The 5 stages of PeerJ

July 16, 2015

I have watched several people go through this sequence.

  1. DENIAL. PeerJ? What even is this thing? I’ll send my work to a real journal, thanks.
  2. THAWING. Huh, so-and-so published in PeerJ, it must not be that bad.
  3. GRUDGING SUBMISSION. Oh, okay, I’ll send them this one thing. I still have reservations but I want this out quickly. And I’m tired of getting rejected because some asshat thinks my paper isn’t sexy enough.
  4. AWAKENING. Wow, that was a lot faster, easier, and less painful than I expected. And the result is awesome.
  5. ACCEPTANCE. Why would I send my work anywhere else? No, really, I’m trying to think of a reason.

PeerJ

Now that the new Wilson and Allain (2015) paper has redescribed Rebbachisaurus, we can use it to start thinking about some other specimens. Particularly helpful is this beautiful rotating animation of the best dorsal vertebra (here captured at the point of the rotation where we’ve viewing it in right anterolateral):

rebbachisaur-dorsal-rotation

As I briefly discussed on Twitter, seeing this made me think of my baby, Xenoposeidon. Now that specimen, beautiful though it is, preserves only the lower one third of the vertebra. But there are some clear commonalities, and they’re clearer if you look at the animation.

Xenoposeidon-TNF

Most obviously, there are laminae running up and down the anterior and posterior margins of the lateral face of Xeno’s neural arch, and those same laminae seem to exist in Rebbachisaurus. We didn’t name these laminae in the Xeno paper, but if they’re the same thing as in Rebbachisaurus, then they’re ACPLs and PCDL — anterior centroparapophyseal and posterior centodiapophyseal laminae.

If that’s right, then we misinterpreted the site of the parapophysis in Xenoposeidon. We (Taylor and Naish 2007) thought it was at the cross-shaped junction of laminae near the anterodorsalmost preserved part of the vertebra. In Rebbachisaurus, this cross exists, but it’s merely where the CPRL (centroprezygapophyseal lamina) intersects the ACPL.

But there’s more. In Xenoposeidon, the base of the CPRL (if that’s what it is) forms a “V” shape with an accessory lamina that proceeds posterodorsally from the same origin. (This is one of the features that’s apparent on the more damaged right side of Xeno as well as the nicer left side.) That lamina also seems to exist in Rebbachisaurus — but with the whole vertebra to consider, we can see that it’s not an accessory lamina, but a perfectly well-behaved CPOL (centropostzygapophseal lamina).

So if Xeno is indeed a rebbachisaurid, then the two branches of the “V” go to support the pre- and postzygs, and the laminae running up the anterior and posterior margins of the centrum support the parapophyses and diapophyses respectively. There are actually two crosses on each side of the neural arch: one at the intersection of CPRL and ACPL, the other at the intersection of CPOL and PCDL; but in the Xeno specimen, the posterior cross is lost, having been just above where the break occurs at the top of the neural arch.

Here’s what I mean:

reconstructed-as-rebbachisaur

In case it’s not clear, the grey lines are an (extremely crude) reconstruction, the blue lines label the important laminae, and the red circles highlight the two crosses.

Hmm. The more I look at this, the more convincing I find it.

But there’s more! The anterior aspect of the Rebbachisaurus vertebra also bears a notable resemblance to what we see in Xeno, with a pair or arched laminae forming a vaulted roof to the neural canal.

 

rebbachisaur-dorsal-rotation2

Jeff Wilson spotted the same thing in a sequence of comments on my tweets, saying:

That’s not a bad call—the infrazygapophyseal region of that vert is elongate, and there is a nice CPRF and those closely positioned TPRLs could mean that prz’s are close to one another or even conjoined. It’s tantalizing, but not much to go on. Would be nice to prep out CPRF & work out laminae on lat sfc.

Jeff is right that more preparation would help to figure this out.

