Back in business

May 31, 2018

Many thanks to all of the good folks in the radiology department at the Hemet Valley Medical Center, especially John Yasmer, DO, my partner in crime, and Heather Salzwedel, who did all of the actual work of scanning while the rest of us stood around making oooh and aaah noises.

Further bulletins as events warrant.

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I know, I know — you never believed this day would come. And who could blame you? Nearly thirteen years after my 2005 SVPCA talkSweet Seventy-Five and Never Been Kissed, I am finally kicking the Archbishop descriptive work into gear. And I’m doing it in the open!

In the past, I’ve written my academic works in LibreOffice, submitted them for peer-review, and only allowed the world to see them after they’ve been revised, accepted and published. More recently, I’ve been using preprints to make my submitted drafts public before peer review. But there’s no compelling reason not to go more open than that, so I’ll be writing this paper out in the open, in a public GitHub repository than anyone can access. That also means anyone can file issues if they thing there’s something wrong or missing, and anyone can submit pull-requests if they have a correction to contribute.

I’ll be writing this paper in GitHub Flavoured Markdown so that it displays correctly right in the browser, and so that patches can be supported. That will make tables a bit more cumbersome, but it should be manageable.

Anyway, feel free to follow progress at https://github.com/MikeTaylor/palaeo-archbishop

The very very skeletal manuscript is at https://github.com/MikeTaylor/palaeo-archbishop/blob/master/archbishop-manuscript.md

I got an email a couple of days ago from Maija Karala, asking me a question I’d not come across before (among several other questions): how much poop did Argentinosaurus produce in a day?

I don’t recall this question having been addressed in the literature, though if anyone knows different please shout. Having thought about it a little, I sent the following really really vague and hand-wavy response.

Suppose Argentinosaurus massed 73 tonnes (Mazzetta et al. 2004). In cattle, food intake varies roughly with body mass to the power 0.7 (Taylor et al. 1986), so let’s assume that the same is true of sauropods.

Let’s also assume that sauropods are like scaled-up elephants, in that both would have subsisted on low-quality forage. Wikipedia says elephants “can consume as much as 150 kg (330 lb) of food and 40 L (11 US gal) of water in a day.” Let’s assume that the “as much as” suggests we’re talking about a big elephant here, maybe 6 tonnes. So Argentinosaurus is 73/6 = 12 times as heavy, which means its food intake would be 12 ^ 0.7 = 5.7 times as much. That’s 850 kg per day.

Hummel et al. (2008, table 1) show that for a range of foods, the indigestible “neutral detergent fibre” makes up something around half of the mass, so let’s assume that’s the bulk of what gets pooped out, and halve the input to get about 400 kg of poop per day.

References

  • Hummel, Jürgen, Carole T. Gee, Karl-Heinz Südekum, P. Martin Sander, Gunther Nogge and Marcus Clauss. 2008. In vitro digestibility of fern and gymnosperm foliage: implications for sauropod feeding ecology and diet selection. Proceedings of the Royal Society B, 275:1015-1021. doi:10.1098/rspb.2007.1728
  • Mazzetta, Gerardo V., Per Christiansen and Richard A. Farina. 2004. Giants and Bizarres: Body Size of Some Southern South American Cretaceous Dinosaurs. Historical Biology 2004:1-13.
  • Taylor, C. S., A. J. Moore and R. B. Thiessen. 1986. Voluntary food intake in relation to body weight among British breeds of cattle. Animal Science 42(1):11-18.

You could drive several trucks through the holes in that reasoning, but it’s a start. Can anyone help to refine the reasoning, improve the references, and get a better estimate?

Remember this broken Giraffatitan dorsal vertebra, which Janensch figured in 1950?

It is not only cracked in half, anteroposteriorly, it’s also unfused.

Here’s a better view of the broken face, more clearly showing that the neural canal is (a) much taller than wide – unlike all vertebrate spinal cords – and (b) almost entirely situated ventral to the neurocentral joint, getting close to the condition in the perverted Camarasaurus figured by Marsh.

Here’s a dorsal view, anterior to the top, with Mike’s distal forelimbs for scale.

