A pox on your numbered references, redux
April 2, 2013
Folks,
I am preparing a manuscript for PLOS ONE, which uses numbered references rather than author+date citations like sane journals. And I am hating it. I am taking perfectly good statements like:
Juvenile sauropods have proportionally short cervicals (Wedel et al. 200: 368–369, Fig. 14, and Table 4)
And reformatting them as:
Juvenile sauropods have proportionally short cervicals [31]: 368–369, Fig. 14, and Table 4.
Which doesn’t look right at all.
My question: how, when using numbered references, can I properly refer to page-range and figure number? Because there has to be a way — doesn’t there?
Surely it can’t be the case that in the culture of numbered-reference journals, you just don’t bother to specify with any more precision than pointing at a 46-page paper? I know Science ‘n’ Nature don’t care much about science or nature, but they can’t be that sloppy, can they? And if they are, I’d be horrified to find that the PLOS journals are so infected with me-too that they’re prepared to copy such poor practice?
The House of Lords’ terribly disappointing report on Open Access
February 22, 2013
A while back, I submitted evidence to the House of Lords’ inquiry into Open Access — pointlessly, as it turns out, since they were too busy listening to the whining of publishers, and of misinformed traditionalist academics who hadn’t taken the trouble to learn about OA before making public statements about it.
Today the Lords’ report [PDF version] is out, summarised here. And it’s a crushing disappointment. As I’d feared, this inquiry didn’t represent an opportunity to forge ahead, but a retreat. The RCUK’s excellent OA policy is to be emasculated by a more gradual implementation, the acceptance of longer embargoes and a toning down of the preference for Gold over Green. (While there is case for Green in the abstract, the form of Green required by the RCUK policy is much weaker that its form of Gold, in that it doesn’t require a liberal licence such as would enable text-mining, use in education, etc.)
On top of that, RCUK have been criticised for “lack of clarity”: quite unfair since their policy is pretty explicit and in any case has twice been clarified on their blog. This is not a hard resource to find: anyone honestly concerned about a perceived lack of clarity could find it in ten seconds of googling. RCUK also caught criticism for lack of consultation — also unfairly, as they made a call for comments which I also responded to.
RCUK has responded apologetically to all this — “Lessons have been learned and we will continue to actively engage with the academic and publishing sectors” as though the publishing sector has any right to a say. I would much rather RCUK had shown the balls to stick with the leadership they initially provided, but I assume they’re under political pressures and were left with no choice. Instead, venality from publishers, ignorance from certain academics and cowardice from the Lords has conspired to strip the UK of its leadership in OA, and reduce it to being a follower.
As Nature News editor Richard Van Noorden said, “In other words, RCUK in response promises nothing it wasn’t doing already”. And the reason was rather diplomatically stated by ICL researcher Stephen Curry: ”Not 100% convinced their lordships have mastered topic”. You can say that again.
Taking a step back — and a deep breath — the weakened RCUK policy is still A Good Thing — just a much less good thing than it could have been, and was on track to be. At a time when radical new journals like eLife and PeerJ are showing just how much better our publishing ecosystem can be, it’s desperately disappointing to see the Lords backing an approach to OA that will mean we
- keep paying $5333 per article in subscriptions,
- don’t see the work until two years after it’s fresh,
- even then get only a draft instead of the final versions, and
- don’t have permission to actually do anything with it.
What I would like to see from RCUK now is a statement that, if the public that funds our research is to face yet longer embargoes before it can see that work, it must at least be allowed to use it when it gets it. RCUK must insist on CC BY for the Green arm of its policy.
Giving it both barrels at the Guardian
January 17, 2013
My new article is up at the Guardian. This time, I have taken off the Conciliatory Hat, and I’m saying it how I honestly believe it is: publishing your science behind a paywall is immoral. And the reasons we use to persuade ourselves it’s acceptable really don’t hold up.
Read Choose open access: publishing your science behind a paywall is immoral
Because for all that we rightly talk about the financial efficiencies of open access, when it comes right down to it OA is primarily a moral, or if you prefer idealogical, issue. It’s not really about saving money, though that’s a welcome side-effect. It’s about doing what’s right.
