Specimen photos with desaturated backgrounds
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?
All I want to do in this post is make people aware that there is a difference between these two things, and occasionally that affects those of us who work in natural history.
In one of his books or essays, Stephen Jay Gould made the point that in natural history we are usually not dealing with whether phenomena are possible or not, but rather trying to determine their frequency. If we find that in a particular population of quail most of the birds eat ants but some avoid them, then we know some things: that quail can tolerate eating ants, that quail are not required to eat ants, and that both strategies can persist in a single population.
This idea has obvious repercussions for paleoart, especially when it comes to “long-tail” behaviors. I dealt with that in this post, and also in the comment thread to this one. But that’s not what I want to talk about today.
Sometimes it is useful to talk about things that never happen, or that have at least never occurred in the sample of things we know of. Obviously how certain you can be in these cases depends on the intensity of sampling and the inherent likelihood of a surprising result, which can be hard to judge. If you argued right now that T. rex lacked feathers because no T. rex specimens have been found with feathers, you’d most likely be wrong; it is almost certainly just a matter of time before someone finds direct evidence of feathers in T. rex, given the number of T. rex specimens waiting to be found and the strength of the indirect evidence (e.g., phylogenetic inference, analogy: ornithomimids are known to be feathered even though most specimens are found without feather impressions). If you argue that sauropods are unique among terrestrial animals in having necks more than five meters long, you’re most likely right; being wrong would imply the existence of some as-yet undiscovered land animal of sauropod size, or with seriously wacky proportions (or both), and our sampling of terrestrial vertebrates is good enough to make that extremely unlikely.
The reason for this post is that sometimes people confuse that last argument, which is about sampling and induction, with the argument from personal incredulity.
For example, in our no-necks-for-sex paper (Taylor et al. 2011), we included this passage:
Sauropoda also had a long evolutionary history, originating about 210 million years ago in the Carnian or Norian Age of the Late Triassic, and persisting until the end-Cretaceous extinction of all non-avian dinosaurs about 65 millions years ago. Thus the ‘necks-for-sex’ hypothesis requires that this clade continued to sexually select for exaggeration of the same organ for nearly 150 million years, a scenario without precedent in tetrapod evolutionary history.
One of the reviewers argued that we couldn’t include that section, because it was just the argument from personal incredulity writ large, like so:
There are no other known cases of X in tetrapod evolutionary history, and therefore we don’t believe that the case in question is the sole exception.
…with the second part of that unstated (by us) but implied. But we disagreed, and argued (successfully) that it was an argument based on sampling, like so:
There are no other known cases of X in tetrapod evolutionary history, and therefore it is unlikely that the case in question is the sole exception.
Now, it is perfectly fair to criticize arguments like that based on the thoroughness of the sampling and the likelihood of exceptions, as discussed above for T. rex feathers. Just don’t mistake arguments like that for arguments from personal incredulity.* On the flip side, if someone makes an argument from personal incredulity, see if the same thing can be restated as an argument about sampling. Maybe they’re correct but just expressing themselves poorly (“I refuse to believe that the moon is made out of cheese”), and maybe they’re wrong and restating things in terms of sampling will help you understand why.
* If you want to get super pedantic about it, they’re both arguments from ignorance. But one of them is at least potentially justifiable by reference to sampling. Absence of evidence is not necessarily evidence of absence, but it may get to be that way as the sampling improves (e.g., there is no evidence of planets closer to the sun than Mercury, and at this point, that is pretty persuasive evidence that no such planets exist).
Parting shot: one thing that has always stuck in my head from Simberloff (1983) is the bit about imagining a large enough universe of possible outcomes. And I’ve always had a perverse fascination with Larry Niven’s “Down in Flames”, in which he pretty much demolished his Known Space universe by assuming that every basic postulate of that universe was false. Neither of these follow directly on from the main point of the post, but they’re not completely unrelated, either. Because I think that they yield a pretty good heuristic for how to do science: imagine what it would take for you to be wrong–imagine a universe in which you are wrong–and then go see if the thing that makes you wrong, whatever it is, can be shown to exist or to work. If not, it doesn’t mean you’re right, but it means you’re maybe less wrong, which, if we get right down to it, is the best that we can hope for.
The photos have nothing to do with the post, they’re just pretty pictures from the LACM to liven things up a little.
References
- Simberloff, D. (1983). Competition theory, hypothesis-testing, and other community ecological buzzwords. The American Naturalist, 122(5), 626-635.
- Taylor, M. P., Hone, D. W., Wedel, M. J., & Naish, D. (2011). The long necks of sauropods did not evolve primarily through sexual selection. Journal of Zoology, 285(2), 150-161.
Brachiosaurus sp. BYU 12866 c5? in left lateral view with CT slices, some corrected for distortion.
Last Tuesday Mike popped up in Gchat to ask me about sauropod neck masses. We started throwing around some numbers, derived from volumetric estimates and some off-the-cuff guessing. Rather than tell you more about it, I should just paste our conversation, minimally edited for clarity and with a few hopefully helpful links thrown in.
BYU 12613, a posterior cervical probably referable to Diplodocus, in dorsal (top), left lateral (left), and posterior (right) views. It most closely resembles C14 of D. carnegii CM 84/94 (Hatcher 1901: plate 3) despite being less than half as large, with a centrum length of 270 mm compared to 642 mm for C14 of D. carnegii. From Wedel and Taylor (in press).