Not that everything about the Rebbachisaurus dorsal is Xeno-ish. Most notably, the lateral foramen is nothing like that of Xeno, being an uninspiringly dull and simple oval rather than the much more elegant foramen-within-a-fossa arrangement that we see in Xeno. But there are other points of commonality, too, such as the flat stretch of bone above the fossa and the way the posterior margin of the neural arch reaches the posterior margin of the centrum.

All in all — while there is plenty of work yet to do — I am increasingly inclined to think that the evidence we currently have suggests Xenoposeidon is a rebbachisaurid. If that’s right, it would be quite an exciting result. It would be the earliest known rebbachisaur, and the only named one from the UK. (Mannion 2009 described, but did not name, a rebbachisaurid scapula from Wessex formation of the Wealden). Could Mannion’s scapula be Xenoposeidon? Unlikely, as it’s 10 million years more recent. But it could be a close relative.

Exciting times!

References

 

Here at SV-POW! Towers, we’re keenly aware that some of our fans are just here for the hardcore sauropod vertebra action. These folks start to shift in their seats when we put up too many posts in a row on open access or rabbits or…okay, mostly just OA and bunnies. If that’s you – or, heck, even if it isn’t – your good day has come. Saddle up. Let’s ride.

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When Brian Engh and I were at the new Natural History Museum of Utah recently, I spotted this cute little juvenile cervical in one of the display cases.

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According to this sign, it’s UMNH 21054, and it was found by Frank DeCourten and prepared by Virginia Tidwell.

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It shares a display case and a sign with what is probably an anterior dorsal, UMNH 21055.

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Now, I don’t mean to brag (okay, maybe a little…) but the number of EKNApod* vertebrae is not large and the number of EKNApod vertebrae I’m not intimately familiar with hovers near zero. This thing was ringing bells – I knew I’d seen it before.

* Early Cretaceous North American sauropod

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Here are few more views. Note the light-colored oblong spot on the top of the condyle in the image above – this may be a pneumatic foramen filled with matrix, or a spot where the cortical bone flaked away to reveal one of the internal pneumatic spaces. Also, check out the fragment of extraneous bone (probably cervical rib) stuck sideways across the top of the centrum, just behind the condyle, in the image immediately below. Both of these features will be important later.

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The vert belongs to a juvenile sauropod because the neural arch is missing – it didn’t fuse to the centrum before the animal died. But it was a big baby; the centrum is maybe just a hair under 40 cm in length, meaning that a world-record giraffe might just maybe have a couple of cervicals of the same length. But basal titanosauriforms typically have 12-13 cervicals, not the whimpy 7 that almost all mammals must make do with, and all-stars like Euhelopus can have up to 17.

Also, this was not from the middle of the neck. No way. The parapophyses are huge, and the centrum is pretty stubby compared to Sauroposeidon or YPM 5294, the Sauroposeidonesque cervical from Unit VII of the Cloverly (pic here). My guess is we’re looking at something past the middle of the neck, where the cervicals start to get proportionally shorter (but sometimes max out in absolute length), maybe a C9 or C10. In Giraffatitan brancai HM SII/MB.R.2181, C10 has a centrum length of 100 cm and makes up about 12% of the 8.5-meter neck. Assuming similar proportions here, UMNH  21054 came from the roughly 3-meter neck of a sauropod about the size of a really big draft horse or a really small elephant.

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But enough noodling about the animal’s size. I knew I’d seen this vert before, but where? Thank goodness for comprehensive signage – I knew the material had been discovered by Frank DeCourten and prepped by Virginia Tidwell. At one of the SVP meetings in Denver, at a reception at the Denver museum, Virginia had invited me into the prep lab to see some EKNApod material from the Long Walk Quarry in Utah. The Long Walk Quarry was Frank DeCourten’s baby – he wrote a couple of papers about it (e.g., DeCourten 1991) and included additional information in his book, Dinosaurs of Utah (1998; second edition in 2013). DeCourten had referred the material to Pleurocoelus because that’s what people did with EKNApods back in the 20th century, but I remembered seeing one cervical that, like Sauroposeidon and YPM 5294, was just too long to match any of the Pleurocoelus material. My ‘Museum Photos’ file has a subfolder titled ‘Denver 2004′ – was the mystery vert in there?

