We’ve noted many times over the years how inconsistent pneumatic features are in sauropod vertebra. Fossae and formamina vary between individuals of the same species, and along the spinal column, and even between the sides of individual vertebrae. Here’s an example that we touched on in Wedel and Taylor (2013), but which is seen in all its glory here:

Taylor and Wedel (2021: Figure 5). Giraffatitan brancai tail MB.R.5000, part of the mounted skeleton at the Museum für Naturkunde Berlin. Caudal vertebrae 24–26 in left lateral view. While caudal 26 has no pneumatic features, caudal 25 has two distinct pneumatic fossae, likely excavated around two distinct vascular foramina carrying an artery and a vein. Caudal 24 is more shallowly excavated than 25, but may also exhibit two separate fossae.

But bone is usually the least variable material in the vertebrate body. Muscles vary more, nerves more again, and blood vessels most of all. So why are the vertebrae of sauropods so much more variable than other bones?

Our new paper, published today (Taylor and Wedel 2021) proposes an answer! Please read it for the details, but here’s the summary:

  • Early in ontogenly, the blood supply to vertebrae comes from arteries that initially served the spinal cord, penetrating the bone of the neural canal.
  • Later in ontegeny, additional arteries penetrate the centra, leaving vascular foramina (small holes carrying blood vessels).
  • This hand-off does not always run to completion, due to the variability of blood vessels.
  • In extant birds, when pneumatic diverticula enter the bone they do so via vascular foramina, alongside blood vessels.
  • The same was probaby true in sauropods.
  • So in vertebrae that got all their blood supply from vascular foramina in the neural canal, diverticula were unable to enter the centra from the outside.
  • So those centra were never pneumatized from the outside, and no externally visible pneumatic cavities were formed.

Somehow that pretty straightforward argument ended up running to eleven pages. I guess that’s what you get when you reference your thoughts thoroughly, illustrate them in detail, and discuss the implications. But the heart of the paper is that little bullet-list.

Taylor and Wedel (2021: Figure 6). Domestic duck Anas platyrhynchos, dorsal vertebrae 2–7 in left lateral view. Note that the two anteriormost vertebrae (D2 and D3) each have a shallow pneumatic fossa penetrated by numerous small foramina.

(What is the relevance of these duck dorsals? You will need to read the discussion in the paper to find out!)

Our choice of publication venue

The world moves fast. It’s strange to think that only eleven years ago my Brachiosaurus revision (Taylor 2009) was in the Journal of Vertebrate Palaeontology, a journal that now feels very retro. Since then, Matt and I have both published several times in PeerJ, which we love. More recently, we’ve been posting preprints of our papers — and indeed I have three papers stalled in peer-review revisions that are all available as preprints (two Taylor and Wedels and a single sole-authored one). But this time we’re pushing on even further into the Shiny Digital Future.

We’ve published at Qeios. (It’s pronounced “chaos”, but the site doesn’t tell you that; I discovered it on Twitter.) If you’ve not heard of it — I was only very vaguely aware of it myself until this evening — it runs on the same model as the better known F1000 Research, with this very important difference: it’s free. Also, it looks rather slicker.

That model is: publish first, then filter. This is the opposite of the traditional scholarly publishing flow where you filter first — by peer reviewers erecting a series of obstacles to getting your work out — and only after negotiating that course to do get to see your work published. At Qeios, you go right ahead and publish: it’s available right off the bat, but clearly marked as awaiting peer-review:

And then it undergoes review. Who reviews it? Anyone! Ideally, of course, people with some expertise in the relevant fields. We can then post any number of revised versions in response to the reviews — each revision having its own DOI and being fixed and permanent.

How will this work out? We don’t know. It is, in part, an experiment. What will make it work — what will impute credibility to our paper — is good, solid reviews. So if you have any relevant expertise, we do invite you to get over there and write a review.

And finally …

Matt noted that I first sent him the link to the Qeios site at 7:44 pm my time. I think that was the first time he’d heard of it. He and I had plenty of back and forth on where to publish this paper before I pushed on and did it at Qeios. And I tweeted that our paper was available for review at 8:44 — one hour exactly after Matt learned that the venue existed. Now here we are at 12:04 my time, three hours and 20 minutes later, and it’s already been viewed 126 times and downloaded 60 times. I think that’s pretty awesome.

