from a slide in my Berlin 11 satellite conference talk):

berlin11-satellite-taylor-what-we-can-do--impact-factor-graph

I was delighted to see that the regression slope is actually negative: in my case at least, the higher the impact factor of the venue I publish in, the fewer citations I get.

There are a few things worth unpacking on that graph.

First, note the proud cluster on the left margin: publications in venues with impact factor zero (i.e. no impact factor at all). These include papers in new journals like PeerJ, in perfectly respectable established journals like PaleoBios, edited-volume chapters, papers in conference proceedings, and an arXiv preprint.

My most-cited paper, by some distance, is Head and neck posture in sauropod dinosaurs inferred from extant animals (Taylor et al. 2009, a collaboration between all three SV-POW!sketeers). That appeared in Acta Palaeontologia Polonica, a very well-respected journal in the palaeontology community but which has a modest impact factor of 1.58.

My next most-cited paper, the Brachiosaurus revision (Taylor 2009), is in the Journal of Vertebrate Palaeontology – unquestionably the flagship journal of our discipline, despite its also unspectacular impact factor of 2.21. (For what it’s worth, I seem to recall it was about half that when my paper came out.)

In fact, none of my publications have appeared in venues with an impact factor greater than 2.21, with one trifling exception. That is what Andy Farke, Matt and I ironically refer to as our Nature monograph (Farke et al. 2009). It’s a 250-word letter to the editor on the subject of the Open Dinosaur Project. (It’ a subject that we now find profoundly embarrassing given how dreadfully slowly the project has progressed.)

Google Scholar says that our Nature note has been cited just once. But the truth is even better: that one citation is in fact from an in-prep manuscript that Google has dug up prematurely — one that we ourselves put on Google Docs, as part of the slooow progress of the Open Dinosaur Project. Remove that, and our Nature note has been cited exactly zero times. I am very proud of that record, and will try to preserve it by persuading Andy and Matt to remove the citation from the in-prep paper before we submit. (And please, folks: don’t spoil my record by citing it in your own work!)

What does all this mean? Admittedly, not much. It’s anecdote rather than data, and I’m posting it more because it amuses me than because it’s particularly persuasive. In fact if you remove the anomalous data point that is our Nature monograph, the slope becomes positive — although it’s basically meaningless, given that all my publications cluster in the 0–2.21 range. But then that’s the point: pretty much any data based on impact factors is meaningless.

References

 

Well, folks, I’m back from Berlin. And what an extraordinary couple of days it was. There were in fact three days of open-access talks, though I was only able to be there for the first two. Day one was the satellite conference, aimed at early-career researchers; days two and three were the much larger main conference, attended mostly by heavy hitters: senior librarians, university administrators, a sprinkling of politicians, and of course some researchers and publishers.

It was my privilege to speak at both satellite and main conferences. This post is really just to advertise those talks. Why am I doing this? Because I’m convinced that they’re by far the most important talks I’ve ever given. It’s great fun to talk about Barosaurus at SVPCA, or about intervertebral cartilage in Bonn, but if someone says to me that that work doesn’t really matter in a cosmic sense, I’ll be hard put to find reasons why they’re wrong. But open access has profound and immediate consequences for health, industry, education, third-world development, and more fields than I can list.

So here are the talks.

Satellite meeting talk

berlin11-satellite-taylor-what-we-can-do

First up, at the satellite conference, my subject was: Towards universal Open Access: what we can do about it, and who should do it. My goal here was to help researchers see what practical steps they can take right now towards the open-access goal that we all aspire to. I covered six areas:

  1. Publish our own work open access (whether Gold or Green)
  2. Review for Open Access journals
  3. Edit for Open Access journals
  4. Advocate Open Access policies
  5. Deprecate journal rank
  6. Talk about Open Access

Along the way, we talked about the open-access citation advantage, the (mostly non-) problem of article processing charges, the complete non-problem of “predatory open-access publishers”, the acceptable length of Green-OA embargoes (zero), the SV-POW! decision tree, publishers’ lack of control over what you do before you sign the copyright transfer, the inability of impact factor to predict citation count (post to come), the childishness of evaluating individuals by journal rank, and the knotty problem of who should take responsibility for fixing our current broken system.

