Imaging bone cells in 420-million-year-old jawless fish

March 31, 2021

The early armored fish Bothriolepis, which Yara Haridy affectionately refers to as a “beetle mermaid”. Art by Brian Engh, dontmesswithdinosaurs.com.

If I had to sum up my main research program over the past 20+ years, it would be, “Why pneumatic bone?” Or as I typically put it in my talks, most bone has marrow inside, so if you find bone with air inside, someone has some explaining to do (f’rinstance).

One of the reasons I like hanging out with Yara Haridy is that she is interested in an even more fundamental question: “Why bone?” And also “How bone?” And she has a paper out today that gives us new insights into the form and function of bone cells — osteocytes — in some of the earliest vertebrates that had them (Haridy et al. 2021; if you’re in TL;DR mode, here’s the link). 

Bones have multiple functions in vertebrate bodies: they’re a mechanical framework for our muscles, and a mineral reservoir, and form armor in many taxa, and are involved in hormone regulation, and doubtless other things that we are still discovering, even now. To fulfill those functions, bone tissue has to be formed in the first place, it has to be maintained, and it has to be able to be reshaped as an individual grows. Derived extant vertebrates, including humans, have an impressive array of cellular machinery to make all those things happen. Central to most of those operations are osteocytes, the cells inside living bone, which maintain intimate connections to extracellular bone tissue and to other osteocytes via fine, tentacle-like processes.

Individual osteocytes look something like the Flying Spaghetti Monster. The central portion of the FSM, with the meatballs, is the osteocyte body, and the noodly appendages are the processes.

Now imagine that you cloned the FSM many, many times, and the resulting array of FSMs stayed in physical contact with each other via their noodly appendates, forming a network.

Then imagine that you entombed all of the cloned FSMs in concrete. This is more or less what cellular bone — the kind you find in humans, dinosaurs, and even some jawless fish — looks like on the microscopic scale: osteocytes (the FSMs) and their processes (the noodly appendages) embedded in space-filling stuff (the bone matrix). Some critters, including teleost fish, have acellular bone, but I don’t have time for those unbelievers today.

When an animal dies and decomposes, the osteocytes and their processes decay away, leaving behind the spaces that they used to occupy. The big spaces that hold osteocytes are called lacunae, and the little tunnels that hold the osteocyte processes (noodly appendages, in this metaphor) are canaliculi. Collectively, the lacunae and canaliculi form the lacunocanalicular network or LCN.

Those spaces can then be filled by matrix — not extracellular bone matrix, but future rock matrix, like mud and clay. In point of fact, not all of the spaces are filled with matrix. Even in their 420-million-year-old fish, Yara and colleagues found some osteocyte lacunae that had not been filled with matrix, and were filled by air instead. Whether the lacunocanalicular network is filled with matrix or air, its preservation in fossil bone has turned out to be a boon for paleontologists, because we can ‘see’ the sizes and shapes of osteocytes, and their level of connectivity, by studying the lacunae and canaliculi they left behind. 

Histological thin section of bone in the osteostracan Tremataspis mammillata (MB.f.TS.463), imaged with transmitting light microscopy showing osteocyte lacunae (osl) and canaliculi (ca); scale bar, 100 microns. Haridy et al. (2021: fig 2A).

Traditionally osteocyte lacunae and canaliculi in fossil bone have been imaged by taking thin sections of the specimens and looking at them under microscopes.

Synchrotron tomography of bone of Bothriolepis trautscholdi (MB.f.9188a) with the vasculature and osteocytes segmented; scale bar, 0.4 mm. (D) Close-up of tomography in (C) showing the resolution of the osteocyte lacunae volumes; scale bar, 10 microns. bs, bone sample; vs, vasculature channels. Modified from Haridy et al. (2021: fig. 2C-D).

If you’re fancy, you can also do synchrotron tomography, which is fine enough to show osteocyte lacunae — the colored blobs in the image on the right, above.

Those methods have their limitations. Light microscopy will reveal both lacunae and canaliculi in 2D, but it’s hard to get a 3D understanding of the lacunocanalicular network that way (at least in fossils; in modern samples it can be done with confocal miscoscopy). Synchrotron tomography can resolve lacunae in 3D, but not canaliculi, sort of like a map that shows only cities but not the highways that connect them.

Enter FIB-SEM: focused ion beam scanning electron microscopy. An ion gun blasts the specimen with a beam of gallium ions, which vaporizes a slice of the specimen that is less than 1 micron thick, and an SEM images the freshly exposed face. If you do this over and over again, you can build up a 3D model of the stuff that once occupied the volume that got zapped. 

FIB-SEM tomography imaging and processing of the fossil jawless vertebrate Tremataspis mammillata (MB.f.9025). (A and B) FIB-SEM setup showing the FIB in relation to the SEM both aimed at the region of interest. (C) Bone surface with an excavate area made by the FIB. (D) Internal wall of the excavated area lined with small black dots that are the fossil osteocyte lacunae. (E) Single osteocyte lacuna from the surface that is scanned; the single SEM image shows the lacunae and canaliculi in black and the mineralized bone in gray; scale bar, 5 microns. (F and G) An image stack is obtained, and 3D made of fossil LCN can be made. Haridy et al. (2021: fig 3).

FIB-SEM is fine enough to resolve both osteocyte lacunae and canaliculi — the lacunocanalicular network or LCN — in three dimensions, in fossil specimens where confocal light microscopy doesn’t always work very well. And the resolution is pretty insane. The rough edges on the 3D models of the LCN aren’t sampling artifacts, they’re accurately reflecting the real morphology of the walls of the lacunae and canaliculi as they were preserved in the fossil bone.

But wait — that’s not all! Not only can FIB-SEM show us osteocyte lacunae and canaliculi in incredible detail in three dimensions, it can also help us figure out at least some of what osteocytes were doing. Together, osteocytes and their processes can sense mechanical strain in bone, trigger bone remodeling, and resorb and lay down bone from the walls of the lacunae and canaliculi. That last process starts with osteocytic osteolysis — the resorption of bone matrix (= osteolysis) from the lacunae and canaliculi by the osteocytes themselves (as opposed to the more familiar destruction of bone at a larger spatial scale by osteoclasts), which is typically followed by the replacement of new matrix where the old bone used to be. Lots of extant vertebrates do osteocytic osteolysis, especially those that have a high demand for calcium and phosphorus in physiologically challenging times. Examples including migrating salmon, lactating mice, and lactating humans. But when did that capacity evolve — did the earliest osteocytes already have the ability to resorb and replace bone? As Yara said to me when she was telling me about her new paper, “We think we know how things work by looking at extant animals, but we’re looking at this highly pruned tree, and we can’t just assume that things worked the same way earlier in our evolutionary history.” 

