Saurischian laminae and fossae v2 - Adam Marsh 2015

[Hi folks, Matt here. I’m just popping in to introduce this guest post by Adam Marsh (UT Austin page, LinkedIn, ResearchGate). Adam is a PhD student at UT Austin’s Jackson School of Geosciences, currently working for a semester as a Visiting Student Researcher at my old stomping ground, Berkeley’s UCMP.  Adam’s been working at Petrified Forest National Park in the summers and most of his research is on the Navajo Nation in Arizona. His major interest is in how we perceive extinctions in the fossil record. Specifically, he’s exploring the geochronology of the Glen Canyon Group to look at the biotic response to the end-Triassic mass extinction. He’s also working on an overhaul of the early saurischian dinosaurs of western North America – hence this post. It’s timely because I was just talking in the last post about putting together infographics to spread your ideas; here Adam’s very nice diagram serves as a quick guide and pointer to several papers by Jeff Wilson and colleagues. Many thanks to Sarah Werning for suggesting that Adam and I get acquainted over vertebrae. Update the next day: both the diagram above and the PDF linked below have been updated to fix a couple of typos. Also, there are now black and white versions – see below.]

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If you’re like me, you don’t count sheep when you fall asleep, you count laminae. These struts of bone and their affiliated fossae connect and span between major structural features on vertebral neural arches such as prezygapophyses, postzygapophyses, parapophyses, diapophyses, hyposphenes, hypantra, and the neural spine. Presumably, laminae bracket and fossae house outgrowths of pneumatic diverticula from the respiratory system, which has been covered extensively on this blog in sauropodomorph dinosaurs.

Talking about these complicated structures is cumbersome; they’ve been called buttresses, ridges, struts, etc. throughout descriptive skeletal literature. But what we call things is important, especially when we introduce laminae and other vertebral structures to the rigors of phylogenetic systematics, where homologous apomorphies reign supreme. In order to avoid arguing about whether one structure is called the potato or the tomato, Jeff Wilson and others introduced a strategy of naming vertebral laminae (Wilson, 1999) and the fossae (Wilson et al., 2011) that they surround using the same vertebral landmarks that most tetrapod anatomists agree upon (see the parade of –apophyses above). The process is very simple. Vertebral laminae are named for the two structures that they connect; the prezygodiapophyseal lamina (prdl) connects the prezygapophysis and the diapophysis, so each neural arch will have two prdls. Vertebral fossae are named for the two major laminae that constrain them; the prezygocentrodiapophyseal fossa (prcdf) opens anterolaterally and is delineated dorsally by the prezygodiapophyseal lamina and ventrally by the anterior centrodiapophyseal lamina. Again, each neural arch will have two prcdfs. Those of you who are black belt vertebral anatomists, to borrow a favorite phrase from my advisor, might be interested in serial variation and how these structures change up and down the vertebral column. Until I get my act together and publish some cool new saurischian data, I will refer you to Wilson (2012). [We’ve also touched on serial variation in laminae in this post and this one. – MJW]

Saurischian laminae and fossae v2 bw - Adam Marsh 2015

Same thing in black and white, with labels

 

You might have noticed that the names are a mouthful and take up their fair share of typed characters. In my research of early saurischian dinosaurs, I’ve run across quite a few of these laminae everywhere from herrerasaurids to sauropodomorphs to coelophysoids to Dilophosaurus. Even though I’ve drawn, photographed, and written about various laminae and fossae, I still need to remind myself of what goes where and what it’s called. Believe me, vertebral lamina nomenclature does not lend itself well to Dem Bones covers. As a result, I’ve put together a reference figure that might be useful for those of you who are dealing with this or even teaching it to students. At the very least, you can put it on the ceiling above your bed so that it’s the first thing you see when you open your eyes in the morning.