Here are a few tweets that went out as I was giving this talk: “a blistering, fantastic presentation“, “Can we get a twitter round of applause … Absolutely BRILLIANT presentation“, “TOTALLY BRILLIANT“, “This is why we HAVE to record these conferences. Not recording that presentation would be a crime“, “It was AWESOME!“, and finally my favourites: “making you not just know #openaccess , but feel it” and “Mike’s talks at the #Berlin11 conference was 1of the most emotional 1′s I have ever seen!

I actually don’t know whether it’s going to be possible for people who missed the live stream to watch this talk. That was the plan, but I heard a rumour that the recording went wrong. If a video does becomes available, I’ll let you know. In the mean time, you can at least get the slides [PowerPoint or exported PDF]. They are CC By.

Main meeting talk

berlin11-main-Taylor-CUT-DOWN

In the main conference, I used my slot to remind us all that Open Access is about sharing, unity and sanity, not about money. Because I was addressing a more senior audience that necessarily has to think more about practicalities, finances, ways and means, I wanted to take the opportunity to remember that those are not the issues that gave birth to Open Access; rather, it started out as an unabashedly idealistic movement (as reading any of the three great declarations will show you). I don’t want us to walk away from that high-ground and be reduced to thinking only about practicalities, important though they are.

Publishers and their associates often say — rightly, as far as they go — that “Scientific and technical publishing is a business“. But no-one goes into it because of they money they can make. Everyone involved in doing or publishing research surely got into that business because their eyes were on a higher prize. So the burden of my talk was that publishing research is a mission; that far from “getting rid of the idealists“, we should cherish them; and that we should encourage rather than curb our own idealistic tendencies.

Perhaps the most satisfying part of the whole conference was giving this talk — you might almost call it a preach — and watching the nodding agreement spread across the audience. Folks, we’re about a great work. Let’s not forget that. Let’s not sell ourselves short.

The main session was unfortunately not livecast, and to the best of my knowledge, there were never any plans to record it. But as with my satellite talk, you can at least get the slides [PowerPoint or exported PDF]. They are CC By.

Where next?

Since I made the slides available for download immediately after the talks (three days ago for the satellite meeting, two days ago for the main meeting), I’ve been surprised and delighted to see the download numbers — currently standing at 641 for the satallite talk and 939 for the main talk. The tweet announcing the main talk has also been retweeted 34 times and favourited 26 times. I hope that shows that I struck a chord.

I have an informal invitation to deliver the main-session talk next year to an Italian university, which I’ll be pleased to do once we’re able to sort out the details. I’m not sure whether more invitations are likely to be forthcoming, but I’ll mention them here if they do materialise.

I’d like to finish by thanking my employer, Index Data. As most of you know, I am not a career academic: I work on sauropods in my spare time (and advocate open access in my spare spare time), earning my living as a computer programmer. By the time the invitations to speak at the Berlin conferences came in, I’d already booked up my annual leave allowance, so I had to ask for permission to take unpaid days for the conference. Instead, Index Data gave me two more paid days — because they, like me, believe in the importance of open access.

This is all the more laudable since, if anything, universal open access will harm our business. A significant part of what we build is authentication mechanisms to allow people (legitimate) access to paywalled resources. Once everything is open, no-one will need to pay us to do that. It’s greatly to Index Data’s credit that, despite this, they want to help us push on towards a goal that will benefit society as a whole.

References

  • Taylor, Michael P. Monday 18 November 2013. Towards universal Open Access: what we can do about it, and who should do it. Berlin 11 Satellite Conference for students and early-career researchers. [Slides PPT] [Slides PDF]
  • Taylor, Michael P. Tuesday 19 November 2013. Open Access is about sharing, unity and sanity, not about money. Berlin 11 Open Access Conference: 10th Anniversary of the Berlin Declaration. [Slides PPT] [Slides PDF]

As I mentioned a few days ago, Matt and I have a couple of papers in the new PLOS ONE Sauropod Gigantism collection. We were each lead author on one and second author on the other, so for convenience’s sake we’ll refer to them as my paper (Taylor and Wedel 2013c on neck cartilage) and Matt’s paper (Wedel and Taylor 2013b on caudal pneumaticity.)