Yara wanted to investigate when osteolytic osteolysis first evolved when she started her dissertation in 2018, but she didn’t know that FIB-SEM existed. Then she was visiting a neutron tomography facility in Berlin and she saw a poster on the wall about people using FIB-SEM to image corrosion in batteries on ultra-fine scales. She thought, “Wow, the corrosion pits in the batteries look like osteocytes!” The rest you probably figured out faster than it’s taking me to write this sentence: together with her collaborators, she got some samples of bone from the jawless fish Tremataspis and Bothriolepis and zapped them with the FIB-SEM.

Osteocytic osteolysis as a mechanism for early mineral metabolism. (A to C) Illustrations depicting the process of osteocytic osteolysis; the phases are stasis phase, dissolution phase, and redeposition phase, respectively. (D) Single SEM image from the FIB-SEM acquisition showing the air-filled osteocyte lacunae and canaliculi of T. mammillata. (E) Same SEM image as in (D) with contrast shifted to show the demineralized zone surrounding the lacunae. (F and G) 3D render of the stack of images from (D and E) T. mammillata (MB.f.9025). The 3D model shows several osteocytes and their canaliculi, with the red areas showing where the “areas of low density” were found. ald, area of low density; os, osteocyte. Scale bar, 5 microns.

And, wonder of wonders, some of the osteocyte lacunae in Tremataspis were surrounded by a halo of less-dense bone, which is evidence for osteocytic osteolysis. Now, Yara and colleagues can’t be sure whether the bone is less dense because it was being resorbed when the animal died — the actual lytic or bone-destructive phase — or because new bone was being laid down after the old bone had been resorbed; naturally the new bone is less dense as it being formed than it will be when it is complete. They also can’t be sure why the process was occurring in that one individual Tremataspis. Mice only do osteocytic osteolysis when they’re lactating, and salmon only do it when they’re migrating, so the presence of osteocytic osteolysis might indicate that the Tremataspis in question was doing something stressful related to its ecology or life history — both topics we know almost nothing about.

Yara and colleagues didn’t find any evidence of osteocytic osteolysis in their Bothriolepis sample, but this is one of those ‘absence of evidence is not evidence of absence’ things — you wouldn’t find evidence of osteocytic osteolysis in my skeleton either, despite a long ancestral history, because I’m skeletally healthy, not fasting or migrating, and not lactating. Possibly other Bothriolepis individuals that were going through a rough patch, metabolically speaking, would show osteocytic osteolysis. So far, as a species, we’ve only looked at the one sample, from the one individual.

I asked Yara what she wanted people to take away from her new paper. Her response:

  1. We have technology can image fossil bone cells at the same resolution that we can see modern bone cells.
  2. Bone metabolism was going on 420 million years ago, in the earliest osteocytes, the same way it happens in modern mammals, including humans. 

I expect that we will see a lot more FIB-SEM papers on fossils in years to come. That research program started today, with the publication of Haridy et al. (2021). I often sign off posts with “stay tuned”, and this time I really mean it.

Reference

Yara Haridy, Markus Osenberg, André Hilger, Ingo Manke, Donald Davesne, and Florian Witzmann. 2021. Bone metabolism and evolutionary origin of osteocytes: Novel application of FIB-SEM tomography. Science Advances 7(14): eabb9113. DOI: 10.1126/sciadv.abb9113.

Posted by Matt Wedel
Filed in 3D models, Art, Brian Engh, life restorations, stinkin' fish, why bone
11 Comments »

Analysing the distribution of complete sauropod necks

March 27, 2021

Matt dropped me a line midweek about the catalogue of complete sauropod necks, with some interesting thoughts. He broke down the necks as listed across a basic phylogeny of sauropods, and counted the occurrences:

Simplified phylogeny of Sauropoda, showing counts of complete and near-complete necks. Captions: C, complete and described; U, complete but undescribed; –1, missing the atlas but otherwise complete; O, other near-complete necks; T, total.

Matt and I were both surprised to see that non-neosauropods are quite well represented, both inside and outside of Mamenchisauridae — although it’s a pity that two of those ten specimens are of Jobaria, for which we have next to zero information.

Diplodocoids are surprisingly poorly represented, with essentially just one each in Dicraeosauridae and Diplodocidae that are complete. And brachiosaurids are a black hole, with absolutely no representation — see the 2015 preprint for details on how unconvincing the neck of Giraffatitan is.

But camarasaurids are crushing it, probably just by being the most abundant sauropods of all time in terms of individual specimens in museums. (Of course when we say “camarasaurids”, we just mean Camarasaurus, which is the only named sauropod currently considered to belong to Camarasauridae unless you follow Mateus and Tschopp (2013) in considering Cathetosaurus to be generically distinct. But Matt and I both suspect that Camarasaurus is way over-lumped, so we’ll see how this pans out over the next decade or two.)

It’s surprising, though, that the second and third best represented sauropods in museums, Diplodocus and Apatosaurus, are both barely represented in terms of complete necks. And while it’s encouraging to see quite a few complete and nearly-complete necks among somphospondyls, including titanosaurs,it’s disappointing that about half of them are not yet described.

References

Posted by Mike Taylor
Filed in necks
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The catalogue of complete sauropods necks nears completion

March 24, 2021

A couple of months ago, I asked for your help in compiling a list of all known complete sauropods necks. This has gone really well, and I want to thank everyone who chipped in, and all the various authors I have contacted for details as a result.

My next step is to take the raw data in the Google spreadsheet that I have been maintaining, and write it up as prose for the paper that I am shortly going to resubmit, having first done so back in 2015. And I thought it would make sense to draft that section here on SV-POW!, so I can get any further feedback before I finalize it for the manuscript.

Young and Zhao (1972:figure 3). Mamenchisaurus hochuanensis holotype CCG V 20401 as is occurred in the field.

So here goes: any additional comments at this stage will be welcome!

