September 24, 2013
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.
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 Paleobiology: five 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.
September 23, 2013
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!
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.
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.
- 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
September 20, 2013
Let’s take another look at that Giraffatitan cervical. MB.R.2180:C5, from a few days ago:
That’s a pretty elongate vertebra, right? But how elongate, exactly? How can we quantify whether it’s more or less elongate than some other vertebra?
The traditional answer is that we quantify elongation using the elongation index, or EI. This was originally defined by Upchurch (1998:47) as “the length of a vertebral centrum divided by the width across its caudal face”. Measuring from the full-resolution version of the image above, I make that 1779/529 pixels, or 3.36.
But then those doofuses Wedel et al. (2000:346) came along and said:
When discussing vertebral proportions Upchurch (1998) used the term elongation index (EI), defined as the length of the centrum divided by the width of the cotyle. Although they did not suggest a term for the proportion, Wilson & Sereno (1998) used centrum length divided by the height of the cotyle as a character in their analysis. We prefer the latter definition of this proportion, as the height of the cotyle is directly related to the range of motion of the intervertebral joint in the dorsoventral plane. For the purposes of the following discussion, we therefore redefine the EI of Upchurch (1998) as the anteroposterior length of the centrum divided by the midline height of the cotyle.
Since then, the term EI has mostly been used in this redefined sense — but I think we all agree now that it would have been better for Wedel et al to have given a new name to Wilson and Sereno’s ratio rather than apply Upchurch’s name to it.
Aaaanyway, measuring from the image again, I give that vertebra an EI (sensu Wedel et al. 2000) of 1779/334 = 5.33. Which is 58% more elongate than when using the Upchurch definition! This of course follows directly from the cotyle being 58% wider than tall (529/334 pixels).
So one of principal factors determining how elongate a vertebra seems to be is the shape of its cotyle. And that’s troublesome, because the cotyle is particularly subject to crushing — and it’s not unusual for even consecutive vertebrae from the same column to be crushed in opposite directions, giving them (apparently) wildly different EIs.
Here’s an example (though not at all an extreme one): cervicals 4 and 6 of the same specimen, MB.R.2180 (formerly HM SI), as the multi-view photo above:
Measuring from the photos as before, I make the width:height ratio of C4 683/722 pixels = 0.95, and that of C6 1190/820 pixels = 1.45. So these two vertebrae — from the same neck, and with only one other vertebrae coming in between them — differ in preserved cotyle shape by a factor of 1.53.
And by the way, this is one of the best preserved of all sauropod neck series.
Let’s take a look at the canonical well-preserved sauropod neck: the Carnegie Diplodocus, CM 84. Here are the adjacent cervicals 13 and 14, in posterior view, from Hatcher (1901: plate VI):
For C14 (on the left), I get a width:height ratio of 342/245 pixels = 1.40. For C13 (on the right), I get 264/256 pixels = 1.03. So C14 is apparently 35% broader than its immediate predecessor. I absolutely don’t buy that this represents how the vertebrae were in life.
FOR EXTRA CREDIT: what does this tell us about the reliability of computer models that purport to tell us about neck posture and flexibility, based on the preserved shapes of their constituent vertebrae?
So what’s to be done?
The first thing, as always in science, is to be explicit about what statements we’re making. Whenever we report an elongation index, we need to clearly state whether it’s EI sensu Upchurch 1998 or EI sensu Wedel et al. 2000. Since that’s so cumbersome, I’m going propose that we introduce two new abbreviations: EIH (Elongation Index Horizonal), which is Upchurch’s original measure (length over horizontal width of cotyle) and EIV (Elongation Index Vertical), which is Wilson and Sereno’s measure (length over vertical height of cotyle). If we’re careful to report EIH and EIV (or better still both) rather than an unspecified EI, then at least we can avoid comparing apples with oranges.
But I think we can do better, by combining the horizontal and vertical cotyle measurements in some way, and dividing the length by the that composite. This would give us an EIA (Elongation Index Average), which we could reasonably expect to preserve the original cotyle size, and so to give a more reliable indication of “true” elongation.
The question is, how to combine the cotyle width and height? There are two obvious candidates: either take the arithmetic mean (half the sum) or the geometric mean (the square root of the product). Note that for round cotyles, both these methods will give the same result as each other and as EIH and EIV — which is what we want.
Which mean should we use for EIA? to my mind, it depends which is best preserved when a vertebra is crushed. If a 20 cm circular cotyle is crushed vertically to 10cm, does it tend to smoosh outwards to 30 cm (so that 10+30 = the original 20+20) or to 40 cm (so that 10 x 40 = the original 20 x 20)? If the former, then we should use arithmetic mean; if the latter, then geometric mean.
Does anyone know how crushing works in practice? Which of these models most closely approximates reality? Or can we do better than either?