Mine is very simple in concept (although it ended up at 17 pages and 23 figures). It’s all about addressing one of the overlooked variables in reconstructing the postures of the necks of sauropods (and indeed of all tetrapods). That is, the spacing between consecutive vertebrae, and the effect this has on “neutral pose”.

The concept of “neutral pose” goes back to the DinoMorph work of Stevens and Parrish (1999). They defined it (p. 799) as follows: “We determined the neutral poses for each animal, wherein the paired articular facets of the postzygapophyses of each cervical vertebra were centered over the facets of the prezygapophyses of its caudally adjacent counterpart.”

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Taylor and Wedel (2013c: Figure 3). Articulated sauropod vertebrae. Representative mid-cervical vertebra of Giraffatitan brancai, articulating with its neighbours. The condyle (ball) on the front of each vertebra’s centrum fits into the cotyle (socket) at the back of the preceding one, and the prezygapophyses articulate with the preceding vertebra’s postzygapophyses. These vertebrae are in Osteological Neutral Pose, because the pre- and postzygapophyseal facets overlap fully.

One of the more fundamental flaws in Stevens and Parrish (1999) is the assumption that animals habitually rest their necks in neutral pose — an assumption that is unsupported by evidence and, as it turns out, false (Vidal et al. 1986, Taylor et al. 2009). But let’s leave that aside for the moment, and consider what neutral pose actually represents.

The fact that there is even such a thing as neutral articulation between two consecutive vertebrae is due to there being three points of contact between those vertebra: as with the legs of a tripod, three points is the minimum number you need to fix an object in three-dimensional space. Two of these points are at the zygapophyses, as noted in the original definition above. The third point is the articulation between the centra.

The centrum has been curiously overlooked in discussions of neutral pose, but needless to say its length is crucial in establishing what is neutral. In the image above, if the centrum was longer, then the angle between the consecutive vertebrae would need to be raised in order to keep the zygapophyses articulated.

And of course it was longer in life, because of the cartilage in between the consecutive centra. (The use of the more specific term “osteological neutral pose” goes some way to recognising that tissues other than bone have been overlooked, but the problem has not really been addressed or even properly acknowledged in published works before our paper.)

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Taylor and Wedel (2013c: Figure 5). Intervertebral gaps in camel necks. Head and neck of dromedary camels. Top: UMZC H.14191, in right lateral view, posed well below habitual posture, with apparently disarticulated C3/C4 and C4/C5 joints. Photograph taken of a public exhibit at University Museum of Zoology, Cambridge, UK. Bottom: OUMNH 17427, in left lateral view, reversed for consistency with Cambridge specimen. Photograph taken of a public exhibit at Oxford University Museum of Natural History, UK. Inset: detail of C4 of the Oxford specimen, showing articulations with C3 and C5. The centra are separated by thick pads of artificial ‘‘cartilage’’ to preserve spacing as in life.

You simply can’t ignore cartilage when modelling neck postures and expect to get anything resembling a meaningful result. That is, presumably, the reason why the habitual posture of rabbits in life exceeds the most extended posture we were able to obtain when manipulating dry vertebrae of a hare: compare Vidal et al. (1986: fig. 4) with Taylor et al. (2009: fig. 1).

How big is the effect? That depends on the thickness of the cartilage and the height of the zygapophyses above the center of rotation. Here is an illustration that we should have put in the paper, but which inexplicably neither of us thought of:

figNEW-angle-at-zygs

Influence of intervertebral cartilage on vertebral articulation angle. Consider the posterior vertebra (black) as fixed. The blue vertebra represents neutral pose of the preceding vertebra with centra abutting and zygapophyseal facets maximally overlapped. The red vertebra indicates neutral pose once intervertebral cartilage is added between the vertebra (where else?) The green lines show the angle by which the more anterior vertebra must be inclined in order to accommodate the cartilage, and the magenta line shows the height of the zygapophyseal articulation above the center of rotation between the two vertebrae.

Here’s some elementary trigonometry. Suppose the intervertebral cartilage is x distance thick at mid-height of the centra, and that the height of the zygs above this mid-height point (the magenta line) is y. The triangle between the middle of the condyle of the posterior vertebra, the middle of the cotyle of the anterior one and the zygapophyseal articulation is near enough a right-angled triangle as makes no odds.