Unambiguously complete necks are known from published accounts of only a few sauropod specimens. In chronological order of description, the following specimens were found with their necks complete and articulated, and have been adequately described:

  • CM 11338, a referred specimen of Camarasaurus lentus described by Gilmore (1925). This is a juvenile specimen, and thus does not fully represent the adult morphology. (McIntosh et al. 1996:76 claim that this specimen is the holotype, but this is not correct: YPM 1910 is the holotype — see below.)
  • CM 3018, the holotype of Apatosaurus louisae, described by Gilmore (1936). The neck was separated from the torso but articulated from C1–C15, though the last three cervicals were badly crushed: see below for details.
  • CCG V 20401, the Mamenchisaurus hochuanensis holotype, described by Young and Zhao (1972). Each vertebra is broken in half at mid-length, with the posterior part of each adhering to the anterior part of the its successor; and all the vertebrae are badly crushed in an oblique plane.
  • ZDM T5402, a Shunosaurus lii referred specimen, described in Chinese by Zhang (1988), with English figure captions. Figure 22 depicts the atlas. Unlike the holotype T5401, this specimen is mature.
  • BYU 9047, the Cathetosaurus lewisi holotype, described by Jensen (1988). (Jensen incorrectly gives the specimen number as BYU 974.) This specimen was redescribed, and the species referred to Camarasaurus, by McIntosh et al. (1996). Although all 12 cervicals are present, “10–12, particularly 12, have suffered such severe damage that it is impossible to restore them” (McIntosh et al. 1996:76).
  • MACN-N 15, the holotype of Amargasaurus cazaui MACN-N 15, described by Salgado and Bonaparte (1991) who desribed “22 presacral vertebrae articulated with each other and attached to the skull and sacrum, relatively complete” (Salgado & Bonaparte 1991:335, translated.
  • ZDM 0083, the holotype of Mamenchisaurus youngi, described in Chinese by Ouyang and Ye (2002) with English figure captions. Figure 14 depicts the atlas and axis.
  • MUCPv-323, the holotype of Futalognkosaurus dukei, initially described by Calvo et al. 2007a and redescribed by Calvo et al. 2007b. The neck was found in two articulated sections which fit together without needing additional vertebrae in between (Jorge O. Calvo, pers. comm., 2021).
  • SSV12001, the holotype of Xinjiangtitan shanshanesis, described by Zhang et al. (2018). The original description of this specimen by Wu et al. 2013 included only the last two cervicals, which were the only ones that had been excavated at that time.

A few additional specimens are known to have complete and articulated necks, but have not yet been described:

  • USNM 13786, a referred subadult specimen of Camarasaurus lentus recently mounted at the Smithsonian. The specimen “was almost completely buried before the sinews had allowed the bones to separate” (letter from Earl Douglass to William J. Holland, 22 August 1918), and photographs kindly supplied by Andrew Moore show that the atlas was preserved.
  • MNBH TIG3, the holotype of Jobaria tiguidensis. Sereno et al. (1999:1343) assert that this species has 12 cervicals in all and say “One articulated neck was preserved in a fully dorsiflexed, C-shaped posture”. Sereno (pers. comm., 2021) confirms that the articulated neck is MNBH TIG3
  • SMA 002, referred to Camarasaurus sp. Tschopp et al. (2016), in a description of its feet, say that this specimen “lacks only the vomers, the splenial bones, the distal end of the tail, and one terminal phalanx of the right pes. The bones are preserved in three dimensions and in almost perfect articulation”.
  • MAU-Pv-LI-595, the “La Invernada” Titanosaur. Filippi et al. (2016) give a very brief account in an abstract. Filippi, pers. comm, 2021) says that the entire preserved specimen was articulated.
  • MAU-Pv-AC-01, an unnamed titanosaur mentioned in abstracts by Calvo et al. (1997) and Coria and Salgado (1999). The specimen was found in perfect articulation from skull down to the last caudal vertebrae (Rodolfo Coria, pers. comm., 2021).

The first cervical (the atlas) in sauropods is very different in form from the other vertebrae, and small and fragile. Consequently it is easily lost. Some further specimens have necks that are complete and articulated from C2 (the axis) backwards:

  • MB.R.4886, the holotype of Dicraeosaurus hansemanni, described by Janensch (1929), has a neck that complete and well preserved from C2 to C12 (the last cervical). Janensch referred to this as “specimen m” and writes “It was found articulated from the 19th caudal vertebra to the 9th cervical vertebra inclusive. The proximal part of the neck from the 8th cervical vertebra up to the axis was bent ventrally and lay at right angles to the distal part of the neck.” (Janensch 1929:41).
  • PMU 233, the holotype of Euhelopus zdanskyi, described by Wiman (1929) as “exemplar a” and redescribed by Wilson and Upchurch (2009).
  • ZDM T5401, the subadult holoype of Shunosaurus lii, described in Chinese by Zhang et al 1984. The quarry map (Zhang et al. 1984:figure 1) suggests that the atlas is missing.
  • MCT 1487-R, informally known as “DGM Series A”, described by Powell (2003). Gomani (2005:9) summarises as “12 cervical vertebrae, except the atlas, preserved in articulation with three proximal dorsal vertebrae”.
  • GCP-CV-4229, the holotype of Spinophorosaurus nigerensis, described by Remes et al. (2009). The specimen was found in very good condition and well articulated from C2 to C13, the last cervical. The atlas seems to be missing (Remes, pers. comm., 2021.

One other sauropod is complete from the first cervical, but probably not to the last:

  • MOZ-Pv1232, the holotype of Lavocatisaurus agrioensis, described by Canudo et al. (2018). This is complete from C1-C11. Canudo’s guess is that this is complete neck (Canudo, pers. comm, 2021), but the specimen doesn’t demand that conclusion and no known eusauropod has fewer than 12 cervicals.

Other sauropod specimens have necks that are complete and articulated from further back in the cervical sequence:

  • YPM 1910, Camarasaurus lentus, a mounted specimen described by Lull (1930). The neck is complete from C2 or C3, Lull was uncertain which.
  • SMA 0004, Kaatedocus siberi, described by Tschopp and Mateus (2012). Cervicals 3-14 are preserved.
  • AODF 888 (informally “Judy”), probably referrable to Diamantinasaurus, briefly described by Poropat et al. (2019). Preserved from C3 or maybe C4. “One posterior cervical (XIII or XIV) found several metres from articulated series, but appears to slot nicely into the gap between the articulated cervical series and the unprepared thoracic section, which might include at least one additional cervical (XIV or XV)” (Poropat, pers. comm. 2021).