Update (8:48am): thanks for Emanuel Tschopp for pointing out (below) what I should have remembered: that Chure et al.’s (2010) description of Abydosaurus introduces “aEI”, which is the same as one of my proposed definitons of EIA. So we should ignore the last four paragraphs of this post and just use aEI. (Their abbreviation is better, too.)
- Hatcher, Jonathan B. 1901. Diplodocus (Marsh): its osteology, taxonomy and probable habits, with a restoration of the skeleton. Memoirs of the Carnegie Museum 1:1-63 and plates I-XIII.
- Upchurch, Paul. 1998. The phylogenetic relationships of sauropod dinosaurs. Zoological Journal of the Linnean Society 124:43-103.
- Wedel, Mathew J., Richard L. Cifelli and R. Kent Sanders. 2000b. Osteology, paleobiology, and relationships of the sauropod dinosaur Sauroposeidon. Acta Palaeontologica Polonica 45(4):343-388.
- Wilson, J. A. and Paul C. Sereno. 1998. Early evolution and higher-level phylogeny of sauropod dinosaurs. Society of Vertebrate Paleontology, Memoir 5:1-68.
September 11, 2013
We’ve blogged a lot of Bob Nicholls‘ art (here, here, and here) and we’ll probably continue to do so for the foreseeable future. We don’t have much choice: he keeps drawing awesome things and giving us permission to post them. Like this defiantly shaggy Apatosaurus, which was probably the star of the Morrison version of Duck Dynasty. Writes Bob:
On my way home at the airport I did a sketch of your giant Apatosaurus* – see attachment. My thought was that massive thick necks were probably pretty sexy things to apatosaurs, so maybe sexually mature individuals used simple feathers (stage 1, 2 or 3?) to accentuate the neck profile. The biggest males would of course have the most impressive growths so in the attached sketch your giant has one of the biggest beards in Earth’s history! What do you think of this idea?
Well, I think it’s awesome. And entirely plausible, for reasons already explained in this post.
“Now, wait,” you may be thinking, “I thought you guys said that sauropod necks weren’t sexually selected.” Actually we made a slightly different point: that the available evidence does not suggest that sexual selection was the primary driver of sauropod neck elongation. But we also acknowledged that biological structures are almost never single-purpose, and although the long necks of sauropods probably evolved to help them gather more food, there is no reason that long necks couldn’t have been co-opted as social billboards. This seems especially likely in Apatosaurus, where the neck length is unremarkable** but the neck fatness is frankly bizarre (and even inspired a Star Wars starfighter!).
I also love the “mobile ecosystem” of birds, other small dinosaurs, and insects riding on this Apatosaurus or following in its train. It’s a useful reminder that we have no real idea what effect millions of sauropods would have on the landscape. But it’s not hard to imagine that most Mesozoic terrestrial ecosystems were sauropod-driven in a thousand cascading and ramifying chains of cause and effect. I’d love to know how that worked. At heart, I’m still a wannabe chrononaut, and all my noodlings on pneumaticity and sauropod nerves and neural spines and so on are just baby steps toward trying to understand sauropod lives. Safari by way of pedantry: tally-ho!
For other speculative apatosaurs, see:
** Assuming we can be blasé about a neck that is more than twice as long (5 m) as a world-record giraffe neck (2.4 m), for garden variety Apatosaurus, or three times that length for the giant Oklahoma Apatosaurus (maybe 7 m).
September 9, 2013
I was at the Oklahoma Museum of Natural History in March to look at their Apatosaurus material, so I got to see the newly-mounted baby apatosaur in the “Clash of the Titans” exhibit (more photos of that exhibit in this post). How much of this is real (i.e., cast from real bones, rather than sculpted)? Most of the vertebral centra, a few of the neural arches, some of the limb girdle bones, and most of the long bones of the limbs. All of the missing elements–skull, neural arches, ribs, appendicular bits–were sculpted by the OMNH head preparator, Kyle Davies. Kyle is one of those frighteningly talented people who, if they don’t have what they need, will just freaking build it from scratch. Over the years he has helped me out a LOT with the OMNH sauropod material–including building a clamshell storage jacket for the referred scapula of Brontomerus so we could photograph it from the lateral side–so it’s about time I gave him some props.
Case in point: this sweet atlas-axis complex that Kyle sculpted for the juvenile Apatosaurus mount.
Most fish, amphibians, and other non-amniote tetrapods only have a single specialized vertebra for attaching to the skull. But amniotes have two: a ring- or doughnut-shaped first cervical vertebra (the atlas) that articulates with the occipital condyle(s) of the skull, and a second cervical vertebra (the axis) that articulates with the atlas and sometimes with the skull as well. Mammals have paired occipital condyles on the backs or bottoms of our skulls, so our skulls rock up and down on the atlas (nodding “yes” motion), and our skull+atlas rotates around a peg of bone on the axis called the odontoid process or dens epistrophei (shaking head “no” motion). As shown in the photos and diagrams below, the dens of the axis is actually part of the atlas that fuses to the second vertebra instead of the first. Also, reptiles, including dinosaurs and birds, tend to have a single ball-shaped occipital condyle that fits into the round socket formed by the atlas, so their “yes” and “no” motions are less segregated by location.
