In a move that will surprise no-one who’s been paying attention, my and Matt’s presentation of vertebral orientation at the 1st Palaeo Virtual Congress is now up as a PeerJ preprint. Sadly, with the end of the conference period on 15th December, the page for my talk has been deleted, along with some interesting comments. But here at SV-POW!, we have no truck with ephemerality, hence this more permanent manifestation of our work.

Matt’s preprint consists of the abstract, and has the slide deck as a supplementary data file. That’s what he submitted to the conference, with attendees invited to page through it. By contrast, I recorded a video of my talk. I am trying to get that attached to my preprint, but as things stand it’s not there because it’s too big (at 65 Mb).

Meanwhile — and indeed in perpetuity — you can just watch it on YouTube, where I also uploaded it. In the end, that may be a more practical way of making video available anyway, but I do want the preservational benefit of lodging it with a preprint.

Remember, we’re working on the paper in the open. We’d love to get input from you all, and especially from anyone who’s run into this problem before with other taxa. Please, if you have fifteen minutes spare, watch the talk and leave any comments you have: here, on the preprint, on the YouTube page, or as issues in the GitHub tracker!

Reference

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If you were curious about the Wedel et al. presentation on the Snowmass Haplocanthosaurus at the 1st Palaeo Virtual Congress but didn’t attend the event, it is now preserved for posterity and freely available to the world as a PeerJ Preprint (as promised). Here’s the link.

I’ll have much more to say about this going forward, but for now here are slides 20 and 21 on the intervertebral joint spaces. This is obviously just the same vert cloned three times and articulated with itself. With the digital rearticulation of the reconstructed and retrodeformed caudal series still in progress, we cloned caudal 3, the only vertebra that preserves both sets of zygapophyses, to get a rough estimate of the sizes and shapes of the soft tissues that filled the intervertebral spaces and neural canal.

The reconstructed intervertebral discs (in blue) are very crude and diagrammatic. The reason I’m putting these particular slides up is to get the cited references out in the open on the blog, to start correcting the misapprehension that all non-mammalian amniotes have exclusively synovial intervertebral joints (see the discussion in the comments on this post). In the list below I’m including Banerji (1957), which is not cited in the presentation but which I did cite in that comment thread; it’s an important source and at least for now it is a free download. These refs are just the tip of a very big iceberg. One of my goals for 2019 is to do a series of posts reviewing the extensive literature on amphiarthrodial (fibrocartilaginous) intervertebral joints in living lepidosaurs and birds. Stay tuned!

And please go have a look at the presentation if you are at all interested or curious. As we said in the next to last slide, “this research is ongoing, and we welcome your input. If there are facts or hypotheses we haven’t considered but should, please let us know!”

References

This was an interesting exercise. It was my first time generating a poster to be delivered at a conference since 2006. Scientific communication has evolved a lot in the intervening decade, which spans a full half of my research career to date. So I had a chance to take the principles that I say that I admire and try to put them into practice.

It helped that I wasn’t working alone. Jann and Brian both provided strong, simple images to help tell the story, and Mike and I were batting ideas back and forth, deciding on what we could safely leave out of our posters. Abstracts were the first to go, literature cited and acknowledgments were next. We both had the ambition of cutting the text down to just figure captions. Mike nailed that goal, but my poster ended up being slightly more narrative. I’m cool with that – it’s hardly text-heavy, especially compared with most of my efforts from back when. Check out the text-zilla I presented at SVP back in 2006, which is available on FigShare here. I am happier to see, looking back, that I’d done an almost purely image-and-caption poster, with no abstract and no lit cited, as early as 1999, with Kent Sanders as coauthor and primary art-generator – that one is also on FigShare.

I took 8.5×11 color printouts of both my poster and Mike’s, and we ended up passing out most of them to people as we had conversations about our work. That turned out to be extremely useful – I had a 30-minute conversation about my poster at a coffee break the day before the posters even went up, precisely because I had a copy of it to hand to someone else. Like Mike, I found that presenting a poster resulted in more and better conversations than giving a talk. And it was the most personally relaxing SVPCA I’ve ever been to, because I wasn’t staying up late every night finishing or practicing my talk.

