February 12, 2014
Today (12th February) is the one-year anniversary of the first PeerJ papers! As Matt put it in an email this morning:
Hard to believe it’s been a year already. On the other hand, it’s also hard to believe that it’s only been a year. PeerJ is just such an established part of my worldview now.
That’s exactly right. PeerJ has so completely rewritten the rule-book (on price, speed and quality of service) that now when I’m thinking about new papers I’m going to write, the question I ask myself is no longer “Where shall I send this?” but “Is there any reason not to send it to PeerJ?”
Yesterday in the comments of a post on The Scholarly Kitchen, Harvey Kane asked me “I am curious as to where you get the notion that publishing OA is less expensive and in some way “better” than the traditional model?” My reply was (in part):
My notion that OA publishing yields better results than traditional is rooted in the online-only nature of articles, which allows them to ignore arbitrary limits on word-count, number of figures, use of colour, etc., and to exploit online-only formats such as video, 3d models, CT-slice stacks, etc. In my own field of vertebrate palaeontology, it’s now routine to see in PLOS ONE descriptive articles that are many times more comprehensive than their equivalents in traditional journals — see for example the recent description of the frog Beelzebufo.
Of course there is nothing specific to open-access about this: there is no technical reason why an online-only subscription journal shouldn’t publish similarly detailed articles. But my experience so far has been that they don’t — perhaps because they are tied to the mindset that pages and illustrations are limited resources.
For Beelzebufo in PLOS ONE, read baby Parasaurolophus in PeerJ, which we described as “the world’s most open-access dinosaur“. This paper is 83 pages of technicolour goodness, plus all the 3d models you can eat. And the crazy thing is, this sort of detail in descriptive papers is not even exceptional any more — see for example the recent description of Canardia in PLOS ONE, or this analysis of croc respiration in PeerJ
Years ago, I said that in the Archbishop descriptions I wanted to raise the bar for quality of illustration. Well, I’ve taken so long over getting the Archbishop done that the bar has been raised, and now I’m scrambling to catch up. Certainly the illustrations even in our 2011 description of Brontomerus are starting to look a bit old-fashioned.
And of course, the truly astonishing thing about PeerJ is that it does this so very cheaply. Because I’m already a member (which cost me $99), the Archbishop description is going to be free to me to publish this year. (This year for sure!) If we also get our Barosaurus neck preprint published properly this year,then I’ll have to find $100 to upgrade my Basic membership to Enhanced. That’s cheap enough that it’s not even worth going through the hassle of trying to get Bristol to pay for me. And if I ever hit a year when I publish three or more papers, I’ll upgrade once more (for another $100) to the Investigator plan and then that’s it: I’m done paying PeerJ forever, however many papers I publish there. (Matt jumped straight to the all-you-can-eat plan, so he wouldn’t even have to think about it ever again.)
PeerJ’s pricing is making PLOS ONE’s $1350 APC look distinctly old-fashioned; and the $3000 charged by the legacy publishers (for a distinctly inferior product) is now frankly embarrassing. You might expect that as such low prices, PeerJ’s quality of service would suffer, but that’s not been our experience: editing, reviewing, typesetting and proofing for our neck-anatomy paper were all up there with the best we’ve received anywhere.
And it’s great to see that it’s not just minor researchers like Matt and me who are persuaded by PeerJ: they’ve now accumulated a frankly stellar list of 20 universities (so far) with institutional plans for researchers to publish there. When I say “stellar” I mean that the list includes Harvard, MIT, Cambridge, Berkeley, Stanford, Johns Hopkins, UCL, Carnegie Mellon, Duke … the list goes on.
We can only hope that the next year, and the next ten and twenty, are as successful for PeerJ as the first has been; and that other New Generation publishers will join it in pushing the field forward.
I leave the last word to Matt:
I’m getting Vicki a lifetime membership for Valentine’s Day. Because I’m a romantic.
She’s a lucky, lucky woman.
“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.“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.
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:
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:
Those photos were pretty persuasive; and a closer examination of the specimen on that same trip was to prove conclusive.
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!
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)!