Four main vertebral laminae are present plesiomorphically in archosaurs: the anterior and posterior centrodiapophyseal laminae, the prezygodiapophyseal lamina, and the postzygodiapophyseal lamina. This means that the prezygocentrodiapophyseal, postzygocentrodiapophyseal, and centrodiapophyseal fossae are present, and sometimes the top of the transverse process is concave between the neural spine and the zygapophyses to form the spinodiapophyseal fossa. I know that a certain sister group of Sauropodomorpha can get disparaged around these parts, but the truth is that theropods build long necks, too, and sometimes in very different ways than sauropodomorphs. When you are writing about the various vertebral buttresses and chonoses, don’t get frustrated with the names, because Wilson and his colleagues have actually made it much easier for us to talk to one another about presumably homologous structures without needing an additional degree in civil engineering.

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Here’s the figure again in PDF form: Marsh, Adam 2015 saurischian laminae and fossae diagram v2

And in black and white for those who prefer it that way: Marsh, Adam 2015 saurischian laminae and fossae diagram v2 bw

References

A couple of weeks ago, Mike sent me a link to this interview with ecologist James O’Hanlon, who made this poster (borrowed from this post on O’Hanlon’s blog):

O'Hanlon et al isbeposter

We had a short email exchange which quickly converged on, “This would work well for some projects, but not for others.” That’s the same conclusion I came to in my recent review of my own paper titles: I am increasingly enamored of titles that are full sentences, because then if all someone reads is your title, they still know what you found. But not every paper can be summarized so neatly.

Beginning a tight little internet eddy that will be complete at the end of this post, Andy Farke posted my paper title review post on Facebook and it fired some discussion in the comments. Victoria Arbour wrote, “I’m trying to move more towards ‘sentence’ titles, but it’s difficult to come up with something that’s concise, accurate and nuanced sometimes!” I responded, “Totally agreed. There’s no one size fits all solution. I have no idea how John Foster and I could have turned the Snowmass Haplocanthosaurus title into a sentence that wouldn’t have been a disaster. ‘Concise, accurate, and nuanced’ are all good goals, but they pull in different directions.”

But it got me thinking about the different ways that we can craft our results for effective delivery. The default package is long-form: the paper. Not just long, but narrowly targeted: just about every sub-sub-subfield has a core of diehards who will read your paper because it’s right in their wheelhouse and they basically have to, to stay caught up. You were going to reach them anyway. The real question – the question that, iterated over all of your papers, will decide the shape of your career – is who else are you going to reach? The answer is going to depend a lot on serendipity, but you can improve your chances by building something easily digestible – scattering the seeds of your results over as many brains as possible, to increase the number of successful germinations (which in this metaphor could be anything from citations to one-off collaborations to life-long friendships). Here’s what I have so far.

Four ways to efficiently package your results

I almost wrote, “four ways to weaponize and aerosolize your science”. You’re trying to infect people with your ideas. Here are some potential delivery mechanisms.

First, and already mentioned: a good title. Not “Aspects of the history, anatomy, taxonomy and palaeobiology of good heavens I have lost feeling in my extremities” but, whenever possible, something that either tells people what you found (the sentence title) or at least indicates that you found something interesting (the question title, some ‘hook’ titles – “Why giraffes have short necks”). See these three posts for more.

Wedel and Taylor 2013 bifurcation Figure 9 - bifurcatogram

Congratulations, now you’ve read Wedel and Taylor 2013a (to a first approximation). What are you going to do with all the time we just saved you?

Second, a summary figure. Discussed here. Nice because once people have seen that figure, they basically have your results in one convenient, portable, easily-digestible package. Downside: figures are usually entombed in papers, so this doesn’t count as an outreach maneuver unless you let the figure out into the wild some other way. Blog it, put it on Facebook, do something with it so that it functions as a funnel, catching people and pointing them toward your work.

