Here’s an odd thing. Over and over again, when a researcher is mistreated by a journal or publisher, we see them telling their story but redacting the name of the journal or publisher involved. Here are a couple of recent examples.

First, Daniel A. González-Padilla’s experience with a journal engaging in flagrant citation-pumping, but which he declines to name:

Interesting highlight after rejecting a paper I submitted.
Is this even legal/ethical?
EDITOR-IN-CHIEF’S COMMENT REGARDING THE INCLUSION OF REFERENCES TO ARTICLES IN [REDACTED]
Please note that if you wish to submit a manuscript to [REDACTED] in future, we would prefer that you cite at least TWO articles published in our journal WITHIN THE LAST TWO YEARS. This is a polict adopted by several journals in the urology field. Your current article contains only ONE reference to recent articles in [REDACTED].

We know from a subsequent tweet that the journal is published by Springer Nature, but we don’t know the name of the journal itself.

And here is Waheed Imran’s experience of editorial dereliction:

I submitted my manuscript to a journal back in September 2017, and it is rejected by the journal on September 6, 2020. The reason of rejection is “reviewers declined to review”, they just told me this after 3 years, this is how we live with rejections. @AcademicChatter
@PhDForum

My, my question is, why in such situations do we protect the journals in question? In this case, I wrote to Waheed urging him to name the journal, and he replied saying that he will do so once an investigation is complete. But I find myself wondering why we have this tendency to protect guilty journals in the first place?

Thing is, I’ve done this myself. For example, back in 2012, I wrote about having a paper rejected from “a mid-to-low ranked palaeo journal” for what I considered (and still consider) spurious reasons. Why didn’t I name the journal? I’m not really sure. (It was Palaeontologia Electronica, BTW.)

In cases like my unhelpful peer-review, it’s not really a big deal either way. In cases like those mentioned in the tweets above, it’s a much bigger issue, because those (unlike PE) are journals to avoid. Whichever journal sat on a submission for three years before rejecting it because it couldn’t find reviewers is not one that other researchers should waste their time on in the future — but how can they avoid it if they don’t know what journal it is?

So what’s going on? Why do we have this widespread tendency to protect the guilty?

You! Shall not! Pass!

August 22, 2020

OK, technically this is MB.R.3822, a dorsal vertebra of Giraffatitan brancai formerly known as HMN Ar1, in posterior view, rendered from a 3D scan provided by Heinrich Mallison.

But you can’t tell me that when you look at that you don’t see Gandalf shouting at a balrog.

This just in from John Conway:

John doesn’t say much about it in the tweet where he unveiled this piece: just “A new #painting, of a Saltapotamus”. His website is just a little more forthcoming:

Saltapotamus

Saltasaurus was a small (for a sauropod) sauropod from the Late Cretaceous of Argentina. It had a some armour, and a lot of girth.

This reminds me very strongly of Obesethocoelicaudia, a fat restoration of Opisthocoelicaudia that John kindly did for Matt and me to use in our 2014 SVPCA talk, “Slender Giants”:

(Saltasaurus and Opisthocoelicaudia are both derived titanosaurs, and in most phylogenies they come out as pretty closely related.)

Is this kind of restoration credible? After all, it’s a long way from how we’ve been used to seeing Saltasaurus. Here, for example, is how E. Guanuco restored a group of four Saltasaurus individuals in Powell (2003: plate 78):

In this illustration they are tubby in a Normanpedia kind of way, but nothing very different from how (say) Apatosaurus was being restored not too long before then.

But the truth is that lots of animals have flesh envelopes very different from what you might predict based on the skeleton alone. Exhibit A, the inspiration for John’s new piece: the humble hippopotamus. Skeleton:

And life appearance:

It seems more than reasonable that across a clade as diverse, disparate and long-lived as the sauropods, there would have been some that were similarly heavy with flesh. In fact, I think it would be special pleading to argue that there were not.

Which specific sauropods were obese? That is much harder to tell. Hippos can be very heavy with little penalty as they spend much of their time in the water. Perhaps the same was true of some sauropods. If that’s so, then our quest must be for sauropods whose skeletons show adaptations for a semi-aquatic lifestyle, and on that basis Opisthocoelicaudia may have at least two feature supporting this interpretation: very robust limb bones and (if the interpretation of Borsuk-Bialynicka 1977: figure 5 is to be trusted) a transversely broad torso.

References

  • Powell, Jaime E. 2003. Revision of South American Titanosaurid dinosaurs: palaeobiological, palaeobiogeographical and phylogenetic aspects. Records of the Queen Victoria Museum 111:1-94.

 

Long before Matt and others were CT-scanning sauropod vertebrae to understand their internal structure, Werner Janensch was doing it the old-fashioned way. I’ve been going through old photos that I took at the Museum für Naturkunde Berlin back in 2005, and I stumbled across this dorsal centrum:

Dorsal vertebra centum of ?Giraffatitan in ventral view, with anterior to top.