* R. McNeill Alexander (1985, 1989) did estimate the mass of the neck of Diplodocus, based on the old Invicta model and assuming a specific gravity of 1.0. Which was a start, and waaay better than no estimate at all. Still, let’s pretend that Mike meant “tried based on the actual fossils and what we know now about pneumaticity”.
The stuff about putting everything off until April is in there because we have a March 31 deadline to get a couple of major manuscripts submitted for an edited thingy. And we’ve made a pact to put off all other sciencing until we get those babies in. But I want to blog about this now, so I am.
Another thing Mike and I have been talking a lot about lately is the relation between blogging and paper-writing. The mode we’ve seen most often is to blog about something and then repurpose or rewrite the blog posts as a paper. Darren paved the way on this (at least in our scientific circle–people we don’t know probably did it earlier), with “Why azhdarchids were giant storks“, which became Witton and Naish (2008). Then last year our string of posts (starting here) on neural spine bifurcation in Morrison sauropods became the guts–and most of the muscles and skin, too–of our in-press paper on the same topic.
But there’s another way, which is to blog parts of the science as you’re doing them, which is what Mike was doing with Tutorial 20–that’s a piece of one of our papers due on March 31.
Along the way, we’ve talked about John Hawks’ model of using his blog as a place to keep his notes. We could, and should, do more of that, instead of mostly keeping our science out of the public eye until it’s ready to deploy (which I will always favor for certain projects, such as anything containing formal taxonomic acts).
And I’ve been thinking that maybe it’s time for me–for us–to take a step that others have already taken, and do the obvious thing. Which is not to write a series of blog posts and then decide later to turn it into a paper (I wasn’t certain that I’d be writing a paper on neural spine bifurcation until I had written the second post in that series), but to write the paper as a series of blog posts, deliberately and from the outset, and get community feedback along the way. And I think that the sauropod neck mass project is perfect for that.
Don’t expect this to become the most common topic of our posts, or even a frequent one. We still have to get those manuscripts done by the end of March, and we have no shortage of other projects waiting in the wings. And we’ll still post on goofy stuff, and on open access, and on sauropod stuff that has nothing to do with this–probably on that stuff a lot more often than on this. But every now and then there will be a post in this series, possibly written in my discretionary blogging time, that will hopefully move the paper along incrementally.
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Alexander, R.M. 1985. Mechanics of posture and gait of some large dinosaurs. Zoological Journal of the Linnean Society, 83(1): 1-25.
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Alexander, R.M. 1989. Dynamics of Dinosaurs and Other Extinct Giants. Columbia University Press.
- Hutchinson, J.R., Bates, K.T., Molnar, J., Allen, V., and Makovicky, P.J. 2011. A computational analysis of limb and body dimensions in Tyrannosaurus rex with implications for locomotion, ontogeny, and growth. PLoS ONE 6(10): e26037. doi:10.1371/journal.pone.0026037
- Taylor, M.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.
- Wedel, M.J., and Taylor, M.P. In press. Neural spine bifurcation in sauropod dinosaurs of the Morrison Formation: ontogenetic and phylogenetic implications. PalArch’s Journal of Vertebrate Paleontology.
- Witton, M.P., and Naish, D. 2008. A reappraisal of azhdarchid pterosaur functional morphology and paleoecology. PLoS ONE 3(5): e2271. doi:10.1371/journal.pone.0002271
The Recapture Creek sauropod: the reveal
March 3, 2013
If you’re just joining us, this post is a follow-up to this one, in which I considered the possible size and identity of the Recapture Creek femur fragment, which “Dinosaur Jim” Jensen (1987: page 604) said was “the largest bone I have ever seen”.
True to his word, Brooks Britt at BYU got back to me with measurements of the Recapture Creek femur fragment in practically no time at all:
Length 1035 mm, width 665 mm. However, you cannot trust the measurements because Jensen put a lot of plaster on the proximal half of the bone.
Now, taking plaster off a bone is not going to make it any larger. So the plastered-up specimen is the best case scenario for the RC femur to represent a gigapod. And I know the stated width of 665 mm is the max width of the proximal end, because I sent Brooks a diagram showing the measurements I was requesting. The length is a little less than anticipated, and doesn’t quite jibe with the max proximal width–I suspect a little might have broken off from the distal end where the preservation looks not-so-hot.
Based on those measurements, it looks like Jensen got the scale bar in Figure 8 in his 1987 paper approximately right–if anything, the scale bar is a little undersized, but only by 5% or so, which is actually pretty good as these things go (scale bars without measurements are still dag-nasty evil, though). By overlapping Jensen’s photo with the femur of the Brachiosaurus altithorax holotype (FMNH P25107) to estimate the size of the element when complete, I get a total length of 2.2 meters–exactly the same size as the Brachiosaurus holotype. If the Recapture Creek femur is from a Camarasaurus, which I don’t think we can rule out, it was 2 meters long when complete, or 11% longer and 37% more massive than the big C. supremus AMNH 5761–about 35 tonnes or maybe 40 on the outside. So it’s a big bone to be sure, but it doesn’t extend the known size range of Morrison sauropods.