Third, a punchy poster, like O’Hanlon’s. This has a similar caveat as the summary figure: if the only place people can see it is in its native environment (the paper, the scientific meeting), it’s still only preaching to the converted. Get it out where other people can see it. Second caveat: if the poster doesn’t point to something outside of itself, it doesn’t really count as outreach material. The best part of O’Hanlon’s poster is the QR code. If anyone is unhappy with how brief the poster is, they can follow the link and go down the rabbit hole. The depth of the engagement is in the user’s hands. Corollary: if your poster doesn’t have a QR code or a (tiny)URL, it’s a dead end. Why not make it into a gateway? It’s not a question of either/or, it’s an opportunity for yes/and.

ankylosaur heads by Victoria Arbour

Fourth, an infographic, like this one Victoria Arbour made to summarize some of the results from her big 2013 paper on Alberta ankylosaurs (borrowed from here). I thought it was ingenious when I first saw it (on Facebook), and I still do. You know why? Because I know jack about ankylosaurs, but this thing makes them seem both cool and tractable. Victoria is conveying, “There is structure here, and it makes sense. Let me guide you through it.” I instantly wanted something like this for every group of dinosaurs. You know who will appreciate you building something like this? Every other person besides the half-dozen grognards who work on the exact same thing you do (and maybe them, too). Gratitude leads to citations – people will go out of their way to cite your work just because they want other people to know about it.

Conclusions: give people a destination, give them choices, give them something

Three final points about all of this. First, none of these things work if there’s nowhere for interested parties to go, or nothing for them to find when they get there. If there’s a paper already, it had better justify the interest that made people look at it. Don’t let your catchy title be like the trailer for that movie that was 2 minutes of awesome and 1:58 of zzzzzzz. If there’s no paper yet, what are you pointing people to – a blog, a research website, a PeerJ preprint, some files on FigShare, a YouTube video, your open notebook, what? Give them somewhere to go. Immediate implication: if there’s nowhere else for interested people to go, why are you presenting now? Again: don’t build dead-ends, build gateways.

Next, if you think that crafting a second, tighter package strictly for the purposes of promotion is a bit gauche, here’s another perspective: you’re giving people more choices about how to engage with your work. A paper alone presents a very limited set of options. Read me (or skim me, or look at my figures), or don’t. Some people don’t have the activation energy that requires, and by ‘some people’ I mean everyone outside of your little niche. Most of them will never know that your work even exists. Craft something that will reach those people and give them an easy way in. Even for those closer to home, it may still make their lives easier. Have I actually read Arbour and Currie (2013)? No, but I looked at the pretty figures, because I saw the infographic on Facebook. So when I do need to know something about ankylosaurs (hey, stranger things have happened), I know where to turn – and who to cite. I, the user, have options. Give your users more options, and you may find that you get more users.

Third, it pays to stop and think about how people who aren’t in your narrow sub-sub-subfield are going to find out about your work. Do you have a blog? A Facebook account? Active on a mailing list or a forum? As long as that figure or poster or infographic sits in its native habitat, it’s only reaching the converted. Put it on your blog or on Facebook, now it’s something else, carrying your ideas out into the world: a missive, a missile, a missionary – all from the Latin mittere, ‘to send’. You’re already doing the work. Package it, neatly and tightly, and send it.

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Many thanks to Victoria Arbour for permission to post her diagram, and for her patience over the 23 months that it has taken me to get around to doing so. You really should go check out Arbour and Currie (2013) – the figures are stunning – and Victoria’s extensive and entertaining series of blog posts that followed. That rabbit hole starts here.

References

 

Brontosaurus, the animal formerly known as Apatosaurus, the animal formerly known as Brontosaurus.

YPM 1980: Brontosaurus excelsus, the animal formerly known as Apatosaurus excelsus, the animal formerly known as Brontosaurus excelsus.

Today is a good day for sauropod science. Since we’re not getting this up until the afternoon, you’ve probably already seen that Emanuel Tschopp and colleagues have published a monstrous specimen-level phylogenetic analysis of Diplodocidae and, among other things, resurrected Brontosaurus as a valid genus. The paper is in PeerJ so you can read it for free (here).

