Cool URIs don’t change

November 26, 2020

It’s now 22 years since Tim Berners-Lee, inventor of the World Wide Web, wrote the classic document Cool URIs don’t change [1]. It’s core message is simple, and the title summarises it. Once an organization brings a URI into existence, it should keep it working forever. If the document at that URI moves, then the old URI should become a redirect to the new. This really is Web 101 — absolute basics.

So imagine my irritation when I went to point a friend to Matt’s and my 2013 paper on whether neural-spine bifurcation is an ontogenetic character (spoiler: no), only to find that the paper no longer exists.

Wedel and Taylor (2013b: figure 15). An isolated cervical of cf. Diplodocus MOR 790 8-10-96-204 (A) compared to D. carnegii CM 84/94 C5 (B), C9 (C), and C12 (D), all scaled to the same centrum length. Actual centrum lengths are 280 mm, 372 mm, 525 mm, and 627 mm for A-D respectively. MOR 790 8-10-96-204 modified from Woodruff & Fowler (2012: figure 2B), reversed left to right for ease of comparison; D. carnegii vertebrae from Hatcher (1901: plate 3).

Well — it’s not quite that bad. I was able to go to the web-site’s home page, navigate to the relavant volume and issue, and find the new location of our paper. So it does still exist, and I was able to update my online list of publications accordingly.

But seriously — this is a really bad thing to do. How many other links might be out there to our paper? All of them are now broken. Every time someone out there follows a link to a PalArch paper — maybe wondering whether that journal would be a good match for their own work — they are going to run into a 404 that says “We can’t run our website properly and can’t be trusted with your work”.

“But Mike, we need to re-organise our site, and —” Ut! No. Let’s allow Sir Tim to explain:

We just reorganized our website to make it better.

Do you really feel that the old URIs cannot be kept running? If so, you chose them very badly. Think of your new ones so that you will be able to keep then running after the next redesign.

Well, we found we had to move the files…

This is one of the lamest excuses. A lot of people don’t know that servers such as Apache give you a lot of control over a flexible relationship between the URI of an object and where a file which represents it actually is in a file system. Think of the URI space as an abstract space, perfectly organized. Then, make a mapping onto whatever reality you actually use to implement it. Then, tell your server.

If you are a responsible organization, then one of the things you are responsible for is ensuring that you don’t break inbound links. If you want to reorganize, fine — but add the redirects.

And look, I’m sorry, I really don’t want to pick on PalArch, which is an important journal. Our field really needs diamond OA journals: that is, venues where vertebrate paleontology articles are free to read and also free to authors. It’s a community-run journal that is not skimming money out of academia for shareholders, and Matt’s and my experience with their editorial handling was nothing but good. I recommend them, and will proabably publish there again (despite my current irritation). But seriously, folks.

And by the way, there are much worse offenders than PalArch. Remember Aetogate, the plagiarism-and-claim-jumping scandal in New Mexico that the SVP comprehensively fudged its investigation of? The documents that the SVP Ethics Committee produced, such they were, were posted on the SVP website in early 2008, and my blog-post linked to them. By July, they had moved, and I updated my links. By July 2013, they had moved again, and I updated my links again. By October 2015 they had moved for a third time: I both updated my links, and made my own copy in case they vanished. Sure enough, by February 2019 they had gone again — either moved for a fourth time or just quietly discarded. This is atrocious stewardship by the flagship society of our discipline, and they should be heartily ashamed that in 2020, anyone who wants to know what they concluded about the Aetogate affair has to go and find their documents on a third-party blog.

Seriously, people! We need to up our game on this!

Cool URIs don’t change.

 

 


[1] Why is this about URIs instead of URLs? In the end, no reason. Technically, URIs are a broader category than URLs, and include URNs. But since no-one anywhere in the universe has ever used a URN, in practice URL and URI are synonymous; and since TBL wrote his article in 1998, “URL” has clearly won the battle for hearts and minds and “URI” has diminished and gone into the West. If you like, mentally retitle the article “Cool URLs don’t change”.

Here’s a bit of light relief, in the middle of all those looong posts about Supersaurus and its buddies. When Matt and I were at NAMAL on the last day of the 2016 Sauropocalypse, we took a bunch of tourist shots. Two of them were of a skull and first three cervical vertebrae from what I take to be Diplodocus or something close, and happened to be from sufficiently close angles that they make a pretty good anaglyph. Here it is!

(If you don’t have the 3D glasses that you need to see this, get some. Seriously, how many times do I have to tell you?)

If anyone out there is familiar with NAMAL (on indeed with diplodocid skulls) and can confirm or contradict my identification, I’d appreciate it. Best of all would be a photo of the signage associated with this specimen, such as I should have taken.

By the way, if you’re not used to the ways of sauropods, you might be thinking “Mike, you dummy, there are only two vertebrae there”. But in saropods, the atlas (1st cervical) is a tiny, inconsequential element that frequently fuses to the axis (2nd cervical). So what looks like the first cervical here is really 1+2. If you look closely, you can see the blades of the atlas projecting backwards and upwards, across the surface of the axis.

You know the drill. For ground-level Diplodocus, go here, for Apatosaurus, go here.

In a word, amazingly. After 6 days (counting public galleries last Sunday), 4300 photos, 55 videos, dozens of pages of notes, and hundreds of measurements, we’re tired, happy, and buzzing with new observations and ideas.

We caught up with some old friends. Here Mike is showing an entirely normal and healthy level of excitement about meeting CM 584, a specimen of Camarasaurus from Sheep Creek, Wyoming. You may recognize this view of these dorsals from Figure 9 in our 2013 PeerJ paper.

We spent an inordinate amount of time in the public galleries, checking out the mounted skeletons of Apatosaurus and Diplodocus (and Gilmore’s baby Cam, and the two tyrannosaurs, and, and…).

I had planned a trip to the Carnegie primarily to have another look at the Haplocanthosaurus holotypes, CM 572 and CM 879. I was also happy for the chance to photograph and measure these vertebrae, CM 36034, which I think have never been formally described or referred to Haplocanthosaurus. As far as I know, other than a brief mention in McIntosh (1981) they have not been published on at all. I’m planning on changing that in the near future, as part of the larger Haplocanthosaurus project that now bestrides my career like a colossus.

The real colossus of the trip was CM 555, which we’ve already blogged about a couple of times. Just laying out all of the vertebrae and logging serial changes was hugely useful.

Incidentally, in previous posts and some upcoming videos, we’ve referred to this specimen as Brontosaurus excelsus, because McIntosh (1981) said that it might belong to Apatosaurus excelsus. I was so busy measuring and photographing stuff that it wasn’t until Friday that I realized that McIntosh made that call because CM 555 is from the same locality as CM 563, now UWGM 15556, which was long thought to be Apatosaurus excelsus but which is now (i.e., Tschopp et al. 2015) referred to Brontosaurus parvus. So CM 555 is almost certainly B. parvus, not B. excelsus, and in comparing the specimen to Gilmore’s (1936) plates of CM 563, Mike and I thought they were a very good match.

Finding the tray of CM 555 cervical ribs was a huge moment. It added a ton of work to our to-do lists. First we had to match the ribs to their vertebrae. Most of them had field numbers, but some didn’t. Quite a few were broken and needed to be repaired – that’s what I’m doing in the above photo. Then they all had to be measured and photographed.

It’s amazing how useful it was to be able to reassociate the vertebrae with their ribs. We only did the full reassembly for c6, in part because it was the most complete and perfect of all of the vertebrae, and in part because we simply ran out of time. As Mike observed in his recent post, it was stunning how the apatosaurine identity of the specimen snapped into focus as soon as we could see a whole cervical vertebra put back together with all of its bits.

We also measured and photographed the limb bones, including the bite marks on the radius (above, in two pieces) and ulna (below, one piece). Those will of course go into the description.

And there WILL BE a description. We measured and photographed every element, shot video of many of them, and took pages and pages of notes. Describing even an incomplete sauropod skeleton is a big job, so don’t expect that paper this year, but it will be along in due course. CM 555 may not be the most complete Brontosaurus skeleton in the world, but our ambition is to make it the best-documented.

In the meantime, we hopefully left things better documented than they had been. All of the separate bits of the CM 555 vertebrae – the centra, arches, and cervicals ribs – now have the cervical numbers written on in archival ink (with permission from collections manager Amy Henrici, of course), so the next person to look at them can match them up with less faffing about.

We have people to thank. We had lunch almost every day at Sushi Fuku at 120 Oakland Avenue, just a couple of blocks down Forbes Avenue from the museum. We got to know the manager, Jeremy Gest, and his staff, who were unfailingly friendly and helpful, and who kept us running on top-notch food. So we kept going back. If you find yourself in Pittsburgh, check ’em out. Make time for a sandwich at Primanti Bros., too.