Several necks are probably nearly complete, but it is not possible to knew due to their not being found in articulation:

  • CM 84, the holotype of Diplodocus carnegii, described by Hatcher (1901). C2–C15 are preserved, though not all in articulation; C11 may be an intrusion: see below for details.
  • ZDM T5701, the holotype of Omeisaurus tianfuensis, described by He et al. (1988). The neck was not articulated (He et al. 1988:figure 1), and was missing “two elements or so” (He et al. 1988:120).
  • QJGPM 1001, the holotype of Qijianglong guokr, described by Xing et al. (2015). On page 8, the authors say “The axis to the 11th cervical vertebra were fully articulated in the quarry. The atlas intercentrum and the 12th–17th cervical vertebrae were closely associated with the series.”
  • MNBH TIG9, a referred specimen of Jobaria tiguidensis. Wilson (2012:103) writes that this specimen “includes a partially articulated series of 19 vertebrae starting from the axis and extending through the mid-dorsal vertebrae.”
  • MNBH TIG6, another referred specimen of Jobaria tiguidensus, which has not been mentioned in the literature. Sereno (pers. comm., 2021) says that it is “a subadult partial skeleton with excellent neck” and that “the sequence was articulated from C2–11. Most of the ribs were attached as well.”

At the time of writing, the Paleobiology Database (https://paleobiodb.org/) lists more than 270 sauropod species. The nine unambigously complete and articulated necks therefore represent only one in 30 known sauropod species.

Note. The Jobaria tiguidensis individuals previously had specimen numbers beginning MNN, but the Musee National du Niger changed its name to Musée National Boubou Hama and the specimen numbers have changed with it.

Posted by Mike Taylor
Filed in help SV-POW!, necks, papers by SV-POW!sketeers
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Amazing things are out there waiting to be noticed

March 22, 2021

It is said that, some time around 1590 AD, Galileo Galilei dropped two spheres of different masses from the Leaning Tower of Pisa[1], thereby demonstrating that they fell at the same rate. This was a big deal because it contradicted Aristotle’s theory of gravity, in which objects are supposed to fall at a speed proportional to their mass.

Aristotle lived from 384–322 BC, which means his observably incorrect theory had been scientific orthodoxy for more than 1,900 years before being overturned[2].

How did this happen? For nearly two millennia, every scientist had it in his power to hold a little stone in one hand and a rock in the other, drop them both, and see with his own eyes that they fell at the same speed. Aristotle’s theory was obviously wrong, yet that obviously wrong theory remained orthodox for eighty generations.

My take is that it happened because people — even scientists — have a strong tendency to trust respected predecessors, and not even to look to see whether their observations and theories are correct. I am guessing that in that 1,900 years, plenty of scientists did indeed do the stone-and-rock experiment, but discounted their own observations because they had too much respect for Aristotle.

But even truly great scientists can be wrong.

Now, here is the same story, told on a much much smaller scale.

Well into the 2010s, it was well known that in sauropods, caudal vertebrae past the first handful are pneumatized only in diplodocines and in saltasaurine titanosaurs. As a bright young sauropod researcher, for example, I knew this from the codings in important and respected phylogenetic analysis such as those of Wilson (2002) and Upchurch et al. (2004).

Until the day I visited the Museum für Naturkunde Berlin and actually, you know, looked at the big mounted Giraffatitan skeleton in the atrium. And this is what I saw:

That’s caudal vertebrae 24–26 in left lateral view, and you could not wish to see a nicer, clearer pneumatic feature than the double foramen in caudal 25.

That observation led directly to Matt’s and my 2013 paper on caudal pneumaticity in Giraffatitan and Apatosaurus (Wedel and Taylor 2013) and clued us into how much more common pneumatic hiatuses are then we’d realised. It also birthed the notion of “cryptic diverticula” — those whose traces are not directly recorded in the fossils, but whose presence can be inferred by traces on other vertebrae. And that led to our most recent paper on pneumatic variation in sauropods (Taylor and Wedel 2021) — from which you might recognise the photo above, since a cleaned-up version of it appears there as Figure 5.

The moral

Just because “everyone knows” something is true, it doesn’t necessarily mean that it actually is true. Verify. Use your own eyes. Even Aristotle can be wrong about gravity. Even Jeff Wilson and Paul Upchurch can be wrong about caudal pneumaticity in non-diplodocines. That shouldn’t in any way undermine the rightly excellent reputations they have built. But we sometimes need to look past reputations, however well earned, to see what’s right in front of us.

Go and look at fossils. Does what you see contradict what “everyone knows”? Good! You’ve discovered something!

 

References

Notes

1. There is some skepticism about whether Galileo’s experiment really took place, or was merely a thought experiment. But since the experiment was described by Galileo’s pupil Vincenzo Viviani in a biography written in 1654, I am inclined to trust the contemporary account ahead of the unfounded scepticism of moderns. Also, Viviani’s wording, translated as “Galileo showed this by repeated experiments made from the height of the Leaning Tower of Pisa in the presence of other professors and all the students” reads like a documentary account rather than a romanticization. And a thought experiment, with no observable result, would not have demonstrated anything.

2. Earlier experiments had similarly shown that Aristotle’s gravitational theory was wrong, including in the works of John Philoponus in the sixth century — but Aristotle’s orthodoxy nevertheless survived until Galileo.

 

Posted by Mike Taylor
Filed in 100% totally real, caudal, credit where it's due, Giraffatitan, Just Plain Wrong, opportunities, papers by SV-POW!sketeers, pneumaticity, Tails, Thinking it through
14 Comments »

Tutorial 39: how not to conclude a talk or paper

March 19, 2021

“And in conclusion, this new fossil/analysis shows that Lineageomorpha was more [here fill in the blank]:

  • diverse
  • morphologically varied
  • widely distributed geographically
  • widely distributed stratigraphically

…than previously appreciated.” 

Yes, congratulations, you’ve correctly identified that time moves forward linearly and that information accumulates. New fossils that make a group less diverse, varied, or widely distributed–now that’s a real trick.

Okay, that was snarky to the point of being mean, and here I must clarify that (1) I haven’t been to a conference in more than a year, so hopefully no-one thinks I’m picking on them, which is good, because (2) I myself have ended talks this way, so I’m really sniping at Old Matt.