I’m expecting some kick-back on this one. Fire away; I’ll enjoy the discussion.
Welcome Kaatedocus: this is how to illustrate a sauropod
December 20, 2012
A couple of days ago, a paper by Tschopp and Mateus (2012) described and named a new diplodocine from the Morrison Formation, Kaatedocus siberi, based on a beautifully preserved specimen consisting of a complete skull and the first fourteen cervical vertebrae.
Unfortunately, the authors chose to publish their work in the Journal of Systematic Palaeontology, a paywalled journal, which means that most of you reading this will be unable to read the actual paper — at least, not unless you care enough to pay £27 for the privilege.
So you’ll just have to take my word for it when I tell you that it’s a fine, detailed piece of work, weighing in at 36 pages. It features lavish illustrations of the skull, but we won’t trouble you with those. The vertebrae are illustrated rather less comprehensively, though still better than in most papers:
Tschopp and Matteus (2012: figure 9). A, Photograph and B, drawings of the mid-cervical vertebrae of the holotype of Kaatedocus siberi (SMA 0004). Photograph in lateral view and to scale, CV 8 shown in the drawings is indicated by an asterisk. Drawings of CV 8 (B) in dorsal (1), lateral (2), ventral (3), posterior (4) and anterior (5) views. Scale bars = 4 cm.
It should be immediately apparent from these lateral views that the vertebra are rather Diplodocus-like. But the hot news is that there is a great raft of free supplementary information, including full five-orthogonal-view photos of all fourteen vertebrae!
Here is just one of them, C6, in glorious high resolution (click through for the full awesome):
Now, folks, that is how to illustrate a sauropod in 2012! The goal of a good descriptive paper is to be the closest thing possible to a proxy for the specimen itself, and you just can’t do that if you don’t illustrate every element from multiple directions. By getting this so spectacularly right, Tschopp and Matteus have made their paper the best illustrated sauropod descriptions for 91 years. (Yes, I am talking about Osborn and Mook 1921.)
It’s just a shame that all the awe-inspiring illustrations are tucked away in supplementary information rather than in the paper itself. Had the paper been published in a PLOS journal, for example, all the goodness could have been in one place, and it would all have been open access.
Is Kaatedocus valid?
There’s a bit of a fashion these days for drive-by synonymisation of dinosaurs, and sure enough no sooner had Brian Switek written about Kaatedocus for his new National Geographic blog than comments started cropping up arguing (or in some cases just stating) that Kaatedocus is merely Barosaurus.
It’s not. I spent a lot of time with true Barosaurus cervicals at Yale this summer, and those of Kaatedocus are nothing like them. Here is Tschopp and Mateus’s supplementary figure of C14:
And here is a posterior vertebra — possibly also C14 — of the Barosaurus holotype YPM 429, in dorsal and right lateral views:
Even allowing for a certain amount of post-mortem distortion and “creative” restoration, it should be immediately apparent that (A) Barosaurus is much weirder than most people realise, and (B) Kaatedocus ain’t it.
There may be more of a case to be made that Kaatedocus is Diplodocus — but that’s the point: it there’s a case, then it needs to be actually made, which means a point-by-point response to the diagnostic characters proposed by the authors in their careful, detailed study based on months of work with the actual specimens.
There seems to be an idea abroad at the moment that it’s somehow more conservative or sober or scientific to assume everything is a ontogenomorph of everything else — possibly catalysed by the Horner lab’s ongoing “Toroceratops” initiative and subsequent cavalier treatment of Morrison sauropods — maybe even by the Amphidocobrontowaassea paper. Folks, there is no intrinsic merit in assuming less diversity. Historically, the Victorian sauropod palaeontologists of England did at least as much taxonomic damage by assumptions of synonymy (everything’s Cetiosaurus or Ornithopsis — whatever that is) as they did by raising new taxa. The thing to do is find the hypothesis best supported by evidence, not presupposing that either splitting or lumping is a priori the more virtuous course.
Sermon ends.
Morrison sauropod diversity
As we’ve pointed out a few times in our published work, sauropod diversity in the Kimmeridgian-Tithonian in general, and in the Morrison Formation in particular, was off-the-scale crazy. There’s good evidence for at least a dozen sauropod genera in the Morrison, and more than fifteen species. Kaatedocus extends this record yet further, giving us a picture of an amazing ecosystem positively abundant with numerous species of giant animals bigger than anything alive on land today.