References

  • Taylor, Michael P. 2009. A re-evaluation of Brachiosaurus altithorax Riggs 1903 (Dinosauria, Sauropoda) and its generic separation from Giraffatitan brancai (Janensch 1914). Journal of Vertebrate Paleontology 29(3):787-806. [PDF]
  • Taylor, Michael P., and Mathew J. Wedel. 2021. Why is vertebral pneumaticity in sauropod dinosaurs so variable? Qeios 1G6J3Q. doi: 10.32388/1G6J3Q [PDF]
  • Wedel, Mathew J., and Michael P. Taylor 2013b. Caudal pneumaticity and pneumatic hiatuses in the sauropod dinosaurs Giraffatitan and Apatosaurus. PLOS ONE 8(10):e78213. 14 pages. doi: 10.1371/journal.pone.0078213 [PDF]

This is a very belated follow-up to “Tutorial 12: How to find problems to work on“, and it’s about how to turn Step 2, “Learn lots of stuff”, into concrete progress. I’m putting it here, now, because I frequently get asked by students about how to get started in research, and I’ve been sending them the same advice for a while. As with Tutorial 25, from now on I can direct the curious to this post, and spend more time talking with them about what they’re interested in, and less time yakking about nuts and bolts. But I hope the rest of you find this useful, too.

Assuming, per Tutorial 12, that you’ve picked something to investigate–or maybe you’re trying to pick among things to investigate–what next? You need a tractable way to get started, to organize the things you’re learning, and to create a little structure for yourself. My recommendation: do a little project, with the emphasis on little. Anyone can do this, in any area of human activity. Maybe your project will be creating a sculpture, shooting and editing a video, learning–or creating–a piece of music, or fixing a lawn mower engine. My central interest is how much we still have to discover about the natural world, so from here on I’m going to be writing as a researcher addressing other researchers, or aspiring researchers.

Arteries of the anterior leg, from Gray’s Anatomy (1918: fig. 553). Freely available courtesy of Bartleby.com.

I’ll start with a couple of examples, both from my own not-too-distant history. A few years ago I got to help some of my colleagues from the College of Podiatric Medicine with a research project on the perforating branch of the peroneal artery (Penera et al. 2014). I knew that vessel from textbooks and atlases and from having dissected a few out, but I had never read any of the primary (journal) literature on it. As the designated anatomist on the project, I needed to write up the anatomical background. So I hit the journals, tracked down what looked like the most useful papers, and wrote a little 2-page summary. We didn’t use all of it in the paper, and we didn’t use it all in one piece. Some sentences went into the Introduction, others into the Discussion, and still others got dropped entirely or cut way down. But it was still a tremendously useful exercise, and in cases like this, it’s really nice to have more written down than you actually need. Here’s that little writeup, in case you want to see what it looks like:

Wedel 2013 anatomy of the perforating branch of the peroneal artery

Pigeon spinal cord cross-section, from Necker (2006: fig. 4).

More recently, when I started working with Jessie Atterholt on weird neural canal stuff in dinosaurs, I realized that I needed to know more about glycogen bodies in birds, and about bird spinal cords generally. I expected that to be quick and easy: read a couple of papers, jot down the important bits, boom, done. Then I learned about lumbosacral canals, lobes of Lachi, the ‘ventral eminences’ of the spinal cord in ostriches, and more, a whole gnarly mess of complex anatomy that was completely new to me. I spent about a week just grokking all the weird crap that birds have going on in their neural canals, and realized that I needed to crystallize my understanding while I had the whole structure in my head. Otherwise I’d come back in a few months and have to learn it all over again. Because it was inherently visual material, this time I made a slide deck rather than a block of text, something I could use to get my coauthors up to speed on all this weirdness, as well as a reminder for my future self. Here’s that original slide deck:

Wedel 2018 Avian lumbosacral spinal cord specializations

If you’re already active in research, you may be thinking, “Yeah, duh, of course you write stuff down as you get a handle on it. That’s just learning.” And I agree. But although this may seem basic, it isn’t necessarily obvious to people who are just starting out. And even to the established, it may not be obvious that doing little projects like this is a good model for making progress generally. Each one is a piton driven into the mountainside that I’m trying to climb: useful for me, and assuming I get them out into the world, useful for anyone I’d like to come with me (which, for an educator and a scientist, means everyone).

A view down the top of the vertebral column in the mounted skeleton of Apatosaurus louisae, CM 3018, showing the trough between the bifurcated neural spines.

If you’re not active in research, the idea of writing little term papers may sound like purgatory. But writing about something that you love, that fascinates you, is a very different proposition from writing about dead royalty or symbolism because you have to for a class.* I do these little projects for myself, to satisfy my curiosity, and it doesn’t feel like work. More like advanced play. When I’m really in the thick of learning a new thing–and not, say, hesitating on the edge before I plunge in–I am so happy that I tend to literally bounce around like a little kid, and the only thing that keeps me sitting still is the lure of learning the next thing. That I earn career beans for doing this still seems somewhat miraculous, like getting paid to eat ice cream.

* YMMV, history buffs and humanities folks. If dead royalty and symbolism rock your world but arteries and vertebrae leave you cold, follow your star, and may a thousand gardens grow.