And, yeah, new fossils are nice. But for new fossils or new analyses to expand what we know is expected. It’s almost the null hypothesis for science communication–if something doesn’t expand what we know, why are we talking about it? So that find X or analysis Y takes our knowledge beyond what was “previously appreciated” is good, but it’s not a particularly interesting thing to say out loud, and it’s a really weak conclusion.

(Some cases where just being new is enough: being surprisingly new, big expansions [like hypothetically finding a tyrannosaur in Argentina], and new world records.)

Don’t be Old Matt. Find at least one thing to say about your topic that is more interesting or consequential than the utterly pedestrian observation that it added information that was not “previously appreciated”. The audience already suspected that before you began, or they wouldn’t be here.

I showed this post to Mike before I published it, and he said, “What first made you want to work on this project? That’s your punchline: the thing that was cool enough that you decided to invest months of effort into it.” Yes! Don’t just tell the audience that new information exists, tell them why it is awesome.

Posted by Matt Wedel
Filed in rants, Science communication, Tutorial
2 Comments »

Cross-sectional asymmetry of sauropod vertebrae

March 13, 2021

 

FIGURE 7.1. Pneumatic features in dorsal vertebrae of Barapasaurus (A–D), Camarasaurus (E–G), Diplodocus (H–J), and Saltasaurus (K–N). Anterior is to the left; different elements are not to scale. A, A posterior dorsal vertebra of Barapasaurus. The opening of the neural cavity is under the transverse process. B, A midsagittal section through a middorsal vertebra of Barapasaurus showing the neural cavity above the neural canal. C, A transverse section through the posterior dorsal shown in A (position 1). In this vertebra, the neural cavities on either side are separated by a narrow median septum and do not communicate with the neural canal. The centrum bears large, shallow fossae. D, A transverse section through the middorsal shown in B. The neural cavity opens to either side beneath the transverse processes. No bony structures separate the neural cavity from the neural canal. The fossae on the centrum are smaller and deeper than in the previous example. (A–D redrawn from Jain et al. 1979:pl. 101, 102.) E, An anterior dorsal vertebra of Camarasaurus. F, A transverse section through the centrum (E, position 1) showing the large camerae that occupy most of the volume of the centrum. G, a horizontal section (E, position 2). (E–G redrawn from Ostrom and McIntosh 1966:pl. 24.) H, A posterior dorsal vertebra of Diplodocus. (Modified from Gilmore 1932:fig. 2.) I, Transverse sections through the neural spines of other Diplodocus dorsals (similar to H, position 1). The neural spine has no body or central corpus of bone for most of its length. Instead it is composed of intersecting bony laminae. This form of construction is typical for the presacral neural spines of most sauropods outside the clade Somphospondyli. (Modified from Osborn 1899:fig. 4.) J, A horizontal section through a generalized Diplodocus dorsal (similar to H, position 2). This diagram is based on several broken elements and is not intended to represent a specific specimen. The large camerae in the midcentrum connect to several smaller chambers at either end. K, A transverse section through the top of the neural spine of an anterior dorsal vertebra of Saltasaurus (L, position 1). Compare the internal pneumatic chambers in the neural spine of Saltasaurus with the external fossae in the neural spine of Diplodocus shown in J. L, An anterior dorsal vertebra of Saltasaurus. M, A transverse section through the centrum (L, position 2). N, A horizontal section (L, position 3). In most members of the clade Somphospondyli the neural spines and centra are filled with small camellae. (K–N modified from Powell 1992:fig. 16.) [Figure from Wedel 2005.]

Here’s figure 1 from my 2005 book chapter. I tried to cram as much pneumatic sauropod vertebra morphology into one figure as I could. All of the diagrams are traced from pre-existing published images except the horizontal section of the Diplodocus dorsal in J, which is a sort of generalized cross-section that I based on broken centra of camerate vertebrae from several taxa (like the ones shown in this post). One thing that strikes me about this figure, and about most of the CT and other cross-sections that I’ve published or used over the years (example), is that they’re more or less bilaterally symmetrical. 

We’ve talked about asymmetrical vertebrae before, actually going back to the very first post in Xenoposeidon week, when this blog was only a month and a half old. But not as much as I thought. Given how much space asymmetry takes up in my brain, it’s actually weird how little we’ve discussed it.

The fourth sacral centrum of Haplocanthosaurus CM 879, in left and right lateral view (on the left and right, respectively). Note the distinct fossa under the sacral rib attachment on the right, which is absent on the left.

Also, virtually all of our previous coverage of asymmetry has focused on external pneumatic features, like the asymmetric fossae in this sacral of Haplocanthosaurus (featured here), in the tails of Giraffatitan and Apatosaurus (from Wedel and Taylor 2013b), and in the ever-popular holotype of Xenoposeidon. This is true not just on the blog but also in our most recent paper (Taylor and Wedel 2021), which grew out of this post.

Given that cross-sectional asymmetry has barely gotten a look in before now, here are three specimens that show it, presented in ascending levels of weirdness.

First up, a dorsal centrum of Haplocanthosaurus, CM 572. This tracing appeared in Text-fig 8 in my solo prosauropod paper (Wedel 2007), and the CT scout it was traced from is in Fig 6 in my saurischian air-sac paper (Wedel 2009). The section shown here is about 13cm tall dorsoventrally. The pneumatic fossa on the left is comparatively small, shallow, and lacks very distinct overhanging lips of bone. The fossa on the right is about twice as big, it has a more distinct bar of bone forming a ventral lip, and it is separated from the neural canal by a much thinner plate of bone. The fossa on the left is more similar to the condition in dorsal vertebrae of Barapasaurus or juvenile Apatosaurus, where as the one on the right shows a somewhat more extensive and derived degree of pneumatization. The median septum isn’t quite on the midline of the centrum, but it’s pretty stout, which seems to be a consistent feature in presacral vertebrae of Haplocanthosaurus.

