I had an email out of the blue this morning, from someone I’d not previously corresponded with, asking me an important question about PeerJ. I thought it was worth sharing the question, and its answer, more generally. So here it is.
Do you have any insight into the PeerJ business model? When I try to persuade people to publish in PeerJ, a very common response is that the journal can’t possibly last because the numbers don’t add up.
And indeed PeerJ’s financial model does seem too good to be true: rather than charging an APC of $1350 (as PLOS ONE does) or $3000 (as the legacy publishers do for their not-really-open hybrid articles), PeerJ charges just $99 per author — which buys not just the right to publish one article, but one per year for life. (Or you can pay $300 for the right to publish any number of papers forever.)
PeerJ is a privately owned company and does not disclose its internal financial details. Since I have no connection with PeerJ (other than being a very satisfied customer), I know nothing of the financials.
But here is what we do know.
1. PeerJ is run by Pete Binfield, who has more experience of running open-access megajournals than anyone alive, and he’s confident enough in the financial model to have staked his own livelihood on it.
2. The principal outside investor in PeerJ is Tim O’Reilly, who has more experience of making money from free-to-read content than anyone alive, and he’s confident enough in the financial model to have staked a seven-figure sum on it.
3. Most importantly, the content in PeerJ is safe forever, because it’s fully, properly, BOAI-compliant open access, licenced using CC By, and archived at PubMed Central. So even if the worst happened, if PeerJ went bankrupt, everything published in it would live on.
4. Since CC-By documents cannot be re-enclosed if their publisher is acquired, even if PeerJ were acquired by a predatory barrier-based publisher such as Elsevier, the articles would remain safe.
5. We have got into the habit of paying far too much for publishing. On average paywalled papers cost the world more than $5000 each. Legacy publishers typically charge APCs of $3000 or so. Yet born-digital publishers such as Ubiquity Press need charge only $500, and show the breakdown of that cost. (And note that $80 of that is set aside to cover waivered articles for which no fee is paid.) Against that analysis, PeerJ’s fees don’t look crazy. The truth is that, as well as their 35% profit-margins, legacy publishers’ costs are sky-high because they are dragging around the carcass of print-based publishing.
6. Numerous universities are confident enough of the PeerJ model that they have signed up for institutional plans. You know, little universities like Cambridge, UCL and Bristol (UK), and Harvard, MIT and Cornell (USA).
Putting it all together, we see that the PeerJ financial model is roughly in alignment with other new-model publishers, that the details are persuasive enough to convince the world-leading experts who know about them, that the open-access papers published in PeerJ will be freely available to the world forever, whatever happens — which is more than we can say for articles “published” behind paywalls, and that the world’s leading universities are on board.
In short, there is no rational reason not to publish in PeerJ (unless you’re statistically illiterate enough to think that its lack of an impact factor is of any scientific significance).
March 22, 2015
We adopted a couple of 6-week-old box turtles today.
They are Three-Toed Box Turtles, Terrapene carolina triunguis, and they are insanely adorable.
This one seemed oddly familiar…had I encountered it before?
UPDATE: The last few images here are an homage to Mike’s Gilmore sequence from slide 96 in our 2012 SVPCA talk on Apatosarus minimus (link). I would have linked to it sooner, but I couldn’t find the right blog post. Because there wasn’t one. Memory!
March 17, 2015
I have a new paper out today in PeerJ: “Ecological correlates to cranial morphology in leporids (Mammalia, Lagomorpha)”, with coauthors Brian Kraatz, Emma Sherratt, and Nick Bumacod. Get it free here.
I know, I know, I have fallen from grace. First Aquilops, now rabbits. And, and…skulls! I know what you’re thinking: that maybe I’m not just experimenting with the non-vertebrae of non-sauropods anymore – maybe I have an actual problem. But I don’t. I can quit anytime! You’ll see.
Actually rabbits are the freakiest of all mammals and their skulls are wicked cool. They have double incisors, with the second set right behind the first, hence the name Duplicidentata for rabbits and their close relatives. They have weird fenestrations in their maxillae (pretty much all taxa) and parietal and occipital bones (some more than others) – I’ll come back to that in a bit. And, as we discuss in our new paper, you can tell something about how a rabbit runs by looking at its skull. I thought it would be fun to relate how we figured that out, and why.