Doing little projects is such a convenient and powerful way to make concrete progress that it has become my dominant mode. As with the piece that I wrote about the perforating branch of the peroneal artery, the products rarely get used wholesale in whatever conference presentation or research paper I end up putting together, but they’re never completely useless. First, there is the benefit to my understanding that I get from assembling them. Second, they’re useful for introducing other people to the sometimes-obscure stuff I work on, and nothing makes you really grapple with a problem like having to explain it to others. And third, these little writeups and slideshows become the Lego bricks from which I assemble future talks and papers. The bird neural canal slide deck became a decent chunk of our presentation on the Snowmass Haplocanthosaurus at the 1st Palaeontological Virtual Congress (Wedel et al. 2018)–and it’s about to become something even better.

The operative word at the start of the last paragraph is ‘concrete’. I don’t think this was always the case, but now that I’m in my mid-40s ‘what I know’ is basically equivalent to ‘what I remember’, which is basically equivalent to ‘what I’ve written down’. (And sometimes not even then–Mike and I both run across old posts here on SV-POW! that we’ve forgotten all about, which is a bit scary, given how often we put novel observations and ideas into blog posts.) Anyway, this is why I like the expression ‘crystallize my understanding’: the towers of comprehension that I build in my head are sand castles, and if I don’t find a way to freeze them in place, they will be washed away by time and my increasingly unreliable cerebral machinery.

Really nice Stegosaurus plate on display at Dinosaur National Monument.

Also, if I divide my life into the things I could do and the things I have done, only the things in the latter category are useful. So if you are wondering if it’s worthwhile to write a page to your future self about valves in the cerebral arteries of rats, or all of the dinosaurs from islands smaller than Great Britain, or whatever strange thing has captured your attention, I say yes, go for it. Don’t worry about finding something novel to say; at the early stages you’re just trying to educate yourself (also, talks and papers need intro and background material, so you can still get credit for your efforts). I’ll bet that if you set yourself the goal of creating a few of these–say, one per year, or one per semester–you’ll find ways to leverage them once you’ve created them. If all else fails, start a blog. That might sound flip, but I don’t mean for it to. I got my gig writing for Sky & Telescope because I’d been posting little observing projects for the readers of my stargazing blog.

A final benefit of doing these little projects: they’re fast and cheap, like NASA’s Discovery missions. So they’re a good way to dip your toes into a new area before you commit to something more involved. The more things you try, the more chances you have to discover whatever it is that’s going to make you feel buoyantly happy.

You may have noticed that all of my examples in this post involved library research. That’s because I’m particularly interested in using little projects to get started in new lines of inquiry, and whenever you are starting out in a new area, you have to learn where the cutting edge is before you can move it forward (Tutorial 12 again). Also, as a practical consideration, most of us are stuck with library research right now because of the pandemic. Obviously this library research is no substitute for time in the lab or the field, but even cutters and diggers need to do their homework, and these little projects are the best way that I’ve found of doing that.

P.S. If you are a student, read this and do likewise. And, heck, everyone else who writes should do that, too. It is by far the advice I give most often as a journal editor and student advisor.

P.P.S. As long as you’re reading Paul Graham, read this piece, too–this whole post was inspired by the bit near the end about doing projects.

References

This beautiful image is bird 52659 from Florida Museum, a green heron Butorides virescens, CT scanned and published on Twitter.

(The scan is apparently from MorphoSource, but I can’t find it there.)

There is lots to love here: for example, you can see that the long bones of the arm are pneumatic, because the margins of the bones show up more strongly than the cores. But you won’t be surprised that I am interested mostly in the neck.

As you can see, while the vertebrae of the neck are pulled back into a strong curve, the trachea doesn’t bother, and just sort of hangs there from the base of the head to the top of the lungs, cheerfully crossing over (i.e. passing to the side of) the vertebral sequence. So the trachea here is not much more than half the length of the vertebral sequence.

Now this is the opposite of what we see in some birds. Here, for example, is a trumpet manucode Phonygammus keraudrenii (a bird-of-paradise) as illustrated in Katrina van Grouw’s book The Unfeathered Bird:

Yes, all those coils visible in the torso are the trachea, which is many times longer than it needs to be to connect the head to the lungs. Birds-of-paradise do this sort of thing a lot (Clench 1978).

And they are not alone: cranes and others also have elongated and contorted tracheal trajectories. So it’s odd that herons seem to do the opposite.

But the heron is even odder than that. As we have noted before, herons can stretch their necks out to the point where you would scarcely believe the unstretched and stretched animals are the same thing. But they are:

The CT-scanned heron at the top of this post is in a pose intermediate between the two shown here. But since it can adopt the long-necked pose on the right, it’s apparent that the trachea can become long enough to connect the head and lungs in that pose. Which means it must be able to stretch to nearly twice the length we see in the CT scan.

Don’t try this at home, kids!

References

  • Clench, Mary H. 1978. Tracheal elongation in birds-of-paradise. The Condor 80(4):423–430. doi:10.2307/1367193

Herons lie, part 2

July 28, 2020

I just stumbled across this tweet from bird photographer Gloria (@Lucent508). Four photos of the same individual, apparently a Green Heron. In this image, I am juxtaposing the third image (left-right flipped and scaled up) with the first image (filled out on the left with a stretched reflection of part of the background).