Sometimes you’ll hear people use this observation as a working-backwards piece of evidence that Morrison sauropods are oversplit. Nuh-uh. We have to assess taxonomy on its own grounds, then see what it tells us about ecosystem. As Dave Hone’s new paper affirms (among many others), Mesozoic ecosystem were not like modern ones. We have to resist the insidious temptation to assume that what we would have seen in the Late Jurassic is somehow analogous to what we see today on the Serengeti.
Hutton’s (or Lyell’s) idea that “the present is the key to the past” may be helpful in geology. But despite its roots as a branch of the discipline, the palaeontology we do today is not geology. When we’re thinking about ancient ecosystems, we’re talking about palaeobiology, and in that field the idea that the present is the key to the past is at best unhelpful, at worst positively misleading.
Sermon ends.
But isn’t the Kaatedocus holotype privately owned?
You’ve had two sermons already, I’m sure we can all agree that’s plenty for one blog post. I will return to this subject in a subsequent post.
Sermon doesn’t even get started.
References
Publish means “make public”. Paywalls are the opposite of publishing
October 16, 2012
“But Mike”, you say, “What’s wrong with publishers making a profit?”
Nothing is wrong with publishers making a profit.
PLOS made an operating profit of 21.5% in 2011 (though they plough it back into their mission “to accelerate progress in science and medicine by leading a transformation in research communication”.) BioMed Central also makes a profit, and since they are a for-profit company they get to keep it, distribute it to shareholders, or what have you. Good on them.
If you can make money by publishing research, that’s great.
The issue is not publishers who make money. The issue is corporations that go by the title “publishers”, but which in fact make money by preventing publication.
Because “publish” means “make public”. The whole point of a publisher is to make things public. The reason the scientists of 30 years ago sent their papers to a publisher was because having a publisher print them on paper and ship them around the world was the most effective way to make them public. And subscriptions were the obvious way to pay for that work. But now that anything can be made public instantly — “Publishing is not a job any more, it’s a button” — giving papers to a “publisher” that locks them behind a firewall is the opposite of publishing. It’s privating.
–
Yesterday we saw an appalling demonstration of why this is so important. The barrier-based textbook publisher Pearson found that in 2007 a teacher had posted a copy of the Beck Hopelessness Scale on his blog. It’s a 20-question list, intended to help prevent suicide, and totals 279 words. It was published in 1974, and Pearson holds the copyright, selling copies for $120 – $6 per question, or 43¢ per word.
So naturally Pearson saw their profits being eaten into by the free availability of the Beck Scale. Naturally, rather than contacting the blog author, or the network that it’s part of, they sent a DMCA takedown notice to ServerBeach, who host the web server that the blog was on. And naturally ServerBeach shut down the entire site twelve hours later.
This site, Edublogs, is home to 1,451,943 teacher and student blogs. Yes, you read that right. One and a half million blogs.
So to recap: because a teacher five years ago posted a copy of 279-word, 38-year-old questionnaire that costs $120, the publisher shut down 1.5 million blogs. That works out at 0.008¢ per blog.
We could talk all day about all the things that went wrong here — the ludicrously unbalanced DMCA (“half a DeMoCrAcy”), the idiot response of ServerBeach — but I want to focus on one issue. The reason Pearson issued a DMCA takedown is because they make their money by preventing access. It’s the nature of the beast. If your business model is to prevent people from making things public, then this kind of thing is inevitable. Whereas it is literally impossible for PLOS or BMC ever to perpetrate this kind of idiocy because their business model is to make things public. When someone else takes a thing that they have made public and makes it more public, then great! No-one has to issue any DMCA takedowns!
And this is why there is a fundamental, unbridgeable divide between open-access publishers and barrier-based publishers. It’s why no amount of special programmes, limited-time zero-cost access options, reductions in subscription rates, access to back-issues and so on will ever really make any difference. The bottom line is that we want one thing — access to research — and barrier-based “publishers” want the exact opposite.