2004-11-08 SVP 049

In short, yes. Here’s one of the photos I took back in 1994.

2004-11-08 SVP 050

Here’s another, sans flash this time. Check out the white spot on top of the condyle, the bar of float bone stuck sideways across the centrum just behind the spot, and general pattern of breaks – it’s a perfect match for UMNH 21054. Also note the block number on the pink specimen label at the bottom of the image – LWQ8, for Long Walk Quarry.

Three mysteries remain. One, the signage says the vert is from Carbon County, Utah, but the Long Walk Quarry has always been described as being in Emery County. Just a typo, or is there a story there? Two, how much of the animal (or animals) was excavated and prepped? I saw other vertebrae, both larger and smaller, when I was in Denver back on ’04, and DeCourten figured still others that I haven’t yet seen personally. Finally, is anyone working on it? And if not…[cautiously raises hand].

For other posts on the NHMU public galleries, see:

References

  • DeCourten, F.L.  1991.  New data on Early Cretaceous dinosaurs from the Long Walk Quarry and tracksite, Emery County, Utah.  In: T.C. Chidsey, Jr. (ed) Geology of East-Central Utah. Utah Geological Association Publication 19: 311-325.
  • DeCourten, F.L. 1998. Dinosaurs of Utah. University of Utah Press, Salt Lake City, 208pp.

I spent much of yesterday morning at the launch meeting of HEFCE’s new report on the use of metrics, The Metric Tide: Report of the Independent Review of the Role of Metrics in Research Assessment and Management. (Actually, thanks to the combination of a tube strike and a train strike, I spent most of the day stationary in traffic jams, but that’s not important right now.)

There’s a lot to like about the report, which is a fantastically detailed piece of work. (It weighs in at 178 pages for the main report, plus 200 pages for Supplement I and another 85 for Supplement II. I suspect that most people, including me, will content themselves with the Executive Summary, which is itself no lightweight at 12 pages.) Much has been written about it elsewhere — see the LSE’s link farm — but I want to focus on one issue that came up in the discussion.

As we’ve noted here a couple of times before, the REF (Research Excellence Framework) is explicit in disavowing impact factors and other rankings in its assessments: see the answer to this question: How will journal impact factors, rankings or lists, or the perceived standing of publishers be used to inform the assessment of research outputs?, which is:

No sub-panel will make any use of journal impact factors, rankings, lists or the perceived standing of publishers in assessing the quality of research outputs. An underpinning principle of the REF is that all types of research and all forms of research outputs across all disciplines shall be assessed on a fair and equal basis.

The problem is, people tend not to believe it. Universities continue to select which papers to submit to the REF on the basis of what journals they were in. And this propagates all the problems of journal rank and the absurdly disproportionate influence that two or three scientifically weak journals have on the whole field of scholarship.

As Richard Butler said in a comment on an earlier post:

Most people inside UK universities that I have talked to say that journal reputation is being considered by departments when preparing their REF submissions, and this has been documented by various articles in The Guardian and THS.

So that’s the background.

Then at the Metrics Tide launch, the question was asked: what more can HEFCE do to convey that they’re looking for good work, not work from high-IF journals?

That was the only point in the meeting where I stuck my hand up — I had things to say, but at that point the chairman of the panel chipped in with a different question, and the moment had passed. So rather than yank the discussion back to that point, I decided it would be better to blog about it.

There are two possible reasons why universities depend on journal rank in general, and impact factor in particular, when deciding on what papers to submit to the REF.

1. They simply don’t believe what the REF says about not caring what venue a paper is in; or
2. They believe the REF is telling truth, but think that Impact Factor is a good proxy for the qualities that the REF does care about.