 

Getting weirder. Here’s a section through the mid-centrum of C6 of CM 555, which is probably Brontosaurus parvus. That specific vert has gotten a lot of SV-POW! love over the years: it appears in several posts (like this one, this one, and this one), and in Fig 19 in our neural spine bifurcation paper (Wedel and Taylor 2013a). The section shown here is about 10cm tall, dorsoventrally. In cross-section, it has the classic I-beam configuration for camerate sauropod vertebrae, only the median septum is doing something odd — rather than attaching the midline of the bony floor of the centrum, it’s angled over to the side, to attach to what would normally be the ventral lip of the camera. I suspect that it got this way because the diverticulum on the right either got to the vertebra a little ahead of the one on the left, or just pneumatized the bone faster, because the median septum isn’t just bent, even the vertical bit is displaced to the left of the midline. I also suspect that this condition was able to be maintained because the median septa weren’t that mechanically important in a lot of these vertebrae. We use “I-beam” as a convenient shorthand to describe the shape, but in a metal I-beam the upright is as thick or thicker than the cross bits. In contrast, camerate centra of sauropod vertebrae could be more accurately described as a cylinders or boxes of bone with some holes in the sides. I think the extremely thin median septum is just a sort of developmental leftover from the process of pneumatization.

EDIT 3 days later: John Whitlock reminded me in the comments of Zurriaguz and Alvarez (2014), who looked at asymmetry in the lateral pneumatic foramina in cervical and dorsal vertebrae of titanosaurs, and found that consistent asymmetry along the cervical column was not unusual. They also explicitly hypothesized that the asymmetry was caused by diverticula on one side reaching the vertebrae earlier than diverticula on other other side. I believe they were the first to advance that idea in print (although I should probably take my own advice and scour the historical literature for any earlier instances), and needless to say, I think they’re absolutely correct.

Both of the previous images were traced from CTs, but the next one is traced from a photo of a specimen, OMNH 1882, that was broken transversely through the posterior centrum. To be honest, I’m not entirely certain what critter this vertebra is from. It is too long and the internal structure is too complex for it to be Camarasaurus. I think an apatosaurine identity is unlikely, too, given the proportional length of the surviving chunk of centrum, and the internal structure, which looks very different from CM 555 or any other apatosaur I’ve peered inside. Diplodocus and Brachiosaurus are also known from the Morrison quarries at Black Mesa, in the Oklahoma panhandle, which is where this specimen is from. Of those two, the swoopy ventral margin of the posterior centrum looks more Diplodocus-y than Brachiosaurus-y to me, and the specimen lacks the thick slab of bone that forms the ventral centrum in presacrals of Brachiosaurus and Giraffatitan (see Schwarz and Fritsch 2006: fig. 4, and this post). So on balance I think probably Diplodocus, but I could easily be wrong.

Incidentally, the photo is from 2003, before I knew much about how to properly photograph specimens. I really need to have another look at this specimen, for a lot of reasons.

Whatever taxon the vertebra is from, the internal structure is a wild scene. The median septum is off midline and bent, this time at the top rather than the bottom, the thick ventral rim of the lateral pneumatic foramen is hollow on the right but not on the left, and there are wacky chambers around the neural canal and one in the ventral floor of the centrum. 

I should point out that no-one has ever CT-scanned this specimen, and single slices can be misleading. Maybe the ventral rim of the lateral foramen is hollow just a little anterior or posterior to this slice. Possibly the median septum is more normally configured elsewhere in the centrum. But at least at the break point, this thing is crazy. 

What’s it all mean? Maybe the asymmetry isn’t noise, maybe it’s signal. We know that when bone and pneumatic epithelium get to play together, they tend to make weird stuff. Sometimes that weirdness gets constrained by functional demands, other times not so much. I think it’s very seductive to imagine sauropod vertebrae as these mechanically-optimized, perfect structures, but we have other evidence that that’s not always true (for example). Maybe as long as the articular surfaces, zygapophyses, epipophyses, neural spine tips, and cervical ribs — the mechanically-important bits — ended up in the right places, and the major laminae did a ‘good enough’ job of transmitting forces, the rest of each vertebra could just sorta do whatever. Maybe most of them end up looking more or less the same because of shared development, not because it was so very important that all the holes and flanges were in precisely the same places. That might explain why we occasionally get some really odd verts, like C11 of the Diplodocus carnegii holotype.

That’s all pretty hand-wavy and I haven’t yet thought of a way to test it, but someone probably will sooner or later. In the meantime, I think it’s valuable to just keep documenting the weirdness as we find it.

References

Posted by Matt Wedel
Filed in camarasaurs, cervical, cross sections, diplodocids, Diplodocus, dorsal, Haplocanthosaurus, pneumaticity, sacral, Saltasaurus, titanosaur
8 Comments »

Good experiences of peer-review at Qeios

March 9, 2021

A month after I and Matt published our paper “Why is vertebral pneumaticity in sauropod dinosaurs so variable?” at Qeios, we were bemoaning how difficult it was to get anyone to review it. But what a difference the last nineteen days have made!

In that time, we’ve had five reviews, and posted three revisions: revision 2 in response to a review by Mark McMenamin, version 3 in response to a review by Ferdinand Novas, and version 4 in response to reviews by Leonardo Cotts, by Alberto Collareta, and by Eduardo Jiménez-Hidalgo.

Taylor and Wedel (2021: Figure 2). Proximal tail skeleton (first 13 caudal vertebrate) of LACM Herpetology 166483, a juvenile specimen of the false gharial Tomistoma schlegelii. A: close-up of caudal vertebrae 4–6 in right lateral view, red circles highlighting vascular foramina: none in Ca4, two in Ca5 and one in Ca6. B: right lateral view. C: left lateral view (reversed). D: close-up of caudal vertebrae 4–6 in left lateral view (reversed), red circles highlighting vascular foramina: one each in Ca4, Ca5 and Ca6. In right lateral view, vascular foramina are apparent in the centra of caudal vertebrae 5–7 and 9–11; they are absent or too small to make out in vertebrae 1–4, 8 and 12–13. In left lateral view (reversed), vascular foramina are apparent in the centra of caudal vertebrae 4–7 and 9; they are absent or too small to make out in vertebrae 1–3, 8, and 10–13. Caudal centra 5–7 and 9 are therefore vascularised from both sides; 4 and 10–11 from one side only; and 1–3, 8 and 12–13 not at all.

There are a few things to say about this.

First, this is now among our most reviewed papers. Thinking back across all my publications, most have been reviewed by two people; the original Xenoposeidon description was reviewed by three; the same was true of my reassessment of Xenoposeidon as a rebbachisaur, and there may have been one or two more that escape me at the moment. But I definitely can’t think of any papers that have been under five sets of eyes apart from this one in Qeios.

Now I am not at all saying that all five of the reviews on this paper are as comprehensive and detailed as a typical solicited peer review at a traditional journal. Some of them have detailed observations; others are much more cursory. But they all have things to say — which I will return to in my third point.