Consider the angle θ between the green lines. Sin(θ) = opposite/hypotenuse = x/y, and by similarity, the additional angle of inclination of the anterior vertebra is also θ.

But for small angles (and this is generally a small angle), sin(θ) ≈ θ. So the additional inclination in radians = cartilage thickness divided by zygapophyseal height. For example, in vertebrae where the zygs are 23 cm above the mid-height of the centra, adding 4 cm of intervertebral cartilage adds about 4/23 = 0.174 radians = 10 degrees of extra inclination. (That’s pretty similar to the angle in the illustration above. Eyeballing the cartilage thickness and zyg height in the illustration suggests that 23:4 ratio is about right, which is a nice sanity-check of this method.)

millionaire-stupid-contestant4

At this point, I am cursing my own stupidity for not putting this diagram, and the very simple calculation, into the paper. I guess that can happen when something is written in a hurry (which to be honest this paper was). The formula is so simple — and accurate enough within tolerances of inevitable measurement error — that we really should have used it all over the place. I guess that will have to go in a followup now.

Anyway — next time, we’ll address this important related question: how thick, in fact, was the cartilage between the cervicals of sauropods?

References

A few bits and pieces about the PLOS Collection on sauropod gigantism that launched yesterday.

2013-10-29-SauropodEbook1-thumb

First, there’s a nice write-up of one of our papers (Wedel and Taylor 2013b on pneumaticity in sauropod tails) in the Huffington Post today. It’s the work of PLOS blogger Brad Balukjian, a former student of Matt’s from Berkeley days. The introduction added by the PLOS blogs manager is one of those where you keep wanting to interrupt, “Well, actually it’s not quite like that …” but the post itself, once it kicks in, is good. Go read it.

Brad also has a guest-post on Discover magazine’s Crux blog: How Brachiosaurus (and Brethren) Became So Gigantic. He gives an overview of the sauropod gigantism collection as a whole. Well worth a read to get your bearings on the issue of sauropod gigantism in general, and the new collection in particular.

PLOS’s own community blog EveryONE also has its own brief introduction to the collection.

And PLOS and PeerJ editor Andy Farke, recently in these pages because of his sensational juvenile Parasaurolophus paper, contributes his own overview of the collection, How Big? How Tall? And…How Did It Happen?

Finally, if you’re at SVP, go and pick up your free copy of the collection. Matt was somehow under the impression that the PLOS USB drives with the sauropod gigantism collection would be distributed with the conference packet when people registered. In fact, people have to go by the PLOS table in the exhibitor area (booth 4 in the San Diego ballroom) to pick them up. There are plenty of them, but apparently a lot of people don’t know that they can get them.

References

This is an exciting day: the new PLOS Collection on sauropod gigantism is published to coincide with the start of this year’s SVP meeting! Like all PLOS papers, the contents are free to the world: free to read and to re-use.  (What is a Collection? It’s like an edited volume, but free online instead of printed on paper.)

There are fourteen papers in the new Collection, encompassing neck posture (yay!), nutrition (finally putting to bed the Nourishing Vomit Of Eucamerotus hypothesis), locomotion, physiology and evolutionary ecology. Lots every sauropod-lover to enjoy.

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Taylor and Wedel (2013c: Figure 12). CT slices from fifth cervical vertebrae of Sauroposeidon. X-ray scout image and three posterior-view CT slices through the C5/C6 intervertebral joint in Sauroposeidon OMNH 53062. In the bottom half of figure, structures from C6 are traced in red and those from C5 are traced in blue. Note that the condyle of C6 is centered in the cotyle of C5 and that the right zygapophyses are in articulation.

Matt and I are particularly excited that we have two papers in this collection: Taylor and Wedel (2013c) on intervertebral cartilage in necks, and Wedel and Taylor (2013b) on pneumaticity in the tails of (particularly) Giraffatitan and Apatosaurus. So we have both ends of the animal covered. It also represents a long-overdue notch on our bed-post: for all our pro-PLOS rhetoric, this is the first time either of has had a paper published in a PLOS journal.

Wedel and Taylor (2013b: Figure 4). Giraffatitan brancai tail MB.R.5000 (‘Fund no’) in right lateral view. Dark blue vertebrae have pneumatic fossae on both sides, light blue vertebrae have pneumatic fossae only on the right side, and white vertebrae have no pneumatic fossae on either side. The first caudal vertebra (hatched) was not recovered and is reconstructed in plaster.