I’ve already been pinged by lots of folks asking for my thoughts on this. I know that the return of Brontosaurus is what’s going to catapult this paper into the spotlight, but I hope what everyone takes away from it is just what a thorough piece of work it is. I’ve never seen so many phylogenetic characters illustrated so well. It sets a new standard, and anyone who wants to overturn this had better roll up their sleeves and bring a boatload of data. I’m also very, very happy that it’s open-access so everyone in the world can see it, use it, question it, tear it apart or build on it. Getting Brontosaurus back is just gravy. Although, being pro-brontosaur enough to have named a dinosaur in honor of Brontosaurus, I’m also pretty happy about that. If you need a quick guide to who’s who now, A. ajax and A. louisae are still Apatosaurus, and B. excelsus, B. yahnahpin (formerly Eobrontosaurus), and B. parvus (originally Elosaurus) are all Brontosaurus. For more details, go read the paper.

A louisae from Wikipedia - full

Apatosaurus lousiae CM 3018: still Apatosaurus. Photo from Wikipedia.

My personal feelings aside, a lot of people are asking how solid is this generic re-separation. I haven’t read the entire paper yet – it’s 299 pages long, for crying out loud – but the separation of Brontosaurus and Apatosaurus seems solid enough. Tschopp et al. didn’t do it lightly, they justify their decision in detail. I don’t hold with the idea that just because two taxa are sisters, means that they cannot be separated generically. As usual in phylogenetic taxonomy, it comes down to what we decide as a community constitutes “diagnosably distinct”. Tschopp et al. have actually put some thought into what that might mean here, and whether you agree with them or not, they’ve at least made all of their evidence and reasoning explicit. That’s both an opportunity and a challenge for critics: an opportunity to pin down exactly where and why you may disagree, and a challenge to do exactly that. You can’t just sit back and say, “I think the analysis is flawed” or “I wouldn’t have coded that character that way” (well, you can, but if that’s all you say, no-one is obliged to take that kind of lazy, drive-by criticism seriously). There are 477 characters here, most of them illustrated, for 81 OTUs, and a lot of post-hoc discussion of the results. So whether you agree with the authors or not, in whole or in part, both fans and critics should dig in and build on this work. Is it the last word on diplodocid taxonomy? Of course not. But it does move the field forward significantly, and the Tschopp et al. should be applauded for that.

There’s a lot more in there than just bringing back Brontosaurus. “Diplodocus” hayi is elevated to its own genus, Galeamopus. Neither of those things are super surprising. There have been rumors since the 90s at least that Brontosaurus might be coming back, and everyone has known for a while that D. hayi was a bit wonky. I was also not surprised to see Australodocus returned to Diplodocidae – when I saw the type material in 2011, it looked diplodocid to me (based on some characters I’ll have to unpack in some other post). More surprising to me are the sinking of Dinheirosaurus into Supersaurus, the finding that Tornieria is not particularly close to Diplodocus, and the uncertain positions of AMNH 460, the American Museum mount, which is an indeterminate apatosaurine pending further study, of FMNH 25112, the Field Museum “Apatosaurus”, which might not even be an apatosaurine at all(!). In several cases, Tschopp et al. come right out and say that X is going to need further study, so if you want to work on sauropods and you’re stuck for project ideas, go see what needs doing.

AMNH mounted Apatosaurus with Taylor for scale

AMNH 460: we don’t know who this is anymore.

As I was scanning the paper again while composing the last paragraph, I almost fell down the rabbit hole. So much interesting stuff in this paper. Even if all you care about is morphology, the hundred or so figures illustrating the phylogenetic characters ought to keep you happy for a very long time. I look forward to reading through the vertebral characters in detail and seeing what I’ve been missing all these years.

I’m contractually obliged to point out that the authors chose to publish the complete peer-review history of the paper, so you can see what the editor (Andy Farke) and reviewers had to say. As always, I think this transparency (and credit for the reviewers) is great for science, and I can’t wait until it’s the norm at more journals.

