Here’s Easty dirty, with a dull-looking shell and a pretty serious ‘tub ring’ of hard-water stains around the crown of her carapace. This shot is a few years old, but she looks about the same now when she’s filthy. But here’s how she cleans up:

On Saturday I gave her a good soak in some warm distilled water and scrubbed her shell with a toothbrush. She shined up beautifully. I should have tried shooting a video, because the keratinous scutes on her shell are a bit translucent, and when full sunlight hits them they take on a depth and luster that I had not previously appreciated (heh).

I shot some reference images in the cardinal directions. If you need dorsal, lateral, or ventral views of an adult female Three-toed box turtle, Terrapene carolina triunguis, it’s your lucky day.

The lateral view is interesting, because you can clearly see the joint between the two halves of her plastron, both of which can raise like drawbridges to completely seal her behind an impenetrable wall of bone and keratin. You can also tell that her posterior plastron is gently convex, which is a female trait. As in many other turtles, male box turtles tend to have at least a gently concave posterior plastron, to help them stay on top of the females during mating.

And a ventral view, giving a good look at her plastron. Note her tiny, tiny tail, with the swelling for the vent just visible in the shadow of the plastron, about even with the edge of the carapace — that’s another female trait, whereas males have longer tails and a more distal vent for mating. You can also see yellow lines cutting across some of the scutes of her plastron — those are the outlines of her plastral bones showing through the overlying keratin. As in carapace, the keratinous scutes overlap the edges of the bones to form a sort of biological plywood. A lot of the growth lines have been worn off of her plastron, which is totally normal, but for the most part you can tell where the growth centers were originally located.

I also gave baby turtle a proper bath, with supervision. Baby box turtles can swim just fine, but if the water is inconveniently deep they can sometimes get flipped over on their backs, be unable to right themselves, and drown. She really did not like not having something to haul out on, so I put in the black jar lid you see in the photo. This particular pic is overexposed, which was a happy accident, because now you can see that the apparently dark and featureless areas of her shell and head are in fact very intricately patterned (compare to her dry photo at the top of this post). I’m really looking forward to seeing how her colors come in over the next few years.

And here’s her plastron. Baby turtle is a different subspecies from Easty — she’s a true Eastern box turtle, Terrapene carolina carolina — so she should have stronger patterns on both her carapace and her plastron when she gets bigger. Her head my also be more vibrantly colored, although Easty is no slouch in that department.

I put the two of them next to each other for a very closely-supervised comparison shot. I had been worried that Easty might have a go at baby turtle, but actually the opposite was true. The wee monster frankly terrorized Easty by nipping at her toes –and this was after eating two small slugs from the back yard — so I brought that experiment to a swift end, and got nipped on the finger for my trouble. I happened to be filming when baby turtle nipped Easty’s toe and my finger, and I will try to get those videos cleaned up and posted soon. Watch this space.

Click to embiggen. Trust me on this.

What I think of as our phylogenetically-extended nuclear family grew by one this week: we got a baby box turtle. We got her from a local hobbyist, who hatched her last summer. We haven’t named her yet, so for now she’s just Baby Tiny Turtle. Unlike Easty, who is the three-toed subspecies, Terrapene carolina triunguis, baby turtle is an Eastern box turtle sensu stricto, Terrapene carolina carolina, so she might end up being quite colorful (f’rinstance). She already has pretty complex patterns of lines and spots on the sides and top of her head and on her beak, but she’s so small that you can’t really see them unless you take a photo and zoom in.

(Aside: how do we know she’s a she and not a he? Personally I’d be lost, but the guy who hatched her says that at this age he can sex the babies correctly about 80% of the time, based on the position of the cloaca — it’s farther from the base of the tail in males. If she turns out to be a he, we’ll love him just the same, we’ll just keep him away from Easty.)

Speaking of her size, here’s an obligatory random-objects-for-scale photo. Baby turtle was closer in size to that US quarter when she hatched. You can tell that she’s grown a bit already because each scute on her shell has a outer rim of smooth new keratin. It’s a bit bittersweet, because I want her to grow big and strong and healthy, but I will miss the tiny turtle days when she is bigger. 

If you just want to die of cuteness, watch this video of her trying to eat some banana. She got it all down eventually, but with a little more adventure than either of us expected. If you turn up the volume, you can hear me talking her through it. That was entirely for my benefit, because I’m a big ole softy who talks to animals a lot, and she got through just fine on her own.

Full bulletins as events warrant.

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.

Henry and Cheeto

This past summer, I got into a Facebook conversation with Steve Kary about turtles and tortoises. He was posting photos of Henry, his Russian tortoise (Agrionemys horsfieldii, formerly Testudo horsfieldii), and I was struck by how not-big Henry is. I am not a tortoise expert and what little direct experience I have is with desert tortoises and the big-to-giant species like Sulcatas and the Galapagos and Aldabra giant tortoises. I know the popular pet species like Greek and Russian tortoises and the small African species much less well. Offhand, Henry looked about as big as our three-toed box turtle, Easty (Terrapene carolina triunguis), so I asked Steve if he’d mind posting a photo with a scale bar. This is what Steve sent:

Clockwise from the top we have an ink pen, a 75-million-year-old caudal centrum of a crocodile, a bottle cap, a Nebulon-B frigate from Star Wars Armada, a screwdriver, a nail clipper, a small bottle of Tylenol, and a coin. Oh, and a DVD of an awesome movie.