Second, Qeios has further decoupled the functions of peer review. Traditional peer review combines three rather separate functions: A, Checking that the science is sound before publishing it; B, assessing whether it’s a good fit for the journal (often meaning whether it’s sexy enough); and C, helping the authors to improve the work. When PLOS ONE introduced correctness-only peer-review, they discarded B entirely, reasoning correctly that no-one knows which papers will prove influential[1]. Qeios goes further by also inverting A. By publishing before the peer reviews are in (or indeed solicited), it takes away the gatekeeper role of the reviewers, leaving them with only function C, helping the authors to improve the work. Which means it’s no surprise that …

Third, all five reviews have been constructive. As Matt has written elsewhere, “There’s no way to sugar-coat this: getting reviews back usually feels like getting kicked in the gut”. This is true, and we both have a disgraceful record of allowing harshly-reviewed projects to sit fallow for far too long before doing the hard work of addressing the points made by the reviewers and resubmitting[2].

The contrast with the reviews from Qeios has been striking. Each one has sent me scampering back to the manuscript, keen to make (most of) the suggested changes — hence the three revised versions that I’ve posted in the last fortnight. I think there are at least two reasons for this, a big one and a small one.

  • The big reason, I think, is that the reviewers know their only role is to improve the paper. Well, that’s not quite true: they also have some influence over its evaluation, both in what they write and in assigning a 1-to-5 star score. But they know when they’re writing their reviews that whatever happens, they won’t block publication. This means, firstly, that there is no point in their writing something like “This paper should not be published until the authors do X”; but equally importantly, I think it puts reviewers in a different and more constructive mindset. They feel themselves to be allies of the authors rather than (as can happen) adversaries.
  • The smaller reason is it’s easier to deal with one review at a time. I understand why journals solicit multiple reviews: so the handling editor can consider them all in reaching a decision. I understand why the authors get all the reviews back at once. But that process can’t help but be discouraging: because, once the decision has been made, they’re all on hand and there’s no point in stringing them out. One at a time may not be better, exactly; but it’s emotionally easier.

Is this all upside? Well, it’s too early to say. We’ve only done this once. The experience has certainly been more pleasant — and, crucially, much more efficient — than the traditional publishing lifecycle. But I’m aware of at least two potential drawbacks:

First, the publish-first lifecycle could be exploited by cranks. If the willingness to undergo peer-review is the mark of seriousness in a researcher — and if non-serious researchers are unwilling to face that gauntlet — then a venue that lets you make an end-run around peer-review is an obvious loophole. How serious a danger is this? Only time will tell, but I am inclined to think maybe not too serious. Bad papers on a site like Qeios will attract negative reviews and low scores, especially if they start to get noticed in the mainsteam media. They won’t be seen as having the stamp of having passed peer-review; rather, they will be branded with having publicly failed peer-review.

Second, it’s still not clear where reviewers will come from. We wrote about this problem in some detail last month, and although it’s worked out really well for our present paper, that’s no guarantee that it will always work out this well. We know that Qeios itself approached at least one reviewer to solicit their comments: that’s great, and if they can keep doing this then it will certainly help. But it probably won’t scale, so either a different reviewing culture will need to develop, or we will need people who — perhaps only on an informal basis — take it on themselves to solicit reviews from others. We’re interested to see how this develops.

Anyway, Matt and I have found our first Qeios experience really positive. We’ve come out of it with what I think is a good paper, relatively painlessly, and with much less friction than the usual process. I hope that some of you will try it, too. To help get the process rolling, I personally undertake to review any Qeios article posted by an SV-POW! reader. Just leave a comment here to let me know about your article when it’s up.

 

Notes

[1] “No-one knows which papers will prove influential”. As purely anecdotal evidence for this claim: when I wrote “Sauropod dinosaur research: a historical review” for the Geological Society volume Dinosaurs: A Historical Perspective, I thought it might become a citation monster. It’s done OK, but only OK. Conversely, it never occurred to me that “Head and neck posture in sauropod dinosaurs inferred from extant animals” would be of more than specialist interest, but it’s turned out to be my most cited paper. I bet most researchers can tell similar stories.

[2] One example: my 2015 preprint on the incompleteness of sauropod necks was submitted for publication in October 2015, and the reviews[3] came back that same month. Five and a half years later, I am only now working on the revision and resubmission. If you want other examples, we got ’em. I am not proud of this.

[3] I referred above to “harsh reviews” but in fact the reviews for this paper were not harsh; they were hard, but 100% fair, and I found myself agreeing with about 90% of the criticisms. That has certainly not been true of all the reviews I have found disheartening!

 

Posted by Mike Taylor
Filed in caudal, open access, papers by SV-POW!sketeers, Peer review, stinkin' crocs
16 Comments »

Burpee PaleoFest 2020: my last conference

March 8, 2021

Last spring I was an invited speaker at PaleoFest at the Burpee Museum of Natural History in Rockford, Illinois. I meant to get these photos posted right after I got back. But I flew back from Illinois on Monday, March 9, 2020, and by the following weekend I was throwing together virtual anatomy labs for the med students. You know the rest. 

The wall of ceratopsians at the Burpee Museum. Every museum should have one of these.

I had a fantastic time at PaleoFest. The hosts were awesome, the talks were great, the Burpee is a cool museum to explore, and the swag was phenomenal.

An ontogenetic series of Triceratops skulls. Check out how the bony horn cores switch from back-curving to forward-curving. The keratin sheaths over the horn cores elongated, but they didn’t remodel, so adult trikes probably had S-curving horns.

I know I poke a lot of fun at non-sauropods around here, but the truth is that I’m a pan-dino-geek at heart. When I’m looking at theropods and ceratopsians I am mostly uncontaminated by specialist knowledge or a desire to work on them, so I can relax, and squee the good squee.

I’m a sucker for dinosaur skin. It’s just mind-blowing that we can tell more or less what it would feel like to pet a dinosaur.

Among the memorable talks last year: Win McLaughlin educated me about rhinos, which are a heck of a lot weirder than I thought; Larisa DeSantis gave a mind-expanding talk about mammalian diets, evolution, and environmental change; and Holly Woodward explained in convincing detail why “Nanotyrannus” is a juvenile T. rex.

The pride of the Burpee Museum: Jane, the juvenile T. rex.