So, as before, caveat estimator when working from scaled illustrations of single partial bones of possibly immense sauropods.
Now, here’s a weird thing. Let’s assume for the sake of this discussion that the Recapture Creek femur is from a brachiosaur. That gives us three individual Late Jurassic brachiosaurids–the Recapture Creek animal, the Brachiosaurus altithorax holotype, and the mounted Giraffatitan brancai–that are almost exactly the same size in limb bone dimensions (although B.a. had a longer torso). But we know that brachiosaurids got bigger, as evidenced by the XV2 specimen of Giraffatitan, and based on the lack of scapulocoracoid fusion in both FMNH P25107 and the mounted Giraffatitan. So why do we keep finding these (and smaller) subadults, and so few that were XV2-sized? I know that there gets to be a preservation bias against immense animals (it’s hard to bury a 50-tonne animal all in one go), but I would not think the 13% linear difference between these subadults and XV2-class adults would be enough to matter. Your thoughts?
Reference
How big was the Recapture Creek sauropod?
February 28, 2013
From Jensen (1987, page 604):
“In 1985 I found the proximal third of an extremely large sauropod femur (Figs. 8A, 12A) in a uranium miner’s front yard in southern Utah. The head of this femur is 1.67 m (5’6″) in circumference and was collected from the Recapture Creek Member of the the Morrison Formation in Utah near the Arizona border. It is the largest bone I have ever seen.”
Jensen included not one but two figures of this immense shard of excellence. Here they are:
Jensen 1987, Figure 8
Jensen 1987, Figure 12
The specimen was heavily reconstructed, as you can see from the big wodge of unusually smooth and light-colored material in the photo. So we can’t put much stock in that part of the specimen.
Unfortunately, the only measurement of the specimen that Jensen gives in the paper is that circumference; there are no straight-line linear measurements, and the figures both have the dreaded scale bars. Why dreaded? Check this out:
As you can see, when the scale bars are set to the same size, the bones are way off (the scale bar in the drawing is 50 cm). This is not an uncommon problem. I make the Fig 8 version 30% bigger in max mediolateral width of the entire proximal end, and still 17% bigger in minimum diameter across the femoral head, as measured from the slight notch on the dorsal surface (on the right in this view).
Can we figure out which is more accurate based on the internal evidence of the paper? For starters, the Fig 12 version is a drawing (1), that does not match the outline from the photo (2), and the hand-drawn scale bar (3) does not actually coincide with any landmarks (4), and that’s plenty of reasons for me not to trust it.
What about that circumference Jensen mentioned? Unfortunately, he didn’t say exactly where he took it, just that the head of the femur had a circumference of 1.67 meters. Is that for the entire proximal end, or for the anatomical head that fits in the acetabulum, er wot? I’m afraid the one measurement given in the paper is no help in determining which of the figures is more accurately scaled.
The obvious thing to do would be to see if this bone is in the BYU collections, and just measure the damn thing. More on that at the end of the post.
In the meantime, Jensen said that the shape of the Recapture Creek femur was most similar to the femur of Alamosaurus, or to that of Brachiosaurus among Morrison taxa, and he referred it to Brachiosauridae. So how does this thing–in either version–compare with the complete femur of FMNH P25107, the holotype of Brachiosaurus altithorax?
The Recapture Creek femur fragment compared to the complete femur of the Brachiosaurus altithorax holotype FMNH P25107
The first thing to notice is that the drawn outline from Figure 12 is a much better match for the Brachiosaurus altithorax femur–enough so that I wonder if Jensen drew it from the Recapture Creek specimen, or just traced the B.a. proximal femur and scaled it accordingly (or maybe not accordingly, since the scale bars don’t match).
But let’s get down to business: how long would the complete femur have been?
Using the scale bar in the photograph from Figure 8 (on the left in above image), I get a total femur length of 2.36 meters. Which is long, but only 7.7% longer than the 2.19-meter femur of FMNH P25107, and therefore only 25% more massive. So, 35 tonnes to Mike’s 28-tonne B.a., or maybe 45 tonnes to a more liberal 36-tonne B.a. Big, yeah, but not world-shattering.
Using the scale bar in the drawing from Figure 12 (on the right in the above image)–which, remember, is 50 cm, not 1 meter–I get a total femur length of about 1.9 meters, which is considerably smaller than the B.a. holotype. That is very much at odds with Jensen’s description of it as “the largest bone I have ever seen”, and given that we have many reasons for not trusting the scale bar in the drawing, it is tempting to just throw it out as erroneous.
So it would seem that unless Jensen got both scale bars too big, the Recapture Creek brachiosaur was at most only a shade bigger than the holotype specimen of Brachiosaurus altithorax.
But wait–is the Recapture Creek brachiosaur a brachiosaur at all? Jensen didn’t list any characters that pushed him toward a brachiosaurid ID, and I don’t know of any proximal femur characters preserved in the specimen that would separate Brachiosaurus from, say, Camarasaurus. And in fact a camarasaur ID has a lot to recommend it, in that Camarasaurus femora have very offset heads (the ball- or cylinder-like articular surface at the top end sticks out a big more to engage with the hip socket–see Figure 12 up near the top of the post), moreso than in many other Morrison sauropods, and that would make them better matches for the Recapture Creek femur photo. Here’s what the comparo looks like:
The Recapture Creek femur fragment compared with a complete femur of Camarasaurus.