Where has it put that long neck in the lower image? We know it’s in there somewhere, but one thing is for sure: herons lie!

See also: Herons lie (and so do shoebills), and the whole ongoing Necks Lie sequence.

My thanks to Gloria for having taken the excellent photographs that made this post possible.

For those following the saga of Oculudentavis (the beautiful tiny dinosaur preserved in amber that turned out to be a lizard), three more things.

Xing et al. 2020, Extended Data Fig. 2. Computed tomography scan of HPG-15-3 in palatal view, with the mandibles removed, and an isolated quadrate. a, Full palatal view. Dashed square box in a indicates the region enlarged in b [not shown]. bp, basipterygoid process; bs, basisphenoid plate; bsr, basisphenoid rostrum; ch, choana; dt, developing tooth; pt, pterygoid; pp, papillae; pmc, medial contact of the palatal processes of the premaxillae.

First, I’ve updated the timeline in Friday’s post to include several more events, kindly pointed out by commenters Pallas1773 and Ian Corfe. Check back there to better understand the increasingly confusing sequence of events.

Second, David Marjanovic provided an excellent summary of the ICZN issues in a message on the Dinosaur Mailing List. (Summary: you can’t invalidate a name by retracting the paper in which it was erected.) David knows the details of the code as well as anyone, so his analysis is well worth reading.

Finally — and annoyingly, I can’t remember who put me on to this — an interesting Chinese-language article was published two days ago about the retraction [link] [Google translation]. (Apparently the word translated “oolong” should be “mistake”.) It contains a statement from Xing Lida, lead author of the original paper, on the reason for the retraction:

The reporter found that the key to retracting the manuscript was “research progress has been made on a new specimen with a more complete preservation of the same origin discovered by the author team.” The team realized that the skull of the new specimen was very similar to HPG-15-3, but the skeleton behind the head showed a typical squamosaurus form and should be classified as squamosaurus. This indicates that HPG-15-3 is likely to belong to the squamatosaurus, which is different from the initial conclusion.

But the article goes on to note that “there are many loopholes in this withdrawal statement”. It contains some illuminating analysis from Oliver Rauhut and Per Ahlberg, including this from Rauhut: “The main problem of the paper is that the author basically preconceived that the specimen was a bird and analyzed it under this premise (this is not necessarily intentional)“. And it claims:

As early as the evening of March 19, the corresponding author of the paper said in an interview with Caixin Mail, “She recognized the questioner’s conclusion-this is more likely to be a lizard than a bird.”

And this of course was nearly three months before the same author (Jingmai O’Connor) lead-authored the preprint reasserting the avian identity of Oculudentavis.

The more I read about all this, the stranger it seems.

Update (22 August 2020)

A new paper at Zoosystema (Dubois 2020) summarises the nomenclatural situation, citing SV-POW! in passing, and concludes that the name remains nomenclaturally valid despite the retraction of the paper in which is was named — quite rightly.

References

 

Since we wrote about the putative tiny bird Oculudentavis (Xing et al. 2020) last time, things have become rather weirder. I want to discuss two things here: how we got to where we are, and what happens to the zoological name Oculudentavis khaungraae.

Xing et al. 2020, Extended Data Fig. 1. Close-up photographs of HPG-15-3. Part a, Entire skull in left lateral view. The black arrows indicate decay products from the soft tissue of the dorsal surface of the skull and the original position of skull, which drifted before the resin hardened. Scale bars, 2 mm.

First, how we got here. The timeline is a little confused but it seems to go like this:

  • 11 March: Xing et al. (2020) name Oculudentavis khaungraae, describing it as a bird. [link]
  • 11 March: In a Facebook thread on the day the paper is published, Tracey Ford claims that at least some of the authors were told at a symposium by lizard workers that their specimen was a lizard.
  • 12 March: Mickey Mortimer (very quick work!) publishes a blog-post titled “Oculudentavis is not a theropod”, making a solid argument. [link]; see also the followup post [link]
  • 13 March: Andrea Cau, working independently, publishes a blog post in Italian titled “Doubts about the dinosaurian (and avian) state of Oculudentavis” (translated), also making a solid case [link]
  • 13 March: Wang Wei et al. (the same authorship team as in the next entry) publish a detailed, technical Chinese-language article arguing that Oculudentavis is a squamate. [link] [Google translation]
  • 18 March: Li et al. (2020), in a BioRxiv preprint, formally dispute the identity of Oculudentavis, suggesting it is a squamate. [link].
  • 3 May: at the monthly meeting of the Southern California Paleontological Society, where Jingmai O’Connor gives the talk on “The evolution of dinosaurian flight and the rise of birds” she is allegedy “quite upfront about Oculudentavis being a lizard” [link]
  • 29 May: a note is added to the online version of Xing et al. 2020 stating “Editor’s Note: Readers are alerted that doubts have been expressed about the phylogenetic placement of the fossil described in this paper. We are investigating and appropriate editorial action will be taken once this matter is resolved.” [link]. (Steven Zhang later says on Facebook, “I’ve been reliably told by one of the coauthors of the Li et al. commentary piece, Nature rejected the comment from publication but then flagged up the matter as an Editor’s Note.”)
  • 14 June: O’Connor et al. (2020) (mostly the same authors as of the original description) reassert the avian identity of Oculudentavis. [link]
  • 22 July 2020: the original article (Xing et al. 2020) is retracted, with the reason given as “We, the authors, are retracting this Article to prevent inaccurate information from remaining in the literature. Although the description of Oculudentavis khaungraae remains accurate, a new unpublished specimen casts doubts upon our hypothesis regarding the phylogenetic position of HPG-15-3.” [link]