Anyway, the whole shebang is often referred to as the atlas-axis complex, and that’s the reconstructed setup for a baby Apatosaurus in the photo above. In addition to making a dull-colored one for the mount, Kyle made this festive version for the vert paleo teaching collection. Why so polychromatic?
Because in fact he built two: the fully assembled one two photos above, and a completely disassembled one, some of which is shown in this photo (I had to move the bigger bits out of the tray so they wouldn’t block the key card at the back). I originally composed this post as a tutorial. But frankly, since Kyle did all of the heavy lifting of (a) making the thing in the first place, (2) making a color-coded key to it, and (d) giving me permission to post these photos, it would be redundant to walk through every element. So think of this as a self-study rather than a tutorial.
Oh, all right, here’s a labeled version. Note that normally in an adult animal the single piece of bone called the atlas would consist of the paired atlas neural arches (na1) and single atlas intercentrum (ic1), and would probably have a pair of fused cervical ribs (r1). Everything else would be fused together to form the axis, including the atlas pleurocentrum (c1), which forms the odontoid process or dens epistrophei (etymologically the “tooth” of the axis).
Here’s the complete Romer (1956) figure from the key card, with a mammalian atlas-axis complex for comparison. Incidentally, the entire book this is drawn from, Osteology of the Reptiles, is freely available online.
And here’s the complete Gilmore (1936) figure. Sorry for the craptastic scan–amazingly, this one is NOT freely available online as far as I can tell, and Mike and I have been trying to get good scans of the plates for years. Getting back on topic, single-headed atlantal cervical ribs have been found in several sauropods, especially Camarasaurus where several examples are known, so they were probably a regular feature, even though they aren’t always preserved.
Also, as noted in this post, it is odd that in this specimen of Apatosaurus the cervical ribs had not fused to the first two vertebrae, even though they normally do, and despite the fact that the vertebrae had fused to each other, even though they normally don’t. Further demonstration, if any were needed, that sauropod skeletal fusions were wacky.
For comparison to the above images, here is the atlas-axis complex in the synapsid Varanops, from Campione and Reisz (2011: fig. 2C).
Those proatlas thingies are present in some sauropods, but that’s about all I know about them, so I’ll say no more for now.
There is a good overview of the atlas-axis complex with lots of photos of vertebrae of extant animals on this page.
Previous SV-POW! posts dealing with atlantes and axes (that’s right) include:
- A fused atlas and axis in Apatosaurus
- Yet more uninformed noodling on the future of scientific publishing and that kind of thing
- Another mystery: embossed laminae and “unfossae”
- Tutorial 15: the bones of the sauropod skeleton
- Campione, N.E. and Reisz, R.R. 2011. Morphology and evolutionary significance of the atlas−axis complex in varanopid synapsids. Acta Palaeontologica Polonica 56 (4): 739–748.
- Gilmore, C.W. 1936. Osteology of Apatosaurus with special reference to specimens in the Carnegie Museum. Memoirs of the Carnegie Museum 11: 175-300.
- Romer, A.S. 1956. Osteology of the Reptiles. University of Chicago Press, Chicago. 772 pp.
September 6, 2013
Those familiar with Lull (1919: plate II: figure 2) will recognise this as “vertebra Q” of the Barosarus lentus holotype YPM 429, in ventral view.
Stay tuned for more exciting Barosaurus-related news!
Lull, R. S. 1919. The sauropod dinosaur Barosaurus Marsh. Memoirs of the Connecticut Academy of Arts and Sciences 6:1-42 and plates I-VII.
September 4, 2013
I recently handled the revisions on a paper that hopefully will be in press very soon. One of the review comments was “Be very careful not to make ad hominem attacks”.
I was a bit surprised to see that — I wasn’t aware that I’d made any — so I went back over the manuscript, and sure enough, there were no ad homs in there.
There was criticism, though, and I think that’s what the reviewer meant.
Folks, “ad hominem” has a specific meaning. An “ad hominem attack” doesn’t just mean criticising something strongly, it means criticising the author rather than the work. The phrase is Latin for “to the man”. Here’s a pair of examples:
- “This paper by Wedel is terrible, because the data don’t support the conclusion” — not ad hominem.
- “Wedel is a terrible scientist, so this paper can’t be trusted” – ad hominem.
What’s wrong with ad hominem criticism? Simply, it’s irrelevant to evaluation of the paper being reviewed. It doesn’t matter (to me as a scientist) whether Wedel strangles small defenceless animals for pleasure in his spare time; what matters is the quality of his work.