However nice they are, however much their hearts are in the right place, they want one thing and we want the opposite. And that just won’t do.
They’re going to have to go. All of them.
Saturday Night in New York City
June 17, 2012
It’s five to ten on Saturday night. Matt and I are in New York City. We could be at the all-you-can-eat sushi buffet a couple of blocks down from our hotel, or watching a film, or doing all sorts of cool stuff.
Instead, we’re in our hotel room. Matt is reformatting the bibliography of our neck-elongation manuscript, and I am tweaking the format of the citations.
Just sayin’.
A completely pointless mini-rant on journal guidelines
June 15, 2012
I am finalising an article for submission to Palaeontologia Electronica. Regarding the acknowledgements, the Contrubutor Instructions say: “Initials are used rather than given names.”
WHY?! What on earth is gained by forcing authors to thank R. Cifelli instead of Rich Cifelli for access to specimens?
And of course this is the tiniest tip of the pointless-reformatting iceberg. Do not get me started on citations and reference, tables, figure captions, headings and all the rest.
The utter, utter pointlessness of such rules is irking me more with each submission I make. It’s indicative of the long-entrenched power-balance that we’ve all internalised, where authors are supplicants to journals, of whom we craved the boon of publication.
This. Is. Stupid.
We take highly trained scientists and put them to work doing tedious, time-consuming, error-prone clerical work which has the net result of reducing the utility of the paper.
Bring on the revolution.
See, this is why publishers irritate me so much
May 17, 2012
I just read this in a Times Higher Eduction report on David Willetts’s recent speech:
Graham Taylor, director of academic publishing at the Publishers Association, said … that publishers would be content with a “leveraged acceleration” of moves towards author-pays open access (the “gold” model) – provided that funding to pay the associated article fees was in place.
What publishers would not accept, Mr Taylor made clear, was Research Councils UK’s suggestion, in its draft new open-access policy, that authors could choose instead to deposit their papers in open-access repositories within an “overly short” embargo period of six months after publication.
Oh, so publishers “will not accept” Green OA?
Where the hell do they get the arrogance to assume that a funding body needs their permission to say how their money is going to be spent? If the government gives me £300 to build a shed and stipulates that it has to be made from renewable wood, the timber yard does not get to say say it “will not accept” that condition.
It’s none of the publishers’ damned business what conditions funding bodies impose on recipients. None. None of their business. At all. Until the publishers start being funders they have no say in the funder-recipient relationship. None.
Am I repeating myself? Very well; I contain multitudes.
Here’s how it works, publishers. The funding body supplies the money, which means it lays down the rules. If the funder says “author must deposit final accepted manuscript in public repository six months after publication” (or indeed “immediately on acceptance”), then those are the rules; in accepting a grant, recipients are agreeing to abide by them. You, the publishers, then have a simple choice. You may accept authors’ articles on that basis; or you may decline to publish them. That’s your prerogative: when I submit my manuscript to your journal, you are at liberty to tell me “the conditions imposed by your funding body make it unattractive for us to publish your work, so we decline your submission”. And then I will go and find another publisher — one that’s not stuck in 1970s.
But that is the only say you have. Funders set the rules. Take it or leave it.
Just because you’ve been living on funding bodies’ money for decades does not mean you get a say in their policy. Tapeworms don’t get to dictate their host’s actions, either. You either provide a service that is acceptable to funders, or you will be bypassed.
That is all.
Don’t write “exhibit” when you mean “have”
May 8, 2012
Question. I am supposed to be meeting up with Mike Taylor at the conference, but we’ve not met before and I won’t recognise him. Do you know what he looks like?
Candidate Answer #1. He’s a bit overweight and has white hair.
Candidate Answer #2. He exhibits mild to moderate abdominal hypertrophy and accelerated ontogenetic degradation in the pigmentation of the cranial integument.
You wouldn’t use answer #2 in Real Life, so don’t use it in your papers. It’s not big, and it’s not clever.
A response to one Elsevier employee, and an open letter to the rest
February 15, 2012
In a comment on the last post, an Elsevier employee wrote:
Elsevier’s support for the Research Works Act comes down to a question of preferring voluntary partnerships to promote access to research, rather than being subjected to inflexible government mandates like the NIH policy, which seek to dictate how journal articles or accepted manuscripts are disseminated without involving publishers.