It’s a bit of a statistical anomaly that after a decade of collaboration in which there was never a Taylor & Wedel or Wedel & Taylor paper, suddenly we have five of them out in a single year (including the Barosaurus preprint, which we expect to eventually wind up as Taylor and Wedel 2014). Sorry about the alphabet soup.

Since Matt is away at SVP this week, I’ll be blogging mostly about the Taylor and Wedel paper this week. When Matt returns to civilian life, the stage should be clear for him to blog about pneumatic caudals.

Happy days!

References

Yesterday I announced that our new paper on Barosaurus was up as a PeerJ preprint and invited feedback.

I woke up this morning to find its third substantial review waiting for me.

That means that this paper has now accumulated as much useful feedback in the twenty-seven hours since I submitted it as any previous submission I’ve ever made.

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Taylor and Wedel (2013b: figure 7). Barosaurus lentus holotype YPM 429, Vertebra S (C?12). Left column from top to bottom: dorsal, right lateral and ventral views; right column: anterior view. Inset shows displaced fragment of broken prezygapophysis. Note the narrow span across the parapophyses in ventral view, and the lack of damage to the ventral surface of the centrum which would indicate transverse crushing.

It’s worth reviewing the timeline here:

  • Monday 23rd September, 1:19 am: I completed the submission process.
  • 7:03 am: the preprint was published. It took less than six hours.
  • 10:52 am: received a careful, detailed review from Emanuel Tschopp. It took less than four hours from publication, and so of course less than ten from submission.
  • About 5:00 pm: received a second review, this one from Mark Robinson. (I don’t know the exact time because PeerJ’s page doesn’t show an actual timestamp, just “21 hours ago”.)
  • Tuesday 24th September, about 4:00 am: received a third review, this from ceratopsian-jockey and open-science guru Andy Farke.

Total time from submission to receiving three substantial reviews: about 27 hours.

It’s worth contrasting that with the times taken to get from submission to the receipt of reviews — usually only two of them — when going through the traditional journal route. Here are a few of mine:

  • Diplodocoid phylogenetic nomenclature at the Journal of Paleontology, 2004-5 (the first reviews I ever received): three months and 14 days.
  • Revised version of the same paper at PaleoBios, 2005 (my first published paper): one month and 10 days.
  • Xenoposeidon description at Palaeontology, 2006: three months and 19 days, although that included a delay as the handling editor sent it to a third, tie-breaking, reviewer.
  • Brachiosaurus revision at the Journal of Vertebrate Paleontology, 2008: one month and 11 days.
  • Sauropod neck anatomy (eventually to be published in a very different form in PeerJ) at Paleobiologyfive months and two days.
  • Trivial correction to the Brachiosaurus revision at the Journal of Vertebrate Paleontology, 2010: five months and 11 days, bizarrely for a half-page paper.

Despite the wide variations in submission-to-review time at these journals, it’s clear that you can expect to wait at least a month before getting any feedback at all on your submission at traditional journals. Even PeerJ took 19 days to get the reviews of our neck-anatomy paper back to us.

So I am now pretty such sold on the pre-printing route. As well as getting this early version of the paper out there early so that other palaeontologists can benefit from it (and so that we can’t be pre-emptively plagiarised), issuing a preprint has meant that we’ve got really useful feedback very quickly.

I highly recommend this route.

By the way, in case anyone’s wondering, PeerJ Preprints is not only for manuscripts that are destined for PeerJ proper. They’re perfectly happy for you to use their service as a place to gather feedback for your work before submitting it elsewhere. So even if your work is destined for, say, JVP, there’s a lot to be gained by preprinting it first.

I was very pleased, on checking my email this morning, to see that my and Matt’s new paper, The neck of Barosaurus was not only longer but also wider than those of Diplodocus and other diplodocines, is now up as a PeerJ preprint!

Figure6-vertebra-q-composite

Taylor and Wedel (2013b: figure 6). Barosaurus lentus holotype YPM 429, Vertebra Q (C?13). Top row: left ventrolateral view. Middle row, from left to right: anterior view, with ventral to the right; ventral view; posterior view, with ventral to the left. Bottom row: right lateral view, inverted. Inset shows diapophyseal facet on right side of vertebra, indicating that the cervical ribs were unfused in this individual despite its great size. Note the broad, flat prezygapophyseal facet visible in anterior view.

