Figure 3. BIBE 45854, articulated series of nine mid and posterior cervical vertebrae of a large, osteologically mature Alamosaurus sanjuanensis. Series is estimated to represent the sixth to fourteenth cervical vertebrae. A, composite photo-mosaic of the cervical series in right lateral view; identification of each vertebra indicated by C6 to C14, respectively. B, line drawing based on the photo-mosaic in A. C, line drawing in B with labels shown and vertebral fossae indicated by solid grey fill; cross-hatching represents broken bone surfaces and reconstructive material. Abbreviations: C, cervical vertebra; cdf, centrodiapophyseal fossa; clf, centrum lateral fossa; pocdf, postzygapophyseal centrodiapophyseal fossa; prcdf, prezygapophyseal centrodiapophyseal fossa; prcdf1, dorsal prezygapophyseal centrodiapophyseal fossa; prcdf2, ventral prezygapophyseal centrodiapophyseal fossa; sdf, spinodiapophyseal fossa; spof, spinopostzygapophyseal fossa; sprf, spinoprezygapophyseal fossa. (Tykoski and Fiorillo 2016)

Have you been reading Justin Tweet’s series, “Your Friends the Titanosaurs“, at his awesomely-named blog, Equatorial Minnesota? If not, get on it. He’s been running the series since June, 2018, so this notice is only somewhat grotesquely overdue. The latest installment, on Alamosaurus from Texas and Mexico, is phenomenal. I have never seen another summary or review that pulled together so much of the relevant literature and explained it all so well. Seriously, that blog post deserves to be a review paper; it could be submitted pretty much as-is, although it would be even better with his two other Alamosaurus posts integrated (this one, and this one). It’s great work, is what I’m saying, and it needs to be acknowledged.

In particular, I was struck by the note by Anonymous in 1941 on the discovery of a cervical vertebra 1.2 meters long. I’d never heard of that ref, and I’ve never seen that vert, but at 120cm it would be in the top 7 longest cervical vertebrae on the planet (see the latest version of the list in this post), narrowly beating out the 118-cm cervical of Puertasaurus. In fairness, the preserved cervical of Puertasaurus is probably a posterior one, and more anterior cervicals might have been longer. Then again, in the big Alamosaurus neck the longest verts are pretty darned posterior, so…we need more Puertasaurus.

EDIT a few hours later: Thanks to the kind offices of Justin Tweet, I’ve now seen Anonymous (1941), and the exact wording is, “A single vertebra, or neck joint bone, is three feet across, only two inches less than four feet long, and in its present fossilized state weighs 600 pounds.” ‘Two inches less than four feet long’ is 46 inches or a hair under 117cm, which puts the supposed giant cervical just behind Puertasaurus after all, but still firmly in the top 10. And depending on how one interprets the passage in Anonymous (1941), it might not have been any bigger than BIBE 45854–see this comment for details.

Big cervical showdown. From the top left: BYU 9024, originally referred to Supersaurus but more likely representing a giant Barosaurus (137cm); the single available cervical of Puertasaurus (118cm); a world-record giraffe neck (2.4m); Alamosaurus referred cervical series BIBE 45854, longest centra are ~81cm; Sauroposeidon holotype OMNH 53062, longest centrum is 125cm. This image makes it very clear that whatever Sauroposeidon was doing, it was a way different thing from Alamosaurus.

Crucially, the longest vertebrae in the BIBE 45854 series are about 80 or 81 cm long, which means that a 1.2-meter cervical would be half again as large. That is a pretty staggering thought, and that individual of Alamosaurus–assuming it was the same taxon as BIBE 45854, and not some other, longer-necked critter–would definitely be a contender for the largest sauropod of all time.

Illustrations here are of the big Alamosaurus cervical series from Big Bend, which was comprehensively described by Ron Tykoski and Tony Fiorillo in 2016, and which we have covered in these previous posts:

References

  • Anonymous. 1941. Find dinosaur neck bone nearly four feet long. The Science News-Letter 39(1):6–7.
  • Tykoski, R.S. and Fiorillo, A.R. 2016. An articulated cervical series of Alamosaurus sanjuanensis Gilmore, 1922 (Dinosauria, Sauropoda) from Texas: new perspective on the relationships of North America’s last giant sauropod. Journal of Systematic Palaeontology 15(5):339-364.

Picture is unrelated. Seriously. I’m just allergic to posts with no visuals. Stand by for more random brachiosaurs.

Here’s something I’ve been meaning to post for a while, about my changing ideas about scholarly publishing. On one hand, it’s hard to believe now that the Academic Spring was almost a decade ago. On the other, it’s hard for me to accept that PeerJ will be only 8 years old next week–it has loomed so large in my thinking that it feels like it has been around much longer. The very first PeerJ Preprints went up on April 4, 2013, just about a month and a half after the first papers in PeerJ. At that time it felt like things were moving very quickly, and that the landscape of scholarly publishing might be totally different in just a few years. Looking back now, it’s disappointing how little has changed. Oh, sure, there are more OA options now — even more kinds of OA options, and things like PCI Paleo and Qeios feel genuinely envelope-pushing — but the big barrier-based publishers are still dug in like ticks, and very few journals have fled from those publishers to re-establish themselves elsewhere. APCs are ubiquitous now, and mostly unjustified and ruinously expensive. Honestly, the biggest changes in my practice are that I use preprint servers to make my conference talks available, and I use SciHub instead of interlibrary loan.

But I didn’t sit down to write this post so I could grumble about the system like an old hippie. I’ve learned some things in the past few years, about what actually works in scholarly publishing (at least for me), and about my preferences in some areas, which turn out to be not what I expected. I’ll focus on just two areas today, peer review, and preprints.

