November 27, 2014
Despite the flagrant trolling of its title, Nature‘s recent opinion-piece Open access is tiring out peer reviewers is mostly pretty good. But the implication that the rise of open-access journals has increased the aggregate burden of peer-review is flatly wrong, so I felt obliged to leave a comment explaining why. Here is that comment, promoted to a post of its own (with minor edits for clarity):
Much of what is said here is correct and important. Although it would be nice if Nature could make a bit more of an effort to avoid the obvious conflict-of-interest issues that lead it to title the piece so misleadingly as an attack on open access. I am glad that so many of the other commenters on this piece saw straight through that rather snide piece of propaganda.
Only one important error of interpretation here, I think. I quote:
The rise of the open-access (OA) movement compounds this effect [i.e. the increasing number of articles needing peer-review.] The business case for online OA journals, to which authors pay submission fees, works best at high volume. And for many of these journals, submitted work is published as long as it is methodologically sound. It does not have to demonstrate, for example, the novelty or societal relevance that some traditional journals demand.
The implication is that journals of this kind (PLOS ONE, PeerJ, the various Frontiers journals) increase the total peer-review burden. In fact, the exact opposite is the case. They greatly reduce the the total amount of peer reviewing.
It’s an open secret that nearly every paper eventually gets published somewhere. Under the old regime, the usual approach is to “work down the ladder”, submitting the same paper repeatedly to progressively less prestigious journals until it reached one that was prepared to publish work of the supplied level of sexiness. As a result, many papers go through four, five or more rounds of peer-review before finally finding a home. Instead, such papers when submitted to a review-for-soundness-only venue such as PLOS ONE require only a single round of review. (Assuming of course that they are indeed methodologically sound!)
The rise of review-for-soundness-only journals (“megajournals”) is an unequivocal improvement in the scientific publishing landscape, and should be welcomed by all parties: authors, who no longer have to submit to the monumental waste of time and effort that is the work-down-the-ladder system; readers, who get access to new research much more quickly; and editors and reviewers who no longer have to burn hours re-reviewing and re-re-reviewing perfectly good papers that have already been repeatedly rejected for a perceived lack of glamour.
November 22, 2014
Matt’s post yesterday was one of several posts on this blog that have alluded to Clay Shirky’s now-classic article How We Will Read [archived copy]. Here is the key passage that we keep coming back to:
Publishing is not evolving. Publishing is going away. Because the word “publishing” means a cadre of professionals who are taking on the incredible difficulty and complexity and expense of making something public. That’s not a job anymore. That’s a button. There’s a button that says “publish,” and when you press it, it’s done.
In ye olden times of 1997, it was difficult and expensive to make things public, and it was easy and cheap to keep things private. Privacy was the default setting. We had a class of people called publishers because it took special professional skill to make words and images visible to the public. Now it doesn’t take professional skills. It doesn’t take any skills. It takes a WordPress install.
… and of course as SV-POW! itself demonstrates, it doesn’t even need a WordPress install — you can just use the free online service.
This passage has made a lot of people very excited; and a lot other people very unhappy and even angry. There are several reasons for the widely differing responses, but I think one of the important ones is a pun on the word “publish”.
When Shirky uses the word, he is talking about making something public, available to the world. Which after all is its actual meaning.
But when academics use the word “publish” they usually mean something quite different — they mean the whole process that a research paper goes through between submission and a PDF appearing in a stable location (and in some cases, copies being printed). That process involves many other aspects besides actual publishing — something that in fact Shirky goes straight on to acknowledge:
The question isn’t what happens to publishing — the entire category has been evacuated. The question is, what are the parent professions needed around writing? Publishing isn’t one of them. Editing, we need, desperately. Fact-checking, we need. For some kinds of long-form texts, we need designers.
And this is dead on target. Many writers need editors[*], to varying degrees. Fact-checking could be equated with peer-review, which we pretty much all agree is still very important. Most academic publishers do a certain amount of design (although I suspect that in the great majority of cases this is 99% automatic, and probably involves human judgement only in respect of where to position the illustrations).
But due to the historical accident that it used to be difficult and costly to make and distribute copies, all those other tasks — relatively inexpensive ones, back in the days when distribution was the expensive thing — have become bundled with the actual publishing. With hilarious consequences, as they say. You know, “hilarious” in the sense of “tragic, and breathtakingly frustrating”.