I make that a 2.07-meter femur using the photo on the left, and a 1.66-meter femur using the drawing on the right. The one decent femur in the AMNH 5761 Camarasaurus supremus collection is 1.8 meters long, so these results are surprisingly similar to those for the B. althithorax comparison–the drawing gives a femur length shorter than the largest known specimens, and the photo gives a length only slightly longer. A camarasaur with a 2.07 meter femur would be 15% larger than the AMNH C. supremus in linear terms, and assuming isometric scaling, 1.5 times as massive–maybe 38 tonnes to AMNH 5761′s estimated 25. A big sauropod to be sure, but not as big as the largest apatosaurs, and not nearly as big as the largest titanosaurs.
I have always been surprised that the Recapture Creek femur frag has attracted so little attention, given that “Dinosaur Jim” himself called it the biggest bone he had ever seen. But it appears that the lack of attention is justified–whether it was a brachiosaur or a camarasaur, and using the most liberal estimates the scale bars allow, it simply wasn’t that big.
Update about half an hour later: Okay, maybe I was a little harsh here. IF the photo scale bar is right, the Recapture Creek femur might still represent the largest and most massive macronarian from the Morrison Formation (Edit: only if it’s a brachiosaur and not a camarasaur; see this comment), which is something. I suppose I was particularly underwhelmed because I was expecting something up in OMNH 1670-to-Argentinosaurus territory, and so far, this ain’t it. I’ll be interested to see what the actual measurements say (read on).
The Moral of This Story
So, if it wasn’t that big after all, and if no-one has made a stink about it being big before now, why go to all this trouble? Well, mostly just to satisfy my own curiosity. If there was a truly gigantic brachiosaur from the Morrison, it would be relevant to my interests, and it was past time I crunched the numbers to find out.
But along the way something occurred to me: this should be a cautionary tale for anyone who gets all wound up about the possible max size of Amphicoelias fragillimus. As with A. fragillimus, for the Recapture Creek critter we have part of one bone, and at least for this exercise I was working only from published illustrations with scale bars. And as with A. fragillimus, the choice of a reference taxon is not obvious, and the size estimates are all over the place, and some of them just aren’t that big.
It always amuses me when A. fragillimus comes up and people (well, trolls) accuse us of being big ole’ wet blankets that just don’t want to believe in 200-tonne sauropods. It amuses me because it’s wrong on so many levels. Believe me, when we have our sauropod fanboy hats on, we most definitely do want to believe in 200-tonne sauropods. That would rock. But when we put our scientist hats on, wanting and belief go right out the window. We have to take a cold, hard look at the data, and especially at its limitations.
Oh, the other moral is to go buy a tape measure, and use it. Sheesh!
Coda
As I said above, the obvious thing to do would be to just track down the bone and measure it. It does still exist, it’s in the BYU collections, and Brooks Britt has kindly offered to send along some measurements when he gets time. So we should have some real answers before long (and here they are). But I wanted to work through this example without them, to illustrate how much uncertainty creeps in when trying to estimate the size of a big sauropod from published images of a single partial bone.
Reference
The dark side of Sauroposeidon
February 4, 2013
Sauroposeidon holotype OMNH 53062, posterior half of ?C7 and all of ?C8 in left lateral view. Scale bar is in inches.
There’s a lot more Sauroposeidon material these days than there used to be, thanks to the referral by D’Emic and Foreman (2012) of Paluxysaurus and Ostrom’s Cloverly material and the new Cloverly material to my favorite sauropod genus. I’ve seen almost all of this material firsthand, but obviously the specimen I’m most familiar with is the holotype, OMNH 53062. It was the primary thing occupying my mind from the summer of 1996 through the spring of 2000, and it has remained a frequent object of wonder ever since.
The specimen was found lying on its right side in the field, so that side is in better shape, by virtue of having been more deeply buried and thus protected from the ravages of freezing and thawing and other erosional processes. When the jackets were taken out of the ground and prepared, the not-so-well-preserved left sides were prepped first. Then permanent support jackets were made on the left sides, the vertebrae were flipped onto their left sides, the field jackets were removed from their right sides, and the vertebrae were prepped on the right. They’ve been lying in their support jackets, left side down and right side up, ever since. (For more on the taphonomy and recovery of the specimen, see this post and Wedel and Cifelli 2005 [free PDF linked below].)
Now, if I had known what I was doing, I would have photographed the crap out of the left sides before the verts were flipped. But it was my first project and I was learning on the job, and that didn’t occur to me until later.
It also didn’t occur to me that, once flipped, the left sides would be effectively out of reach forever. But the vertebrae are extremely fragile. The bigger verts have cracks running through them, and the jackets flexed noticeably when we took them for CT scanning. I am worried that if we tried to flip the bigger verts today, they might just crumble. Even the surface bone is fragile. I remember once trying to get some dust off one of the verts with a vacuum cleaner hose, and watching in horror as some of the millimeter-thin external bone just flaked off and flew away. That was in the late 1990s, when the verts were still stored in the dusty, drafty WWII-era buildings that had housed the museum collections for ages. Now they’re in what I still think of as the “new” building, which opened in 2000, in a really nice modern collection room with climate and dust control, and I’ve never seen them with any noticeable dust.