Left lateral view.

Right lateral view – note the subtle asymmetries in the pneumatic foramen/camera. A little of that might be taphonomic distortion but I think much of it is real (and expected, most pneumatic systems produce asymmetries).

And postero-dorsal view, really showing the weird neural canal to good advantage. In this photo and in the pure dorsal view, you can see that the two platforms for the “neural arch” – which, as in the aforementioned Camarasaurus, is neither neural nor an arch – converge so closely as to leave only a paper-thin gap.

A few points arise. As explained in this post, it makes more sense to talk about the neurocentral joint migrating up or down relative to the neural canal, which is right where it always is, just dorsal to the articular faces of the centrum.

So far, in verts I’ve seen with “offset” neurocentral joints, the joint tends to migrate dorsally in dorsal vertebrae, putting the canal inside the developmental domain of the centrum (which now includes a partial or total arch in an architectural sense, even though the chunk of bone we normally call the neural arch develops as a separate bit) – as shown in the first post in this series. In sacral and caudal vertebrae, the situation is usually reversed, with the joint shifted down into what would normally be the centrum, and the canal then mostly or completely surrounded by the arch – as shown in the second post in the series. This post then doesn’t really add any new concepts, just a new example.

Crucially, we can only study this in the vertebrae of juveniles and subadults, because once the neurocentral joints are fused and remodeled, we usually can’t tell where the old joint surface was. So it’s like cervicodorsal and caudal dorsal pneumatic hiatuses, in that the feature of interest only exists for part of the ontogeny of the animal, and our sample size is therefore inherently limited. Not necessarily limited by material – most museums I’ve visited have a fair amount of juvenile and subadult material in the collections – but limited in published visibility, in that for many sauropods only the largest and most complete specimens have been monographically described.

So once again, the answer is simply to visit collections, look at lots of fossils, and stay alert for weird stuff – happily, a route that is open to everyone with a legitimate research interest.

Reference

  • Janensch, W. 1950. Die Wirbelsaule von Brachiosaurus brancai. Palaeontographica (Suppl. 7) 3:27-93.

Last Wednesday, May 9, Brian Engh and I bombed out to Utah for a few days of paleo adventures. Here are some highlights from our trip.

We started at a Triassic tracksite on Thursday. But I’m not going to post any pictures of the tracks – those will be coming to a Brian Engh joint near you in the future. Instead, I’m going to talk about this little male collared lizard whose territory included the tracksite. He was fearless – didn’t want to run off and leave us yahoos wandering around his patch of desert unsupervised. Brian tickled his chin at one point.

Getting this close to him is how I got shots like this one:

Click through to the big version, it’s worth it.

One more shot of a couple of cool desert dwellers. I was so fixated on the lizard that I didn’t realize until later that Brian was in the frame, taking a much-needed hydration break.

On Friday we had a temporary breaking of the fellowship. I went to Fruita, Colorado, to visit the Dinosaur Journey museum. You’ve seen photos from DJ here before, from the 2014 Mid-Mesozoic Field Conference and the 2016 Sauropocalypse. Here’s an apatosaur pubis with some obvious bite marks on the distal end. This is on display next to a similarly-bitten ischium, which is shown in the MMFC14 post linked above.

Here’s a big apatosaur cervical, in antero-ventral view, with a dorsal rib draped over its left side. The cervical ribs are not fused in this specimen, so it was probably still growing. Here’s a labeled version:

The short centrum and nearly-vertical transverse processes indicate that this is a pretty posterior cervical, possibly a C13 or thereabouts. This specimen was over the fence in the exhibit area and I couldn’t throw a scale bar at it, but I’d describe it as “honkin'”. Like most of the apatosaur material at DJ, this vert is from the Mygatt-Moore Quarry.

Of course the real reason I was at Dinosaur Journey was to see the Snowmass Haplocanthosaurus that John Foster and I described back in 2014. You may remember that its caudal vertebrae have wacky neural canals. You may also have noticed a recent uptick in the number of posts around here about wacky neural canals. The game is afoot.