How I Stopped Worrying and Learned to Love Peer Review

Surprise #1: I’m not totally against peer review. I realize that the way it is implemented in many places is deeply flawed, and that it’s no guarantee of the quality of a paper, but I also recognize its value. This is not where I was 8 years ago; at the time, I was pretty much in agreement with Mike’s post from November, 2012, “Well, that about wraps it up for peer-review”. But then in 2014 I became an academic editor at PeerJ. And as I gained first-hand experience from the other side of the editorial desk, I realized a few things:

  • Editors have broad remits in terms of subject areas, and without the benefit of peer reviews by people who specialize in areas other than my own, I’m not fit to handle papers on topics other than Early Cretaceous North American sauropods, skeletal pneumaticity, and human lower extremity anatomy.
  • Even at PeerJ, which only judges papers based on scientific soundness, not on perceived importance, it can be hard to tell where the boundary is. I’ve had to reject a few manuscripts at PeerJ, and I would not have felt confident about doing that without the advice of peer reviewers. Even with no perceived importance criterion, there is definitely a lower bound on what counts as a publishable observation. If you find a mammoth toe bone in Nebraska, or a tyrannosaur tooth in Montana, there should probably be something more interesting to say about it, beyond the bare fact of its existence, if it’s going to be the subject of a whole paper.
  • In contentious fields, it can be valuable to get a diversity of opinions. And sometimes, frankly, I need to figure out if the author is a loony, or if it’s actually Reviewer #2 that’s off the rails. Although I think PeerJ generally attracts fairly serious authors, a handful of things that get submitted are just garbage. From what I hear, that’s the case at almost every journal. But it’s not always obvious what’s garbage, what’s unexciting but methodologically sound, and what’s seemingly daring but also methodologically sound. Feedback from reviewers helps me make those calls. Bottom line, I do think the community benefits from having pre-publication filters in place.
  • Finally, I think editors have a responsibility to help authors improve their work, and reviewers catch a lot of stuff that I would miss. And occasionally I catch something that the reviewers missed. We are collectively smarter and more helpful than any of us would be in isolation, and it’s hard to see that as anything other than a good thing.

The moral here probably boils down to, “white guy stops bloviating about Topic X when he gains actual experience”, which doesn’t look super-flattering for me, but that’s okay.

You may have noticed that my pro-peer-review comments are rather navel-gaze-ly focused on the needs of editors. But who needs editors? Why not chuck the whole system? Set up an outlet called Just Publish Everything, and let fly? My answer is that my time in the editorial trenches has convinced me that such a system will silt up with garbage papers, and as a researcher I already have a hard enough time keeping up with all of the emerging science that I need to. From both perspectives, I want there to be some kind of net to keep out the trash. It doesn’t have to be a tall net, or strung very tight, but I’d rather have something than nothing.

What would I change about peer review? Since it launched, PeerJ has let reviewers either review anonymously, or sign their reviews, and it has let authors decide whether or not to publish the reviews alongside the paper. Those were both pretty daring steps at the time, but if I could I’d turn both of those into mandates rather than options. Sunlight is the best disinfectant, and I think almost all of the abuses of the peer review system would evaporate if reviewers had to sign their reviews, and all reviews were published alongside the papers. There will always be a-holes in the world, and some of them are so pathological that they can’t rein in their bad behavior, but if the system forced them to do the bad stuff in the open, we’d all know who they are and we could avoid them.

Femur of Apatosaurus and right humerus Brachiosaurus altithorax holotype on wooden pedestal (exhibit) with labels and 6 foot ruler for scale, Geology specimen, Field Columbian Museum, 1905. (Photo by Charles Carpenter/Field Museum Library/Getty Images)

Quo Vadis, Preprints?

Maybe the advent of preprints was more drawn out than I know, but to me it felt like preprints went from being Not a Thing, Really, in 2012, to being ubiquitous in 2013. And, I thought at the time, possibly transformative. They felt like something genuinely new, and when Mike and I posted our Barosaurus preprint and got substantive, unsolicited review comments in just a day or two, that was pretty awesome. Which is why I did not expect…

Surprise #2: I don’t have much use for preprints, at least as they were originally intended. When I first confessed this to Mike, in a Gchat, he wrote, “You don’t have a distaste for preprints. You love them.” And if you just looked at the number of preprints I’ve created, you might get that impression. But the vast majority of my preprints are conference talks, and using a preprint server was just the simplest way to the get the abstract and the slide deck up where people could find them. In terms of preprints as early versions of papers that I expect to submit soon, only two really count, neither more recent than 2015. (I’m not counting Mike’s preprint of our vertebral orientation paper from 2019; he’s first author, and I didn’t mind that he posted a preprint, but neither is it something I’d have done if the manuscript was mine alone.)

My thoughts here are almost entirely shaped by what happened with our Barosaurus preprint. We put it up on PeerJ Preprints back in 2013, we got some useful feedback right away, and…we did nothing for a long time. Finally in 2016 we revised the manuscript and got it formally submitted. I think we both expected that since the preprint had already been “reviewed” by commenters, and we’d revised it accordingly, that formal peer review would be very smooth. It was not. And the upshot is that only now, in 2021, are we finally talking about dealing with those reviews and getting the manuscript resubmitted. We haven’t actually done this, mind, we’re just talking about planning to make a start on it. (Non-committal enough for ya?)

Why has it taken us so long to deal with this one paper? We’re certainly capable — the two of us got four papers out in 2013, each of them on a different topic and each of them substantial. So why can’t we climb Mount Barosaurus? I think a big part of it is that we know the world is not waiting for our results, because our results are already out in the world. We’re the only ones being hurt by our inaction — we’re denying ourselves the credit and the respect that go along with having a paper finally and formally published in a peer-reviewed journal. But we can comfort ourselves with the thought that if someone needs our observations to make progress on their own project, we’re not holding them up. Just having the preprint out there has stolen some of our motivation to the get the paper done and out, apparently enough to keep us from doing it at all.

Mike pointed out that according to Google Scholar, our Barosaurus preprint has been cited five times to date, once in its original version and four times in its revised version. But to me, the fact that the Baro manuscript has been cited five times is a fail. Because all of my peer-reviewed papers from 2014-2016, which have been out for less long, have been cited more. So I read that as people not wanting to cite it. And who can blame them? Even I thought it would be supplanted by the formally-published, peer-reviewed paper within a few weeks or months.