Anyway, the left sides are now obscured by their supporting jackets and will remain that way for the foreseeable future. And I don’t have a complete set of photos of the left sides of the verts. But I do have one, of the back half of ?C7 and all of ?C8, and a scan of it appears at the top of this post. It’s a scan of a physical photograph because it was taken in late 1996 or early 1997–no-one I knew had a digital camera, and if you wanted a digital version of a photograph, you shot it on a film camera, had a big print made, and scanned that on a flatbed scanner.
Here’s another version with the vertebrae outlined:
When I and everyone else thought that Sauroposeidon was a brachiosaur, I was pretty sure that these were C7 and C8, out of a total of 13 cervicals, just like Giraffatitan. And it still might be so–a future analysis might find that the newly-expanded Sauroposeidon is a brachiosaurid after all, and even if not, Gomani (2005) posited a primitive cervical count of 13 for titanosaurs. If that’s true, then possibly 13 cervicals are primitive for all titanosauriforms, and the increases beyond that–to 17 in Euhelopus and 14-17 in more derived titanosaurs like Futalognkosaurus and Rapetosaurus–were deviations from that primitive pattern.
But.
If Sauroposeidon was a basal somphospondyl, as posited by D’Emic and Foreman (2012) and as found in the phylogenetic analysis of D’Emic (2012), then maybe it was more like Euhelopus than Giraffatitan, and maybe it had more than 13 cervicals. (Note that D’Emic [2012] found Sauroposeidon to be a basal somphospondyl but outside the Euhelopodidae, so even in his analysis, Euhelopus could have gotten its extra cervicals independently of Sauroposeidon.) That’s an interesting prospect, since the 11.5-meter neck estimate for Sauroposeidon I made back in 2000 was based on the conservative assumption of 13 cervicals. If Sauroposeidon had more cervicals, they were probably mid-cervicals (nobody adds more dinky C3s, or stubby cervico-dorsals*–that would be silly), and therefore between 1 and 1.25 meters long. So if the individual represented by OMNH 53062 had 15 cervicals, as Mike hypothetically illustrated in this post, its neck might was probably more like 14 meters long, and if it had 17 cervicals, like Euhelopus and Rapetosaurus, its neck might have topped 16 meters–as long or longer than that of Supersaurus.
Now, I’m not saying that Sauroposeidon had a 16-meter neck. The conservative estimate is still 13 cervicals adding up to 11.5 meters. But the possibility of a longer neck is tantalizing, and can’t be ruled out based on current evidence. As usual, we need more fossils.
Happily, now that Sauroposeidon is known from Oklahoma, Texas, and Wyoming, and is one of the best-represented EKNApods instead of one of the scrappiest, the chances that we’ll find more of it–and recognize it–are looking good. I will keep my fingers firmly crossed–as they have been for the last 17 years.
* Radical pedantry note: of course we have very good evidence of sauropods getting more cervical vertebrae by recruiting dorsals into the cervical series. So, for example, 13 cervicals and 12 dorsals are supposed to be primitive for neosauropods, but diplodocids have 15 and 10, respectively–the obvious inference being that the first two dorsals got cervicalized. So in this narrow meristic sense, sauropods definitely did add cervicodorsals. But my point above is about the morphology of the verts themselves–once diplodocids had those two extra cervicals at the end, the former cervicodorsals were free to become more “cervicalized” in form. So effectively–in terms of the shapes of their necks–diplodocids added mid-cervicals.
References
- D’Emic, M.D. 2012. The early evolution of titanosauriform sauropod dinosaurs. Zoological Journal of the Linnean Society 166: 624–671.
- D’Emic, M.D., and B.Z. Foreman. 2012. The beginning of the sauropod dinosaur hiatus in North America: insights from the Lower Cretaceous Cloverly Formation of Wyoming. Journal of Vertebrate Paleontology 32(4): 883-902.
- Gomani, Elizabeth M. 2005. Sauropod dinosaurs from the Early Cretaceous of Malawi, Africa. Palaeontologia Electronica 8(1):27A (37 pp.)
- Wedel, M.J., and Cifelli, R.L. 2005. Sauroposeidon: Oklahoma’s native giant. Oklahoma Geology Notes 65 (2):40-57.
…and that, ladies and gentlemen, is why you code Brachiosaurus and Giraffatitan separately
January 23, 2013
D’Emic (2012: figure 5)
Now this is super-freakin’ cool, and I’ve been meaning to blog about it for a while. In Mike D’Emic’s recent titanosauriform phylogeny (D’Emic 2012), he (correctly) included Brachiosaurus and Giraffatitan as separate OTUs, and, hey, whaddayaknow, they’re not sister taxa anymore: Brachiosaurus is more closely related to a trio of Early Cretaceous North American brachiosaurids than it is to Giraffatitan.
The potential for someone to find this result was there ever since Mike broke Brachiosaurus and Giraffatitan apart, as a previously composite OTU, in his 2009 paper. It just hadn’t materialized. In fact, some authors have gone out of their way to not find this out, by keeping the old composite coding. That seems…unwise, in retrospect. Whether one agreed with Mike on the nomenclatural point of generic separation or not, not coding the two taxa as separate OTUs (especially after Mike had done that work for them) was a poor phylogenetic decision–in essence, it constrained Brachiosaurus and Giraffatitan to be sister taxa in the analysis, and outlawed any more interesting results–like the one obtained by D’Emic (2012)–before the software even started crunching trees.
