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

 

For reasons that I will explain in a later post, I am parting with one of my most treasured possessions: the badger skull that I extracted from my roadkill specimen four years ago.

As a farewell, I finally photographed it properly from all the cardinal directions, and prepared this multiview:

Don’t forget to click though for the full resolution version!

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 think we’ve all had enough of the Impact Factor as a way of measuring the quality of journals. From Ginny Barbour’s forensic account of negotiating PLoS Medicine’s IF back in 2006, via Stephen Curry’s measured rant back in 2012 (“if you use impact factors you are statistically illiterate”) and Björn Brembs’ survey of how very widespread IF negotations are in 2016, to all the recent negotiations with Clarivate about which journals should even have IFs, it’s become increasingly obvious that the Impact Factor is not a metric, it’s a negotiation.

And of course this means that the reason any journal has the particular IF it has is competely opaque.

The world needs a much more transparent metric of journal quality, and I am here to offer it! The Objective Quality Factor (QOF) is assigned in a wholly straightforward way that anyone can understand:

Your journal obtains an OQF of x by paying me x pounds.

That’s it. As soon as I acknowledge your payment, you have the right to display your OQF on the journal home page and in marketing materials.

If another journal in your field obtains a higher OQF than yours, and you need to regain your journal’s position at the top of the totem pole, all you need do is send me more money.

Payments via PayPal to ebay@miketaylor.org.uk please!

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

Black Lives Matter

June 9, 2020

Mark Witton says this better than I could:

Like many white folks, I have traditionally assumed that simply not being racist was doing my part, and that the actions of others would eventually convert society at large to seeing race as the non-issue it should be. I have also felt that, as a white, straight male from a middle-class background, my voice would add nothing to this conversation or – worse – be seen as patronising or virtue signalling.

I now realise that this view was incorrect. The fact that people of colour are still fighting against global systemic marginalisation and persecution shows that being non-racist isn’t enough, and that we must be outspokenly anti-racist, even if we have never experienced racial discrimination ourselves. Some may accuse me of jumping on a bandwagon with this. That’s accurate, but I don’t care. This is a wagon we should all be on, and I’m ashamed for not being on-board earlier.

Go and read his post. I endorse it.

And remember: the opposite of Black Lives Matter is not All Lives Matter; it’s Black Lives Don’t Matter. Don’t be That Guy.

Here’s one of my most prized possessions: a cannon bone from a giraffe. I got it last fall from Necromance, a cool natural history store in LA. Originally they had a matched pair on display in the front window. Jessie Atterholt got one of them last summer, and I got the other a few months later.

The cannon bones of hoofed mammals consist of fused metacarpals (in the forelimbs) or metatarsals (in the hindlimbs). In this case, the giraffe cannon bone in the top photo is the one from the right forelimb, consisting of the fused 3rd and 4th metacarpals, which correspond to the bones in the human hand leading to the middle and ring fingers. Only my third metacarpal is traced in the top photo. For maximum homology goodness I should have traced MC4, too, but I’m lazy.

I didn’t know that this was a right forelimb cannon bone when I got it. In fact, I only figured that out this afternoon, thanks to the figures and text descriptions in Rios et al. (2016), which I got free through Palaeontologia Electronica (you can too). The weirdly large and perfectly circular holes at the ends of my cannon bone were clearly drilled out by somone, I guess maybe for mounting purposes? At first I thought it might have been to help the marrow cook out of the shaft of the bone during simmering and degreasing, but none of the drilled holes intersect the main marrow cavity, they’re just in the sponge of trabecular bone at the ends of the element.

This post is a sequel to one from last year, “Brachiosaurus and human metacarpals compared“, which featured metacarpal 3 from BYU 4744, the partial skeleton of Brachiosaurus from Potter Creek, Colorado. I know what everyone’s thinking: can we make these two high-browsing giants throw hands?

Yes, yes we can. The giraffe cannon bone is 75.5cm long, and the brachiosaur metacarpal is 57cm long, or 75.5% the length of the giraffe element. I scaled the two bones correctly in the above image. My hands aren’t the same size because they’re at different distances from the camera, illustrating the age-old dictum that scale bars are not to be trusted.

The Potter Creek brachiosaur is one of the largest in the world–here’s me with a cast of its humerus–but ‘my’ giraffe is not. World-record giraffes are about 19 feet tall (5.8m), and doing some quick-and-dirty cross-scaling using the skeleton photo above suggests that the metacarpal cannon bone in a world-record giraffe should be pushing 90cm. So the giraffe my cannon bone is from was probably between 15.5 and 16 feet tall (4.7-4.9m), which is still nothing to sniff at.

I don’t know how this bone came to be at Necromance. I assume from an estate sale or something. I only visited for the first time last year, and at that time they had three real bones from giraffes out in the showroom: the two cannon bones and a cervical vertebra. They might have put out more stuff since–it’s been about six months since I’ve been there–but all of the giraffe bones they had at that point have been snapped up by WesternU anatomists. Jessie and I got the cannon bones, and Thierra Nalley got the cervical vertebra, which is fair since she works on the evolution of necks (mostly in primates–see her Google Scholar page here). I don’t know if there are any photos of Thierra’s cervical online, but Jessie did an Instagram post on her cannon bone, which is nearly as long as her whole damn leg.

There will be more anatomy coming along soon, and probably some noodling about sauropods. Stay tuned!

Reference

Ríos M, Danowitz M, Solounias N. 2016. First comprehensive morphological analysis on the metapodials of Giraffidae. Palaeontologia Electronica 19(3):1–39.

 

 

Credit: anonymous tattoo, Grant Harding for the caption.

Update. Here is the Instagram post that Grant got this from. Unfortunately it seems to be from an account that specialises in reposting others’ work without attribution, so we don’t know where the tattoo photo originated.

My eldest son Dan went out to visit his girlfriend Beth, shortly before the Coronavirus crisis began, during her university placement in Toulouse. While they were there, they bought me this gift:

As you can see, it’s a Lego-like self-assembly kit; but as you can also see from the mug in the background, it’s tiny. As  best I can make out, the blocks are half the length and width of Lego blocks, and about third the height. The whole model is about seven or eight inches (18-20 cm) from nose to tail.

Here’s a very quick walk-round, so you can appreciate the 3d shape.

I am properly impressed with this. It has the shape of the ribcage right, and the hips and shoulders, and the proportions are right so that it conveys with absolute conviction the quality of brachiosaurosity. It has a very posable neck that can be placed in a realistic life posture, and there are even hints of scapulae and ilia.

I made only one change from the instructions: I reoriented the forefoot so that we have a vertically oriented arcade of metacarpals rather than a plantigrade forefoot.

It was a very picky build. The instructions recommend using Nanoblock tweezers, sold separately, but I just used my big clumsy fingers, so that ribs and legs and things were constantly falling off. The process was rather like what this video shows, but much slower.

If you want one of your own, you can get it from Amazon UK or from Amazon US. I recommend it for serious sauropod lovers, but would be infuriating for children, and requires patience and precision to assemble.

Oh, and kit came with plenty of spare parts, in case you lose some of them: enough that Dan was able to make a juvenile with the leftovers.