While we do appreciate that you’re trying to engage us here, you’re going to have to show a little more effort than just parroting the company line. To be frank, this is a load of crap.
First off, if the NIH pays for the research, the NIH should have a say in how the results of that research are disseminated. We don’t have to talk in oblique terms about what “involving publishers” means, because everyone’s motives are perfectly transparent and known to everyone else. The NIH wants the research results available to everyone who wants them with a minimum of hassle and ideally at no cost to the user, which is understandable since the NIH has already paid for it once. The researchers want the research results available to everyone who wants them with a minimum of hassle and ideally at no cost. And the readers want the research results available to everyone who wants them with a minimum of hassle and ideally at no cost. The publishers–and let’s be specific here and note that we’re really talking about corporate for-profit publishers–want to maximize their profits by selling the research community’s results back to them with just enough “added value” to justify their claim of ownership of those results, and to do that by maximizing costs (whether hassle is something they deliberately set about to create or just a stupid side-effect of the roadblocks set up to restrict access is an open question).
So the corporate for-profit publishers’ motives are directly opposed to everyone else’s: those who pay for the research, those who carry it out, and those who consume it.
What’s going on here is that those latter three groups are (very belatedly) realizing that it’s completely bogus to have all of their desires thwarted by the one player in the game who gives the least and charges the most.
Alternatively I could just cite Cameron Neylon’s wonderful observation that, “Publishers never really did have a business model, they had a public subsidy.”
Also: “voluntary partnerships to promote access to research” my ass. How does Elsevier expect to continue making such immense profits if the other “partners” are in the relationship voluntarily? In any case, all this talk about “promoting access to research” is more folderol. If you want people to have access to research, you just give them access (it’s not hard). If your corporation can’t find a way to do that and satisfy shareholders, boo-hoo. To riff on a great phrase by Tom Holtz, “Sorry if that makes some people feel bad, but I’m not in the ‘make the corporate parasites fattening at the public teat feel good’ business; I’m one of the researchers you’ve been screwing.”
I’ll also note that Elsevier and the other corporate for-profit publishers have had a LOT of opportunities to cultivate goodwill among researchers, and not taken them. For starters–and I am not the first or even the thousandth person to mention this–why not charge a reasonable download fee of, say, $1-5 per paper, instead of $30-50? We all know it’s an outrageous ripoff, but no-one is making any moves to change it. Putting together fake journals full of paid ads masquerading as papers doesn’t look so good either. But surely paying off Congresspeople to sponsor a bill that most funding agencies, researchers, and readers–you know, the groups you’re allegedly trying to engage in conversation–view as actively evil has been the biggest misstep.
So, what do I want Elsevier to do? I want it to do what Mike suggested–throw its support behind the FRPAA–and then restructure itself as an open-access publisher. That will probably mean saying goodbye to 30+% annual profit margins, but hey, wake up. If PLoS ONE can offer no length limits, no full color figure limits, and full BOAI-compliant open access for $1350, charging $3000 for an inferior product is the definition of a broken business model.
Such a restructuring is probably impossible for Elsevier, given its corporate mandate to maximize profits for shareholders, and if so, I’ll settle for it just dying. Karma’s a bitch. I signed the declaration of independence, so Elsevier’s already dead to me anyway.
Note that I’m speaking here of the corporation dying, not its constituent humans. Although there must be a few real worms in there to have conceived all of the shenanigans that Elsevier has perpetrated recently, I’m sure that the vast majority of Elsevier employees are honest people of good conscience. If you’re one of them, what I’d like you, personally, to do is either agitate for change from within, if you can pursue that course wholeheartedly, or go work somewhere else. Elsevier isn’t the only publisher in the world. There’s a reason why some people won’t work for the tobacco industry or companies that make land mines: their consciences won’t let them.
If, on the other hand, you choose to not only identify with Elsevier but to try to defend the practices that got it into this mess, don’t be surprised if you don’t get much sympathy from the people your corporation is currently screwing and actively seeking to screw even harder in the future, and don’t complain if we call BS on your arguments and fire back with our own.