So anyway, back to the coolness inherent in D’Emic’s tree. Of course, like all phylogenetic results this is just a hypothesis and it is subject to revision based on new information blah blah blah…but it is really interesting that there is now some phylogenetic support for an endemic radiation of brachiosaurids in North America (bonus goofy observation–you can’t spell ‘endemic’ without D’Emic). Or perhaps Lauriasia–I would kill to know where the British brachiosaurids (or basal titanosauriforms) fit into this story, and Lusotitan, and the apparently tiny Croatian carbonate platform brachiosaurs.
Also super-interesting that, if this tree is accurate, these endemic Early Cretaceous brachiosaurids were living alongside a giant basal somphospondyl in the form of Sauroposeidon, which came from heaven knows where. Look who it’s surrounded by–Ligabuesaurus is from Argentina, Tastavinsaurus is from Spain, and the euhelopodids are from eastern Asia. Evidently there was also a global radiation of basal somphospondyls. And why are all the Early Cretaceous North American brachiosaurids small–smaller than Brachiosaurus and Giraffatitan, anyway (at least until we find bigger individuals of the former)–while Sauroposeidon is so big? Or is that just an effect of tiny sample sizes, and one lucky strike in the form of the Sauroposeidon holotype?
So much cool stuff to think about. I don’t usually get this much enjoyment out of a tree unless it has lights and ornaments.
References
- D’Emic, M.D. 2012. The early evolution of titanosauriform sauropod dinosaurs. Zoological Journal of the Linnean Society 166: 624–671.
- Taylor, M.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.
Plateosaurus is pathetic
January 16, 2013
This photograph is of what I consider the closest thing to the Platonic Ideal sauropod vertebra: it’s the eighth cervical of our old friend the Giraffatitan brancai paralectotype MB.R.2181. (previously known as “Brachiosaurus” brancai HM S II — yes, it’s changed genus and specimen number, both recently, but independently.)
And if you look very carefully, down at the bottom, you can see the same vertebra, C8, of the prosauropod Plateosaurus. Pfft.
This photo was taken down in the basement of the Museum für Naturkunde Berlin, on the same 2008 trip where Matt took the “Mike in Love” photo from two days ago. For anyone who didn’t recognise the specific vertebra I was in love with in that picture, shame on you! It is of course our old friend the ?8th dorsal vertebra of the same specimen, which we’ve discussed in detail here on account of its unique spinoparapophyseal laminae, its unexpectedly missing infradiapophyseal lamina and its bizarre perforate anterior centroparapophyseal laminae.
2000 AD’s flagrantly plagiarised Brontosaurus
October 18, 2012
Another blast from the past:
Like the recent Compsognathus, this is a card from the “Flesh” card-game that was printed across several progs (issues) of the comic 2000 AD in 1977. This one is from the back cover of Prog 10. (Click through the picture for the whole back cover.)
What’s interesting about this one is how very flagrant a rip-off it is of Rudolph Zallinger’s 1960 painting of Brontosaurus being attacked by Allosaurus:
I know this painting best from Dinosaurs and other Prehistoric Reptiles, a 1966 book that I had as a boy, and which I believe is the same thing as the Giant Golden Book of Dinosaurs. Here is a high-resolution scan of my copy of that book, pages 24-25. (Click through for 5472 by 3669 version.)
And while I’m here, I may as well throw in my scan of the “Brachiosaurus” (i.e. Giraffatitan)on pages 20-21. (Click through for 5431 by 3162 version.)
I will leave it to others to point out which other classic piece of sauropod art this one plagiarises.
Posting palaeo papers on arXiv
September 28, 2012
Over on Facebook, where Darren posted a note about our new paper, most of the discussion has not been about its content but about where it was published. We’re not too surprised by that, even though we’d love to be talking about the science. We did choose arXiv with our eyes open, knowing that there’s no tradition of palaeontology being published there, and wanting to start a new tradition of palaeontology being routinely published there. Having now made the step for the first time, I see no reason ever to not post a paper on arXiv, as soon as it’s ready, before — or maybe even instead of — submitting it to a journal.
(Instead of? Maybe. We’ll discuss that below.)
The key issue is this: science isn’t really science until it’s out there where it can be used. We wrote the bulk of the neck-anatomy paper back in 2008 — the year that we first submitted it to a journal. In the four years since then, all the observations and deductions that it contains have been unavailable to the world. And that is stupid. The work might just as well never have been done. Now that it’s on arXiv, that’s over. I was delighted to get an email less than 24 hours after the paper was published, from an author working on a related issue, thanking us for posting the paper, saying that he will now revise his own in-prep manucript in light of its findings, and cite our paper. Which of course is the whole point: to get our science out there where it can do some damage.