FMNH 25112 formerly Apatosaurus

FMNH 25112: what even IS that thing?

In addition to the paper, there’s also an interview with lead author Emanuel Tschopp on the PeerJ blog, and a nice shout-out for SV-POW!

Parting shot: why did Tschopp et al. get different results than anyone had previously? Because they used more specimens and more taxa – more data full stop. That’s also why their paper warrants serious consideration. It’s serious work. Let’s go stand on their shoulders.

Reference

Tschopp E, Mateus O, Benson RBJ. (2015) A specimen-level phylogenetic analysis and taxonomic revision of Diplodocidae (Dinosauria, Sauropoda) PeerJ 3:e857 https://dx.doi.org/10.7717/peerj.857

This abomination — a proposal for a “UK National Licence” for open-access papers, making them available only in the UK, is not an April Fool joke. It’s a serious proposal, put forward by HEPI, the Higher Education Policy Institute, which styles itself “the UK’s only independent think tank devoted to higher education” (though I note without comment that they routinely partner with Elsevier).

It’s desperately disappointing that British academics should propose something as small-minded and xenophobic as this, which I can only refer to as the UKIP Licence.  Let’s start counting some of the ways this is a terrible, terrible idea.

1. It’s not open access by any existing definition of the term. For example, the Budapest Open Access Initiative, which first coined the term, describes OA as “free availability on the public internet” (i.e. not a subnet), “permitting any users” (i.e. not just British users) “without financial, legal, or technical barriers” (i.e. no filtering on IP addresses).

2. It positions the UK as the one country in the world willing to poison the open-access well, prepared to destroy value for 199 countries in the hope of increasing it for one. This makes it a classic prisoner’s-dilemma “defect” strategy — an approach which has been shown by multi-algorithm tournaments to reliably downgrade the defector’s outcome.

3. British people gain more when 200 countries are working on advances in health, education, etc., than when only one is. This tiny-minded licence, if adopted, would hobble British innovation, health and education, as well as that of the rest of the world.

4. Most important, it’s mean. We have to be better than this. Publishing research about diseases that kill millions in third-world countries, then preventing scientists in those countries from reading that research is not just stupid, it’s despicable. It’s hard to imagine behaviour more unrepresentative of the values that we like to imagine the UK embodies.

Oh, and 5. it won’t work, of course. Barring access by IP address is a notoriously flawed approach, which hides content from Brits abroad while allowing access to anyone anywhere who knows how to use a Web proxy.

Putting it all together, this is about the most misguided proposal imaginable. I would like to see its authors, both of them senior at UCL, withdraw it with all possible haste, and with an appropriate apology.

[I would have left this comment on HEPI’s blog-post announcing their proposal,  but comments are turned off — perhaps not surprisingly. I did leave a version of it on the Times Higher Education article about this.]

Update the next day: see also David Kernohan’s post A local licence for Henbury.

Update 9th April: this post, lightly modified, is published as a letter in today’s Times Higher Education. More importantly, you should all go and read Stephen Curry’s much more dispassionate, but equally critical, analysis of the National Licence proposal.

There’s been some concern over Scientific Reports‘ new scheme whereby authors submitting manuscripts can pay $750 to have them peer-reviewed more quickly. Some members of the editorial board have quit over this development, feeling that it’s unfair to authors who can’t pay. Myself, I feel it at least shows admirable audacity — NPG has found a way to monetise its own lethargy, which is surely what capitalism is all about.

The real problem with this scheme is that $750 is an awful lot to gamble, as a sort of “pre-APC”, at a point when you don’t know whether your article is actually going to be published or not. If the peer-review returns an unfavourable verdict it’s just money down the drain.

So I welcome today’s announcement that, for only a slightly higher payment of a round $1000, it’s now possible to bypass peer-review completely, and move directly to publication. This seems like a much fairer deal for authors, and of course it streamlines the publication process yet further. Now authors can obtain the prestigious Nature Publishing Group imprint in a matter of a couple of days.

Onward and upward!