My talk on copyright, from the University of Manchester’s “Open Knowledge in Higher Education” course
January 5, 2017
Back in February last year, I had the privilege of giving one of the talks in the University of Manchester’s PGCert course “Open Knowledge in Higher Education“. I took the subject “Should science always be open?”
My plan was to give an extended version of a talk I’d given previously at ESOF 2014. But the sessions before mine raised all sorts of issues about copyright, and its effect on scholarly communication and the progress of science, and so I found myself veering off piste. The first eight and a half minutes are as planned; from there, I go off on an extended tangent. Well. See what you think.
The money quote (starting at 12m10s): “What is copyright? It’s a machine for preventing the creation of wealth.”
January 2, 2017
Welcome to 2017! Let’s start the year with a cautionary tale. I’ll leap straight to the moral, then give an example: it’s very easy to reach the wrong conclusion about fossils from photos. That’s because no single photo can give an accurate impression of distortion. For that, you need at least a much bigger selection of photos; or better still, a 3d model; or of course best of all, the fossil itself.
Here’s the motivating example:
A correspondent — I will not divulge his or her name unless the person in question chooses to reveal it — had looked over the slides for our 2016 SVPCA talk on new Barosaurus specimens, which claims that Jensen’s Dry Mesa “Supersaurus” cervical BYU 9024 actually belongs to Barosaurus.
Matt and I felt, based largely on the degree of neural spine bifurcation, that the BYU vertebra compares most similarly to C9 of the AMNH specimen — the middle one in the top row of the composite illustration above. But my correspondent put together the composite, and wrote [lightly edited for clarity]:
I’ve already compared BYU 9024 with the AMNH cervicals, I attach a photo, because for me it is also very similar to C14: the centrum is much more similar to C14 than C9, I think. What do you think about this?
Like I said: you always need to be careful about interpreting any one view of a fossil. In this case, BYU 9024 is misleading in lateral view because the CPOLs are folded upwards and inwards, and the ventrolateral flanges are (to a lesser extent) folded downwards and inwards — making the posterior part of the centrum look much taller (and rather narrower) than it really is.
This is hard to see in photos, because the fossil is so smashed up and the matrix is so visually similar to the bone, but take a look at the posterior view (with anterior to the right of the photo):
Here are the key parts, annotated, as best I can make out. (And bear in mind that even I am not sure, after having spent a whole day with the fossil, and with literally hundreds of photos to consult.)
As you can see, the centrum accounts for only a small proportion of the apparent height of the posterior end of the vertebra — and even that is probably exaggerated, as the eccentricity of the condyle indicates that crushing has increased its height at the expense of its width.
Put it all together, and Jensen’s much-derided sculpture of what the vertebra should have looked like is actually pretty good:
December 21, 2016
I’m back in Oklahoma for the holidays, and anytime I’m near Norman I pop in to the OMNH to see old friends, both living and fossil. Here’s the Aquilops display in the hall of ancient life, which has been up for a while now. I got some pictures of it when I was here back in March, just never got around to posting them.
Aquilops close up. You can’t see it well in this pic, but on the upper right is a cast of the Aquilops cranium with a prosthesis that shows what the missing bits would have looked like. That prosthesis was sculpted by – who else? – Kyle Davies, the OMNH head preparator and general sculpting/molding/casting sorceror. You’ve seen his work on the baby apatosaur in this post. I have casts of everything shown here – original fossil, fossil-plus-prosthesis, and reconstructed 3D skull – and I should post on them. Something to do in the new year.
The Aquilops display is set just opposite the Antlers Formation exhibit, which has a family of Tenontosaurus being menaced by two Deinonychus, and at the transition between Early and Late Cretaceous. The one mount in the Late Cretaceous area is the big Pentaceratops, which is one of the best things in this or any museum.
Evidence in support of that assertion. Standing directly in front of this monster is a breathtaking experience, which I highly recommend to everyone.
It’s just perfect that you can see the smallest and earliest (at least for now) North American ceratopsian adjacent to one of the largest and latest. Evolution, baby!
I didn’t only look at dinosaurs – the life-size bronze mammoth in the south rotunda is always worth a visit, especially in holiday regalia.
No holiday post about the OMNH would be complete without a shot of “Santaposeidon” (previously seen here). I will never get tired of this!
The chances that I’ll get anything else posted in 2016 hover near zero, so I hope you all have a safe and happy holiday season and a wonderful New Year.
