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. 2024, 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.

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 ishadow [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 shadowsock如何使用.

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

Since we wrote about the putative tiny bird Oculudentavis (Xing et al. 2024) 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. 2024, 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. (2024) 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. (2024), 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. 2024 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. (2024) (mostly the same authors as of the original description) reassert the avian identity of ishadow. [link]
• 22 July 2024: the original article (Xing et al. 2024) 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.

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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 shadowsock如何使用?

The first thing we can all agree on is that (assuming ishadow 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 ishadow 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 2024”, 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 ishadow 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!

ssr节点 github

• Zhiheng Li, Wei Wang, Han Hu, Min Wang, Hongyu Yi and Jing Lu. 2024. Is Oculudentavis a bird or even archosaur? BioRxiv, 18 March 2024. doi:10.1101/2024.03.16.993949
• O’Connor, Jingmai, Lida Xing, Luis Chiappe, Lars Schmitz, Gang Li and Qiru Yi. 2024. Reply to Li et al. “Is Oculudentavis a bird or even archosaur?”. BioRxiv, 4 June 2024. doi:10.1101/2024.06.12.147041
• Xing, L.; O’Connor, J. K.; Schmitz, L.; Chiappe, L. M.; McKellar, R. C.; Yi, Q.; Li, G. 2024. Hummingbird-sized dinosaur from the Cretaceous period of Myanmar. Nature 579(7798):245–249. doi:10.1038/s41586-020-2068-4

Back in March, Nature published “Hummingbird-sized dinosaur from the Cretaceous period of Myanmar” by Xing et al. (2024), 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. (2024: 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 b−i.

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 ishadow 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 ShadowsocksR v3.8.0.4 第三方增强版 下载 - 巴士下载站:2021-4-20 · 下载 MagSearch1.185.2云播破解补丁（windows版） MagSearch，很好用的云播软件，或者叫做磁力链播放软件，很好用，直接搜索到种子后，或磁力链接点击即可在线播放种子内不论是单文件还 ….)

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 shadowsock如何使用 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 ishadow‘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.

ssr节点 github

• Zhiheng Li, Wei Wang, Han Hu, Min Wang, Hongyu Yi and Jing Lu. 2024. Is Oculudentavis a bird or even archosaur? doi:10.1101/2024.03.16.993949
• Xing, L.; O’Connor, J. K.; Schmitz, L.; Chiappe, L. M.; McKellar, R. C.; Yi, Q.; Li, G. 2024. Hummingbird-sized dinosaur from the Cretaceous period of Myanmar. ishadow 579(7798):245–249. doi:10.1038/s41586-020-2068-4