You can see a transverse crack running across it, and sure enough the front and back are actually broken apart. Here there are:

The same dorsal vertebral centrum of ?Giraffatitan, bisected transversely in two halves. Left: anterior half in posterior view; right: posterior half in anterior view. I had to balance the anterior half on my shoe to keep it oriented corrrectly for the photo.

This does a beautiful job of showing the large lateral foramina penetrating into the body of the centrum and ramifying further into the bone, leaving only a thin midline septum.

But students of the classics will recognise this bone immediately as the one that Janensch (1947:abb. 2) illustrated the posterior half of in his big pneumaticity paper:

It’s a very strange feeling, when browsing in a collection, to come across a vertebra that you know from the literature. As I’ve remarked to Matt, it’s a bit like running into, say, Cameron Diaz in the corner shop.

Reference

  • Janensch, W. 1947. Pneumatizitat bei Wirbeln von Sauropoden
    und anderen Saurischien. Palaeontographica, supplement
    7:1-25.

I’ve got a problem. For a paper I’m working on, I need to run a phylogenetic analysis based on that of Mannion et al. (2013) — the Lusotitan paper. The most recent version of that matrix, greatly expanded from the original version, is that of Mannion et al. (2019) — the Jiangshanosaurus paper — so I am working from that matrix.

But what exactly do I do with that Matrix? The analysis protocol is described on pages 12-13 of the PDF:

Several unstable and fragmentary taxa were excluded from the analyses (Astrophocaudia, Australodocus, Brontomerus, Fukuititan, Fusuisaurus, Liubangosaurus, Malarguesaurus, Mongolosaurus). Using equal weighting of characters, this pruned data matrix was analysed using the ‘Stabilize Consensus’ option in the ‘New Technology Search’ in TNT v. 1.5. Searches employed sectorial searches, drift and tree fusing, with the consensus stabilized five times, prior to using the resultant trees as the starting topologies for a ‘Traditional Search’, using Tree Bisection-Reconstruction. We then re-ran the analysis, using the same pruned matrix and protocol, but also applying extended implied weighting in TNT.

There is no problem downloading TNT: it’s freely available thanks to subsidy by the Willi Hennig Society. But the program is tricky to use, and documentation is rather cryptic. You drive TNT with scripts that look like this (short excerpt):

ttags =;
<tag generating commands>
ttags );
tsave *tags.tre;
save * <tree number>;
tsave /;

It seems, for example that = and ) are values that the ttags command accepts. But I’ve not been able to find documentation that spells out such things. (There is a help command, but its output too is cryptic.)

So here is my problem: how do I translate the Mannion et al. (2019) protocol into a TNT script? If anyone can help me with this, I will acknowledge the heck out of them the paper that eventually emerges from this rubble.

(Why not just ask Phil Mannion, you ask? I’ve been talking with Phil and he has been super-helpful: but he’s been using a Windows-only version of TNT in which you don’t write scripts, but invoke various menu options, so he’s not able to help with this directly.)

Thank you!

References

 

As John himsef admits in the tweet that announced this picture, it’s five years late … but I am prepared to forgive that because IT’S NEVER TOO LATE TO BRONTOSMASH!

As always, John’s art is not just scientifically accurate, but evocative. Here’s a close-up of the main action area:

As you see, he has incorporated the keratinous neck spikes that we hypothesized, based on the distinct knobs that are found at the ventrolateral ends of apatosaurine cervical rib loops.

John has also incorporated a lot of blood — which is exactly what you get when elephant seals collide:

By the way, if John’s BRONTOSMASH! art can be said to be five years late — so can the actual paper. It was of course at SVPCA 2015 that we first presented our apatosaur-neck-combat hypothesis (Taylor et al. 2015), and it’s not at all to our credit that nearly five years later, we have not even got a manuscript written. We really need to get our act together on this project, so consider this post my apology on behalf of myself, Matt, Darren and Brian.

Reference

  • Taylor, Michael P., Mathew J. Wedel, Darren Naish and Brian Engh. 2015. Were the necks of Apatosaurus and Brontosaurus adapted for combat?. p. 71 in Mark Young (ed.), Abstracts, 63rd Symposium for Vertebrate Palaeontology and Comparative Anatomy, Southampton. 115 pp. doi:10.7287/peerj.preprints.1347v1

Herons lie, part 2

July 28, 2020

I just stumbled across this tweet from bird photographer Gloria (@Lucent508). Four photos of the same individual, apparently a Green Heron. In this image, I am juxtaposing the third image (left-right flipped and scaled up) with the first image (filled out on the left with a stretched reflection of part of the background).

Where has it put that long neck in the lower image? We know it’s in there somewhere, but one thing is for sure: herons lie!

See also: Herons lie (and so do shoebills), and the whole ongoing Necks Lie sequence.

My thanks to Gloria for having taken the excellent photographs that made this post possible.

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