I have a lot of stuff to say about the conference, the field trip, the citability of abstracts and posters (TL;DR: I’m for it), and so on, but unfortunately no time right now. I’m just popping in to get this posted while it’s still fresh. Like Mike’s poster, this one is now published alongside my team’s abstract on PeerJ PrePrints.

I will hopefully have much more to say about the content in the future. This is a project that Jann, Brian, and I first dreamed up over a decade ago, when we were grad students at Berkeley. Mike provided the impetus for us to get it moving again, and kindly stepped aside when I basically hijacked his related but somewhat different take on ontogeny and serial homology. When my fall teaching is over, I’m hoping that the four of us can take all of this, along with additional examples found by Mike that didn’t make it into this presentation, and shape it into a manuscript. I’ll keep you posted on that. In the meantime, the comment field is open. For some related, previously-published posts, see this one for the baby sauropod verts, this one for CM 555, and this one for Plateosaurus.

Flying over Baffin Island on the way home.

And finally, since I didn’t put them into the poster itself, below are the full bibliographic references. Although we didn’t mention it in the poster, the shell apex theory for inferring the larval habits of snails was first articulated by G. Thorson in 1950, which is referenced in full here.

Literature Cited

If you don’t get to give a talk at a meeting, you get bumped down to a poster. That’s what’s happened to Matt, Darren and me at this year’s SVPCA, which is coming up next week. My poster is about a weird specimen that Matt and I have been informally calling “Biconcavoposeidon” (which I remind you is not a formal taxonomic name).

Here it is, for those of you who won’t be at the meeting (or who just want a preview):

But wait — there’s more. The poster is now also formally published (Taylor and Wedel 2017) as part of the PeerJ preprint containing the conference abstract. It has a DOI and everything. I’m happy enough about it that I’m now citing it in my CV.

Do scientific posters usually get published? Well, no. But why not? I can’t offhand think of a single example of a published poster, though there must be some out there. They are, after all, legitimate research artifacts, and typically contain more information than published abstracts. So I’m happy to violate that norm.

Folks: it’s 2017. Publish your posters.

References

  • Taylor, Michael P., and Mathew J. Wedel. 2017. A unique Morrison-Formation sauropod specimen with biconcave dorsal vertebrae. p. 78 in: Abstract Volume: The 65th Symposium on Vertebrate Palaeontology and Comparative Anatomy & The 26th Symposium on Palaeontological Preparation and Conservation. University of Birmingham: 12th–15th September 2017. 79 pp. PeerJ preprint 3144v2. doi:10.7287/peerj.preprints.3144v2/supp-1

“Biconcavoposeidon”

August 15, 2017

Here is a fascinating sequence of five consecutive posterior dorsal vertebra — AMNH FARB 291 from the”Big Bone Room” at the AMNH:

AMNH FARB 291, five consecutive posterior dorsal vertebrae of a probably brachiosaurid sauropod, in right lateral view. The vertebrae are embedded in a plaster block, which has been desaturated in this image.

Matt and I first saw this specimen back in February 2009, when we were mostly there to look at Apatosarusminimus (and then again in 2012). As soon as our eyes lit on it, we couldn’t help but be captivated by its bizarre biconcave centra. We immediately started flippantly referring to it as “Biconcavoposeidon” — the ugliest name we could come up with — and in our subsequent discussions the name has stuck (often abbreviated to “BCP”).

  • Taxonomic note: for avoidance of doubt, “Biconcavoposeidon” is not and will never be a formal taxonomic name, only an informal specimen nickname. If at some future point we conclude that this specimen represents a new taxon, and name it, we will definitely not use the name “Biconcavoposeidon”. If you ever use the name, please do not set it in italics.

As you can see in this front view, the specimen is sheared: the upper part of the vertebrae have been displaced to their left (which is the right as we see it in this image):

AMNH FARB 291, most anterior of five consecutive posterior dorsal vertebrae of a probably brachiosaurid sauropod, in anterior view.

Apart from the shearing, though, and the truncation of the neural spines shortly above the transverse processes, the specimen is in pretty good nick. Crucially, it’s not been “restored” in plaster to conceal what is and is not real bone — unlike many specimens of that era. It came out of the Bone Cabin quarry in 1898, back when scientific information was routinely discarded in order to obtain a more beautiful-looking specimen.