A long time ago in a graduate seminar far, far away…
1950: DuBrul, Laskin, and Moss
I met Brian Kraatz at Berkeley, where he and I were part of the cohort of students that came into the Integrative Biology Department in the fall of 2001 (faithful readers may remember Brian from his work tracking oliphaunts from, gosh, three years ago already). We took a lot of classes together, including a seminar by Marvalee Wake on evolutionary morphology. I’m pretty sure that seminar was the first time I’d actually read DuBrul and Laskin (1961), “Preadaptive potentialities of the mammalian skull: an experiment in growth and form”, or as I think of it, “How to turn a rat skull into a pika skull for fun and profit.”
Pikas (Ochotonidae) are the sister group to rabbits (Leporidae) and together these groups make up crown Lagomorpha. If you’re not familiar with pikas, Brian describes them as starting with bunny rabbits and then making them even cuter and cuddlier. Seriously, go do an image search for ‘pika’ and try not to die of cute overload.
Pikas are interesting because in many ways their skulls are intermediate between those of rodents, especially rats, and rabbits. This is maybe not surprising since rodents are the sister group to lagomorphs and are united with them in the clade Glires. E. Lloyd DuBrul was all over this rat-pika-rabbit thing back in the mid-twentieth century. Here’s an illustration from DuBrul (1950: plate 2; labels added by me):
So DuBrul knew from pikas and in particular he had the idea that you could maybe just tweak a rat skull – say, by knocking out the basicranial sutures in a baby rat to limit the growth of the skull base – and produce a gently domed skull like that of a pika. That’s what DuBrul and Laskin (1961) is all about. They did that experiment and here are their results (DuBrul and Laskin (1961: plate 3). Normal rat skull on the right, and dotted in the bottom diagram; experimental “pika-morph” rat skull on the left, and solidly outlined below.
What’s going on here morphogenetically is that the facial skeleton is getting tilted down and away from the back end of the skull. DuBrul was hip to that, too – here’s a relevant image from his 1950 paper (plate 4; labels added by me):
The common reference point against which these skulls are registered is the cranial base (the floor of the braincase just forward of the foramen magnum). Again, the pika is a pretty good intermediate between the rat and a ‘normal’ rabbit, and the dang-near-dog-sized Flemish Giant rabbit takes the lagomorph face-tilting thing to its extreme. (‘Flemish Giant rabbit’ is another entertaining image search that I will leave you as homework.)
Turns out there’s another way you can get rat skulls with different geometries: you can cut off their legs and make them walk on two feet. In an experiment that you might have trouble getting past an Institutional Animal Care and Use Committee today, Moss (1961) lopped off the forefeet or hindfeet in two experimental batches of rats, to see what effect this would have on their skulls. I’ll let Moss speak for himself on this one (Moss, 1961: pp. 301-303, emphasis in the original):
Circumnatal amputation of the forelimbs has successfully produced what are in essence “bipedal rats,” i.e., rats whose habitual mode of kinetic and static posture is permanently altered. […] The animals never became bipedal in the exact sense; that is, they never walked erect on two limbs at all times. […] Nevertheless, bipedal posture and motion were more frequently observed than in controls. […]
Animals whose hind limbs were removed represented another picture. They most certainly did not walk about on their intact forelimbs. Neither did they seem able to use their hind limb stumps as satisfactory substitutes. Their gait was not uniform and seemed to consist in a series of short pushes or hops. The most noticeable thing about them was, among other things, apparent accentuation of their cervical vertebral curvature. The sum of these changes was an upward rotation of the skull.
He wasn’t kidding: when the two groups of bipedal rats grew up, their facial skeletons were tilted relative to the control group, but in different directions (Moss, 1961: fig 3; ‘fore’ and ‘hind’ refer to which limbs the animals had left to locomote with):
Brian and I read Moss back at Berkeley, too. In fact, we were minor Moss junkies. If you’re interested in how living forms come into being, you owe it to yourself to read Moss (1968), “A theoretical analysis of the functional matrix”.