We owe a huge thanks to Calder Dudgeon, who took us up to the skylight catwalk to get the dorsal-view photos of the mounted skeletons (see this post), and especially to Dan Pickering, who moved pallets in collections using the forklift, and moved the lift around the mounted skeletons on Tuesday. Despite about a million ad hoc requests, he never lost patience with us, and in fact he found lots of little ways to help us get our observations and data faster and with less hassle.

Our biggest thanks go to collections manager Amy Henrici, who made the whole week just run smoothly for us. Whatever we needed, she’d find. If we needed something moved, or if we needed to get someplace, she’d figure out how to do it. She was always interested, always cheerful, always helpful. I usually can’t sustain that level of positivity for a whole day, much less a week. So thank you, Amy, sincerely. You have a world-class collection. We’re glad it’s in such good hands.

What’s next? We’ll be posting about stuff we saw and learned in the Carnegie Museum for a long time, probably. And we have manuscripts to get cranking on, some of which were already gestating and just needed the Carnegie visit to push to completion. As always, watch this space.

References

This is what it’s like. The lack of narration is deliberate. We have other videos, which we’ll post at other times, with lots of yap. This one is just for reference, in case later on we need to know what the ischia look like in posterior view, or how the scapulocoracoid is curved, or whatever.

The Apatosaurus louisae walk-around video will be up in the near future. And a similar thing for both skeletons from the second floor balcony. Watch this space!

Mike’s and Matt’s excellent adventure in Pittsburgh continues! Today was Day 4, and just as yesterday offered us a unique opportunity to see the mounted Dipodocus and Apatosaurus skeletons up close on a lift, so today we got to look the two mounts from directly above!

Thanks to our host Amy Henrici and to Calder Dudgeon, we were able to go up to the maintenance balconies above the dinosaur hall, and from there we were able to see this:

It was a little bit scary up there: here’s Matt’s vertical panorama photo of me. Just below the balcony I’m standing on you can see another, which is actually far below up but further back. Below that is the main balcony that overlooks the hall. And below that, the hall itself, showing Diplodocus from above:

We think this is a first: we don’t know of any published photos of mounted sauropods from above — but now, there are some. Let’s take a closer look at the torsos:

Diplodocus carnegii holotype CM 84, torso, in dorsal view, anterior to right.

Apatosaurus louisae holotype CM 3018, torso, in dorsal view, anterior to left.

You can immediately see from here that Apatosaurus is a much broader animal than Diplodocus. That much, we could have guessed. What’s more interesting is that Apatosaurus seems to be slightly broader at the shoulders than at the hips, whereas the opposite is the case in Diplodocus.

This observation left us wondering what’s known about the relative widths of the forelimb and hindlimb articulations in extant animals. What, from the modern bestiary, has hips broader than its shoulders, and what has shoulders wider than its hips? We have no idea. Does anyone know if this has been studied, or better yet summarised?

Four huge beasts

March 13, 2019

Left to right: Allosaurus fragilis, Apatosaurus louisae, Homo sapiens, Diplodocus carnegii.

Hot news! Matt and I will be spending the week of 11th-15th March at the Carnegie Museum in Pittsburgh: the home of the world’s two most definitive sauropods!

The Carnegie Diplodocus, CM 84, is the original from which all those Diplodocus mounts around the globe were taken, and so by far the most-seen sauropod in the world — almost certainly the most-seen dinosaur of any kind.

Diplodocus carnegii mounted holotype specimen CM 84 at the Carnegie Museum, Pittsburgh. Photo by Scott Robert Anselmo, CC By-SA. From Wikimedia.

Like most dinosaur-loving Brits, I grew up with this specimen, in the form of the cast that until recently graced the central hall of the Natural History Museum in London. It defined my concept of what a sauropod is. But I’ve never seen the original before, and I am stoked about it.

Also like most Brits — and American dinophiles often find this hard to believe — I never saw an Apatosaurus skeleton, or indeed any Apatosaurus material, when I was growing up, or even for several years after I started functioning as a palaeontologist. We just don’t have the material over here, so when I saw the mounted Brontosaurus holotype at the Yale Peabody Museum in 2009, it was a big moment for me.