Note that ad hominems can also be positive — and they are just as useless there. Here’s another pair of examples:
- “I recommend publication of Naish’s paper because his work is explained carefully and in detail” — not ad hominem.
- “I recommend publication of Naish’s paper because he is a careful and detailed worker” — ad hominem.
It makes no difference whether Naish is a careful and detailed worker, or if he always buys his wife flowers on their anniversary, or even if he has a track-record of careful and detailed work. What matters is whether this paper, the one I’m reviewing, is good. That’s all.
As it happens the very first peer-review I ever received — for the paper that eventually became Taylor and Naish (2005) on diplodocoid phylogenetic nomenclature — contained a classic ad hominem, which I’ll go ahead and quote:
It seems to me perfectly reasonable to expect revisers of a major clade to have some prior experience/expertise in the group or in phylogenetic taxonomy before presenting what is intended to be the definitive phylogenetic taxonomy of that group. I do not wish to demean the capabilities of either author – certainly Naish’s “Dinosaurs of the Isle of Wight” is a praiseworthy and useful publication in my opinion – but I question whether he and Taylor can meet their own desiderata of presenting a revised nomenclature that balances elegance, consistency, and stability.
You see what’s happening here? The reviewer was not reviewing the paper, but the authors. There was no need for him or her to question whether we could meet our desiderata: he or she could just have read the manuscript and found out.
(Happy ending: that paper was rejected at the journal we first sent it to, but published at PaleoBios in revised form, and bizarrely is my equal third most-cited paper. I never saw that coming.)
I was recently bemoaning the lack of published diplodocid cervical illustrations in dorsal view. Subsequently I mentioned that Upchurch et al. (2005) had illustrated five cervicals of an Apatosaurus specimen.
I was overlooking one other paper that contains such an illustration. Which is a bit embarrassing, as it’s one of ours. In fact, it’s our most recent paper, Wedel and Taylor (2013) on sauropod neural spine bifurcation. The very first figure in that paper (the first of 25!) is relevant to my interests. So here it is:
Click through for glorious high-resolution goodness!
Upchurch, Paul, Yukimitsu Tomida, and Paul M. Barrett. 2005. A new specimen of Apatosaurus ajax (Sauropoda: Diplodocidae) from the Morrison Formation (Upper Jurassic) of Wyoming, USA. National Science Museum Monographs No. 26. Tokyo. ISSN 1342-9574.
Wedel, M.J., and Taylor, M.P. 2013. Neural spine bifurcation in sauropod dinosaurs of the Morrison Formation: ontogenetic and phylogenetic implications. Palarch’s Journal of Vertebrate Palaeontology 10(1): 1-34. ISSN 1567-2158.
September 2, 2013
Every year I invest many days’ effort into preparing a 20-minute talk for SVPCA. Then I deliver it to maybe 80 people, and that’s the end — it’s over. It seems like a terrible waste of effort, and it occurred to me that I should make a video of this year’s talk, Barosaurus revisited: the concept of Barosaurus (Dinosauria: Sauropoda) is based on erroneously referred specimens (which at the last minute I retitled Barosaurus revisited: the concept of Barosaurus (Dinosauria: Sauropoda) is not based on erroneously referred specimens).
But I don’t know how to do that. What I want is a simple program, for either Ubuntu GNU/Linux or MacOS, which will record both the video of my screen (as I step through PowerPoint slides) and the audio of the microphone (as I give the talk), resulting in a single video file that I can upload to YouTube.
Can anyone recommend such a program?
I got an almost immediate suggestion from @Stephen_Curry that I use ProfCast. I downloaded the trial version, but it insists on running official Microsoft PowerPoint, which I don’t have. (I prepare my talks using OpenOffice’s low-rent PowerPoint-alike.) Rats.
@emckiernan13 cleverly suggested that I do a Google hangout (on air, recording to YouTube) with me as the only participant. So far I’ve not been able to get this to work. It won’t start a video hangout unless I have at least one other live person on the call; and although I can make it go in and out of capture mode, I can’t find a way to get hold of the captured stream.
Has anyone done this successfully?
September 1, 2013
Last time, I asked if anyone has dorsal-view photos of the cervical vertebrae of Diplodocus. No responses yet, and I do urge you to chip in if you have any ideas. But here’s something to keep us positive: Apatosaurus cervicals!
This is Plate 1 from Upchurch et al.’s (2005) excellent descriptive monograph of a specimen of Apatosaurus ajax, NSMT-PV 20375. It shows cervicals 3, 6, 7, 12 and 14, each in left lateral, dorsal and right lateral view; and C14 in ventral view. Click through for the glorious full-resolution version (5183 × 2876).
Here is a close-up of C12 in dorsal view.