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.

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

 

I am still building up to a big post on vertebral orientation, but in the meantime, check out this caudal vertebra of a Komodo dragon, Varanus komodoensis. This is right lateral view–the vert is strongly procoelous, and the articular ends of the centrum are really tilted relative to the long axis. I find this encouraging, for two reasons. First, it helped me clarify my thinking on how we ought to orient vertebrae, which Mike wrote about here and here. And second, it gives me some hope, because if we can figure out why tilting your articular surfaces makes functional sense in extant critters like monitors, maybe we can apply those lessons to sauropods and other extinct animals.

This is LACM Herpetology specimen 121971. Many thanks again to Neftali Camacho for access and assistance, and to Jessie Atterholt for basically doing all the other jobs while I was faffing about with this Komodo dragon.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

And this one is looking behind, back toward Hanksville.

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

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

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

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

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

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

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

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

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

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