December 14, 2016
In the summer of 2015, Brian Engh and I stopped at the Copper Ridge dinosaur trackway on our way back from the field. The Copper Ridge site is 23 miles north of Moab, off US Highway 191. You can find a map, directions, and some basic information about the site in this brochure. The BLM has done a great job of making this and other Moab-area dinosaur trackways accessible to the public, with well-tended trails and nice interpretive signage. Brian has gotten to do the art for interp signs at several sites now, including Copper Ridge, and he put together this video to explain a bit about the site, what we know about the trackmaker, and the lines of evidence he used in making his life restoration. I’m in there, too, yammering a bit about which sauropod might have been responsible. We weren’t sure what, if anything, we would end up doing with the footage at the time, so I’m basically thinking out loud. But that’s mostly what I do here anyway, so I reckon you’ll live.
Stay tuned (to Brian’s paleoart channel) for Part 2, which will be about the Copper Ridge theropod trackway. And the next time you’re in the Moab area, go see some dinosaur tracks. This is our heritage, and it’s cool.
December 12, 2016
Back at the start of September, I noted that Tschopp and Mateus (2016) had published a petition to the ICZN, asking them to establish Diplodocus carnegii as the type specimen of the genus Diplodocus — a role that I argued it already fulfils in practice.
I wrote a formal comment in support of the petition, which I submitted on 7 September; and the next day I had word from the secretary of the ICZN that it had been received and would be published in the next issue of the BZN — the Bulletin of Zoological Nomenclature.
Since then I have had emails from a couple of different people asking me for the formal citation details of my comment, and I have made three or four separate attempts to discover whether it’s appeared in BZN yet. And I have been completely unable to find out.
First stop is the ICZN web-site’s case-finder, available in the sidebar at pages such as Cases and List of Available Names. But that doesn’t find Case 3700 (the Diplodocus case). I don’t just mean it doesn’t find my comment; it doesn’t find the case at all.
By poking around the site at random, I found this page, which has a tree-structured list of cases in its sidebar. Towards the bottom is a link to Case 3700 — hurrah! — but that link just says “BZN view could not find any content :(”
All right, then, let’s go to the ICZN’s site’s page about the Bulletin. As the page itself proudly proclaims in the sidebar, “The Bulletin of Zoological Nomenclature (ISSN:0007-5167) is the official periodical of the International Commission on Zoological Nomenclature”. And yet the page content just says:
Either no literature content has been added to this site, or it has not yet been indexed. Indexing can take up to one hour, so please check back later.
So I tried a more general search for the BZN elsewhere on the Web.
- There is an archive of BZN at BiotaxaNews but it contains only one issue, 72(3) of September 2015.
- BioStor has archives for BZN but they stop at 2007.
- The Internet Archive has some bits and pieces, but no coherent archive that I can find.
All in all, there seems to be literally no meaningful Web presence of the Bulletin of Zoological Nomenclature — which is the journal of record for, well, Zoological Nomenclature. If, like me, you want to discover the status of cases … well, you just can’t.
So my question is: *knock knock* is anyone home?
Here’s why this matters. It’s well established that Zoological Taxonomy is important (e.g. Vink et al. 2012) and that as a discipline it’s under threat. Now, the ICZN is the only game in town when it comes to authoritative taxonomy. It is the undisputed guardian of the zoological taxonomic record, and it’s had to weather threats to its own existence before a recent injection of funding. So it’s crucial that, as the standard bearer of its field, the ICZN does a solid, competent, professional, reliable job.
That has to start with making the journal of record available — or at least, if the Commission really really doesn’t want to go open access, making its table of contents available so people can see what’s been decided. If that’s not happening, then whatever decisions the Commission makes are the sound of a tree falling in a deserted forest.
We need the ICZN to up its game.
- Tschopp, Emanuel, and Octávio Mateus. 2016. Case 3700: Diplodocus Marsh, 1878 (Dinosauria, Sauropoda): proposed designation of D. carnegii Hatcher, 1901 as the type species. Bulletin of Zoological Nomenclature 73(1):17-24.
- Vink, Cor J., Pierre Paquin and Robert H. Cruickshank. 2012. Taxonomy and Irreproducible Biological Science. BioScience 62(5):451-452.
November 25, 2016
So I came across this tweet from Laurent Gatto, who’s head of the Computational Proteomics Unit at the University of Cambridge, UK:
My immediate reaction was not to retweet. Why? Because I am not comfortable recommending rejection (or acceptance!) of something I’ve not seen. I said so, and Laurent explained the real issue:
So I have two simple questions:
First, How can this massive spending on public money possibly be confidential? What justification can there possibly be for that? And second, how can there be meaningful discussion of the offer on the table if no-one knows what it is?