The upshot of all of this is that although neither Brian nor I had done anything with our deep (and, okay, deeply weird) knowledge of how to experimentally jack up rat skulls by the time we graduated from Berkeley, we were also primed to be thinking about how skulls attain their shapes – especially the skulls of rodents and rabbits.
2009: American Museum of Natural History
I went to the AMNH in February, 2009, to visit Brian, who was on a postdoc there at the time, and to spend one day looking at sauropods with Mike, who was over from England for a conference. What Brian and I planned to work on was the fenestration of rabbit skulls, because I’m always interested in the strategic loss of bone from skeletal structures. We spent probably half a day talking about that, and I filled a whole page in my notebook with related noodlings:
But as the sketch on the right shows, it didn’t take us long to figure out that there was something even more interesting to do with rabbit skulls. Brian had a whole shedload of rabbit skulls from different taxa sitting on his desk, and we noticed pretty quickly that one of the primary ways they varied was in the tilt of the facial skeleton relative to the back of the skull. Here’s the very next page of my notes from that trip:
The skull up top belongs to Caprolagus, the Hispid hare, which I tend to think of as the “bulldozer hare”. Seriously, it looks like a tank. It doesn’t bound or even hop, it scrambles. Here, stare into the abyss:
That rabbit will cut you, man. And just look at how flat its skull is. Even in life Caprolagus looks more rodent-y than rabbit-y. Or, more precisely, more Ochotona-y.
At the the other extreme are taxa like Bunolagus and Pronolagus, which really push the “I’m going to cute you to death by dint of my incredible bunnosity” thing:
As Brian and I started going through skulls of as many extant rabbits as we could, we noticed that the flatter-skulled taxa, with less pronounced facial tilt, tended to be the stolid, foursquare scramblers like Caprolagus, whereas the speed demons tended to have more strongly tilted skulls. It also seemed like the latter group were achieving that pronounced facial tilt by changing the geometry of the occipital region of the skull. Look back up at the red quadrilaterals I drew on the Caprolagus and Bunolagus skulls in my notebook – those mark the basioccipital ventrally and the dorsal exposure of the supraoccipital. Perhaps unsurprisingly, supraoccipital length is not the whole story; it turns out that some face-tilters get that way by having longer or more strongly arched parietals, BUT it remains true that if you find a rabbit skull with a long dorsal exposure of the supraoccipital, it will also have pronounced facial tilt.
ANYWAY, by my last night in New York, Brian and I decided that the best way to attack this would be to go down to the basement and stay up most of the night drinking beer and measuring rabbit skulls. We then tried to correlate the various measurements and angles with information on the locomotor and burrowing habits of each species. That was a big job, and after a couple of years with little forward progress (to be fair, Brian was moving across the country and taking his first tenure-track job in this interval, and I was helping birth a sauropod) we brought in Brian’s graduate student, Nick Bumacod, to do most of it. Later on the three of us were forced to acknowledge that we knew enough statistics to get ourselves into trouble but not enough to get back out. Brian had taken a geometric morphometrics course for which Emma Sherratt was a TA, and he started bugging her for help with the stats. Emma has been involved in writing new software packages for R, and we realized that the paper would be a lot stronger if we just brought her on as an author and gave her free rein with the data. Along the way Brian and Nick were giving presentations on the project everywhere from the local Western Area Vert Paleo meeting to the World Lagomorph Conference in Vienna. I got my name on four abstracts along the way, which I think is record abstract-to-paper ratio for me (especially considering that 90% of my effort on the paper was invested in a single evening in 2009 over a couple of six-packs).
But enough navel-gazing, what did we find?
2015: Rabbit skulls reveal their mode of locomotion
Our results, which you can read for free, support the hunch that Brian and I had back in 2009: slow-moving rabbits that locomote by scrambling or scampering instead of hopping tend to have less facial tilt, and faster-moving saltatorial (hopping) and cursorial (leaping and bounding) rabbits have more facial tilt. Interestingly, facial tilt does not distinguish the saltators from the cursors. So the break here is between scrambling and any kind of hopping or leaping, but not between hoppers and leapers.