Mike then pointed me to his 2015 post, “Four different reasons to post preprints”, and asked how many of those arguments still worked for me now. Number 2 is good, posting material that would otherwise never see the light of day — it’s basically what I did when I put my dissertation on arXiv. Ditto for 4, which is posting conference presentations. I’m not moved by either 1 or 3. Number 3 is getting something out to the community as quickly as possible, just because you want to, and number 1 is getting feedback as quickly as possible. The reason that neither of those move me is that they’re solved to my satisfaction by existing peer-reviewed outlets. I don’t know of any journals that let reviewers take 2-4 months to review a paper anymore. I don’t know how much credit for the acceleration should go to PeerJ, which asks for reviews in 10 to 14 days, but surely some. And I don’t usually have a high enough opinion of my own work to think that the community will suffer if it takes a few months for a paper to come out through the traditional process.

(If it seems like I’m painting Mike as relentlessly pro-preprint, it’s not my intent. Rather, I’d dropped a surprising piece of news on him, and he was strategically probing to determine the contours of my new and unexpected stance. Then I left the conversation to come write this post while the ideas were all fresh in my head. I hope to find out what he thinks about this stuff in the comments, or ideally in a follow-up post.)

Back to task: at least for me, a preprint of a manuscript I’m going to submit anyway is a mechanism to get extra reviews I don’t want*, and to lull myself into feeling like the work is done when it’s not. I don’t anticipate that I will ever again put up a preprint for one of my own manuscripts if there’s a plausible path to traditional publication.

* That sounds awful. To people who have left helpful comments on my preprints: I’m grateful, sincerely. But not so grateful that I want to do the peer review process a second time for zero credit. I didn’t know that when I used to file preprints of manuscripts, but I know it now, and the easiest way for me to not make more work for both of us is to not file preprints of things I’m planning to submit somewhere anyway.

So much for my preprints; what about those of other people? Time for another not-super-flattering confession: I don’t read other people’s preprints. Heck, I don’t have time to keep up with the peer-reviewed literature, and I have always been convinced by Mike’s dictum, “The real value of peer-review is not as a mark of correctness, but of seriousness” (from this 2014 post). If other people want me to part with my precious time to engage with their work, they can darn well get it through peer review. And — boomerang thought — that attitude degrades my respect for my own preprint manuscripts. I wouldn’t pay attention to them if someone else had written them, so I don’t really expect anyone else to pay attention to the ones that I’ve posted. In fact, it’s extremely flattering that they get read and cited at all, because by my own criteria, they don’t deserve it.

I have to stress how surprising I find this conclusion, that I regard my own preprints as useless at best, and simultaneously extra-work-making and motivation-eroding at worst, for me, and insufficiently serious to be worthy of other people’s time, for everyone else. It’s certainly not where I expected to end up in the heady days of 2013. But back then I had opinions, and now I have experience, and that has made all the difference.

The comment thread is open. What do you think? Better still, what’s your experience?

Xinjiangtitan when originally described, from Wu et al. (2013)

We’re way late to this party, but better late than never I guess. Wu et al. (2013) described Xinjiangtitan shanshanesis as a new mamenchisaurid from the Middle Jurassic of China. At the time of the initial description, all of the dorsal and sacral vertebrae had been uncovered, as well as a handful of the most posterior cervicals and most anterior caudals.

Xinjiangtitan revealed, from Zhang et al. (2018)

Jump a few years forward 2018, when Zhang et al. described the complete cervical series of Xinjiangtitan, based on further excavation of the holotype (they also changed some of the element identifications in the original description). It’s pretty insane: 

  • 18 cervical vertebrae, same as Mamenchisaurus youngi, and one less than M. hochuanensis, all discovered in articulation;
  • 10 of those vertebrae have centrum lengths of 1 meter or more;
  • the longest centrum, that of C12, is 123cm long;
  • the total lengths of the separate cervical vertebrae (not articulated) add up to about 15 meters;
  • even assuming that the condyles of the vertebrae were fully buried in the cotyles, the total length of articulated neck would still be 13.36 meters. 

Now, some caveating. Zhang et al. (2018) report two different lengths for most the cervicals: a maximum centrum length, which includes the anterior condyle, and a “minimum centrum length” without the anterior condyle. Reporting cervical lengths minus the condyle is fairly common–Janensch did it for what is now Giraffatitan (“ohne condylus”), McIntosh (2005) did it for the AMNH Barosaurus, Tschopp and Mateus (2017) did it for Galeamopus pabsti, and so on. In the freely available but as-yet-not-formally-published 4th chapter of my dissertation (Wedel 2007), I referred to the length without the condyle as the “functional length”, and I explicitly assumed that it was “the length that each vertebra contributes to the total neck length”. At the time I assumed that condyles were always fully buried in cotyles in life, because I didn’t know about camel necks (see Taylor and Wedel 2013b: fig. 21 and this post). 

Why am I bringing up all these minutiae? Because I’m really interested in the actual length of the neck of Xinjiangtitan in life, and that’s not so very straightforward to figure out. I’ll start with what Zhang et al. wrote, then proceed to their measurements, and then discuss their map.

At the start of the Description section, Zhang et al. (2018: p. 3) wrote:

In SSV12001, the cervical series is almost completely articulated and is exposed laterally (Figure 2). The long neck (at least 14.9 m) is well-preserved with a total of 18 cervical vertebrae. This measurement was estimated based on the maximum centrum length including the anterior condyles with the space for the cartilage assumed.

How much space is assumed for the cartilage? They don’t say, and it’s not clear, but one reading is that they just added up the total lengths of all the cervical centra and assumed that the cotyles were completely full of cartilage. Which is not so crazy as it might sound, since that’s exactly what happens in camels. But let’s see what their tables of measurements say.