But as cool as they were, the Triassic tracks, the collared lizard, and even the Snowmass Haplo were only targets of opportunity. Brian and I had gone to Utah for this:

That photo was taken by Paige Wiren of Salt Lake City, on the day that she discovered that bone eroding out of a riverbank, just as you see it.

Here’s Paige with the element, which proved to be the left femur of an apatosaurine sauropod. It’s face down in these photos, so we’re looking at the medial side. The articular head is missing from the proximal end – it should be facing toward Paige’s right knee in the above photo – but other than that and a few negligible nicks and dings, the femur was complete and in really good shape.

Paige did the right thing when she found the femur: she contacted a paleontologist. Specifically, she asked a friend, who in turn put her in touch with Carrie Levitt-Bussian, the paleontology Collections Manager at the Natural History Museum of Utah. Based on Paige’s photos and maps, Carrie was able to identify the element as a dinosaur femur, probably sauropod, within the territory of the BLM Hanksville Field Office. John Foster, the Director of the Museum of Moab, has a permit to legally collect vertebrate fossils from that area, and he works on sauropods, so Carrie put Paige in touch with John and with ReBecca Hunt-Foster, the district paleontologist for the BLM’s Canyon Country District in Utah.

Now, I know there’s a lot of heated rhetoric surrounding the Bureau of Land Management, but whatever your political bent, remember this: those are our public lands. Therefore the fossils out there are the collective property of all of us, and we should all be upset if they get poached or vandalized. Yes, that is a big problem – the Brontomerus type quarry was partially poached before the bones we have now were recovered, and vandalism at public fossil sites in Utah made the national news while we were out there.

So that’s what we went to do: salvage this bone for science and education before it could be lost to erosion or asshats. Brian and I were out there to assist John, ReBecca, and Paige, who got to see her find come out of the ground and even got her hands dirty making the plaster jacket. Brian and John headed out to the site Friday morning and met up with Paige there, and ReBecca and I caravanned out later in the day, after I got back from Fruita.

But I’m getting ahead of myself a bit. We didn’t have to jacket the whole thing. It had naturally broken into three pieces, with thin clay infills at the breaks. So we just slid the proximal and middle thirds away as we uncovered them, and hit any loose-looking pieces with consolidant. The distal third was in more questionable shape, so we did make a partial jacket to hold it together.

We also got to camp out in gorgeous country, with spectacular (and welcome) clouds during the day and incredible starry skies at night.

We floated the femur out of the site using the Fosters’ canoe at the end of the day on Saturday, and loaded up to head back to Moab on Sunday. At one point the road was empty and the sky was not, so I stood on the center line and took some photos. This one is looking ahead, toward I-70 and Green River.

And this one is looking behind, back toward Hanksville.

Here are John and Brian with the femur chunks in one of the back rooms of the Museum of Moab. The femur looks oddly small here, but assembled it was 155 cm (5’1″) long and would have been 160 (5’3″) or more with the proximal head. Smaller than CM 3018 and most of the big mounted apatosaurs, but nothing to sneeze at.

What happens to it next? It will be cleaned, prepped, and reassembled by the volunteers and exhibit staff at the Museum of Moab, and eventually it will go on public display. Thousands of people will get to see and learn from this specimen because Paige Wiren made the right call. Go thou and do likewise.

That was the end of the road for the femur (for now), but not for Brian and me. We had business in Cedar City and St. George, so we hit the road Sunday afternoon. Waves of rainclouds were rolling east across Utah while we were rolling west, with breaks for sunlight in between. I miiiight have had to swerve a couple of times when all the scenery distracted me from driving, and I definitely made an obnoxious number of stops to take pictures.

I don’t remember which scenic overlook this was, but it was a pretty darned good view. This is another one that will reward embiggening – check out those mesas marching off into the distance.

In Cedar City we were guests of Andrew R.C. Milner, Site Paleontologist and Curator at the St. George Dinosaur Discovery Site at Johnson Farm (SGDS). We spent most of Monday at SGDS, getting our minds comprehensively blown by the amazing trace and body fossils on display. It was my first time visiting that museum, but it sure as heck won’t be the last.