Why would that be so? We don’t know for sure yet, but our top hypothesis is that if you’re moving fast, it pays to see the ground in front of you more clearly, and getting your nose down out of the way probably helps with that. This is pretty similar to the hypothesis that tyrannosaurs have pinched nasals for better binocular vision (Stevens, 2006). Rabbits are prey animals and probably can’t afford to point their eyes forward, and they may need wide nasal airways as air intakes while they’re sprinting. Tilting the nose down may be the next best thing.
Some circumstantial support for this comes from the Caviidae, the family of South American rodents that includes guinea pigs, cavies, maras, and capybaras. Here’s another plate from DuBrul (1950: plate 6) contrasting the flatter skull of the guinea pig (Cavia porcellus, top) with the decidedly arched skull of the mara or Patagonian hare (Dolichotis magellanica, bottom). Compare the mara skull to the sectioned rabbit skull in the other DuBrul plate, above – there aren’t a lot of obvious characters to separate the two (beyond the lack of double incisors in the mara).
Despite being commonly referred to as ‘hares’ and looking a lot like short-eared rabbits, maras are rodents that evolved their rabbit-like form independently. The acquisition of pronounced facial tilt in two separate lineages of small fast-moving herbivorous mammals is further evidence for the influence of locomotor mode on skull form. Irritatingly, I think we neglected to mention the guinea pig : mara :: pika : rabbit correspondence in the paper. Oh well, it wasn’t our novel observation, and we did cite DuBrul (1950).
We found lots of other interesting things, too. The PCA plots we produced from our data separate the living rabbits in unexpected ways. The length of the diastema (the toothless portion of the upper jaw) and the diameter of the auditory bulla seem to be particularly important. Diastema length isn’t too hard to figure out – most of the face-tilters have long diastemas, and the flat-heads tend to have short ones. We have no idea what bulla diameter means yet. I mean, obviously something to do with hearing, but we don’t have any ecological variables in our analysis to address that because we didn’t see it coming. So there’s a chunk of new science waiting to be done there.
Speaking of new science, or at least a relatively new thing in science, we published the full peer-review history alongside the paper, just as Mike and I did back in 2013 and as Mike did with his stand-alone paper last December. More than 80% of PeerJ authors elect to publish the peer review histories for their papers. I can’t wait until it’s 100%. PeerJ reviews are citeable – each one gets a DOI and instructions on how to cite it – and I’m tired of having my effort as a peer reviewer used once and then thrown away forever.
If you’ve been reading this whole post with gritted teeth, wondering why we were using linear measurements instead of geometric morphometrics, chillax. Brian and Emma are on that. They’ve been CT scanning the skulls of as many extant rabbits as possible and plotting landmarks for 3D morphometrics – if you were at SVP last fall, you may have seen their talk (Kraatz and Sherratt, 2014). So stay tuned for what will soon be a new ongoing series, Rabbit Skulls: The Next Generation. (Update: pilot episode here.)
I probably won’t be on that voyage. I’ve had fun getting acquainted with a completely different part of the tree of life, but there are an awful lot of shards of excellence – busted-up sauropod vertebrae, that is – crying out for my attention, and I need to stop neglecting them. I’m done with rabbit skulls, I promise. I’m going clean. (Wish me luck!)
- DuBrul, E. L. (1950). Posture, locomotion and the skull in Lagomorpha. American Journal of Anatomy, 87(2), 277-313.
- DuBrul, E. L., & Laskin, D. M. (1961). Preadaptive potentialities of the mammalian skull: an experiment in growth and form. American Journal of Anatomy, 109(2), 117-132.
- Kraatz, B., and Sherratt, E. (2014). Evolution, ecology, and modularity of the lagomorph skull. Journal of Vertebrate Paleontology, 35(3, Supplement), 162A.