I was pleased partly because of the very quick work on PeerJ’s part. I submitted the preprint at 1:22am last night, then went to bed. Almost immediately I got an automatic email from PeerJ saying:

Thank you for submitting your manuscript, “The neck of Barosaurus was not only longer but also wider than those of Diplodocus and other diplodocines” (#2013:09:838:0:0:CHECK:P) – it has now been received by PeerJ PrePrints.

Next, it will be checked by PeerJ staff, who will notify you if any alterations are required to the manuscript or accompanying files.

If the PrePrint successfully passes these checks, it will be made public.

You will receive notification by email at each stage of this process; you can also check the status of your manuscript at any time.

Lots to like here: the quickness of the response, the promise of automatic email updates, and the one-click link to check on progress (as opposed to the usual maze of Manuscript Central options to navigate).

Sure enough, a couple of hours later the next automatic email arrived, telling me that Matt had accepted PeerJ’s email invitation to be recognised as the co-author of the submission.

And one hour ago, just as I was crawling out of bed, I got the notification that the preprint is up. That simple.

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Taylor and Wedel (2013b: Figure 9). Partial reconstruction of the Barosaurus lentus holotype YPM 429, cervical vertebra R, approximating its undamaged state by allowing for dorsoventral crushing, shearing and loss of some extremities. Anterior and posterior views scaled to 125% of uncorrected width and 80% of uncorrected height. Dorsal view scaled to 80% of uncorrected height; condyle moved forward and cotyle scaled to 50% of uncorrected width to allow for shearing. Lateral view scaled to 125% of uncorrected height, and sheared backwards 15 degrees. Metapophyses and postzygapophyses drawn in multiple views based on vertebrae Q and S and AMNH 6341 material.

I’m also pleased because we managed to get this baby written so quickly. It started life as our talk at SVPCA in Edinburgh (Taylor and Wedel 2013a), which we delivered 25 days ago having put it together mostly in a few days running up to the conference — so it’s zero to sixty in less than a month. Every year we promise ourselves that we’ll write up our talks, and we never seem to get around to it, but this year I started writing on the train back from Edinburgh. By the time I got home I had enough of a hunk of text to keep me working on it, and so we were able to push through in what, for us, is record time.

Now here’s what we’d like:

We want this paper’s time as a preprint to be time well spent — which means that we want to improve it. To do that, we need your reviews. Assuming we get some useful comments, we plan to release an updated version pretty soon; and after some number of iterations, we’ll submit the resulting paper as a full-fledged PeerJ paper.

So if you know anything about sauropods, about vertebra, about deformation, about ecology, or even about grammar or punctuation, please do us a favour: read the preprint, then get over to its PeerJ page and leave your feedback. You’ll be helping us to improve the scientific record. We’ll acknowledge substantial comments in the final paper, but even the pickiest comments are appreciated.

Because we want to encourage this approach to bringing papers to publication, we’d ask you please do not post comments about the paper here on SV-POW!. Please post them on the PeerJ preprint page. We’ve leaving comments here open for discussion of the preprinting processes, but not the scientific content.

References

  • Taylor, Michael P., and Mathew J. Wedel. 2013a. Barosaurus revisited: the concept of Barosaurus (Dinosauria: Sauropoda) is based on erroneously referred specimens. (Talk given as: Barosaurus revisited: the concept of Barosaurus (Dinosauria: Sauropoda) is not based on erroneously referred specimens.) pp. 37-38 in Stig Walsh, Nick Fraser, Stephen Brusatte, Jeff Liston and Vicen Carrió (eds.), Programme and Abstracts, 61st Symposium on Vertebrae Palaeontology and Comparative Anatomy, Edinburgh, UK, 27th-30th August 2013. 33 pp.
  • Taylor, Michael P., and Mathew J. Wedel. 2013b. The neck of Barosaurus was not only longer but also wider than those of Diplodocus and other diplodocines. PeerJ PrePrints 1:e67v1 http://dx.doi.org/10.7287/peerj.preprints.67v1
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