Because the alternative is horrible, really. Horribly wasteful, horribly dispiriting, horribly retarding for science. For example, a couple of weeks ago in his SVPCA talk, David Norman was lamenting again that he never got around to publishing the iguanodont systematic work that was in his dissertation, I-don’t-know-how-many-years-ago. The result of that interminable delay is that others have done other, conflicting iguanodont systematic work, and Norman is now trying belatedly to undo that and bring his own perspective. A terrible an unnecessary slowing of ornithopod science, and a waste of duplicated effort. (Thankfully it’s only ornithopods.)
And of course David Norman is very far from being alone. Pretty much any palaeontologist you talk to will tell you of a handful of papers — many more in some cases — that were finished many years previously but have never seen the light of day. (I still have a couple myself, but there is no point in resurrecting them now because progress has overtaken them.) I wonder what proportion of all Ph.D work ever sees the light of day? Half? Less? It’s crazy.
Figure 8. Sauropod cervical vertebrae showing anteriorly and posteriorly directed spurs projecting from neurapophyses. 1, cervical 5 of Sauroposeidon holotype OMNH 53062 in right lateral view, photograph by MJW. 2, cervical 9 of Mamenchisaurus hochuanensis holotype CCG V 20401 in left lateral view, reversed, from photograph by MPT. 3, cervical 7 or 8 of Omeisaurus junghsiensisYoung, 1939 holotype in right lateral view, after Young (1939, figure 2). (No specimen number was assigned to this material, which has since been lost. D. W. E. Hone personal communication, 2008.)
Publish now, publish later
So, please folks: we all need to be posting our work on preprint servers as soon as we consider it finished. It doesn’t mean that the posted versions can’t subsequently be obsoleted by improved versions that have gone through peer-review and been published in conventional journals. But it does mean that the world can know about the work, and build on it, and get the benefit of it, as soon as it’s done.
You see, we have a very fundamental problem in academia: publishing fulfils two completely separate roles. Its primary role (or at least the role that should be primary) is to make work available to the community; the secondary role is to provide a means of keeping score — something that can be used when making decisions about who to appoint to jobs, when to promote, who gets grants, who gets tenure and so on. I am not going to argue that the latter shouldn’t happen at all — clearly a functioning community needs some way to infer the standing of its participants. But I do think it’s ridiculous when the bean-counting function of publication trumps the actual publication role of publication. Yet we’ve all been in a position where we have essentially complete work that could easily go on a blog, or in the PalAss newsletter, or in a minor journal, or somewhere — but we hang onto it because we want to get it into a Big Journal.
Let me say again that I do realise how unusual and privileged my own position is: that a lot of my colleagues do need to play the Publication Prestige game for career reasons (though it terrifies my how much time some colleagues waste squeezing their papers into two-and-a-half-page format in the futile hope of rolling three sixes on the Science ‘n’ Nature 3D6). Let’s admit right now that most palaeontologists do need to try to get their work into Proc B, or Paleobiology, or what have you. Fair enough. They should feel free. But the crucial point is this: that is no reason not to post pre-prints so we can all get on with actually benefitting from your work in the mean time.
Actually, I feel pretty stupid that it’s taken me this long to realise that all my work should go up on arXiv.
Figure 11. Archosaur cervical vertebrae in posterior view, Showing muscle attachment points in phylogenetic context. Blue arrows indicate epaxial muscles attaching to neural spines, red arrows indicate epaxial muscles attaching to epipophyses, and green arrows indicate hypaxial muscles attaching to cervical ribs. While hypaxial musculature anchors consistently on the cervical ribs, the principle epaxial muscle migrate from the neural spine in crocodilians to the epipophyses in non-avial theropods and modern birds, with either or both sets of muscles being significant in sauropods. 1, fifth cervical vertebra of Alligator mississippiensis, MCZ 81457, traced from 3D scans by Leon Claessens, courtesy of MCZ. Epipophyses are absent. 2, eighth cervical vertebra ofGiraffatitan brancai paralectotype HMN SII, traced from Janensch (1950, figures 43 and 46). 3, eleventh cervical vertebra of Camarasaurus supremus, reconstruction within AMNH 5761/X, “cervical series I”, modified from Osborn and Mook (1921, plate LXVII). 4, fifth cervical vertebra of the abelisaurid theropod Majungasaurus crenatissimus,UA 8678, traced from O’Connor (2007, figures 8 and 20). 5, seventh cervical vertebra of a turkey, Meleagris gallopavo, traced from photographs by MPT.
Exceptions?
So are there any special cases? Any kinds of papers that we should keep dry until they make it into actual journals? I can think of two classes that you could argue for — one of them convincingly, the other not.
First, the unconvincing one. When I discussed this with Matt (and half the fun of doing that is that usually neither of us really knows what we think about this stuff until we’re done arguing it through), he suggested to me that we couldn’t have put the Brontomerus paper on arXiv, because that would have leaked the name, creating a nomen nudum. My initial reaction was to agree with him that this is an exception. But when I thought about it a bit more, I realised there’s actually no compelling reason not to post such a paper on arXiv. So you create a nomen nudum? So what? Really: what is the negative consequence of that? I can’t think of one. OK, the name will appear on Wikipedia and mailing lists before the ICZN recognises it — but who does that hurt? No-one that I can think of. The only real argument against posting is that it could invite scooping. But is that a real threat? I doubt it. I can’t think of anyone who would be barefaced enough to scoop a taxon that had already been published on arXiv — and if they did, the whole world would know unambiguously exactly what had happened.