But my favorite presentation of the conference was Susie Maidment’s talk on stegosaurs. It was one of the those great talks in which the questions I had after seeing one slide were answered on the next slide, and where by end of the presentation I had absorbed a ton of new information almost effortlessly, by  just listening to an enthusiastic person talk almost conversationally about their topic. And when I say “effortlessly”, I mean for the audience–I know from long experience that presentations like that are born from deep, thorough knowledge of one’s topic, deliberate planning, and rehearsal.

The big T. rex mount is pretty great, too.

That’s not to slight the other speakers, of course. All the talks were good, and that’s not an easy thing to pull off. Full credit to Josh Matthews and the organizing committee for putting on such an engaging and inspiring conference.

Did I say the swag was phenomenal? The swag was phenomenal. Above are just a few of my favorite things: a Burpee-plated Rite-in-the-Rain field notebook, a fridge magnet, a cool sticker, and at the center, My Precious: a personalized Estwing rock hammer. Estwing makes nice stuff, and a lot of paleontologists and field geologists carry Estwing rock hammers. Estwing is also based in Rockford, and they’ve partnered with the Burpee Museum to make these personalized rock hammers for PaleoFest, which is pretty darned awesome.

I already had an Estwing hammer–one of blue-grip models–which is good, because the engraved one is going in my office, not to the field. (If you’re wondering why my field hammer looks so suspiciously unworn, it’s because my original was stolen a few years ago, and I’m still breaking this one in. By doing stuff like this.)

There’s a little Burpee logo with a silhouette of Jane down at the end of the handle, so I had to take Jane to meet Jane.

Parting shot: I grew up in a house out in the country, about 2 miles outside of the tiny town of Hillsdale, Oklahoma, which is about 20 miles north of Enid, which is about 100 miles north-northwest of Oklahoma City. Hillsdale is less than an hour from Salt Plains National Wildlife Refuge, where you can go dig for selenite crystals like the ones shown above. The digging is only allowed in designated areas, to avoid unexploded ordnance from when the salt plains were used as a bombing range in World War II, and at certain times of year, to avoid bothering the endangered whooping cranes that nest there.

I don’t know how many times I went to Salt Plains to dig crystals as a kid, either on family outings or school field trips, but it was a lot. I still have a tub of them out in the garage (little ones, nothing like museum-quality). And there are nice samples, like the one shown above, in the mineral hall of just about every big natural history museum on the planet. One of my favorite things to do when I visit a new museum is go cruise the mineral display and find the selenite crystals from Salt Plains. I’ve seen Salt Plains selenite in London, Berlin, and Vienna, and in most of the US natural history museums that I’ve visited for research or for fun. The farm boy in me still gets a little thrill at seeing a little piece of northwest Oklahoma, from a place that I’ve been and dug, on display in far-flung cities.

I already credited Josh Matthews for organizing a fabulous conference, but I need to thank him for being such a gracious host. He helped me arrange transportation, saw that all my needs were met, kept me plied with food and drink, and drove me to Chicago, along with a bunch of other folks, for a Field Museum visit before my flight home, which is how I got this awesome photo, and also these awesome photos. Thanks also to my fellow speakers, for many fascinating conversations, and to the PaleoFest audience, for bringing their A game and asking good questions. I didn’t know that PaleoFest 2020 would be my last conference for a while, but it was certainly a good one to go out on.

Posted by Matt Wedel
Filed in Burpee Museum of Natural History, Ceratopsians, conferences, integument, museums, navel blogging, PaleoFest, stinkin' ornithischians, stinkin' theropods, Things I should have posted a year ago, travel, Tyrannosaurus
12 Comments »

Elsevier charge $37.95 for access to an unformatted manuscript with intrusive watermarking and the illustrations removed

March 3, 2021

Today should be a day of rejoicing, as it brings us a new sauropod: Arackar licanantay Rubilar-Rogers et al. 2021., a small titanosaur from Chile.

It’s not, though. Because not only is this paper behind a paywall in Elsevier’s journal Cretaceous Research, but the paywalled paper is what they term a “pre-proof” — a fact advertised in a tiny font half way down the page rather than in a giant red letters at the top.

“Pre-proof” is not a term in common usage. What does it mean? It turns out to be an unformatted, double-spaced, and line-numbered manuscript. In other words, this is an AAM (author’s accepted manuscript) of the kind that the authors could have deposited in their institutional repository for anyone to read for free.

But wait — there’s more! By way of “added value”, Elsevier have slapped a big intrusive “journal pre-proof” watermark across the middle of every single page, to make it even less readable than a double-spaced line-numbered manuscript already is:

Sample page from “pre-proof” of Rubilar-Rogers et al. 2021. Reproduced under the Fair Dealing doctrine as non-commercial research, criticism / review / quotation, and news reporting (sections 29, 30, 178 of the Copyright, Designs and Patents Act 1988). Get back in your box, Elsevier copyright lawyers.

If you want to see this for yourself, Elsevier will let you download it for $37.95:

Yeah. Thirty-seven dollars and 95 cents.

And now, the punchline. You may be wondering why, when a new sauropod has been announced, I didn’t lead with a nice image of one of the vertebrae? After all, are we not Sauropod Vertebra Picture of the Week?

It’s because there are no images of the vertebra. There are no images of any of the fossil material. In fact, there are no images at all.

Yes. This “pre-proof” omits all twelve illustrations. (We know there are twelve images, because all the figure captions appear at the end.) I have no idea what Arackar licanantay looks like. None at all. And for this, let’s just remind ourselves again, they charge $37.95.

I want to be careful throwing words like “fraud” around, but what I will say is that this is behaviour unbecoming of a major and once-respected multinational corporation. If a publisher’s behaviour ever merited the label “predatory”, surely this is it.

 

References

  • Rubilar-Rogers, David, Alexander O. Vargas, Bernardo González Riga, Sergio Soto-Acuña, Jhonatan Alarcón-Muñoz, José Iriarte-Díaz, Carlos Arévalo and Carolina S. Gutstein. 2021. Arackar licanantay gen. et sp. nov. a new lithostrotian (Dinosauria, Sauropoda) from the Upper Cretaceous of the Atacama Region, northern Chile. Cretaceous Research 104802 (pre-proof). doi:10.1016/j.cretres.2021.104802

 

Posted by Mike Taylor
Filed in stinkin' publishers
16 Comments »