Naturally, I felt compelled to respond in kind:

Here we have Easty with a similarly eclectic selection of small objects. Again from the top: a rat skull in a plastic bottle, a bottle cap, a d20, a small Altoids tin, an ink pen, a nail clipper, a small metal toy from China, and a nickel. Oh, and a DVD of an awesome movie. Yes, Easty is investigating the d20 as a possible food item. She tried to bite it, but since it’s bigger in diameter than her head, all she achieved was to send it shooting across the floor when her beak slammed shut on one of the vertices.

Here I’ve scaled the two photos to the same size. Henry is definitely wider than Easty, and he has a bigger head and chunkier-looking limbs. In fact, having spent most of my life around box turtles, that’s always my thought when I see a small tortoise: “How do they get so much critter into such a small shell?” It may have to do with space packing. Box turtles have to be able to pull everything in all the way so they can raise the drawbridge, as it were, and use their hinged plastron to close everything up tight (hence the name). Most tortoises lack hinged shells and use the tough scales on their legs and feet to complete the defensive perimeter between carapace and plastron. The limbs don’t have to pull all the way in, so they can be a little bigger.

Anyway, if you’d like to join in this pursuit–photographing turtles with collections of random objects–let me know in the comments. You can post your photos there, or I can add them to the body of the post.

Other turtle posts:

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

 

In lieu of any new science today, have some memes, and a wonderful day!

A timeless classic.

In case you’re wondering, that’s “rolling on the beach laughing my telson off”. Horseshoe crabs have been around for 445 million years, about twice as long as mammals, turtles, and dinosaurs.

Made this last Friday afternoon, in lieu of other stuff I should have been doing. I’m gloating now because the campus is closed and I’m untouchable! Mwa-ha-ha-HAAA!!

Natural selection is a pathway to many abilities that some consider to be…fully rad.

The polished face of the block, 1.5″ tungsten cube for scale. The bowtie shapes are the two biconcave vertebral centra.

It is pretty darned satisfying to be heading to the Isle of Wight for SVPCA next week. My only other visit was in the spring of 2004, when Vicki and I were in England on a spring break vacation/research trip. We spent a night at a bed and breakfast in Sandown and visited the Dinosaur Isle museum, where I got to see “Angloposeidon” and the Barnes High brachiosaur in person.

My most tangible memento of that trip is this cut and polished block with two vertebral centra from what I’m guessing is an ichthyosaur. It has a little story.

While we were at Dinosaur Isle I got to see another cut-and-polished specimen, the partial titanosauriform centrum shown above (and memorialized on the blog way back in 2008, when SV-POW! was about 6 months old). I’ve seen others since (like this one), but that was the first such specimen I’d seen in person, and it captured my imagination.

Vicki and I took a bus to get back to the ferry from Sandown, and somewhere in the island interior there was a bus stop at a small collection of buildings, maybe just two or three? One was a rock shop, and I really wanted to pop in and see what they had. The bus driver warned me, sternly, that the bus would be stopped for precisely two minutes, and that if I was not back on board in 120 seconds I’d be left behind.

So I sprinted inside the shop, found this block behind the counter, paid, and dashed back to the bus, arriving with a few seconds to spare. For four years it sat on my desk or on our mantle, then it got boxed up with a bunch of other natural history stuff and was buried in a closet for a decade. I didn’t get around to unboxing it until January, 2018 — you can spot it in the second photo down in this post. Since then it’s lived on my desk at work, or on a bookshelf adjacent to my desk.

One of the things I love best about it is that even in these somewhat weathered, almost certainly non-diagnostic shards of adequacy, the internal structure is beautifully preserved.

This chunk of rock embodies a lot of time — developmental time for the ichthyosaur, to grow such beautiful bones; deep time for these vertebrae, voyaging to us across millions of years; and personal time. In the fifteen-and-a-half years since my last visit to the Isle of Wight, I’ve gone from being a grad student to a professor at a med school (which I did not see coming back in 2004), and Mike and I have gone from being pen pals to frequent coauthors and co-travelers (and we’re still pen pals).

I think it’s only right that I pressure Mike into stopping at that rock shop, if it’s still there, so I can find a companion piece. Stay tuned.

Last September I spent a day in the LACM Herpetology collections with Jessie Atterholt, looking at weird features in crocs, lizards, snakes, and salamanders. I’ll have more to say about the specific things we were looking for in a month or so, after Jessie’s given her talk at SVPCA. This was just an incidental hit. We were looking at cryptobranchid (literally “hidden gill”) salamanders, because they’re big enough that you don’t need a microscope to see all their weird features. Cryptobranchids include the North American hellbender, Cryptobranchus alleganiensis, and the giant salamanders of China and Japan, Andrias davidianus and Andrias japonicus, respectively, plus a raft of fossil taxa.

This is the mandible of LACM 162475, a specimen of Andrias davidianus, in right lateral view. I’d never spent quality time with the skeleton of a giant salamander, and I was impressed with how evil their teeth are. Just in terms of general outline, these little murder-sticks wouldn’t look out of place in the jaw of a dromaeosaur. Click to enfangenate.

Jessie did an Instagram post on the upper jaw of Cryptobranchus a few months ago, and as long as you’re over there, have a look at the half a pig head that she just plastinated for our colleagues in WesternU’s College of Veterinary Medicine. It’s not the same pig as the one we hemisected last December, but I think it got cut at the same time.