- Kraatz, B.P., Sherratt, E., Bumacod, N., and Wedel, M.J. 2015. Ecological correlates to cranial morphology in leporids (Mammalia, Lagomorpha). PeerJ, 3:e844. https://dx.doi.org/10.7717/peerj.844
- Moss, M. L. (1961). Rotation of the otic capsule in bipedal rats. American Journal of Physical Anthropology, 19(3), 301-307.
- Moss, M. L. (1968). A theoretical analysis of the functional matrix. Acta Biotheoretica, 18(1), 195-202.
- Stevens, K. A. (2006). Binocular vision in theropod dinosaurs. Journal of Vertebrate Paleontology, 26(2), 321-330.
In 2012, Matt and I spent a week in New York, mostly working at the AMNH on “Apatosaurus” minimus and a few other specimens that caught our eye. But we were able to spend a day at the Yale Peabody Museum up in New Haven, Connecticut, to check out the caudal pneumaticity in the mounted Apatosaurus (= “Brontosaurus“) excelsus, YPM 1980, and the bizarrely broad cervicals of the Barosaurus lentus holotype YPM 429.
While we there, it would have been churlish not to pay some attention to the glorious and justly famous Age of Reptiles mural, painted by Rudolph F. Zallinger from 1944-1947.
So here it is, with the Brontosaurus neck for scale:
Click through for high resolution (3552 × 2664).
And here is a close-up of the most important, charismatic, part of the mural:
Again, click through for high resolution (3552 × 2664).
That’s your lot for now. We’ve long promised a proper photo post of the Brontosaurus mount itself, and I’ll try to get that done soon. For now, it’s just scenery.
Just launched: a new open-access journal of vertebrate paleontology, brought to you by the University of Alberta, Canada! It’s called VAMP (Vertebrate Anatomy Morphology Palaeontology), and it charges no APC. Here’s a illustration from one of the two articles in its first issue.
VAMP uses the canonical open-access licence, Creative Commons Attribution 4.0 International (CC By), which means it fulfils both the letter and the spirit of the Budapest Open Access Initiative’s definition of OA.
It’s great that we in vertebrate palaeontology can add this journal to the roster of OA journals in our field, already including Palaeontologia Electronica, Acta Palaeontologica Polonica, Palarch’s Journal of Vertebrate Paleontology, The Fossil Record and others. (Plus of course there is lots of vertebrate palaeontology in PLOS ONE and PeerJ.) I think that as a field, we are ahead of the curve in making the transition towards an all-OA literature.
March 6, 2015
We have a new page on the sidebar – here – where we’re collecting as many museum abbreviations as possible, the idea being that you can copy and paste them into your papers to rapidly populate the ‘Museum Abbreviations’ section. I grabbed about 100 from my own previous papers and a handful of others, so currently the list is highly skewed toward museums with (1) sauropods (2) that I’ve had reason to yap about. I’ve probably missed tons of museums that are important for people working on hadrosaurs or stegosaurs or (shudder) mammals. From here on out the list will grow as people suggest additions and edits in the comments on that page. So please get on over there and contribute!
Completely unrelated eyeball-bait art courtesy of Brian Engh, who writes,
I don’t even remember drawing this, I just found it lying around and spruced it up a bit today. It’s supposed to be some kinda diplodocid, maybe Kaatedocus, but I think the main goal of the drawing was to draw one with a sense of weight that felt right given that their center of mass is supposed to be so far back. I like the idea of them getting startled and popping up every now and again… [see also–MJW]
March 3, 2015
I’ve been taking a long-overdue look at some of the recently-described giant sauropods from China, trying to sort out just how big they were. Not a new pursuit for me, just one I hadn’t been back to in a while. Also, I’m not trying to debunk anything about this animal – as far as I know, there was no bunk to begin with – I’m just trying to get a handle on how big it might have been, for my own obscure purposes.
‘Huanghetitan’ ruyangensis was named by Lu et al. (2007) on the basis of a sacrum, the first 10 caudal vertebrae, some dorsal ribs and haemal arches, and a partial ischium. The holotype is 41HIII-0001 in the Henan Geological Museum. Lu et al. (2007) referred the new animal to the genus Huanghetitan, which was already known from the type species H. liujiaxiaensis (You et al., 2006). However, Mannion et al. (2013) found that the two species are not sister taxa and therefore ‘H.’ ruyangensis probably belongs to another genus, which has yet to be erected. Hence my use of scare quotes around the genus name.