- Taylor, Michael P. 2009. A re-evaluation of Brachiosaurus altithorax Riggs 1903 (Dinosauria, Sauropoda) and its generic separation from Giraffatitan brancai (Janensch 1914). Journal of Vertebrate Paleontology 29(3):787-806.
- Upchurch, Paul, Paul M. Barrett and Peter Dodson. 2004. Sauropoda. pp. 259-322 in D. B. Weishampel, P. Dodson and H. Osmólska (eds.), The Dinosauria, 2nd edition. University of California Press, Berkeley and Los Angeles. 861 pp.
- Wedel, Mathew J., and Michael P. Taylor. 2013. Caudal pneumaticity and pneumatic hiatuses in the sauropod dinosaurs Giraffatitan and Apatosaurus. PLOS ONE 8(10):e78213. 14 pages. doi:10.1371/journal.pone.0078213
- Wilson, J.A. 2002. Sauropod dinosaur phylogeny: critique and cladistic analysis. Zoological Journal of the Linnean Society 136:217-276.
September 25, 2013
This beauty is by Bryan Riolo, aka Algoroth on DeviantART, who also let me use his giant space Cthulhu for my Collect Call of Cthulhu over on Echo Station 5-7. Update: and here, belatedly, is a link to the piece on DA, with Bryan’s thoughts on it.
I love the sense of scale here, with paralititans striding through the surf, the chiaroscuro, and the sheer amount of stuff going on. It reminds me of William Stout’s murals, and lots of atmospheric classic paintings. Sure, there’s a theropod getting his guts rearranged, which I’m always up for, but that’s literally just a sidelight (or sidedark?) in this epic image. In short, I’m diggin’ the art in this paleoart.
For more sauropods stomping theropods, see:
- Genesis of an instant paleo-art classic
- Sauropods stomping theropods: a much neglected theme in palaeo-art
- Sauropods stomping theropods redux
- Brian Engh: Stomp time!
And if your definition of ‘stomping’ encompasses pooping on, vomiting at, and blowing away with sheer awesomeness, you may also enjoy:
September 16, 2013
Because “here’s that Brian Engh sketch of a sauropod literally stomping the guts out of a theropod you ordered” was a bit ungainly for a post title.
Here we have Futalognkosaurus sporting some speculative soft tissues, smooshing some very non-speculative soft tissues out of SeriouslywhogivesacrapwhatitisImjustgladitsdyingvenator. If you just look at the theropod’s face and not the…other stuff, you can imagine that maybe it is laughing. “Oh, ha-ha, you found my tickle spot! Hahaha, stop it! HAHAHA TOO MUCH AAIIIIEEEE–” Schploorrchtbp!!
Futalognkosaurus is clearly saying, “…and I thought they smelled bad on the outside.”
Brian drew this just because we’ve been living up to our mandate lately and posting pictures of sauropod vertebrae. So clearly we gotta do more of that.
For more posts with Brian’s art, go here.
September 15, 2013
I thought I’d done a decent job of illustrating MB.R.2180:C5 last time, but Wedel was not satisfied, demanding ventral and right-lateral views as well as the provided right lateral, anterior, posterior and dorsal.
All right then: here you go!
Here once more, for comparison, is Janensch’s (1950) illustration of the same vertebra:
As you’ll see, I changed the composition of my version, now that I have a right lateral view, to more closely match the composite of Janensch’s figures. The third row of mine is now exactly the same composition as I used for his illustrations, so it’s easier to compare the two.
September 15, 2013
Janensch’s (1950) paper on the vertebral column of Giraffatitan (which he called Brachiosaurus brancai, wrongly as it turns out) is in many ways a superb piece of work. Together with a separate paper on the skull of Giraffatitan and other Tendaguru sauropods (Janensch 1935-6), and yet another on their limbs and girdles (Janensch 1961), it makes up one of the most comprehensive descriptions ever published of any sauropod.
But limitations of the era meant that he wasn’t able to illustrate the vertebrae to the level that we’d hope to see today — certainly nothing like the glorious job Tschopp and Matteus (2012) did on Kaatedocus. As a result, all you get is smallish black-and-white drawings like this one, of C5 of MB.R.2180 (previously known as S I):
As it happens, Matt and I need a dorsal-view brachiosaur vertebra for a paper we’re working on. So I finally got my GIMP on and prepared a nice, high-resolution multiview illustration from the photos that Matt and I took back in 2008. Here it is:
As always, click through for the full-size version, which is 3781 by 2008.