So what is the one real reason not to post a preprint? I think that might be a legitimate choice when publicity needs to be co-ordinated. So while nomenclatural issues should not have stopped us from arXiving the Brontomerus paper, publicity should. In preparation for that paper’s publication day, we did a lot of careful work with the UCL publicity team: writing non-specialist summaries, press-releases and FAQs, soliciting and preparing illustrations and videos, circulating materials under embargo, and so on. In general, mainsteam media are only interested in a story if it’s news, and that means you need to make sure it’s new when they first hear about it. Posting the article in advance on a publicly accessible archive would mess that up, and probably damage the work’s coverage in the press, TV and radio.
Publication venues are a continuum
It’s become apparent to us only gradually that there’s really no clear cut-off where a paper becomes “properly published”. There’s a continuum that runs from least to most formal and exclusive:
SV-POW! — arXiv — PLOS ONE — JVP — Nature
1. On SV-POW!, we write what we want and publish it when we want. We can promise you that it won’t go away, but you only have our word for it. But some of what we write here is still science, and has been cited in papers published in more formal venues — though, as far as I know, only by Matt and me so far.
2. On arXiv, there is a bit more of a barrier to clear: you have to get an existing arXiv user to endorse your membership application, and each article you submit is given a cursory check by staff to ensure that it really is a piece of scientific research rather than a diary entry, movie review or spam. Once it’s posted, the paper is guaranteed to remain at the same URL, unchanged, so long as arXiv endures (and it’s supported by Cornell). Crucially, the maths, physics and computer science communities that use arXiv uncontroversially consider this degree of filtering and permanence sufficient to constitute a published, citeable source.
3. At PLOS ONE, your paper only gets published if it’s been through peer-review — but the reviewing criteria pertain only to scientific soundness and do not attempt to evaluate likely impact or importance.
4. At JVP and other conventional journals, your paper has to make it through a two-pronged peer-review process: it has to be judged both sound scientifically (as at PLOS ONE) and also sufficiently on-topic and important to merit appearing in the journal.
5. Finally, at Nature and Science, your paper has to be sound and be judged sexy — someone has to guess that it’s going to prove important and popular.
Where along this continuum does the formal scientific record begin? We could make a case that all of it counts, provided that measures are taken to make the SV-POW! posts permanent and immutable. (This can be done submitting them to WebCite or to a service such as Nature Precedings used to provide.) But whether or not you accept that, it seems clear that arXiv and upwards is permanent, scientific and citeable.
This raises an interesting question: do we actually need to go ahead and publish our neck-anatomy paper in a more conventional venue? I’m honestly not sure at the moment, and I’d be interested to hear arguments in either direction. In terms of the progress of science, probably not: our actual work is out there, now, for the world to use as it sees fit. But from a career perspective, it’s probably still worth our while to get it into a journal, just so it can sit more neatly on our publication lists and help Matt’s tenure case more. And yet I don’t honestly expect any eventual journal-published version to be better in any meaningful way than the one on arXiv. After all, it’s already benefitted from two rounds of peer-review, three if you count the comments of my dissertation examiners. More likely, a journal will be less useful, as we have to cut length, eliminate illustrations, and so on.
So it seems to me that we have a hard choice ahead of us now. Call that paper done and more onto making more science? Or spend more time and effort on re-publishing it in exchange for prestige? I really don’t know.
For what it’s worth, it seems that standard practice in maths, physics and computer science is to republish arXiv articles in journals. But there are some scientists who routinely do not do this, instead allowing the arXiv version to stand as the only version of record. Perhaps that is a route best left to tenured greybeards rather than bright young things like Matt.
Figure 5. Simplified myology of that sauropod neck, in left lateral view, based primarily on homology with birds, modified from Wedel and Sanders (2002, figure 2). Dashed arrows indicate muscle passing medially behind bone. A, B. Muscles inserting on the epipophyses, shown in red. C, D, E. Muscles inserting on the cervical ribs, shown in green. F, G. Muscles inserting on the neural spine, shown in blue. H. Muscles inserting on the ansa costotransversaria (“cervical rib loop”), shown in brown. Specifically: A. M. longus colli dorsalis. B. M. cervicalis ascendens. C. M. flexor colli lateralis. D. M. flexor colli medialis. E. M. longus colli ventralis. In birds, this muscle originates from the processes carotici, which are absent in the vertebrae of sauropods. F. Mm. intercristales. G. Mm. interspinales. H. Mm. intertransversarii. Vertebrae modified from Gilmore (1936, plate 24).
Citing papers in arXiv
Finally, a practicality: since it’ll likely be a year or more before any journal-published version of our neck-anatomy paper comes out, people wanting to use it in their own work will need to know how to cite a paper in arXiv. Standard procedure seems to be just to use authors, year, title and arXiv ID. But in a conventional-journal citation, I like the way that the page-range gives you a sense of how long the paper is. So I think it’s worth appending page-count to the citations. And while you’re at it, you may as well throw in the figure and table counts, too, yielding the version that we’ve been using:
- Taylor, Michael P., and Mathew J. Wedel. 2012. Why sauropods had long necks; and why giraffes have short necks. arXiv:1209.5439. 39 pages, 11 figures, 3 tables.