Xinjiangtitan cervical vertebra measurements, from Zhang et al. (2018)

Table 1 gives the measurements of the atlas and axis, and Table 2 gives the measurements of all the remaining cervicals. Only “minimum centrum length”–without the condyle–is reported for cervicals 4 and 5, because C3-C5 were articulated as a unit, they haven’t been separated, and without CT scanning or further prep it’s going to be impossible to determine how long they were with the condyles. However, we can infer that the condyles of C4 and C5 are buried in the cotyles of C3 and C4 because (a) only the without-condyle lengths are reported, and (b) the condyles aren’t visible in the figures. File that away, it’s going to be important.

Adding up all of the max centrum lengths, including 165mm for the axis and 30mm for the atlas, per Table 1, I get a total of 14985mm, or 14.985 meters. Because Zhang et al. were so assiduous about their reporting–they really did Measure Their Damn Dinosaur–we can estimate pretty closely how much longer that total would be if it included the condyles of C4 and C5. Subtracting the min length from the max length, we find that the condyle is 70mm long in both C3 and C6, so it’s reasonable to assume the same for the vertebrae in the middle. Adding 140mm to the earlier total gets us up to 15125mm, or 15.125 meters. That’s assuming condyles end even with the rims of the cotyles, and cotyles are completely full of cartilage.

Xinjiangtitan cervicals, from Zhang et al. (2018: fig 3)

Adding up the all of the minimum centrum lengths, again including the axis and atlas, yields a total of 13360mm, or 13.36 meters. I think this smaller total is much more likely to be the actual length of the neck in life, for three reasons:

  1. As mentioned above, the condyles of C4 and C5 of this very specimen are actually buried in the cotyles of the preceding vertebrae. So we don’t need to add any space for cartilage to the summed minimum (without condyle) lengths–there certainly was cartilage between the surfaces of the condyles and cotyles, because that’s how intervertebral joints work, but there was not enough to push the condyles back outside the cotyles, unless we want to engage in some special pleading that C3-C5 were unnaturally smooshed together.
  2. Camels notwithstanding, having the condyles buried in the cotyles is pretty standard for articulated necks of big, long-necked sauropods. In the holotype specimens of Mamenchisaurus hochuanensis and Sauroposeidon, the condyles are not visible in lateral view, because they are completely buried in the cotyles of the preceding vertebrae–see the photos in this post and on this page to confirm that for yourself. In Giraffatitan, just the edges of the condyles are visible sticking out the backs of the cotyles in some of the posterior cervicals–see this post.
  3. The 13.36-meter neck is more consistent with the map of the specimen in the ground than either the 14.9-meter or 15.1-meter totals.

A little unpacking on that last point. Using the dorsal lengths from Wu et al. (2013: table 1)–and assuming that Zhang et al. are correct, and the D1 of Wu et al. is actually cervical 18, but D11 of Wu et al. is actually D10 and D11 together, so there are still 12 dorsals–I get a total length for the articulated dorsal column of 3355mm. Dividing 13360 by 3355 yields a cervical/dorsal ratio of 3.98. Using the screenshot of the map from Zhang et al. (2018: fig. 2), I measured 1505 pixels for the summed cervicals, 380 pixels for the summed dorsals, and 112 pixels for the scale bar. Assuming the scale bar is supposed to be 1 meter (and not 20 meters or 2.0 meters as it is labeled) yields a summed cervical length of 13.4 meters, a summed dorsal length of 3.39 meters, and a cervical/dorsal ratio of 3.96–all admirably close, off by no more than 4cm across 16+ meters, if the neck in the ground was articulated condyle-inside-cotyle. If we assume the map shows a 14.9-meter neck, then both the dorsal series and the scale bar are off by about 12%, which is unreasonable given the high precision of the map if the articulated neck corresponds to the summed minimum lengths.

Mounted skeleton of Omeisaurus tianfuensis: N E C C

Bonus observation #1: the holotype of Mamenchisaurus hochuanensis has a cervical/dorsal ratio of 3.52, but in Omeisaurus tianfuensis the same ratio is 4.09. So Xinjiangtitan is actually a little shorter-necked than Omeisaurus, at least compared to the length of the dorsal series.

Bonus observation #2: the 123-cm cervical of Xinjiangtitan is only the fifth-longest vertebra of anything to date:

  1. BYU 9024, possibly referable to Supersaurus or Barosaurus: 137cm
  2. Price River 2 titanosauriform: 129cm
  3. OMNH 53062, Sauroposeidon holotype: 125cm
  4. KLR1508-77-2, Ruyangosaurus giganteus referred specimen: 124cm
  5. SSV12001, Xinjiangtitan shanshanesis holotype: 123cm
  6. MPEF-PV 3400/3, Patagotitan holotype: 120cm (+?)
  7. MPM 10002, Puertasaurus holotype: 118cm

Getting pretty crowded there in the 120s, but then a big jump to BYU 9024. I’ll have more to say on that in a second.

Just to put a bow on this section, I’m pretty confident, based on all available measurements, taphonomic evidence, and the consilience between the measurements and the map, that the holotype individual of Xinjiantitan had a neck 13.36 meters (43 feet, 10 inches) long in life. 

That’s stunning.

By comparison, the second- and third-longest complete cervical series (of anything, ever, to date) belong to Mamenchisaurus hochuanensis, at 9.5 meters (Young and Zhao 1972, and confirmed by Mike in a basement in Slovenia), and Giraffatitan at 8.5 meters for MB.R.2181 (the larger XV2 specimen would have had a 9.6-meter neck).

Some other contenders, from Taylor and Wedel 2013a (fig 3)

There were things with longer necks, for sure, but none of those necks are complete (yet). Mamenchisaurus sinocanadorum is estimated to have had a neck about 12 meters long, based on the partial cervical series of the holotype. I know there are skeletal reconstructions out there with longer necks, and I will believe them as soon as the specimens they are based on are published. In the aforementioned dissertation chapter, I estimated 11.5 meters for the neck of Sauroposeidon, assuming a brachiosaurid-like cervical count of 13. Note that Mannion et al. (2013) recovered Sauroposeidon as a somphospondyl, and a cervical count of 15 or more as a synapomorphy of Somphospondyli. Adding a couple more 1.2-meter mid-cervicals would bring Sauroposeidon up to perhaps 14 meters. The longest cervicals of Patagotitan are in about the same size class, and we don’t know the cervical count in that monster, either.