(Note: Facebook always seems very ephemeral, so here is a screenshot of the conversation in question:

I am aware that this is only hearsay, and rather vague: what symposium, what lizard workers? But I’ll leave it here as it does seem to be part of the story — judge it as you will.)

The unambiguously strange thing here is the O’Conner et al. preprint, published after O’Connor had seemingly accepted the squamate identity of Oculudentavis, but arguing for an avian identity. The O’Connor et al. rebuttal of Li et al. is pretty clear on its position, stating at the bottom of page 2:

Our parsimony-based phylogenetic analysis run using TNT placed Oculudentavis in Aves … Forcing a relationship with squamates required 10 additional steps.

But it also contains the rather extraordinary statement “Although in the future new information may prove we are incorrect in our original interpretation … this is in no way due to gross negligence” (p3).

I think we have to assume that O’Connor changed her mind between 11 March (the original publication) and 3 May (the SoCal meeting), then changed it back again by 14 June (the rebuttal of Li et al.), and finally accepted her first change of mind had been correct by 22 July (the retraction). But other interpretations are possible.

And of course the key question here lingers: why was the paper retracted, rather than merely corrected? And why does the journal say the authors retracted it, when the lead author says that the journal did it against their will?

Anyway, enough of the past. What of the future of the name Oculudentavis khaungraae?

The first thing we can all agree on is that (assuming Oculudentavis does turn out to be a squamate), the fact that the generic name misidentifies the phylogenetic position of the taxon is neither here nor there. Zoological nomenclature is full of such misnomers: they are not, and never have been, a reason to remove a name from the record.

But the retraction of the article in which the name was published is another matter. Does it mean, as some have argued, that the name is now nomenclaturally void?

I would strongly argue that no, it does not. There are several lines of reasoning.

First, the International Code of Zoological Nomenclature does not mention retractions at all — from which the simplest conclusion to draw is that it does not recognise them, and considers a paper once published to be published forever.

Second, the wording of the code pertains to the act of publication, not to ongoing status. In Article 8 (What constitutes published work), section 8.1 (Criteria to be met) says “A work must … be issued for the purpose of providing a public and permanent scientific record”. And the Oculudentavis paper certainly was issued for that purpose.

Third, the paper is still out there and always will be: even though electronic copies now bear the warning “This article was retracted on 22 July 2020”, there are thousands of copies of Nature 579 in libraries around the world. They can’t all be amended. What’s written is written. Quod scripsi, scripsi.

And this leads us to the final and most fundamental point: you can’t rewrite history: not one line. The simple and unavoidable reality is that the paper was published. That happened. A retraction can’t undo that — all it really amounts to is an expression of regret.

So the paper was published, and still is published, and the name established in it remains, and is forever tied to the type specimen HPG-15-3. If someone describes the “new unpublished specimen” referred to above, they have no choice but to use the established name Oculudentavis khaungraae: they don’t have the option of naming it (say) Oculudentosaurus instead.

At least, that’s how it seems to me. The International Commission on Zoological Nomenclature has been informally invited on Twitter to state a position, but has not responded at the time of writing — but then it’s not tweeted at all since April, so who knows what (if anything) is going on there? I heard somewhere that Oculudentavis is not being discussed on the ICZN mailing list, but I can’t remember where.

Now would be a good time for them to issue some guidance regarding retractions. And hey, ICZN? If you want to use any of my points above, feel free!

References

 

Back in March, Nature published “Hummingbird-sized dinosaur from the Cretaceous period of Myanmar” by Xing et al. (2020), which described and named a tiny putative bird that was preserved in amber from Myanmar (formerly Burma). It’s a pretty spectacular find.

Xing et al. (2020: figure 1). a, Photograph of the amber piece with skull ventrolaterally exposed. b, c, Scan (b) and drawing (c), left lateral view. d, e, Scan (d) and drawing (e), rostral view. f, g, Scan (f) and drawing (g), occipital view. h, i, Scan (h) and drawing (i), dorsal view. de, dentary; fr, frontal; hy, hyoid bone (or bones); jg, jugal; la, lacrimal; mx, maxilla; pa, parietal; pm, premaxilla; po, postorbital; qd, quadrate; sc, scleral ossicle; so, supraoccipital; sq, squamosal; th, teeth. Scale bars, 5 mm; longer scale bar below b applies to bi.