We have here the same vertebra as above: MB.R.2180:C5. On the top row, the long-awaited dorsal view, with anterior to the left; on the bottom row (from left to right): anterior, left lateral and posterior views.
You’ll notice that I’ve illustrated the left side rather than the right that Janensch used. We have photos from both sides, but none of the right-side images came out as cleanly as this one. The anterior and posterior views are pleasantly familiar from Janensch’s figures — although my posterior one is evidently from a slightly more elevated aspect, hence the obscured upper parts of the transverse processes. I also note that Janensch rather sneakily restored the broken parts on both sides of the neurapophysis, and threw in some more prominent spinopostzygapophyseal lamine than the fossil really justifies.
Let’s look more closely at that crucial dorsal view:
It’s now apparent just how narrow brachiosaur cervicals are — at least, those as anterior as C5. You can also see how neatly the spinoprezygapophyseal and spinopostzygapophyseal laminae converge in an “X” shape to form the neurapophysis; and how the prezygapophyseal rami are drawn out almost to a point, with relatively small facets.
- Janensch, W. (1935-36). Die Schadel der Sauropoden Brachiosaurus, Barosaurus und Dicraeosaurus aus den Tendaguru-Schichten Deutsch-Ostafrikas. Palaeontographica (Suppl. 7) 2:147-298.
- Janensch, Werner. 1950. Die Wirbelsaule von Brachiosaurus brancai. Palaeontographica (Suppl. 7) 3:27-93.
- Janensch, Werner. 1961. Die Gliedmaszen und Gliedmaszengurtel der Sauropoden der Tendaguru-Schichten. Palaeontographica (Suppl. 7) 3:177-235.
- Tschopp, Emanuel, and Octávio Mateus. 2012. The skull and neck of a new flagellicaudatan sauropod from the Morrison Formation and its implication for the evolution and ontogeny of diplodocid dinosaurs. Journal of Systematic Palaeontology. doi:10.1080/14772019.2012.746589
September 5, 2013
Back in 2008, Matt and I were at the Museum Für Naturkunde Berlin. We spent some time down in the collections, where we were particularly pleased to see the much-admir’d C8 of Giraffatitan‘s paralectotype, MB.R.2181 (previously known as HMN SII).
While we were down there, we found a C8 from Plateosaurus, too, so we put that next to the Giraffatitan vertebra and shot them together:
I’m just sayin’, is all.
Note: after having written this post, I now see that I wrote an essentially identical one, with an essentially identical image, earlier this year. My memory is definitely going. Oh well: since I’ve written this, I may as well post it anyway.
July 13, 2013
April 25, 2013
Generally when we present specimen photos in papers, we cut out the backgrounds so that only the bone is visible — as in this photo of dorsal vertebrae A and B of NHM R5937 “The Archbishop”, an as-yet indeterminate Tendaguru brachiosaur, in right lateral view:
But for some bones that can be rather misleading: they may be mounted in such a way that part of the bone is obscured by structure. For example — and this is a very minor case — the ventral margins of the centra in the photo above are probably slightly deeper than they appear, because the centra are slightly sunk within the plinth that holds the vertebrae upright.
So I’ve been toying with a different idea: instead of cutting the background out completely, leaving it in place but toning it down. Then the supporting structure is visible, but clearly distinct from the actual bone. (For a more extreme case, see the “Apatosaurus” minimus sacrum.)
Here’s how the image above looks if I desaturate the background:
I’m not sure what to make of this. It looks a bit strange to me, but that might only be the strangeness of unfamiliarity.
And it might not work so well (or indeed it might work better) for photos taken against a busier background.
What do you think?
April 16, 2013
The cervical series of Giraffa camelopardalis angolensis FMNH 34426, articulated by Mike and me and photographed by Mike back in the summer of 2005, cropped and composited by me recently, not previously posted because there’s just too much cool stuff, man. But we’re working on it.
By the way, if you want the details on this critter: