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.

My friend and frequent collaborator Jessie Atterholt has her office in the next building over from mine. When you walk in, you see something that looks approximately like this. Not exactly like this, because I took these photos in February and she’s changed a few things (and I’m rubbish about getting stuff posted in a timely fashion).

The last time I showed an office full of amazing stuff like this, it was Peter Dodson’s. It will come as no surprise that Jessie was Peter’s student at UPenn before she went to Berkeley for her PhD.

The far case holds mostly books and skulls. Dr. A has her own plastination setup for making preserved organs and organisms, and the snake on the second shelf here is one that she prepped herself. One side of the snake still has the skin on, the other half has been skinned to show the muscles. This is crunch week for me so I don’t have time to ID all of the stuff, but alert readers should have no problem spotting some digitally-resurrected Haplocanthosaurus bits.

Mostly skulls on the middle rack. The sirenian skull on the second shelf and the cave bear on the fourth are both casts, but almost everything else is real bone. The bighorn sheep on the middle shelf is a natural mummy.

Here’s a close-up of the top shelf. Other than some 3D-printed human skull bones sitting in front of the brain slice on the left, everything here is real bone, including the lion, baboon, and human skulls, and the giraffe cervicals winding across the top. Jessie’s been collecting since she was a kid and the African megafauna are gifts from a globe-trotting family friend.

The upper shelves here have quite a few of Jessie’s plastinated specimens, both whole organisms and things like hearts and kidneys from various critters.

A close-up of some of Jessie’s coolest anatomical preparations. In back is an internal cast of the lungs and bronchial tree of a cat. The baby rattlesnake died after eating a proportionally gigantic lizard — I was dumb and forgot to flip the snake over to show the lizard inside, plastinated along with its predator. The ground squirrel on the right is another half-fleshed, half-skinned plastinate, and the mouse up front is a classic dissection presentation, preserved forever through plastination.

I’ve heard it said that the difference between a collector and a hoarder is curation. As someone who definitely lurks more on the hoarder end of that spectrum (to paraphrase Dave Barry, if you could see my office you’d be blinded or driven insane), I’m pretty darned jealous of both the breadth of Jessie’s collection, and the skill and taste with which it is displayed. She’s featured some of these specimens on her Instagram, which I strongly recommend.

It’s a miracle!

June 30, 2019

I’ll see your face-of-the-blessed-virgin-in-a-waffle and raise you the fourth dorsal vertebra of the Giraffatitan brancai paralectotype BM.R.2181 (formerly HMN S II) in a dandelion leaf:

I saw this lying on the ground as my friend Nataley was playing a short set at a festival, and it immediately made me think of this:

Janensch (1950:Abb. 54). 17ter Präsakralwirbel (SII), Hinteransicht.

Darren covered this briefly on the Scientific American version of Tetrapod Zoology, but the photos seem to have gone down and who knows how much longer any of that stuff will be up. Plus, he had other things to discuss, so the story has never been told in its entirety. This happened back in April, 2014. Here’s the full writeup I sent to Darren and Mike about it back when:

This happened Sunday afternoon and I thought you’d be interested. London and I let our box turtle, Easty (Terrapene carolina triunguis), crawl around the front yard on sunny days — with supervision, of course. She loves to dig around the edge of the sidewalk and flower bed and eat wood lice, worms, and whatever else comes her way. Sunday we saw her biting this biggish thing that from a distance looked like crumpled up paper. She was really going at it, so I got close to see what she was munching on. It was the head of a rat that our cat, Moe, had killed last week. Easty was snapping off bits of the braincase and eating them.

I had read of turtles scavenging carcasses for minerals but this was the first time I had observed it myself. She kept at it for about 20 minutes, until all of the thin, easily broken parts of the braincase were gone. She didn’t attempt to eat any of the facial skeleton or basicranium. Once she was done, she was done — I tossed the skull in front of her a couple of times and she would stop to smell it, but then walk past it, or even over it on one occasion.

So, there you have it, turtle eats part of rat skull. In keeping with my resolution to blog more about turtles, I’ll try to get some video of Easty feeding later this year. Right now she’s hibernating in a plastic tub on the bottom shelf of our refrigerator, so the hot turtle-feeding action will have to wait. Watch this space!

P.S. The gray ring on Easty’s shell in these photos is a sort of bathtub ring, from soaking in her water dish with just the top of her shell exposed, which she does for about six hours a day when she’s not hibernating. For pictures of Easty with a cleaner shell, please see the previous post. She really is a beautiful turtle.