Today, though, that paper is retracted.

That’s a very rare occurrence for a palaeontology paper. And it raises a lot of questions. The retraction notice reads, in full:

We, the authors, are retracting this Article to prevent inaccurate information from remaining in the literature. Although the description of Oculudentavis khaungraae remains accurate, a new unpublished specimen casts doubts upon our hypothesis regarding the phylogenetic position of HPG-15-3.

But we constantly see papers whose phylogenetic hypotheses are overturned by new specimens. We usually deal with this by writing a new paper. Why, in this case, is there a retraction? Something smells wrong here.

And the plot thickens in Retraction Watch’s account: corresponding author Jingmai O’Connor told them:

I don’t agree with the retraction but there is no point in fighting it, so we all signed it.

I cannot say why Nature chose to retract, I cannot hypothesize on their inner machinations. […] It is also not that unusual for paleontologists to misidentify things and for new information to correct previous hypotheses. However, Nature chose not to publish the Matter’s Arising and instead retracts our paper – they must have their reasons.

This doesn’t add up. The retraction notice explictly states that the authors retracted the original paper — yet the corresponding author says that the journal did it, more or less against the authors’ will.

I don’t know what’s going on here. I agree with O’Connor that “It’s unfortunate because this way science can’t simply correct itself (as it is supposed to do)”. If, as Li et al. (2000) argue, Oculudentavis is actually a squamate (lizard), well, fine: they can publish their conclusion, and the community will arrive at a consensus as to which identification is correct. That’s how it works, right? So why the retraction?

And there’s more: what does this mean for zoological nomenclature? Is the name Oculudentavis khaungraae still nomenclaturally valid? Opinions on this seem to vary (see the Dinosaur Mailing List thread beginning with Ben Creisler’s announcement of the retraction.)

I lean to the interpretation that, since the International Code on Zoological Nomenclature does not mention retractions, it implicitly takes the position that a paper once published is published forever. On that basis, the name Oculudentavis remains valid and attached to the holoype specimen — even if that name, with its -avis suffix, proves to have been poorly chosen in pertaining to a non-bird. (After all, there is plenty of precedent for misleading names staying in place: the whale Basilosaurus is not a saurian, and the clade of “false crocodiles” Pseudosuchia includes the true crocodiles.)

This doesn’t seem to be what Springer Nature wants: in a Facebook exchange forwarded to me by a friend who I will leave anonymous unless he or she chooses to out him or herself, Henry Gee comments “The retraction means the paper is erased from the record, and this includes the name”.

I think this is simply incorrect. But I am no expert: I await comments from those more versed in the intricacies of the ICZN.

At any rate, I can’t help but suspect that something is going on here that’s not being clearly stated. Could it be to do with the fact that Myanmar amber is itself controversial, due to the human rights record of the Myanmar regime? Is it even possible that one or more or the authors of the original Oculudentavis colluded in describing it as a bird when they knew it was something else? I don’t know (and to be 100% clear, I am not accusing anyone of anything). But I do know that Nature‘s vague and possibly misleading retraction notice is not helping, and is not in the spirit of transparency that we aim to cultivate in the sciences.

I’m pretty sure we don’t yet know the full story.

References

 

The new monster redescription of Dilophosaurus by Adam Marsh and Tim Rowe came out in the Journal of Paleontology last week. I’m blogging about it now because the OA link just went live yesterday. So you can get this huge, important paper for free, at this link.

There’s a lot of stuff to love here: beautiful, clear photos of every element from every specimen from multiple angles, interesting anatomical and phylogenetic findings, and of particular interest on this blog, some very cool documentation of serial variation in pneumatic features. Here in Figure 62 we see serial changes in the posterior centrodiapophyseal laminae, which in some of the vertebrae are split around an intermediate fossa, or have accessory laminae.

One thing that I’ve thought a lot about, but written not so much about (yet), is pneumatic features on the ventral surfaces of vertebrae and how they change along the column. So I was excited to see Figure 64, which shows how fossae change serially on both the lateral and the ventral surfaces of the presacral centra. As far as I know, no-one has ever done something like this for a sauropod (please correct me in the comments if I’ve forgotten any examples), but it could be done and the results would be interesting, particularly for taxa like Haplocanthosaurus or Dicraeosaurus that have both lateral and ventral fossae and keels in at least some of the vertebrae.

Here’s Figure 66, a beautiful new skull reconstruction and life restoration, both by Brian Engh. There’s a lot of Engh/Dilophosaurus stuff going on right now, including a new video for the St. George Dinosaur Discovery Site museum (short version here, longer version available at the museum, and I think on Brian’s Patreon page), and, uh, another thing that will be revealed in the not-too-distant future.

I hope everyone is well and safe. When I first realized we were going into quarantine back in March, I had big plans for doing various series of posts here, but almost immediately the demand of getting med school anatomy online ate up all my time and creative energy. Just barely getting back on my feet now. I know Mike has been busier than normal, too. So please be patient with us, and we’ll try to remember to feed the blog now and then.

Reference

Marsh, Adam D., and Rowe, Timothy B. 2020. A comprehensive anatomical and phylogenetic evaluation of Dilophosaurus wetherilli (Dinosauria, Theropoda) with descriptions of new specimens from the Kayenta Formation of northern Arizona. Journal of Paleontology Volume 94, Supplement S78: 1-103. DOI: https://doi.org/10.1017/jpa.2020.14

This is the Jurassic World Legacy Collection Brachiosaurus. I think it might be an exclusive at Target stores here in the US. It turns up on other sites, like Amazon and eBay, but usually from 3rd-party sellers and with a healthy up-charge. Retails for 50 bucks. I got mine for Christmas from Vicki and London. Here’s the link to Target.com if you want to check it out (we get no kickbacks from this).

I thought it would be cool to leverage this thing at outreach events to talk about the new Brachiosaurus humerus that Brian Engh found last year, which a team of us got out of the ground and safely into a museum last October (full story here). But I needed a Brachiosaurus humerus, so I made one, and in this post I’ll show you how to do the same, for next to no money.

Depending on what base you start with and what materials you use, you could build a scale model of a Brachiosaurus humerus at any size. I wanted one that would match the JWLC Brach, so I started by taking some measurements of that. Here’s what I got:

Lengths

  • Head: 45mm
  • Neck: 455mm (x 20 = 9.1m = 29’10”)
  • Torso: 320mm
  • Tail: 320mm
  • Total: 1140 (x 20 = 22.8m = 74’10”)

Heights

  • Max head height: 705mm (x 20 = 14.1m = 46’3″)
  • Withers height: 360mm (x 20 = 7.2m = 23’7″)

The neck length, total length, and head height are pretty close to the mounted Giraffatitan in Berlin. The withers are a little high, as is the bottom of the animal’s belly. I suspect that the limbs on the model are oversized by about 10%. Nevertheless, the numbers say this thing is roughly 1/20 scale.

The largest humeri of Brachiosaurus and Giraffatitan are 213cm, which is about 3mm shy of 7 feet. So a 1/20 scale humerus should be 106.5mm, or 4.2 inches, or four-and-a-quarter if you want a nice, round number.

Incidentally, Chris Pratt is 6’2″ (74 inches), and the Owen Grady action figure is 3.75″, which is 1/20 of 6’3″. So the action figure, the Brachiosaurus toy highly detailed scientific model, and a ~4.2″ humerus model will all be more or less in scale with each other.

I used a chicken humerus for my base. The vast majority of chickens in the US are slaughtered at 5 months, so they don’t get nearly big enough for their humeri to be useful for this project. Fortunately, there’s a pub in downtown Claremont, Heroes & Legends, that has giant mutant chicken hot wings, so I went there and collected chicken bones in the guise of a date. The photo above shows three right humeri (on the left) and one left humerus (on the right) after simmering and an overnight degreasing in a pot of soapy water. I used the same bone clean-up methods as in this post.

What should you do if you don’t have access to giant mutant chicken wings? My method of Brachio-mimicry involves some sculpting, so any reasonably straight bone that bells out a bit at the ends would work. You could use a drumstick in a pinch. Here are my humeri whitening in a tub of 3% hydrogen peroxide from the dollar store down the street.

Brachiosaurid humeri vary somewhat but they all have certain features in common. Here’s the right humerus of Vouivria, modified from Mannion et al. (2017: fig. 19) to show the features of interest to brachiosaur humerus-sculptors. The arrows on the far left point to a couple of corners, one where the deltopectoral crest (dpc in the figure) meets the proximal articular surface, and the other where the articular surface meets the long sweeping curve of the medial border of the humeral shaft.

Here’s a more printer-friendly version of the same diagram. Why did I use Vouivria for this instead of one of the humeri of Brachiosaurus itself? Mostly because it’s a complete humerus for which a nice multi-view was available. Runner-up in this category would have to go to the humerus of Pelorosaurus conybeari figured by Upchurch et al. (2015: fig. 18) in the Haestasaurus paper–here’s a direct link to that figure.

I knew that I’d be doing some sculpting, and I wanted a scale template to work off of, so I made these outlines from the Giraffatitan humerus figured by Janensch (1950) and reproduced by Mike in this post (middle two), and from the aforementioned Pelorosaurus conybeari humerus shown by Mike in this post (outer two). I scaled this diagram so that when printed to fill an 8.5×11 piece of printer paper, the humerus outlines would all be 4.25″–the same nice-round-number 1/20 scale target found above. Here’s a PDF version: Giraffatitan and Pelorosaurus humeri outlines for print.

Here’s the largest of my giant mutant chicken humeri, compared to the outlines. The chicken humerus isn’t bad, but it’s too short for 1/20 scale, the angles of the proximal and distal ends are almost opposite what they should be, and the deltopectoral crest is aimed out antero-laterally instead of facing straight anteriorly. Modification will be required!