That’s why we’re stuck in an idiot world where, when we need someone to peer-review our manuscript, we usually trade away our copyright in exchange (and not even to the people who provide the expert review). If you stop and think about that for a moment, it makes absolutely no sense. When I recently wrote a book about Doctor Who, I had several people proofread it, but I didn’t hand over copyright to any of them. My ability to distribute copies was not hobbled by having had independent eyes look it over. There is no reason why it should have, and there is no reason why our ability to distribute copies of our academic works should be limited, either.
What we need is the ability to pay a reasonable fee for the services we need — peer-review, layout design, reference linking — and have the work published freely.
Well, wouldja lookit that. Looks like I just invented Gold Open Access.
Is publishing just a button? Yes. Making things public is now trivial to do, and in fact much of what so-called publishers now do is labouring to prevent things from being public. But we do need other things apart from actual publishing — things that publishers have historically provided, for reasons that used to make sense but no longer do.
Exactly what those things are, and how extensive and important they are, is a discussion for another day, but they do exist.
[*] Note: the whole issue of academic publishing is further confused by another pun, this one on the word “editor”. When Shirky refers to editors, he means people who sharpen up an author’s prose — cutting passages, changing word choices, etc. Academic editors very rarely do that, and would be resented if they did. In our world, an “editor” is usually the nominally independent third party who solicits and evaluates peer-reviews, and makes the accept/reject decision. Do we need editors, in this academic sense? We’ll discuss that properly another time, but I’ll say now that I am inclined to think we do.
November 21, 2014
…is not actually about scholarly publication. It’s Steve Albini’s keynote address at Melbourne’s Face the Music conference. It’s about the music industry, and how the internet transformed it from a restrictive, top-down oligarchy that mostly benefited middlemen into a more open, level, vibrant ecosystem where artists can get worldwide exposure for free, and yet are often compensated better than they were under the old system. Go read it, and then think about this:
Once the music world met the internet, the problem of getting information from musicians (authors) to listeners (readers) didn’t require any central planning to solve. What little building needed to happen was taken care of by people who were just happy to let the internet work the way it was designed to, and the way it works the most naturally: it makes sharing information almost effortless. Publishers (record labels) still exist, because they offer certain conveniences, but few people are under the delusion that they are necessary.
Over here in academia, we’ve already spent more than a decade wringing our hands over how to manage the shift from a barrier-based publishing world to one based on OA. We’ve put so much time and effort and thought into the problem of how to “save” or “transform” scholarly publishing. Why do we do that? Why not just walk away? Publishing is a button, and anything that we do to lend it any more importance–anything we feed it, in terms of time, effort, energy, or regard–is wasted. Wasted because we deliberately ignore the new reality in favor of propping up a system that performed a job that no-one needs done anymore. I keep wondering when the hell we’re all going to wake up, and start sharing our work the way that musicians and listeners share digital music.
And yet even out here on the crazy-eyed, axe-wielding fringe of the OA movement, we are still conservative. Zen Faulkes published a paper on his blog, and he did it 26 months ago, which is a near eternity in the Shiny Digital Future (it’s 13.4% of the lifespan to date of Google). Mike and I have admired that move, and talk about it, but we haven’t done it. Why not? We could even solicit peer reviews from people we know to be tough but fair reviewers. We all do unpaid editorial and review work for publishers, why not for each other directly? It’s like we’re thinking, “Okay, okay, I’ll review this paper, but only if there’s a publisher somewhere that will benefit from my unpaid labor!”
I suppose that for us, one answer is that PeerJ has given us other options that are just as easy as blogging, like posting preprints. So I am a bit torn: I like PeerJ, I support it, I have several papers in the pipeline that I’m planning on sending there. It offers certain conveniences, like sticking DOIs on everything for us, and tracking all of our metrics. But do we need PeerJ? I wonder if it is just the methadone that will help ease us out of our sad addiction to publishers.
Bonus observation: don’t just translate Albini’s thoughts on music to scholarly publishing, also try doing the reverse. It becomes pretty clear that the central theme of The Scholarly Kitchen is, “How will poor, helpless music listeners survive without all the middlemen to tell them what to listen to? They’ll be so lost.” Keep polishing that brass, guys, and thanks for the patronization!