Here’s the sacrum of ‘H.’ ruyangensis from Lu et al. (2007: fig. 2). The original small scale bar is supposed to be 10cm. You know how I feel about scale bars (or maybe you don’t, in which case read this and this), but in this case the scale seems pretty legit based on limited measurements that are also given in the paper. I comped in the sacrum of Brachiosaurus altithorax FMNH P25107 from this post (many thanks to Phil Mannion for the photos!), and scaled it according to the max width across the second pair of sacral ribs, which Riggs (1904: p. 236) gives as 105 cm. The sacrum of ‘H.’ ruyangensis is a little bigger, but not vastly bigger. ‘H.’ ruyangensis had six sacrals to Brachiosaurus‘s five, so extra length is mostly illusory, whereas the extra width is mostly legit.
According to Lu et al. (2007), the anterior face of the first caudal vertebra in ‘H.’ ruyangensis measures 26.9 cm tall by 32 cm wide, and the centrum is 18.2 cm long. The same measurements in Brachiosaurus are 28 x 33 cm for the anterior face and 16 cm for the centrum length. It’s basically a tie.
What about the big rib? Lu et al. (2007) show a complete dorsal rib of ‘H.’ ruyangensis that is 293 cm long. That’s nothing to sniff at – the longest rib of Brachiosaurus, and the cause for the specific name altithorax (‘tall-bodied’), measures 274.5 cm, so the ‘H.’ ruyangensis rib is about 7% longer. But it’s not the longest rib known for any sauropod. As far as I know, that honor goes to a Supersaurus dorsal rib measuring 305 cm (Lovelace et al., 2008). The biggest Supersaurus caudal also blows away the caudals of both ‘H.’ ruyangensis and Brachiosaurus, with a anterior face 39 cm tall by 46 cm wide. But then diplodocids were all about that bass, so there’s not much point in comparing tail size with a titanosauriform if you’re trying to get a handle on overall body size. Still, the 35-40 ton Supersaurus shows that you can have 3-meter ribs without being anywhere near Argentinosaurus territory, mass-wise.
So what’s the verdict? ‘H.’ ruyangensis was a little bigger than the holotype of Brachiosaurus altithorax, but only by a few percent. It might have been about the same size as the XV2 specimen of Giraffatitan brancai. Or, who knows, it could have had completely different proportions and massed considerably more (or less). But on the current evidence, it doesn’t seem to have been one of the biggest sauropods of all time. I hope we get some more of it one of these days.
- Lovelace, David M., Scott A. Hartman and William R. Wahl. 2008. Morphology of a specimen of Supersaurus (Dinosauria, Sauropoda) from the Morrison Formation of Wyoming, and a re-evaluation of diplodocid phylogeny. Arquivos do Museu Nacional, Rio de Janeiro, 65 (4): 527-544.
- Lu J., Xu, L., Zhang, X., Hu, W., Wu, Y., Jia, S., and Ji, Q. 2007. A new gigantic sauropod dinosaur with the deepest known body cavity from the Cretaceous of Asia. Acta Geologica Sinica, 81: 167-176.
- Mannion, P.D., Upchurch, P., Barnes, R.N., and Mateus, O. 2013. Osteology of the Late Jurassic Portuguese sauropod dinosaur Lusotitan atalaiensis (Macronaria) and the evolutionary history of basal titanosauriforms. Zoological Journal of the Linnean Society, 168(1): 98-206.
- Riggs, E.S. 1904. Structure and relationships of opisthocoelian dinosaurs. Part II, the Brachiosauridae. Field Columbian Museum, Geological Series 2, 6, 229-247.
- You, H., Li, D., Zhou, L., and Ji, Q. 2006. Huanghetitan liujiaxiaensis. a new sauropod dinosaur from the Lower Cretaceous Hekou Group of Lanzhou Basin, Gansu Province, China. Geological Review, 52 (5): 668-674.