Here’s my method for lengthing the humerus: I cut the midshaft of another humerus out, and swapped it in to the middle of the prospective Brachiosaurus model humerus.

To my immense irritation, I failed to get a photo of the lengthened humerus before I started sculpting on it. In the first wave of sculpting, I built up the proximal end and the deltopectoral crest, but missed some key features. On the right, I glued the proximal and distal ends of the donor humerus together; I might make this into a Haestasaurus humerus in the future.

I should mention my tools and materials. I have a Dremel but it wasn’t charged the evening I sat down to do this, so I made all the humerus cuts with a small, cheap hacksaw. I used superglue (cyanoacrylate or CA) for quick joins, and white glue (polyvinyl acetate or PVA) to patch holes, and I put gobs of PVA into the humeral shafts before sealing them up. For additive sculpting I used spackling compound, same stuff you use to patch holes in walls and ceilings, and for reductive sculpting I used sandpaper. I got most of this stuff from the dollar store.

Here we are after a second round of sculpting. The proximal end has its corners now, and the distal end is more accurately belled out, maybe even a bit too wide. It’s not a perfect replica of either the Giraffatitan or Pelorosaurus humeri, but it got sufficiently into the brachiosaurid humerus morphospace for my taste. A more patient or dedicated sculptor could probably make recognizable humeri for each brachiosaurid taxon or even specimen. I deliberately left it a bit rough in hopes that it would read as timeworn, fractured, and restored when painted and mounted. Again, a real sculptor could make some hay here by putting in fake cracks and so on.

The cheap spackling compound I picked up did not harden as much as some other I have used in the past. I had planned on sealing anyway before I painted, and for porous materials a quick, cheap sealant is white glue mixed with water. Here that coat of diluted PVA is drying, and I’m holding up a spare chicken humerus to show how far the model humerus has come.

Before painting, I drilled into the distal end with a handheld electric drill, and used a bamboo barbeque skewer as a mounting rod and handle. I hit it with a couple of coats of gray primer, then a couple of coats of black primer the next day. I could have gotten fancier with highlights and washes and so on, but I was scrambling to get this done for a public outreach event, in an already busy week.

And here’s the finished-for-now product. A couple of gold-finished cardboard gift boxes from my spare box storage gave their lids to make a temporary pedestal. When I get a version of this model that I’m really happy with, either by hacking further on this one or starting from scratch on a second, I’d love to get a wooden or stone trophy base with a little engraved plaque that looks like a proper museum exhibit, and replace the bamboo skewer with a brass rod. But for now, I’m pretty happy with this.

The idea of making dinosaurs out of chicken bones isn’t original with me. I was inspired by the wonderful books Make Your Own Dinosaur Out of Chicken Bones and T-Rex To Go, both by Chris McGowan. Used copies of both books can be had online for next to nothing, and I highly recommend them both.

If this post helps you in making your own model Brachiosaurus humerus, I’d love to see the results. Please let me know about your model in the comments, and happy building!

References

  • Janensch, Werner. 1950. Die Wirbelsaule von Brachiosaurus brancai. Palaeontographica (Suppl. 7) 3: 27-93.
  • Mannion PD, Allain R, Moine O. (2017The earliest known titanosauriform sauropod dinosaur and the evolution of BrachiosauridaePeerJ 5:e3217 https://doi.org/10.7717/peerj.3217
  • Upchurch, Paul, Philip D. Mannion and Micahel P Taylor. 2015. The Anatomy and Phylogenetic Relationships of “Pelorosaurus” becklesii (Neosauropoda, Macronaria) from the Early Cretaceous of England. PLoS ONE 10(6):e0125819. doi:10.1371/journal.pone.0125819

Heinrich Mallison sent me this amazing photo, which he found unattributed on Facebook:

Infuriatingly, I’ve not been able to track down an original source for this: searching for the text just finds a bunch of reposts on meme sites, and Google’s reverse image search just reports a bunch of hits on Reddit:

The line-drawing shows some scientific understanding of bird skeletons, so I imagine someone put real thought into this and is unhappy that the image is propagating uncredited. If that person reads this, please leave a comment: I’d love to credit it properly.

Anyway … what’s going on here?

Birds (like all vertebrates) have two tubes running down the ventral aspect of the neck (i.e. below the vertebrae): the trachea, for breathing, and the oesophagus, for swallowing. But these both open into the back of the mouth and are not piped up past it. I’ve not dissected enough bird heads to show this clearly, but when I was taking Veronica apart the trachea was pretty visibly ending in the mouth cavity, not plumbed up past the mouth into the nasal space:

So yes, I think it’s true: shoebills can bulge their spines out of their mouths.

Why? My best guess that there’s just nowhere else for the spine to go when the neck is retracted. There’s a big empty space in the mouth, why let it go to waste?