The solution to #1 is a just a bigger, bolder statement in the 2020 REF. Instead of being somewhat buried, the 2020 documents should begin with the following statement in 20-point bold font:

Submitted works will be assessed according to their intrinsic quality (clarity, replicability, statistical power, significance) and not according to the venue they appear in. If you use Impact Factors to assess works, you are statistically illiterate.

The solution to #2 is a little more complicated. What it comes down to is education: helping administrators to see and understand that in fact the Impact Factor of the journal that work appears in is not a good proxy for any of the things that we care about.

In short, part of the job that the 2020 REF needs to do is to demonstrate to administrators that submitting high-IF papers is not a good strategy for them. It won’t optimise their REF results. If will give them papers that have no tendency to be highly cited or statistically powerful, but which are more likely to be retracted.

 

This just in: Wilson and Allain’s (2015) redescription of Rebbachisaurus garasbae, the type and only true species of Rebbachisaurus!

Wilson and Allain (2015:figure 3). Holotype of R. garasbae. Dorsal vertebra (MNHN-MRS 1958) in anterior (A), right lateral (B), posterior (C), and dorsal cross-sectional (D) views. Anterior faces top in D. Scale bar equals 20 cm.

Wilson and Allain (2015:figure 3). Holotype of R. garasbae. Dorsal vertebra (MNHN-MRS 1958) in anterior (A), right lateral (B), posterior (C), and dorsal cross-sectional (D) views. Anterior faces top in D. Scale bar equals 20 cm.

Here we see the much-admire’d dorsal vertebra that’s been on display for some time in the French National History Museum, and which we’ve seen here previously:

Jeff Wilson (left) and Ronan Allain (right), with dorsal vertebra of Rebbachisaurus.

Jeff Wilson (left) and Ronan Allain (right), with dorsal vertebra of Rebbachisaurus.

(It’s a shame that photo didn’t make it into the paper, really.)

There’s good and bad news here. The good news is obvious: this is a really important specimen, the type of a whole sauropod family, and it’s been in dire need of redescription because Lavocat’s (1954) paper did a bit of a drive-by on it. It’s great that there’s a proper description at last.

The bad news is, you can’t read it — at least, not unless you’re a JVP subscriber or at a wealthy university. It’s been a while, I think, since we wrote about a non-open access paper here at SV-POW!, and it’s funny how little we seem to have missed them. A lot of the action in vertebrate palaeo, especially for dinosaurs, seems to have moved to open access journals — especially PLOS ONE and PeerJ, but also of course the venerable Palaeontologia Electronica.

FIGURE 13. Holotype of R. garasbae. Right scapula (MNHN-MRS 1957) in medial (A) and lateral (B) views. Abbreviations: ac fo, acromial fossa; ac no, acromial notch; ac ri, acromial ridge; ss, origin of M. subscapularis. Inference of muscle attachment sites is based on comparisons with crocodile pectoral musculature (Meers, 2003). Reconstruction of distal margin of blade based on photograph of scapula in situ (Fig. 2A). Scale bar equals 20 cm.

Wilson and Allain (2015:figure 13). Holotype of R. garasbae. Right scapula (MNHN-MRS 1957) in medial (A) and lateral (B) views. Abbreviations: ac fo, acromial fossa; ac no, acromial notch; ac ri, acromial ridge; ss, origin of M. subscapularis. Inference of muscle attachment sites is based on comparisons with crocodile pectoral musculature (Meers, 2003). Reconstruction of distal margin of blade based on photograph of scapula in situ (Fig. 2A). Scale bar equals 20 cm.

It’s no secret that I am done with JVP (and Palaeontology, and the Journal of Paleontology, not that I’ve ever had a paper in that last one) until they become fully open access journals — and no, a hybrid OA option doesn’t cut it. I’m glad to have that notch on my bedpost, but I don’t feel any need to go back there.

But what I’d forgotten, or perhaps never really registered, is how terribly old-fashioned JVP papers look. No-one is disputing the journal’s high editorial standards or the importance of the work published there; but their tiny fonts, cumbersome two-column layout, and low-resolution black-and-white figures located bizarrely distant from the relevant text all make it feel like a journal badly in need of an overhaul for the 21st Century. I’m not sure what plans the Society has (it’s been years since I was a member) but I’d love to see JVP reinvented as a full-colour open-access journal, primarily online with printed copies only for those who want to pay for them. We’ll see.