BYU 9024, with the mounted (cast, composite) skeleton of Brachiosaurus altithorax and one Mike Taylor for scale

And of course, lurking out there in crazy neck-space is BYU 9024, the immense cervical originally referred to Supersaurus, but which more likely belongs to Barosaurus, and an ungodly huge one. That critter might–might–have had a 17-meter neck.

And I gotta say, in light of Xinjiangtitan, that no longer seems so unreasonable. Because Xinjiangtitan was a big sauropod but not a monster. The dorsal length of 3.3 meters and the femur length of 1.65 meters put it in roughly the same size category as the bigger individual of Jobaria (DL 3.2m, FL 1.8m) or the AMNH 5761 Camarasaurus supremus (DL 2.5m, FL 1.8m). Let’s imagine a Xinjiangtitan with a 2.4-meter femur, the size of Patagotitan or Argentinosaurus. Assuming isometric scaling, that individual would have a 2.4/1.65 = 1.45 x 13.36 = 19.4-meter neck. 

Do we really think such animals never existed?

Food for thought: the holotype individual of Xinjiangtitan was small enough to be buried as a complete skeleton. What about the individuals that were too big to bury in one shot?

Utterly unsurprising, but still nice to see: the highly pneumatic internal structure of the vertebrae of Xinjiangtitan, from Wu et al. (2013)

References

I’m a bit shocked to find it’s now more than five years since Robert Harington’s Scholarly Kitchen post Open Access: Fundamentals to Fundamentalists. I wrote a response in the comments, meaning to also post it here, but got distracted, and then half a decade passed. Here it is, finally. The indented parts are quotes from Harington.


I must admit to being rather tired of the fundamentalism that pervades discussions around open access policies and business models. On the one hand there are the advocates, and through the laws of conservation of energy, the equal and opposite reaction of anti-open access advocacy. There seems little room for rational debate about open access in the midst of such an antagonistic atmosphere.

It’s always a powerful rhetorical move to call your opponent a fundamentalist. It’s also a lazy one. It absolves you from the tedious responsibility of bothering to understand what the opponent actually wants: just dismiss him has a fundamentalist and call it done. I’d hope we’re better than that. At best, this seems like a fine demonstration of the principle that “there seems little room for rational debate about open access in the midst of such an antagonistic atmosphere”.

You want a rational debate? You want to talk about fundamentals? Fine, let’s do that. Here is the most fundamental question of all: what is research for? Our answer to this will profoundly affect every stance we adopt regarding publishing, OA, researcher evalution and more.

The greatest problem we have in discussing these issues is when person A assumes right off the bat that person B has the same answer to that fundamental question, and is then surprised to find that B disagrees over numerous implementation details. All those details flow from the fundamental mismatch. A and B are literally trying to solve two different problems — no wonder they can’t agree on the solution!

So what is research for? Here are three possible answers.

A. Some people believe (or maybe I should say assume) that research is for the world — for the betterment of the lot of society as a whole, the eradication of illness, the understanding of the environment, and generally the benefit of humanity. As pleasant side-effects, it also feeds publishing businesses and advances researchers’ careers.

B. Some people believe (or assume) that research is primarily for the benefit of the economy: that the principle purpose of the whole process is the financial benefit that accrues to publishers and related professions. As pleasant side-effects, it also advances the world’s knowledge and advances researchers’ careers.

C. Some people believe (or assume, or at least give the impression of assuming) that research is mostly about the careers of researchers — about giving them a way to prove their merit and advance up the career ladder. As pleasant side-effects, it also advances the world’s knowledge and feeds publishing businesses.

All of these fundamental positions exist. (There may be others that I missed.) We could probably all classify various individuals into these groups (but I’ll resist the temptation to throw in examples, as that would surely result in an epic sidetrack).

Notice that one can’t reach one of these three positions by any amount of thought about what happens within the research/publication ecosystem. It’s more fundamental than that. That decision has to come from somewhere outside. For example, my own position is no secret: I am an “A”, and the reason is because I feel it follows from the Golden Rule (“Do to others as you would have them do to you”, Luke 6:31) — probably the most universally agreed ethical principle in any religion (and among those who profess none).

And so when Robert Harrington asks:

The real debate here is to understand more about the motivations and needs of a researcher, who may or may not be funded directly. What is the best business model that will allow a researcher to publish work effectively and allow readers access to that work?

That is really two ——quite separate questions that may have completely different answers: 1, what business model will allow a researcher to publish work effectively?; and 2, what business model will allow readers access to that work? If you are an “A”, you’ll care most about the second question; if you’re a “C” you’ll care about the first question; and if you’re a “B” you might still be thinking about the business model mentioned at the start of the question.

It’s fruitless to expect “A”s, “B”c and “C”s to agree on an answer to a question when each group is hearing a different question.

Here’s another example:

The real story here is that the rights and desires of academics are being represented by organizations that do not reflect their needs, and that perhaps do not even understanding them. There is a form of fundamentalism that dictates to academics that this is what you need; just let us lead the way and we will make things right for you.

This statement suggests a “C” mindset: that the rights and desires of researchers are paramount. But if the organisations in question are “A”s (as for example you’d expect the Alliance for Taxpayer Access or RCUK to be), then this complaint is a non-issue. Of course they don’t reflect researchers’ desires — that’s not what they’re there for. They reflect the needs of broader society (which are often aligned with those of researchers, but by no means always).

That’s not a bug. That’s a feature.

And similarly:

I would suggest that there is nothing fundamentally wrong with a subscription model.

This may be true for “B”s (who might prefer the subscription model because they think it yields the most revenue) and for “C”s (who might want to place their work in a specific paywalled journal that is well regarded in their field). But it’s much less likely for “A”s, who see great public benefit in free access, and conversely great harm in arbitrary barriers.

So there you go. Fundamentals.