This is the specimen that I’ll be presenting at SVPCA this year — though only as a poster, unfortunately: there’s no talk for me, Matt or Darren this year. We’ve posted our abstract (including the illustration above) to the nascent PeerJ collection for SVPCA 2017, and we’re looking forward to seeing more of the materials from that conference — abstracts, then manuscripts, then papers — appearing in the collection.

So far as we know, there’s no other sauropod specimen with biconcave posterior dorsal vertebrae. (And, no, Amphicoelias is not an exception, despite its name.) But have we missed any?

Long-time SV-POW! readers will remember that three years ago, full of enthusiasm after speaking about Barosaurus at the Edinburgh SVPCA, Matt and I got that talk written up in double-quick time and had it published as a PeerJ Preprint in less than three weeks. Very quickly, the preprint attracted substantive, helpful reviews: three within the first 24 hours, and several more in the next few days.

This was great: it gave us the opportunity to handle those review comments and get the manuscript turned around into an already-reviewed formal journal submission in less then a month from the original talk.

So of course what we did instead was: nothing. For three years.

I can’t excuse that. I can’t even explain it. It’s not as though we’ve spent those three years churning out a torrent of other awesome papers. We’ve both just been … a bit lame.

Anyway, here’s a story that will be hauntingly familiar. A month ago, full of enthusiasm after speaking about Barosaurus at the Liverpool SVPCA, Matt and I found ourselves keen to write up that talk in double-quick time. It’s an exciting tale of new specimens, reinterpretation of an important old specimen, and a neck eight times as long as that 0f a world-record giraffe.

But it would be crazy to write the new Barosaurus paper without first having dealt with the old Barosaurus paper. So now, finally, three years on, we’ve done that. Version 2 of the preprint is now available (Taylor and Wedel 2016), incorporating all the fine suggestions of the people who reviewed the first version — and with a slightly spiffed-up title. What’s more, the new version has also been submitted for formal peer-review. (In retrospect, I can’t think why we didn’t do that when we put the first preprint up.)

Taylor and Wedel 2016: Figure 3. Barosaurus lentus holotype YPM 429, vertebra R, C?15. Top row: dorsal view; middle row, left to right: posterior, right lateral and anterior views; bottom row: ventral view, from Lull (1919: plate II). Note the apparently very low, undivided neural spine at the intersection of the PRSLs and POSLs, forward-shifted neural arch, broad prezygapophyses, broad, wing-like prezygadiapophyseal laminae, and great width across the diapophyses and across the parapophyses. Abbreviations: dia, diapophysis; para, parapophysis; prz, prezygapophysis; prdl, prezygadiapophyseal lamina; spol, spinopostzygapophyseal lamina; sprl, spinoprezygapophyseal lamina. Scale bar = 500 mm.

Taylor and Wedel 2016: Figure 3. Barosaurus lentus holotype YPM 429, vertebra R, C?15. Top row: dorsal view; middle row: posterior, right lateral and anterior views; bottom row: ventral view, from Lull (1919: plate II). Note the apparently very low, undivided neural spine at the intersection of the SPRLs and SPOLs, forward-shifted neural arch, broad prezygapophyses, broad, wing-like prezygadiapophyseal laminae, and great width across the diapophyses and across the parapophyses. Abbreviations: dia, diapophysis; para, parapophysis; prz, prezygapophysis; prdl, prezygadiapophyseal lamina; spol, spinopostzygapophyseal lamina; sprl, spinoprezygapophyseal lamina. Scale bar = 500 mm.

A big part of the purpose of this post is to thank Emanuel Tschopp, Mark Robinson, Andy Farke, John Foster and Mickey Mortimer for their reviews back in 2013. I know it’s overdue, but they are at least all acknowledged in the new version of the manuscript.

Now we cross our fingers, and hope that the formally solicited reviews for the new version of the manuscript are as helpful and constructive as the reviews in that first round. Once those reviews are in, we should be able to move quickly and painlessly to a formally published version of this paper. (I know, I know — I shouldn’t offer such a hostage to fortune.)

Meanwhile, I will finally be working on handling the reviews of this other PeerJ submission, which I received back in October last year. Yes, I have been lax; but I am back in the saddle now.