I didn’t take nearly enough photos in St. George – too busy helping Brian do some filming for a future project – but I did get this gem. This is a Eubrontes track, from a Dilophosaurus-sized theropod. This is a positive track, a cast of the dinosaur’s foot made by sandy sediment that filled the natural mold formed when the dino stepped into mud. The high clay content of the mud recorded the morphology of the foot in fine detail, including the bumps of individual scales on the foot pads. The vertical streaks were cut into the side of the track by similar scales as the animal’s foot pushed into the mud.

The full story of the Johnson Farm tracks and trackmakers is beautifully told in the book Tracks in Deep Time: The St. George Dinosaur Discovery Site at Johnson Farm, by Jerry Harris and Andrew Milner. I hadn’t read it before, so I picked up a copy in the gift shop and I’ve been devouring it. As a professional scientist, educator, and book author myself, I’m jealous of what Jerry and Andrew produced – both the text and the abundant full-color illustrations are wonderfully clear, and the book is well-produced and very affordable.

From St. George we hit the road home, and rolled into Claremont just before midnight on Monday. It was a whirlwind tour – 1800 miles, three museums, and two fossil sites in six days – and my brain is still fizzing with all of the things we got to see and do.

One of the many pros of having a professional artist as a friend is that minimal hospitality, like letting him crash on my couch, is sometimes rewarded with original art. Brian was already gone when I got up Tuesday morning, but this was waiting for me on the dining room table. (Want your own? Help Brian make more monsters here.)

I owe plenty of thanks myself: to the Foster and Milner families for their near-maximal hospitality, to Julia McHugh of Dinosaur Journey for assistance in collections, to Diana Azevedo, Jalessa Spor, Jerry Harris, and the rest of the SGDS staff for being such gracious hosts, to Brian for being such a great friend and traveling companion, and most of all to Paige Wiren for finding the apato femur and helping us save it for science. You’re all top-notch human beings and I hope our paths cross again soon.

This is the second post in the “bird neural canals are weird” series (intro post here), and it covers the first of five expansions of the spinal cord or meninges in the lumbosacral regions of birds.

The lumbosacral expansion of the spinal cord is not unique to birds and doesn’t require any special explanation. As noted in the slide, all limbed tetrapods and some fishes with sensitive fins have adjacent segments of the spinal cord correspondingly expanded. These expansions house the extra afferent neurons needed to collect sensory inputs from the limbs, the extra efferent neurons needed to provide motor control to the limbs, and the extra interneurons needed for sensory and motor integration (including reflex arcs) – ‘extra’ here meaning ‘more than are required for non-limb neck, trunk, and tail segments’.

Humans have these, too, in our lower cervical vertebrae to run our forelimbs, and in our lower thoracic vertebrae to run our hindlimbs. Recall that the segmental anatomy of the adult human spinal cord corresponds increasingly poorly to the vertebrae the farther we are from the head because of our child-sized spinal cords (see this post for more).

So if the lumbosacral expansion is present in all tetrapods with hindlimbs, why bring it up? My goal is to develop a set of criteria to distinguish the various spinal and meningeal specializations in birds, in part because it’s an interesting challenge in its own right, and in part because doing so may help illuminate some unusual features in sauropods and other non-avian dinosaurs. If we want to be able to detect whether, say, a glycogen body is present, we need to know how to tell the impression left by a glycogen body from the more generalized lumbosacral expansion present in all limbed tetrapods. The key characteristics of the lumbosacral expansion are that the cord (and hence the canal) expands and contracts gradually, over many segments, and that the expansion is in all directions, radially, and not biased dorsoventrally or mediolaterally.

Numbering reflects spinal nerve count – 8 cervical, 12 thoracic, 5 lumbar, and 5 sacral spinal spinal nerves. Cervical expansion for the forelimbs is roughly C5-T1, and lumbosacral expansion for hindlimbs is L2-S3. Gray (1918 image 665).

The one way in which the lumbosacral expansion of birds is weird, at least compared to mammals, is that the magnitude of the change is so great in hindlimb-dominant flightless birds like the ostrich. Here’s a graph from Gray’s Anatomy showing the cross-sectional area of the human spinal cord in square mm, with the head on the left. Note that the swellings for the limbs bump up the cross-sectional area by a quarter to a third, relative to adjacent non-limb areas.