The photos are of the dodo skeleton in the Yorkshire Museum, which I saw at SVPCA back in September. If you’re a dodo-phile like me, you should consider supporting Leon Claessens’s, Kenneth Rijsdijk’s, and Hanneke Meijer’s quest to better understand the skull and feeding mechanics of dodos. Their crowdfunding campaign runs through the end of the year–please go check it out.
November 20, 2014
Back in 2013, when we were in the last stages of preparing our paper Caudal pneumaticity and pneumatic hiatuses in the sauropod dinosaurs Giraffatitan and Apatosaurus (Wedel and Taylor 2013b), I noticed that, purely by chance, all ten of the illustrations shared much the same limited colour palette: pale brows and blues (and of course black and white). I’ve always found this strangely appealing. Here’s a composite:
I’m really happy with this coincidence. In fact I think I might get it printed up as a poster for my office.
(Thought: if I did, would anyone else be interested in buying it?)
Update (a couple of hours later)
At Matt’s suggestion, I switched the order of figures 7 and 8 (the last two on the third row) to get the following version of the image. It breaks the canonical order of the figures, but it’s visually more pleasing.
Now we should write an updated version of the paper that reverses the order in which we refer to figures 7 and 8 :-)
- Wedel, Mathew J., and Michael P. Taylor. 2013. Caudal pneumaticity and pneumatic hiatuses in the sauropod dinosaurs Giraffatitan and Apatosaurus. PLOS ONE 8(10):e78213. 14 pages. doi:10.1371/journal.pone.0078213
November 18, 2014
I’ve been reading The Guinness Book of Animal Facts and Feats (Wood 1982) again. Here’s what he says on pages 98-99 about the strength of crocodiles, and what happens when they bite off more than they can chew.
The strength of the crocodile is quite appalling. Deraniyalga (1939) mentions a crocodile in N. Australia which seized and dragged into the river a magnificent 1 tonne Suffolk stallion which had recently been imported from England, despite the fact that this breed of horse can exert a pull of more than 2 tonnes, and there is at least one record of a full-grown black rhinoceros losing a tug-of-war with a big crocodile. Sometimes, however, even crocodiles over-estimate their strength. One day in the 1860s a hunted named Lesley was a witness when a saurian seized the hind-leg of a large bull African elephant while it was bathing in a river in Natal. The crocodile was promptly dragged up the bank by the enraged tusker and then squashed flat by one of its companions who had hurried to the rescue. The victorious elephant then picked up the bloody carcase with its trunk and lodged it in the fork of a nearby tree (Stokes, 1953). Oswell (1894) says he twice found the skeletons of crocodiles 15 ft 4.6 m up in trees by the river’s bank where they had been thrown by angry elephants. On another occasion a surprised crocodile suddenly found itself dangling 15 ft 4.6 m in mid-air when it foolishly seized a drinking giraffe by the head.
The idea of elephants lodging crocodile corpses up in trees seems too bizarre to be true, but seeing it independently attested by two witnesses makes me more ready to accept it. There’s plenty of Internet chatter about this happening, but I’ve not been able to find photos — or better yet, video — proving that it happens.
- Deraniyalga, P. 1939. The tetrapod reptiles of Ceylon, vol. 1: Testudinates and crocodilians. Colombo Nat. Mus., Ceylon.
- Oswell, W. Cotton. 1894. South Africa fifty years ago. Badminton Library of Sports and Pastimes (Big Game Shooting), London.
- Stokes, C. W. 1953. Sanctuary. Cape Town.
- Wood, Gerald L. 1982. The Guinness Book of Animals Facts & Feats (3rd edition). Guinness Superlatives Ltd., Enfield, Middlesex. 252 pp.
November 16, 2014
At the end of October, we published a short piece called CC-By documents cannot be re-enclosed if their publisher is acquired. In an interesting discussion in the comments, moominoid asked:
Isn’t this what happened when DeGruyter acquired BEPress?
This is the announcement of the acquisition. If you visit the journals now, they are behind paywalls, when they were OA before the acquisition.
Having previously read (and commented favourably on) an interview with bepress CEO Jean-Gabriel Bankier, I was disappointed to think this might be true. I emailed him to ask for clarification, and he passed my message on to Irene Kamotsky, bepress’s Director of Strategic Initiatives. A little later, she send a helpful a detailed response, which I now reproduce with her permission.
Date: 10 November 2014 14:27
From: Irene Kamotsky
To: Mike Taylor
Cc: Jean-Gabriel Bankier
Subject: Re: Previous OA journals enclosed behind paywalls?
I apologize for sitting on this for so long — thank you so much for following up, and for clarifying what was, indeed, always a bit confusing about the bepress-published journals that are now with deGruyter.
To answer your question, the bepress journals were not open access in the formal (Budapest) definition of the term, and they never used a CC license. The copyright was traditional publisher-owned copyright, with permission to authors to post their articles on their websites and university IRs.
The bepress journals did have an unusual access policy: we made all articles available to readers for free, as a way to demonstrate demand and urge libraries to subscribe. Basically, if a guest filled out a short form we would grant them access to the article. We would tally those forms by institution and then call the library and ask them to subscribe. There’s an article in Learned Publishing that describes the model in more detail. It wasn’t open access but it was a good balance for many years. Unfortunately, libraries facing strong budget pressures stopped subscribing. They said “we can’t justify paying for a title that our authors can get for free. We have to spend the money on titles that are otherwise unavailable.”
At the same time, we had already developed our institutional repository and publishing platform called Digital Commons. This platform allowed libraries to host and publish their own faculty’s and students’ journals (among all the other digital scholarly content produced on campus), and this has turned out to be an extremely successful approach. There are now nearly 800 journals published by libraries using Digital Commons, the vast majority of which are open access (and none charge author article fees). You can see a brief overview of this new model in a recent report.
I’d be happy to talk more about the new direction in library-led publishing; I know this is a growing interest among UK libraries. Is this something you’re seeing as well?
Thanks again for getting in touch, and clarifying this point.
November 14, 2014
So how did the YPM come to make such a monstrosity? What was it based on? Tune in next time for the surprising details!
I told him at the time that I’d soon get around to writing a post. But before I did, he wrote a post on this himself: Bully for Camarasaurus. And it’s excellent. Go and read it!
I don’t have a lot to add to what Ben has written, except regarding this:
What Marsh had instead [when restoring the skull for his 1891 “Brontosaurus” reconstruction] were a few fragmentary bits of Camarasaurus cranial material, plus a snout and jaw (USNM 5730) now considered to be Brachiosaurus.
Here’s what Marsh came up with:
But what of the supposed Brachiosaurus skull that he used as a reference? It was finally described 107 years later by Carpenter and Tidwell (1998), in a paper that helpfully also lays out the history behind it. Here’s how it looks:
The skull was found by a crew under the supervision of M. P. Felch in the western part of his Quarry 1, Garden Park, Colorado. Felch reported it to O. C. Marsh in a letter of 8 September 1883. It was found by a meter-long cervical vertebra that probably belonged to Brachiosaurus “which was destroyed during attempts to collect it” (McIntosh and Berman 1975:196). [Of course, Felch and Marsh could hardly have been expected to identify this vertebra correctly, as Brachiosaurus would not be discovered and named for another twenty years (Riggs 1903), and the nature of its neck would not become apparent until Janensch (1914) described the related brachiosaurid Giraffatitan (= “Brachiosaurus“) brancai.]
The Felch skull, along with other material from the quarry, was shipped to Marsh at Yale in October of that year, and was initially assigned the specimen number YPM 1986. At that time it was only partially prepared, hence the rather poor resemblance between the restored version above and Marsh’s hypothetical “Brontosaurus” [= Apatosaurus] skull that was based on it.
It’s notable that Holland (1915) was quite certain that this was not a skull of Brontosaurus, and that a Diplodocus-like skull found with the A. louisae holotype belonged to it. It’s worth reading the skull section of his paper to see just how solid his reasoning was. And it’s extraordinary to think that Osborn’s power, all the way over in New York, was so great that he was able to successfully bully Holland, 370 miles away in Pittsburgh, into not putting the evidently correct skull on the Carnegie Museum’s Apatosaurus mount. That mount remained sadly headless until after Holland’s death.