Wilson and Allain (2015:figure 5). Holotype of R. garasbae. Computed tomography (CT) scans of the dorsal vertebra (MNHN-MRS 1958). A–E, transverse sections; F– G, frontal sections. Abbreviations: acpl, anterior centroparapophyseal lamina; cpol, centropostzygapophyseal lamina; cprf, centroprezygapophyseal fossa; ct, cotyle; lat. spol, lateral spinopostzygapophyseal lamina; med. cprl, medial centroprezygapophyseal lamina; med. spol; medial spinopostzyga- pophyseal lamina; nc, neural canal; pc, pleurocoel; pcdl, posterior centrodiapophyseal lamina; podl, postzygodiapophyseal lamina; posl, postspinal lamina; poz, postzygapophysis; prpl, prezygoparapophyseal lamina; prsl, prespinal lamina; prz, prezygapophysis; sc, subcamerae; spdl, spinodiapophy- seal lamina; se, septum; tpol, intrapostzygapophyseal lamina. Scale bar equals 10 cm for CT images.

Wilson and Allain (2015:figure 5). Holotype of R. garasbae. Computed tomography (CT) scans of the dorsal vertebra (MNHN-MRS 1958). A–E, transverse sections; F– G, frontal sections. Abbreviations: acpl, anterior centroparapophyseal lamina; cpol, centropostzygapophyseal lamina; cprf, centroprezygapophyseal fossa; ct, cotyle; lat. spol, lateral spinopostzygapophyseal lamina; med. cprl, medial centroprezygapophyseal lamina; med. spol; medial spinopostzygapophyseal lamina; nc, neural canal; pc, pleurocoel; pcdl, posterior centrodiapophyseal lamina; podl, postzygodiapophyseal lamina; posl, postspinal lamina; poz, postzygapophysis; prpl, prezygoparapophyseal lamina; prsl, prespinal lamina; prz, prezygapophysis; sc, subcamerae; spdl, spinodiapophyseal lamina; se, septum; tpol, intrapostzygapophyseal lamina. Scale bar equals 10 cm for CT images.

It’s great that Wilson and Allain had the Rebbachisaurus vertebrae CT-scanned, showing just how crazily lightly they are built: see figure 13, especially part A, above. But I have to admit to finding it strange that a 34-page paper that deals in detail with sauropod pneumaticity doesn’t cite anything by either Brooks Britt or our own Matt Wedel — surely the two people who have done the most important work in this area, certainly the most foundational work.

My 2009 paper (Taylor 2009, duh) does get a mention — not, this time, to disagree with me on the generic separation of Giraffatitan from Brachiosaurus, to but to acknowledge its recognition of the spinoparapophyseal lamina (SPPL) that occurs in D?8 of the Giraffatitan paralectotype MB.R.2181 (formerly HMN SII) and has now been recognised also in Rebbachisaurus.

Anyway, this is an important new paper, very well illustrated (apart from the annoyingly avoidable lack of colour) and with typically careful and exhaustive descriptions. It’s going to be very helpful, and it’s reawakened an idea that I once had …

… but that’s for another time.

References

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Now that, faithful readers, is a monument to evolution and its endless forms most beautiful. I’m talking about the wall of ceratopsian skulls at NHMU, of course, not the back of Brian Engh’s head (bottom center).

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If you don’t know them all on sight (yet!), here’s a cheat sheet. I goofed on a couple myself: before I looked at the sheet I figured Coahuilaceratops as Pentaceratops and mistook Kosmoceratops for Vagaceratops. Still, 12 out of 14 isn’t bad for a minor-league ceratopsian scholar such as yours truly.

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Here’s the chasmosaurine-centric view from lower right.

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And the centrosaurine-centric view from distant left.