Streeter (1904: fig. 4)

Here’s the same diagram for an ostrich, again in square mm, again with the head to the left. The lines here are a little different – the “substantia grisea” is the gray matter (mostly neuron cell bodies), and the white matter (axons, mostly myelinated) is divided into the large ventrolateral funiculi (descending motor, ascending pain, temperature, and unconscious proprioception) and the much smaller dorsal funiculi (ascending touch and conscious proprioception). Here the lumbosacral expansion maxes out at more than double the cross-sectional area of the cord in the inter-limb torso segments – and this is just the white and gray matter, and does not include the glycogen body (which is proportionally small in the ostrich, as we’ll see in a future post).

Note that the ostrich does have a much smaller expansion of the spinal cord associated with the forelimbs, but one glance at the graph will tell you that the hindlimbs are a lot more important. This too has implications for fossils. Because the cross-sectional area of the neural canal tends to track the cross-sectional area of the spinal cord (despite the cord not filling the canal), it is possible to make inferences about limb use in fossil taxa based on the relative cross-sectional area of the neural canal along the vertebral column. Emily Giffin published several papers about this in the 1990s (e.g., Giffin 1990, 1995), all of which are worth reading.

Next in this series: the glycogen body.

References

It’s common to come across abstracts like this one, from an interesting paper on how a paper’s revision history influences how often it gets cited (Rigby, Cox and Julian 2018):

Journal peer review lies at the heart of academic quality control. This article explores the journal peer review process and seeks to examine how the reviewing process might itself contribute to papers, leading them to be more highly cited and to achieve greater recognition. Our work builds on previous observations and views expressed in the literature about (a) the role of actors involved in the research and publication process that suggest that peer review is inherent in the research process and (b) on the contribution reviewers themselves might make to the content and increased citation of papers. Using data from the journal peer review process of a single journal in the Social Sciences field (Business, Management and Accounting), we examine the effects of peer review on papers submitted to that journal including the effect upon citation, a novel step in the study of the outcome of peer review. Our detailed analysis suggests, contrary to initial assumptions, that it is not the time taken to revise papers but the actual number of revisions that leads to greater recognition for papers in terms of citation impact. Our study provides evidence, albeit limited to the case of a single journal, that the peer review process may constitute a form of knowledge production and is not the simple correction of errors contained in submitted papers.

This tells us that a larger number of revisions leads to (or at least is correlated with) an increased citation-count. Interesting!

Immediately, I have two questions, and I bet you do, too:

1. What is the size of the effect?
2. How robust is it?

If their evidence says that each additional round of peer-review yields an dozen additional citations, I might be prepared to revise my growing conviction that multiple rounds of peer review are essentially a waste of time. If it says that each round yields 0.0001 additional citations, I won’t. And if the effect is statistically insignificant, I’ll ignore it completely.

But the abstract doesn’t tell me those simple and fundamental facts, which means the abstract is essentially useless. Unless the authors’ goal for the abstract was for it to be an advertisement for the paper — but that’s not what an abstract is for.

In the old days, authors didn’t write abstracts for their own papers. These were provided after the event — sometimes after publication — by third parties, as a service for those who did not have time to read the whole paper but were interesting in its findings. The goal of an abstract is to act as a summary of the paper, a surrogate that a reader can absorb instead of the whole paper, and which summarises the main findings. (I find it interesting that in some fields, the term “précis” or “synopsis” is used: both are more explicit.)

Please, let’s all recognise the painful truth that most people who read abstracts of our papers will not go on to read the full manuscripts. Let’s write our abstracts for those short-on-time people, so they go away with a clear and correct understanding of what our findings were and how strongly they are supported.

References

Rigby, J., D. Cox and K. Julian. 2018. Journal peer review: a bar or bridge? An analysis of a paper’s revision history and turnaround time, and the effect on citation. Scientometrics 114:1087–1105. doi:10.1007/s11192-017-2630-5