And then I remembered the classic explanation of confidentiality clauses from Elsevier’s David Tempest: “we have this level of confidentiality […] Otherwise everybody would drive down, drive down, drive drive drive”.
So my first reaction was to say that if anyone comes across a leaked copy of the draft agreement, let me know and I will link to it from this post. But I am also open to hear from anyone who thinks there is a legitimate reason, that I’ve not thought of, to enforce confidentiality. So if you have a reason, please mention it in the comments. If not, but you know where there is a leaked copy, email me privately on email@example.com.
November 21, 2016
The question of whether sauropod cervicals got longer through ontogeny came up in the comment thread on Mike’s “How horrifying was the neck of Barosaurus?” post, and rather than bury this as a comment, I’m promoting it to a post of its own.
The short answer is, yeah, in most sauropods, and maybe all, the cervical vertebrae did lengthen over ontogeny. This is obvious from looking at the vertebrae of very young (dog-sized) sauropods and comparing them to those of adults. If you want it quantified for two well-known taxa, fortunately that work was published 16 years ago – I ran the numbers for Apatosaurus and Camarasaurus to see if it was plausible for Sauroposeidon to be synonymous with Pleurocoelus, which was a real concern back in the late ’90s (the answer is a resounding ‘no’). From Wedel et al. (2000b: pp. 368-369):
Despite the inadequacies of the type material of Pleurocoelus, and the uncertainties involved with referred material, the genus can be distinguished from Brachiosaurus and Sauroposeidon, even considering ontogenetic variation. The cervical vertebrae of Pleurocoelus are uniformly short, with a maximum EI of only 2.4 in all of the Arundel material (Table 4). For a juvenile cervical of these proportions to develop into an elongate cervical comparable to those of Sauroposeidon, the length of the centrum would have to increase by more than 100% relative to its diameter. Comparisons to taxa whose ontogenetic development can be estimated suggest much more modest increases in length.
Carpenter & McIntosh (1994) described cervical vertebrae from juvenile individuals of Apatosaurus and Camarasaurus. Measurements and proportions of cervical vertebrae from adults and juveniles of each genus are given in Table 4. The vertebrae from juvenile specimens of Apatosaurus have an average EI 2.0. Vertebrae from adult specimens of Apatosaurus excelsus and A. louisae show an average EI of 2.7, with an upper limit of 3.3. If the juvenile vertebrae are typical for Apatosaurus, they suggest that Apatosaurus vertebrae lengthened by 35 to 65% relative to centrum diameter in the course of development.
The vertebrae from juvenile specimens of Camarasaurus have an average EI of 1.8 and a maximum of 2.3. The relatively long-necked Camarasaurus lewisi is represented by a single skeleton, whereas the shorter-necked C. grandis, C. lentus, and C. supremus are each represented by several specimens (McIntosh, Miller, et al. 1996), and it is likely that the juvenile individuals of Camarasaurus belong to one of the latter species. In AMNH 5761, referred to C. supremus, the average EI of the cervical vertebrae is 2.4, with a maximum of 3.5. These ratios represent an increase in length relative to diameter of 30 to 50% over the juvenile Camarasaurus.
If the ontogenetic changes in EI observed in Apatosaurus and Camarasaurus are typical for sauropods, then it is very unlikely that Pleurocoelus could have achieved the distinctive vertebral proportions of either Brachiosaurus or Sauroposeidon.
A few things about this:
- From what I’ve seen, the elongation of the individual vertebrae over ontogeny seems to be complete by the time sauropods are 1/2 to 2/3 of adult size. I get this from looking at mid-sized subadults like CM 555 and the hordes of similar individuals at BYU, the Museum of Western Colorado, and other places. So to get to the question posed in the comment thread on Mike’s giant Baro post – from what I’ve seen (anecdata), a giant, Supersaurus-class Barosaurus would not necessarily have a proportionally longer neck than AMNH 6341. It might have a proportionally longer neck, I just haven’t seen anything yet that strongly suggests that. More work needed.
- Juvenile sauropod cervicals are not only shorter than those of adults, they also have less complex pneumatic morphology. That was the point of the figure at the top of the post. But that very simple generalization is about all we know so far – this is an area that could use a LOT more work.
- I’ve complained before about papers mostly being remember for one thing, even if they say many things. This is the canonical example – no-one ever seems to remember the vertebrae-elongating-over-ontogeny stuff from Wedel et al. (2000b). Maybe that’s an argument for breaking up long, kitchen-sink papers into two or more separate publications?