 

 

Down in flames

August 25, 2018

I first encountered Larry Niven’s story/essay “Down in Flames” in the collection N-Space in high school. This was after I’d read Ringworld and most of Niven’s Known Space stories, so by the time I got to “Down in Flames” I had the context to get it. (You can read the whole thing for free here.)

Here’s the idea, from near the start:

On January 14, 1968, Norman Spinrad and I were at a party thrown by Tom & Terry Pinckard. We were filling coffee cups when Spinny started this whole thing.

“You ought to drop the known space series,” he said. “You’ll get stale.” (Quotes are not necessarily dead accurate.) I explained that I was writing stories outside the “known space” history, and that I would give up the series as soon as I ran out of things to say within its framework. Which would be soon.

“Then why don’t you write a novel that tears it to shreds? Don’t just abandon known space. Destroy it!”

“But how?” (I never asked why. Norman and I think alike in some ways.)

The rest of the piece is just working out the details.

“Down in Flames” brain-wormed me. Other than Ray Bradbury’s “A Sound of Thunder” I doubt if there is another short story I’ve read as many times. Mike once described the act of building something complex and beautiful and then destroying it as “magnificently profligate”, and that’s the exact quality of “Down in Flames” that appeals to me.

I also think it is a terrific* exercise for everyone who is a scientist, or who aspires to be one.

* In both the modern sense of “wonderful” and the archaic sense of “causing terror”.

Seriously, try it. Grab a piece of paper (or open a new doc, or whatever) and write down the ideas you’ve had that you hold most dear. And then imagine what it would take for all of them to be wrong. (When teams and organizations do this for their own futures, it’s called a pre-mortem, and there’s a whole managerially-oriented literature on it. I’d read “Down in Flames” instead.)

It feels like this! Borrowed from here.

Here are some questions to help you along:

  • Which of your chains of reasoning admit more than one end-point? If none of them might lead other places, then either you are the most amazing genius of all time (even Newton and Einstein made mistakes), or you are way behind the cutting edge, and your apparent flawlessness comes from working on things that are already settled.
  • If there is a line of evidence that could potentially falsify your pet hypothesis, have you checked it? Have you drawn any attention to it? Or have you gracefully elided it from your discussions in hopes that no-one will notice, at least until after you’re dead?
  • If there’s no line of evidence that could falsify your pet hypothesis, are you actually doing science?
  • Which of your own hypotheses do you have an emotional investment in?
  • Are there findings from a rival research team (real or imagined) that you would not be happy to see published, if they were accurate?
  • Which hypotheses do you not agree with, that you would be most dismayed to see proven correct?

[And yes, Karl, I know that according to some pedants hypotheses are never ‘proven’. It’s a theoretical exercise already, so just pretend they can be!]

I’ll close with one of my favorite quotes, originally published in a couple of tweets by Angus Johnson in May of 2017 (also archived here):

If skepticism means anything it means skepticism about the things you WANT to be true. It’s easy to be a skeptic about others’ views. Embracing a set of claims just because it happens to fit your priors doesn’t make you a skeptic. It makes you a rube, a mark, a schnook.

So, don’t be that rube. Burn down your house of ideas – or at least, mentally sift through the rubble and ashes and imagine how it might have burned down. And then be honest about that, minimally with yourself, and ideally with the world.

If you’re a true intellectual badass, blog the results. I will. It’s not fair to give you all homework – painful homework – and not take the medicine myself, so I’m going to do a “Down in Flames” on my whole oeuvre in the next a future post. Stay tuned!

Here’s BYU 12866, a mid-cervical of a neosauropod from Dry Mesa Quarry. It’s cataloged as Brachiosaurus, an identification I’ve never found any compelling reason to doubt. It’s definitely brachiosaurid, and for now Brachiosaurus is the only game in town for the Late Jurassic of North America. I expect that will change when more and better material comes to light, based on the different coracoid shapes of the Brachiosaurus holotype and the “Ultrasauros” scapulocoracoid.

I reckon it’s probably a C5 or so, based on its proportions and comparisons with Giraffatitan (for example).

As you can see, it’s a bit distorted, sheared over with the dorsal side to the right and the ventral side to the left.

I don’t think there’s any major anterior/posterior shearing – the zygs are set forward of their respective centrum ends by about the same amount in this specimen as in Giraffatitan.

Kent Sanders and I CT scanned this vert back in the day and those scans made it into several papers, including Wedel et al. (2000b) on Sauroposeidon and Wedel (2005) on sauropod pneumaticity and mass estimates.

I have the original, uncropped, full-res photos, and I’ll probably get them posted at some point (faster if people bug me to do so, so speak up in the comments if you want them). But for now I’m sticking to getting stuff posted quickly, easily, and regularly, and I found these as-is on my hard drive, so here we are.

References

 

Old drawings (of heads)

June 25, 2017

I was organizing my files in DropBox and I found a folder of old drawings I’d almost forgotten about. I drew this back in the late 90s. It was used on a t-shirt by the OU Zoology Department. I got the general idea of making a head out of animals, and the specific idea of using a butterfly wing for the ear, from Wayne Douglas Barlowe’s cover for the novel Wild Seed by Octavia Butler. The snake I stole from ancient Egypt. I think everything else is in there just because I thought it was cool. Note that inverts, fish, herps, birds, and mammals are all represented, with a good balance of aquatic, terrestrial, and volant forms. It looks awfully hippie-dippie from 20 years out, but heck, what doesn’t?

“Solitude” by Mathew Wedel. CC BY-NC 4.0.

Well, this, I suppose.

I drew this about the same time. I was reading The Gnostic Gospels by Elaine Pagels and lots of stuff about ancient monastic traditions and thinking that if the world is an illusion that must be penetrated, then the evidence of one’s senses can only mislead. Also, Vicki was working for the state medical examiner in Oklahoma City and they used wooden dowels to represent the paths of bullets when reconstructing the skulls of those killed by gunfire. So here’s the skull of a monk, with all of the lethal pathways of distraction and temptation clearly marked as such. At last he can contemplate the eternal mysteries in perfect solitude.

