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 firstname.lastname@example.org.
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?
November 18, 2016
Oh man, 2016, you are really working on my nerves.
Sometimes it’s a positive balm to hold a piece of an animal dead and gone for 145 million years, or stare at a thousand vertical feet of sandstone, and know that we are all ants.
These lovelies here intrigue me deeply. They’re the three caudal vertebrae recovered from the Snowmass Haplocanthosaurus that John Foster and I described a couple of years ago. Pretty sure I’ll have more to say about them in the future. For now it’s enough that they’ve come across such a vast gulf of time and given this stressed-out primate a little perspective.
Foster, J.R., and Wedel, M.J. 2014. Haplocanthosaurus (Saurischia: Sauropoda) from the lower Morrison Formation (Upper Jurassic) near Snowmass, Colorado. Volumina Jurassica 12(2): 197–210. DOI: 10.5604/17313708 .1130144
November 2, 2016
I’ve been writing for Sky & Telescope, the American astronomy magazine, for a year now. My first feature article was published last December (details here), my second came out this April (ditto), and my latest is in the current (December 2016) issue, which should be hitting newsstands this week. I’ve also been writing the “Binocular Highlight” column since June.
My latest feature article, “Twelve Steps to Infinity”, is my favorite thing I’ve ever written about astronomy, and maybe my favorite thing I’ve ever written, period.* I’m posting about it here because the concept should be interesting to all students of the past: the speed of light is finite, so when we look out into space, we are also looking back in time. We see the moon as it was 1.28 seconds ago, the sun as it was 8.3 minutes ago, Jupiter anywhere from 33 minutes to over an hour ago, depending on whether we’re on the same side of the sun or not, and Neptune after four hours – at that distance, our 16-light-minute swing around the sun hardly makes a difference. Most of the stars visible to the naked eye are within 2000 light years, which is 2% or less of the diameter of our Milky Way galaxy. With binoculars or a small telescope you can track down numerous external galaxies and see them as they appeared tens of millions of years ago. One of my favorite observations is seeing the light of the quasar 3C 273, which started traveling 2.4 billion years ago, when our single-celled ancestors were gearing up for the Great Oxygenation Event. (If you’d like to replicate that feat yourself, you can get a very capable, “lifetime” telescope for a little over a hundred bucks. I recommend the Orion SkyScanner 100 – see this and this for more information.)
My new Sky & Tel article doesn’t go nearly that far back – in fact, I don’t even make it out of the Cenozoic. But the concept scales all the way out, so if a particular event in Phanerozoic history is near to your heart, there is probably a star, nebula, cluster, or galaxy whose light left at the right time, which you could observe with binoculars or a small telescope (although the distribution is gappy between half a million and 30 million light years, where there just aren’t that many nearby galaxies). The Messier and Caldwell catalogs are good places to start, and there are hordes of online resources (many funded by your tax dollars by way of NASA) you can use to find a match. If I get really motivated I might post a table of easily-observed celestial objects and their lookback times. In the meantime, if you have a date in mind, leave it in a comment and I’ll find something temporally close for you to go look at.
Lots of people provided assistance and inspiration. Steve Sittig, who runs the Hefner Observatory at the Webb Schools here in Claremont, helped me refine the idea through numerous conversations, and did a trial observing run with me last autumn. Fellow paleontologists Alan Shabel and Thierra Nalley guided me on hominid history (needless to say, any remaining errors are mine). My editor at Sky & Telescope, S.N. Johnson-Roehr, made numerous small improvements, and the S&T art department made the article even more beautiful than I had hoped. Finally, the little plesiadapiforms at the end of the piece are there thanks to Pat Holroyd, who introduced me to them when I was at Berkeley. Many thanks, folks!
October 29, 2016
We keep selling out of books, which is a nice problem to have, but still a problem for people who want books. So we’re getting a final shipment this morning, and Mark Hallett and I will be at the JHUP booth signing books, starting at 12:15 and going until we run out of either customers or books.
Many, many thanks to everyone who has gotten a book or just stopped by to chat. We’re humbled by the great response we’ve gotten.
Parting question: someone on Facebook asked if we could sign and mail bookplates for folks who can’t get to our signings. I’m cool with that, just curious about how much interest there might be. Let me know in the comments.
October 28, 2016
The interview that I did for Jisc was conducted via Skype, by the very able Michelle Pauli. We talked for some time, and obviously much of what was said had to be cut for length (and no doubt some repetition).
To my pleasant surprise, though, Michelle prepared a complete transcript of our talk before the cutting started. So in the tradition of DVD movies, I am now able to offer the Deleted Scenes. I hope that some of what follows is of interest.
How would you describe the current state of play of open access in the UK?
I think there are two answers to that. One is it’s enormously encouraging that it’s come so far over the last few years. The other is it’s just terribly discouraging that there’s so very far to go and that so much of the control of how we go about publishing things is still in the hands of organisations that really have no interest — in the full sense — in how science progresses but really are driven primarily by what publishing can do for them commercially.
How about the level of debate in recent times?
The situation is that we have these huge, very well-established publishers that have been running and dominating the game for decades, and commercial consolidations have meant that even the relatively small number of publishers that dominated 20 years ago now are even fewer now — so people like Elsevier and Wiley and Taylor & Francis now control a vast proportion of the overall academic publishing market.