Aaanyway, YPM 1986 was pretty much ignored after Marsh’s abuse of it as a reference for the Brontosaurus reconstruction’s skull. After Marsh’s death in 1899, much of the material collected by Felch was transferred to the Smithsonian (US National Museum of Natural History). The skull was among these specimens, and so was re-catalogued as USNM 5730.
As so often, it was Jack McIntosh who rediscovered this skull and recognised its true affinities. Some time after his tentative identification of the skull as pertaining to Brachiosaurus (presumably on the basis of its resemblance to that of Giraffatitan), Carpenter borrowed the skull, had it more fully prepared, wrote the description, and had a restored model constructed from casts of the preserved elements and models of the missing ones.
Carpenter and Tidwell (1998:fig. 2) also handily showed the restored Felch quarry skull alongside those of other sauropods:
By re-ordering the top row, we can see what a neat intermediate it is between the skulls of Camarasaurus (left) and Giraffatitan (= “Brachiosaurus” of their usage):
I provisionally accepted USNM 5730 as belonging to Brachiosaurus in my re-evaluation of 2009, and included it in my reconstruction (Taylor 2009:fig. 7):
But as noted by Carpenter and Tidwell (1998:82), the lack of comparable parts between the Felch skull and the Brachiosaurus holotype (which remains the only definitive Brachiosaurus material) means that the assignment has to remain tentative.
What we really need is a more complete Brachiosaurus specimen: one with both a skull and good postcervical elements that let us refer it definitively to Brachiosaurus altithorax by comparison with the holotype. And heck, while we’re at it, let’s have a specimen with a good neck, too!
The real question remains: how did Marsh, using a brachiosaur skull as his basis, come up with this?
And stranger still, how someone at the Yale Peabody Museum — we don’t know who — used it, or more likely Marsh’s reconstruction, as a basis for this sculpture:
The Yale mount didn’t go up until 1931 — the last of the Big Four Apatosaurus mounts after the AMNH, Carnegie and Field Museum, which is surprising as it was the first of those specimens to be found. So by the time the skull was sculpted, sauropod skulls were actually reasonably well known. It’s not clear quite how anyone working from a decent reconstruction of, say, a Camarasaurus skull — the one in Osborn and Mook (1921:figure 30), say — could come up with this monster.
The last thing to say is this: it does credit to the YPM that they display this historically important sculpture rather than hiding it away and pretending it never happened. For me, part of the fascination of palaeontology is seeing not just how organisms evolved through prehistory but how ideas evolved through history. It’s great that we can still see important mistakes, alongside their corrections (i.e. the new and lovely skull on the YPM Apatosaurus mount.)
- Carpenter, Kenneth, and Virginia Tidwell. 1998. Preliminary description of a Brachiosaurus skull from Felch Quarry 1, Garden Park, Colorado. Modern Geology 23:69-84.
- Holland, William J. 1915. Heads and tails: a few notes relating to the structure of the sauropod dinosaurs. Annals of the Carnegie Museum 9:273-278.
- Janensch, Werner. 1914. Ubersicht uber der Wirbeltierfauna der Tendaguru-Schichten nebst einer kurzen Charakterisierung der neu aufgefuhrten Arten von Sauropoden. Archiv fur Biontologie, Berlin III, 1(1):81-110.
- Marsh, O. C. 1891. Restoration of Triceratops (with plates XV and XVI). American Journal of Science, 3rd series 41(244):339-342.
- McIntosh, John S., and David, S. Berman. 1975. Description of the palate and lower jaw of the sauropod dinosaur Diplodocus (Reptilia: Saurischia) with remarks on the nature of the skull of Apatosaurus. Journal of Paleontology 49(1):187-199.
- Osborn, Henry Fairfield, and Charles C. Mook. 1921. Camarasaurus, Amphicoelias and other sauropods of Cope. Memoirs of the American Museum of Natural History, n.s. 3:247-387, and plates LX-LXXXV.
- Riggs, Elmer S. 1903. Brachiosaurus altithorax, the largest known dinosaur. American Journal of Science 15(4):299-306.
- Taylor, Michael P. 2009. A re-evaluation of Brachiosaurus altithorax Riggs 1903 (Dinosauria, Sauropoda) and its generic separation from Giraffatitan brancai (Janensch 1914). Journal of Vertebrate Paleontology 29(3):787-806.