Obviously I didn’t get on board the world-is-an-illusion, sensation-is-bad train – skewed pretty hard in the opposite direction, in fact. Possibly because years earlier the Chessmen of Mars by Edgar Rice Burroughs had shown me that pursuing ‘pure’ intellectual and spiritual inquiry would ultimately lead one to a pathetic existence as a disembodied head living in a cave (high culture, meet low culture). Anyway, whatever interest I might have had in that philosophy I exorcised through this drawing. Stripped of any art-making-a-point baggage, I still think it’s pretty bitchin’. I should make t-shirts.

Actually, I probably will make t-shirts of this one if there’s any interest. Hence the CC BY-NC license I put on it, as opposed to the normal CC BY for almost everything else on this site. Look at me, boldly experimenting with new licenses.

This, obviously, is a lot more recent. I was collating all of my scanned drawings and I realized that I’d gone to the trouble of drawing the cranium and lower jaw of Aquilops separately, but I’d never posted the version from before I composited them back into articulation. It is very unlike me to do work and then hide it, so here it is.

It wasn’t until I the post mostly written that I realized that all three drawings are of heads, none of them are saurischians (although the first includes a saurischian, but not the cool kind), and two are stinkin’ mammals (and not the cool kind). I stand ready for your slings and arrows.

For previous posts on my drawings, see:

Wedel 2005 Morrison sauropod cervicals 1 - Diplodocus

When I was back in Oklahoma in March, I met with Anne Weil to see some of the new Apatosaurus material she’s getting out of her Homestead Quarry. It’s nice material, but that’s a post for another day. Anne said something that really resonated with me, which was, “I love it when you guys post about vertebral morphology, because it helps me learn this stuff.” Okay, Anne, message received. This will begin to make things right.

Wedel 2005 Morrison sauropod cervicals 2 - Barosaurus and centra shapes

I spent a week at BYU back in 2005, collecting data for my dissertation. One of the first things I had to do was teach myself how to identify the vertebrae of different sauropods, because BYU has just about all of the common Morrison taxa. These are the notes I made back then.

Wedel 2005 Morrison sauropod cervicals 3 - Brachiosaurus and Apatosaurus

I always planned to do something with them – clean them up, get them into a more usable form. There are a lot of scribbly asides that are probably hard for others to read, and it would be more useful if I put the easily confused taxa next to each other – Barosaurus next to Brachiosaurus, for example. And I didn’t go into serial changes at all.

Wedel 2005 Morrison sauropod cervicals 4 - Camarasaurus and Haplocanthosaurus

Still, hopefully someone will find these useful. If there are things I missed or got wrong, the comment thread is open. And if you want all four spreads in one convenient package, here’s a PDF: Wedel 2005 notes on Morrison sauropod cervicals

Mike and I leave for the Sauropocalypse tomorrow. I’m hoping to post at least a few pretty pictures from the road, as I did for the Mid-Mesozoic Field Conference two years ago. Stand by…

ostrich peeing

cormorant peeing

alligator peeing

Stand by . . . grumpy old man routine compiling . . . 

So, someone at Sony decided that an Angry Birds movie would be a good idea, about three years after the Angry Birds “having a moment” moment was over. There’s a trailer for it now, and at the end of the trailer, a bird pees for like 17 seconds (which is about 1/7 of my personal record, but whatever).

And now I see these Poindexters all over the internet pushing their glasses up their noses and typing, “But everyone knows that birds don’t pee! They make uric acid instead! That’s the white stuff in ‘bird poop’. Dur-hur-hur-hurrr!” I am reasonably sure these are the same people who harped on the “inaccuracy” of the peeing Postosuchus in Walking With Dinosaurs two decades ago. (Honestly, how I didn’t get this written and posted in our first year of blogging is quite beyond my capacity.)

Congratulations, IFLScientists, on knowing One Fact about nature. Tragically for you, nature knows countless facts, and among them are that birds and crocodilians can pee. And since extant dinosaurs can and do pee, extinct ones probably could as well.

So, you know . . . try to show a little respect.

So, you know . . . try to show a little respect.

Now, it is true that crocs (mostly) and birds (always?) release more of their nitrogenous waste as uric acid than as urea. But their bodies produce both compounds. So does yours. We mammals are just shifted waaaay more heavily toward urea than uric acid, and extant archosaurs – and many (but not all) other reptiles to boot – are shifted waaaay more heavily toward uric acid than urea. Alligators also make a crapload of ammonia, but that’s a story for another time.

BUT, crucially, birds and crocs almost always release some clear, watery, urea-containing fluid when they dump the whitish uric acid, as shown in this helpful diagram that I stole from International Cockatiel Resource:

International Cockatiel Resource bird pee guide

If you’ve never seen this, you’re just not getting to the bird poop fast enough – the urine is drying up before you notice it. Pick up the pace!

Sometimes birds and crocs save up a large quantity of fluid, and then flush everything out of their cloacas and lower intestines in one shot, as shown in the photos dribbled through this post. Which has led to some erroneous reports that ostriches have urinary bladders. They don’t, they just back up lots of urine into their colons. Many birds recapture some water and minerals that way, and thereby concentrate their wastes and save water – basically using the colon as a sort of second-stage kidney (Skadhauge 1976).

Rhea peeing by Markus Buhler

Many thanks to Markus Bühler for permission to post his well-timed u-rhea photo.

[UPDATE the next day: To be perfectly clear, all that’s going on here is that the birds and crocs keep their cloacal sphincters closed. The kidneys keep on producing urine and uric acid, and with no way out (closed sphincter) and nowhere else to go (no bladder – although urinary bladders have evolved repeatedly in lizards), the pee backs up into the colon. So if you’re wondering if extinct dinosaurs needed some kind of special adaptation to be able to pee, the answer is no. Peeing is an inherent possibility, and in fact the default setting, for any reptile that can keep its cloaca shut.]