So those organisations obviously exist primarily to make money for their shareholders or their owners. I’m not saying they have no other motivations but that’s their primary motivation and certainly the executives that they hire to run the companies have that goal very much in mind. So it’s not surprising that those companies are desperate to hang onto what is essentially a cash mill for them,where they’re working with content that’s generated by very highly skilled professionals, where they pay no money in exchange for that content, and go onto sell it.
Obviously, they’re desperate to hang on to that market model and, as a result, what we often see from representatives of these publishers is statements that are, I think … charitably you could say are terribly misinformed; a more cynical and perhaps more realistic perspective would be that they’re deliberately misleading and clouding issues, trying to reopen discussions that have long been decided, casting doubt on things that really carry no doubt, forever equivocating and trying to add complexity to what are essentially simple discussions.
So what we end up is with situations where we have groups of people with an interest in open access and scholarly publishing more generally, when you have them gathered together, and we could have been having discussions about how precisely we want to push the whole thing forward; but you always find people from these major publishers as well, always impeding those discussions and throwing up road blocks and ifs and buts and maybes, and slowing things down or bringing them to a complete halt. So that’s what I mean about the quality of the discussion.
Although the quality of the debate within the open access advocacy field is also quite, I can’t think of the word. What word am I looking at here?
It can be disappointingly rancorous at times …
… and the reason is that we’ve got these two routes towards open access which we call Gold and Green. And each of those have advocates, who at times seem to be not so much open access advocates who favour one of the routes but advocates for one of the routes who are actively opposed to the other routes. And that can be unhelpful. But that said, they are some very difficult discussions to reach a conclusion on and I admit I go backwards and forwards on this myself, which of these two approaches is going to be better in the long term.
People talk about gold open access suffering from the fact that it’s expensive. Of course that’s only true if you ignore the money that they spend on subscriptions while they’re running Green open access. So I think a lot of the arguments that are used in favour of either of those routes against the other can be misleading, and probably to some degree is also tied up with the degree of emotional investment people have in the different approaches.
How are things going to move forward? What’s the best way to work with legacy publishers to keep things moving forward or is that not even possible, and then what happens?
Honestly, my take is that the existence of the legacy publishers is a net negative. If I could wave a magic wand and have those publishers cease to exist overnight, I would do it unhesitatingly. Then we’d have a period of two or three months of chaos and then we’d settle into an equilibrium that I think would be much better than what we have at the moment.
I’m not really interested in working with the legacy publishers at the moment. I have often tried to communicate constructively with people from Elsevier in particular and along the way I’ve written lots of blog posts about how I feel Elsevier could change its behaviour in a way that would make it not just tolerable but actively seen as a friend of progress. I’ve reached a point now where I’ve realized that just isn’t going to happen and I don’t really feel that there’s any … while there are individuals at all of those publishers who would very much like to do the right thing, the organisations they are working for just makes it impossible. Not going to work.
We won’t make good progress by for example persuading Elsevier to slightly loosen their requirements on which things can be published as green open access and how long the embargos are and what license they are available under. I think ultimately where we need to get to is somewhere where we just not beholden to these organisations at all and we’re doing what’s best for scholarship rather than what’s best for Elsevier.
Going back to infrastructure, and the possibilities that are there, does the community have to get to own its own infrastructure otherwise you’d have a situation with Elsevier and SSRN and Mendeley and it being taken over again. How does that work?
[Part of the answer was included in the published interview. Then:] Whatever we build absolutely needs to be wrapped around with these kinds of things, and that’s to do with the software being open for example so that if a bad actor does somehow gain control of the organisation then it can be forked and run elsewhere. It’s to do with having financial firewalls between various parts of the organisation. There’s a whole bunch of stuff that they’ve really thought through in detail.
I wonder if you could put on your futurologist hat now and finally say what do you think is going to happen next in open access?
I couldn’t pick one out. There are several possibilities. One is that we’re starting to see deals coming up now where large organisations are getting offsetting for open access article processing charges with the big publishers. What they’re doing is trying to make a sort of revenue-neutral conversion from the current system to a gold open access one. It may be that that eventually catches on and becomes the way that increasing numbers of organisations and countries make things happen. Would I be happy with that? Yeah, I would. Because although I still think it’s bad that these large corporations should have control over the scientific record, I think if it’s freely available to anyone that’s still a huge step forward from where we are now.
Another possibility we’re seeing is that every now and then we’re starting to get stories about universities just cancelling various subscription contracts — or, more realistically, not renewing them when they expire — and finding other ways to make do. Presumably, the money that they were spending on that, they’re investing in other more open forms of scholarly infrastructure. So the long term future that I suppose I would like to see is an increase, an acceleration in that tendency. Resulting in far more money being diverted from subscriptions and being put into other ways of disseminating scholarly outputs.
Will Brexit have any impact on this area?
Yeah, what a horrible thought. A lot of the really good things that have been happening in open access recently have been in the European Union. So you probably know that Horizon 2020 programme has an enormous amount of funding for open access, and for building open access infrastructure, it is responsible for the OpenAire repository which is joining up the scholarly record of European countries all around the continent. The idea of being isolated from all of that is just one of the many awful consequences of the most short sighted political decision in my lifetime.
So yeah, absolutely it’s a setback. Because everything we want to do in academia completely doesn’t respect national boundaries at all. By its very nature what we do is international and we have international collaborators and we work in other countries. So anything like this, that’s to do with rebuilding the historic borders that used to separate our various countries, is a terrible step back not only for academia but for civilisation.