The world needs more things like this. Good on ya, NHMU.

For other NHMU posts, see:

Natural History Museum of Utah: Barosaurus

I wanted to get my initial report on the Joni Mitchell conference out quickly. But since posting it, more thoughts have bubbled up through my mind. I’m thinking here mostly about how a humanities conference varies from a science one. Now of course this is only anecdote, nothing like a scientific survey: my sample size is one conference (for humanities) and only one field for science (vert palaeo, natch), so we should beware of generalising from these observations.

With that understood …

The Minerva Building of the University of Lincoln, where the main conference sessions took place.

The Minerva Building of the University of Lincoln, where the main conference sessions took place.

The Joni conference had mostly parallel sessions: a pair of panels early in the morning, then a pair in the later morning, then three simultaneous panels in the after-lunch session before dropping down to a single plenary session for the later afternoon. (My talk was in one of the three parallel panels, so less well attended than it might otherwise have been.) I don’t know how common this is in humanities conferences, but it’s never done at SVPCA or ProgPal. SVP, of course, does run parallel sessions — but then that is a very big meeting, with thousands of delegates.

I used the word “panel” in that description, which I’ve not come across in science conferences. It refers to one of a set of parallel sessions. The idea is that all the talks in a panel are on a somewhat related subject, and the panel ends with all the speakers coming back to the front together, for a discussion with the audience and among themselves. This is actually a really nice way to run things — much better than the very nominal Q&As at the end of SVPCA talks. It helps you to develop a sense of who people are, as well as digging deeper into the topics. My sense is that this is pretty typical of humanities conferences.

One less positive difference is that it seems far more acceptable in the humanities to read papers out loud from manuscripts. By no means everyone did this, but quite a few did, and it seemed to be thought normal. This did work out well for me in one respect, though. Because of the parallel panels, I missed a talk I would have liked to have heard, on using Joni’s music in therapeutic contexts. But when I later spoke to the author of that paper, she was able to give me a hardcopy of the talk. (I read it today.)

Did I say “Joni”? One aspect of this conference that corresponded pretty well with my prejudices was a sort of liberal guilt that popped up its head from time to time. Most of the speakers referred to our subject as “Joni” rather than “Mitchell”. In the round-table discussion at the end, someone suggesting this implied an unwarranted level of intimacy, and indicated an unconscious sexism on the part of the participants. There was quite a bit of agreement with this, but I don’t buy it. I think we refer to Joni Mitchell as “Joni”, when we don’t refer to Paul Simon as “Paul” for two reasons: one practical, one fundamental. First, because Joni is a rare and distinctive name, whereas Paul could be Paul McCartney; and second because the high level of self-disclosure in Joni’s music creates the impression of intimacy. I don’t think it’s anything to do with her being female and Simon being male.

Similarly, there was some angst about cultural appropriation regarding Joni’s use of jazz idioms, and particularly about her appearance as a black man on the cover of Don Juan’s Reckless Daughter (1977):

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I can certainly see how that cover makes people uncomfortable in 2015, and I can easily imagine that it would have done even in the very different climate of 1977. On the other hand, it felt a bit strange to be part of a 100% white audience debating this. I’m not sure what conclusion would be appropriate, so I won’t attempt one.

Finally, the demographics of the conference were maybe the biggest surprise. I’m not good at noticing race, so I may have missed someone; but as far as I’m aware there was not a single non-caucasian face at the conference. And perhaps even more surprising, in a conference about a feminist icon[*], although the attendance was about 50-50 men and women, the programme was dominated by male speakers. From a quick scan of the programme, I make it 15 men to 7 women, so more than twice as many.

As with most of what I’ve said here, I have no idea what to make of this. I just offer it up as an observation, and I’ll be glad to know what others make of it all.


[*] Joni Mitchell has explicitly disowned the description “feminist” on more than one occasion; but as a woman who not only held her own in man’s world but by most judgements dominated it, she is certainly an admirable example of practical, if not dogmatic, feminism.

 

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