But now, for the first time, I am going to see the definitive apatosaurine specimen, the Apatosaurus louisae holotype CM 3018!

Apatosaurus louisae mounted holotype specimen CM 3018 at the Carnegie Museum, Pittsburgh. Photo by Tadek Kurpaski, CC By. From Wikimedia.

(And I know this is not exactly a new observation here on SV-POW!, but: check out that neck! it’s insane!)

And of course the two big, glamorous mounted sauropods are only the tip of the iceberg. The Carnegie Museum has a ton of awesome material in collection, including Hatcher’s Haplocanthosaurus specimens, the much-loved juvenile apatosaurine cervical sequence CM 555, the Barosaurus cervical sequence CM 1198, and much much more.

We are going to be drowning in sauropods!

I’ll have more to say about this trip shortly, but I just want to close today’s post by saying two things:

First: those of you familiar with the collections at the Carnegie, what are the things that Matt and I should definitely not miss? What will we kick ourselves if we come come without having seen?

And finally: a big thank you to my wife, Fiona, who is finishing up a masters in March and definitely doesn’t need me to be out of the country and unable to help for a week of that final month. She is a marvel, and is sending me anyway.

 

Here’s D10 and the sacrum of Diplodocus AMNH 516 in left lateral and ventral view, from Osborn (1904: fig. 3). Note how the big lateral pneumatic foramina, here labeled ‘pleurocoelia’, start out up at the top of the centrum in D10 and kind of pinch out up there, seemingly entirely absent by S3 (although there is a suspicious-looking shadowed spot above and behind the sacral rib stump labeled ‘r3’). Then on S4 and S5 the big foramina are back, but now they’re low on the centrum, ventral to the sacral ribs. In ventral view, the foramina on D10, S1, and S2 aren’t visible–they’re both over the curve of the centrum, and in the case of S1 and S2, obscured by the sacral ribs. But in S4 and S5, the big lateral foramina are visible in ventral view.

I’ve been interested in a while in this seeming hand-off in centrum pneumatization from dorsolateral, which prevails in the dorsal vertebrae, to ventrolateral, which prevails in the posterior sacral and caudal vertebrae. Almost all sauropod dorsals have the pneumatic foramina quite high on the centrum, sometimes even encroaching on the neural arch. But if sauropod caudals have pneumatic fossae or foramina on the centrum, they’re usually quite low, and almost always below the caudal rib or transverse process (there may also be pneumatic fossae on the neural arch and spine)–for evidence, see Wedel and Taylor (2013b). To me this implies two different sets of diverticula.

I think that in part because sometimes you get both sets of diverticula acting on a single vert. Here’s the centrum of sacral 4 of Haplocanthosaurus CM 879 in right dorsolateral view; anterior is to the right.

Here’s the same thing annotated (yeah, it does look a little like an Ent who is alarmed because his left eye has been overgrown by a huge nasal tumor). This vert has two sets of pneumatic features on the centrum: a big lateral fossa below the sacral rib articulation, presumably homologous with the same feature in S4 of the Diplodocus above; and a smaller dorsolateral fossa above and behind sacral rib articulation.

Unfortunately, CM 879 doesn’t tell us much about how these two sets of diverticula might have changed along the column. The centra of S1-S3 were not found, S5 lacks both sets of fossae, the first caudal has fossae both on the centrum, below the caudal rib, and low on the arch, and the second and subsequent caudals lack both sets of fossae. (I wrote a LOT more about pneumaticity in this individual in my 2009 air sacs paper, which is linked below.)

Working out how these diverticula change serially is a tractable problem. Someone just needs to sit down with a reasonably complete, well-preserved series that includes posterior dorsals, all the sacrals, and the proximal caudals–or ideally several such series–and trace out all of the pneumatic features. As far as I know, that’s never been done, but feel free to correct me if I’ve missed something. I’m neck deep in other stuff, so if someone wants that project, have at it. (If you happen to look into this, I’d be grateful for a heads up, so we don’t run over each other if I do get a yen to investigate further myself.)

References

Diplodocus goes digital

August 21, 2018

No time for a proper post, so here’s a screenshot from Amira of Diplodocus caudal MWC 8239 (the one you saw being CT scanned last post) about to be digitally hemisected. Trust me, you’ll want to click through for the big version. Many thanks to Thierra Nalley for the Amira help.

Further bulletins as time and opportunity allow.