References

  • Taylor, Michael P., and Mathew J. Wedel. 2016. The neck of Barosaurus: longer, wider and weirder than those of Diplodocus and other diplodocines. PeerJ PrePrints 1:e67v2 doi:10.7287/peerj.preprints.67v2

As a long-standing proponent of preprints, it bothers me that of all PeerJ’s preprints, by far the one that has had the most attention is Terrell et al. (2016)’s Gender bias in open source: Pull request acceptance of women versus men. Not helped by a misleading abstract, we’ve been getting headlines like these:

But in fact, as Kate Jeffrey points out in a comment on the preprint (emphasis added):

The study is nice but the data presentation, interpretation and discussion are very misleading. The introduction primes a clear expectation that women will be discriminated against while the data of course show the opposite. After a very large amount of data trawling, guided by a clear bias, you found a very small effect when the subjects were divided in two (insiders vs outsiders) and then in two again (gendered vs non-gendered). These manipulations (which some might call “p-hacking”) were not statistically compensated for. Furthermore, you present the fall in acceptance for women who are identified by gender, but don’t note that men who were identified also had a lower acceptance rate. In fact, the difference between men and women, which you have visually amplified by starting your y-axis at 60% (an egregious practice) is minuscule. The prominence given to this non-effect in the abstract, and the way this imposes an interpretation on the “gender bias” in your title, is therefore unwarranted.

And James Best, in another comment, explains:

Your most statistically significant results seem to be that […] reporting gender has a large negative effect on acceptance for all outsiders, male and female. These two main results should be in the abstract. In your abstract you really should not be making strong claims about this paper showing bias against women because it doesn’t. For the inside group it looks like the bias moderately favours women. For the outside group the biggest effect is the drop for both genders. You should hence be stating that it is difficult to understand the implications for bias in the outside group because it appears the main bias is against people with any gender vs people who are gender neutral.

Here is the key graph from the paper:

TerrellEtAl2016-fig5(The legends within the figure are tiny: on the Y-axes, they both read “acceptance rate”; and along the X-axis, from left to right, they read “Gender-Neutral”, “Gendered” and then again “Gender-Neutral”, “Gendered”.)

So James Best’s analysis is correct: the real finding of the study is a truly bizarre one, that disclosing your gender whatever that gender is reduces the chance of code being accepted. For “insiders” (members of the project team), the effect is slightly stronger for men; for “outsiders” it is rather stronger for women. (Note by the way that all the differences are much less than they appear, because the Y-axis runs from 60% to 90%, not 0% to 100%.)

Why didn’t the authors report this truly fascinating finding in their abstract? It’s difficult to know, but it’s hard not to at least wonder whether they felt that the story they told would get more attention than their actual findings — a feeling that has certainly been confirmed by sensationalist stories like Sexism is rampant among programmers on GitHub, researchers find (Yahoo Finance).

I can’t help but think of Alan Sokal’s conclusion on why his obviously fake paper in the physics of gender studies was accepted by Social Text:it flattered the editors’ ideological preconceptions“. It saddens me to think that there are people out there who actively want to believe that women are discriminated against, even in areas where the data says they are not. Folks, let’s not invent bad news.

Would this study have been published in its present form?

This is the big question. As noted, I am a big fan of preprints. But I think that the misleading reporting in the gender-bias paper would not make it through peer-review — as the many critical comments on the preprint certainly suggest. Had this paper taken a conventional route to publication, with pre-publication review, then I doubt we would now be seeing the present sequence of misleading headlines in respected venues, and the flood of gleeful “see-I-told-you” tweets.

(And what do those headlines and tweets achieve? One thing I am quite sure they will not do is encourage more women to start coding and contributing to open-source projects. Quite the opposite: any women taking these headlines at face value will surely be discouraged.)

So in this case, I think the fact that the study in its present form appeared on such an official-looking venue as PeerJ Preprints has contributed to the avalanche of unfortunate reporting. I don’t quite know what to do with that observation.

What’s for sure is that no-one comes out of this as winners: not GitHub, whose reputation has been wrongly slandered; not the authors, whose reporting has been shown to be misleading; not the media outlets who have leapt uncritically on a sensational story; not the tweeters who have spread alarm and despondancy; not PeerJ Preprints, which has unwittingly lent a veneer of authority to this car-crash. And most of all, not the women who will now be discouraged from contributing to open-source projects.