Aaaanyway, all those white urate solids tend to make bird pee more whitish than yellow, as shown in the photos. I have seen a photo of an ostrich making a good solid stream from cloaca to ground that was yellow, but that was years ago and frustratingly I haven’t been able to relocate it. Crocodilians seem to have no problem making a clear, yellowish pee-stream, as you can see in many hilarious YouTube videos of gators peeing on herpetologists and reporters, which I am putting at the bottom of this post so as not to break up the flow of the rant.

ostrich excreting

You can explore this “secret history” of archosaur pee by entering the appropriate search terms into Google Scholar, where you’ll find papers with titles like:

  • “Technique for the collection of clear urine from the Nile crocodile (Crocodylus niloticus)” (Myburgh et al. 2012)
  • “Movement of urine in the lower colon and cloaca of ostriches” (Duke et al. 1995)
  • “Plasma homeostasis and cloacal urine composition in Crocodylus porosus caught along a salinity gradient” (Grigg 1981)
  • “Cloacal absorption of urine in birds” (Skadhauge 1976)
  • “The cloacal storage of urine in the rooster” (Skadhauge 1968)

I’ve helpfully highlighted the operative term, to reinforce the main point of the post. Many of these papers are freely available – get the links from the References section below. A few are paywalled – really, Elsevier? $31.50 for a half-century-old paper on chicken pee? – but I’m saving them up, and I’ll be happy to lend a hand to other scholars who want to follow this stream of inquiry. If you’re really into the physiology of birds pooling pee in their poopers, the work of Erik Skadhauge will be a gold mine.

Now, to be fair, I seriously doubt that any bird has ever peed for 17 seconds. But the misinformation abroad on the net seems to be more about whether birds and other archosaurs can pee at all, rather than whether a normal amount of bird pee was exaggerated for comedic effect in the Angry Birds trailer.

ostrich excreting 3

In conclusion, birds and crocs can pee. Go tell the world.

And now, those gator peeing videos I promised:

UPDATE

Jan. 30, 2016: I just became aware that I had missed one of the best previous discussions of this topic, with one of the best videos, and the most relevant citations! The post is this one, by Brian Switek, which went up almost two years ago, the video is this excellent shot of an ostrich urinating and then defecating immediately after:

…and the citations are McCarville and Bishop (2002) – an SVP poster about a possible sauropod pee-scour, which is knew about but didn’t mention yet because I was saving it for a post of its own – and Fernandes et al. (2004) on some very convincing trace fossils of dinosaurs peeing on sand, from the Lower Cretaceous of Brazil. In addition to being cogent and well-illustrated, the Fernandes et al. paper has the lovely attribute of being freely available, here.

So, sorry, Brian, that I’d missed your post!

And for everyone else, stand by for another dinosaur pee post soon. And here’s one more video of an ostrich urinating (not pooping as the video title implies). The main event starts about 45 seconds in.

References

tornado debris

Hey, look, there goes my future!

One thing that always bemuses me is the near-absolute serendipity of the academic job market. To get into research careers takes at least a decade of very deliberate, directed work, and then at the end you basically toss your diploma into a whirlwind and see where it lands. After all of that careful planning, almost all of us end up where we do based on the random (to us) set of jobs available in the narrow window in which we’re searching.

Did you dream of being curator at Museum X, or professor at University Y? Well, tough, those jobs went to Dr. Graduated-Two-Years-Sooner and Lucky Nature Paper, PhD, and they’re not retiring for three or four decades. Or maybe your dream job comes open right after you, your spouse, and your kids get settled in at your new acceptable-but-not-quite-dream job. Uproot or stay the course? Or what would be your dream job finally comes open but they’re looking for new junior faculty and you just got tenure at Tolerable State U.

This drastic mismatch between carefulness of preparation and randomness of outcome was present even pre-2008. The craptastic academic job market since then has only whetted the central irony’s keen edge. Getting grants and getting jobs is now basically a lottery. I’m not saying that good jobs don’t go to good people – they almost always do – but there are a lot of good people in jobs they never imagined having. And, sadly, plenty of good people who are now working outside of the field they prepared for because of the vicissitudes of the job market. A handful of years sooner or later and they might be sitting pretty.

This is on my mind because I recently had lunch with a physician friend from work and he was talking about applying for jobs as a doctor. “The first thing everyone tells you,” he said, “is decide what part of the country you want to live in first, then apply for the jobs that are there.” Doctors can do that because there are more than 800,000 of them active in the US. Paleontologists are mighty rarified by comparison – it’s hard to say how many of us there are, but probably not more than 2000 active in vert paleo. So the usual advice for budding biologists and paleontologists is exactly opposite that for physicians: “Forget about living where you want. Go wherever the job is and make the best of it.”

Oddly enough, I don’t remember this ever coming up in grad school. It’s something Vicki and I figured out at the end, as we started the process of applying for positions. There are alternate universes where we are at Marshall (they offered us both jobs, but not as attractive as UC Merced at the time), or at Northern Arizona (which is bittersweet because we have totally fallen in love with Flagstaff just in the past three years), or other places. If I were choosing a job site based on everything other than the institution, I’d spring for somewhere in Arizona or the intermountain west in a heartbeat.

IMG_5787

But with all that said, we are happy here. It’s funny, when we got the job offers down here I thought, “LA? Crap, there goes the outdoor part of my life.” But Claremont has lots of parks, it’s tucked up against the San Gabriels and I can get into the mountains in 30 minutes, or out to the desert in 90. I’m spending more time outdoors than I have since I was a kid growing up in rural Oklahoma.

So I’m not complaining about my personal situation. Vicki and I both landed on our feet – and the fact that we both managed to stick the landing at the same institution is little short of miraculous. But we still had to step into the job market hurricane to get here.

If you’re a grad student and you’re reading this, I didn’t write it to freak you out. Just to let you know that it’s coming, and there are things you can do to improve your chances. Be aggressively curious. Write. Publish. Give good talks (and give lots of talks so you can become good at it). Broaden your skill set – if you’re going into paleo, knowing how to teach human anatomy probably doubles or triples the number of available jobs at any one time, even if many of them are not the jobs you’ve been dreaming of.

Then, at the end, pour yourself one stiff drink and cast your fortune to the winds.

Good luck.

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