Matt’s Brachiosaurus in the wild
February 16, 2020
No, not his new Brachiosaurus humerus — his photograph of the Chicago Brachiosaurus mount, which he cut out and cleaned up seven years ago:
This image has been on quite a journey. Since Matt published this cleaned-up photo, and furnished it under the Creative Commons Attribution (CC By) licence, it has been adopted as the lead image of Wikipedia’s Brachiosaurus page [archvied]:
Consequently (I assume) it has now become Google’s top hit for brachiosaurus skeleton:
Last Saturday, Fiona and I went to Birdland, a birds-only zoo in the Cotswolds, about an hour away from where we live. The admission price also includes “Jurassic Journey”, a walking tour of a dozen or so not-very-good dinosaur models. In an interpretive centre in this area, I found this Brachiosaurus skeletal reconstruction stencilled on the wall:
I immediately knew it was the Chicago mount due to the combination of Giraffatitan anterior dorsals and Brachiosaurus posterior dorsals; but I found it more hauntingly familiar than that. A quick hunt turned up Matt’s seven-year-old post, and when I told Matt about my discovery he filled me in on its use in Wikipedia.
So this is 99% of a good story: we’re delighted that this work is out there, and has resulted in a much better Brachiosaurus image at Birdland than the rather sad-looking Stegosaurus next to it. The only slight disappointment is that I couldn’t find any sign of credit, which they really should have included given that Matt put the image out under CC By rather than in the public domain.
But as Matt said: “Even though I didn’t get credited, I’m always chuffed to see my stuff out in the world.” So true.
Tutorial 19g: Open Access definitions and clarifications, part 7: why your open-access journal should use the CC By licence
October 15, 2019
Matt and I are about to submit a paper. One of the journals we considered — and would have really liked in many respects — turned out to use the CC By-NC-SA license. This is a a very well-intentioned licence that allows free use except for commercial purposes, and which imposes the same licence on all derivative works. While that sounds good, there are solid reasons to prefer the simpler CC By licence. I wrote to the journal in question advocating a switch to CC By, and then I thought the reasoning might be of broader interest. So here’s what I wrote, lightly edited.
First, CC By neatly expresses the one requirement all academics have of their work: that they get credit for it. When we publish papers, we are happy for them to be freely distributed, but also want people to build on them, re-using parts in whatever way helps, provided we’re credited — and that is exactly what CC By enables.
Second, because of this, many funders that require the work their grantees do to be published open access specifically require the CC By licence, in the expectation that it will provide the greatest societal benefit in exchange for their investment. Most famously, this is the case for the Gates Foundation (the largest private foundation in the world), but for a partial list of the many other funders with this policy, see https://www.springernature.com/gp/open-research/funding/funders-requiring-cc-by-for-articles — funders whose grantees, as things stand, are not allowed to publish their work in your journal.
Third, CC By is almost universal among well established and respected open-access journals, including all the PLOS journals, PeerJ, the BioMed Central journals, the Hindawi journals, eLIFE, Nature’s Scientific Reports, and palaeo journals such as Acta Palaeontologica Polonica and Palarch’s Journal of Vertebrate Paleontology. This is important because CC By-licenced journals can’t freely use material published under more restrictive licences such as your journal’s CC By-NC-SA. Instead, authors of such articles must labouriously seek exemptions from the copyright holders of the material they wish to reuse or adapt.
Fourth and last, other online resources also use CC By (or optionally CC By-SA in the case of Wikipedia), which means that, while material from PLOS ONE, Scientific Reports et al. can be freely used in Wikipedia articles, text and illustrations from articles in your journal cannot, limiting its use in outreach. Similarly, even on our own palaeontology blog, we would have concerns about using By-NC-SA materials as we use Patreon to solicit donations and our blog is arguably therefore commercial. (Part of the problem with the NC clause is that there is no rigorous definition of “commercial”.)
For all these reasons, we believe that your journal would better serve its authors, its readers, the academic community and broader society if its articles were published under the CC By licence. We hope that, if you agree, you are able to some point to help the journal make this transition. And if there’s anything Matt or I can do to assist that process, we’ll be happy to.
On the philosophy of what research is for
August 8, 2019
I’m a bit shocked to find it’s now more than five years since Robert Harington’s Scholarly Kitchen post Open Access: Fundamentals to Fundamentalists. I wrote a response in the comments, meaning to also post it here, but got distracted, and then half a decade passed. Here it is, finally. The indented parts are quotes from Harington.
I must admit to being rather tired of the fundamentalism that pervades discussions around open access policies and business models. On the one hand there are the advocates, and through the laws of conservation of energy, the equal and opposite reaction of anti-open access advocacy. There seems little room for rational debate about open access in the midst of such an antagonistic atmosphere.
It’s always a powerful rhetorical move to call your opponent a fundamentalist. It’s also a lazy one. It absolves you from the tedious responsibility of bothering to understand what the opponent actually wants: just dismiss him has a fundamentalist and call it done. I’d hope we’re better than that. At best, this seems like a fine demonstration of the principle that “there seems little room for rational debate about open access in the midst of such an antagonistic atmosphere”.
You want a rational debate? You want to talk about fundamentals? Fine, let’s do that. Here is the most fundamental question of all: what is research for? Our answer to this will profoundly affect every stance we adopt regarding publishing, OA, researcher evalution and more.
The greatest problem we have in discussing these issues is when person A assumes right off the bat that person B has the same answer to that fundamental question, and is then surprised to find that B disagrees over numerous implementation details. All those details flow from the fundamental mismatch. A and B are literally trying to solve two different problems — no wonder they can’t agree on the solution!
So what is research for? Here are three possible answers.
A. Some people believe (or maybe I should say assume) that research is for the world — for the betterment of the lot of society as a whole, the eradication of illness, the understanding of the environment, and generally the benefit of humanity. As pleasant side-effects, it also feeds publishing businesses and advances researchers’ careers.
B. Some people believe (or assume) that research is primarily for the benefit of the economy: that the principle purpose of the whole process is the financial benefit that accrues to publishers and related professions. As pleasant side-effects, it also advances the world’s knowledge and advances researchers’ careers.
C. Some people believe (or assume, or at least give the impression of assuming) that research is mostly about the careers of researchers — about giving them a way to prove their merit and advance up the career ladder. As pleasant side-effects, it also advances the world’s knowledge and feeds publishing businesses.
All of these fundamental positions exist. (There may be others that I missed.) We could probably all classify various individuals into these groups (but I’ll resist the temptation to throw in examples, as that would surely result in an epic sidetrack).
Notice that one can’t reach one of these three positions by any amount of thought about what happens within the research/publication ecosystem. It’s more fundamental than that. That decision has to come from somewhere outside. For example, my own position is no secret: I am an “A”, and the reason is because I feel it follows from the Golden Rule (“Do to others as you would have them do to you”, Luke 6:31) — probably the most universally agreed ethical principle in any religion (and among those who profess none).
And so when Robert Harrington asks:
The real debate here is to understand more about the motivations and needs of a researcher, who may or may not be funded directly. What is the best business model that will allow a researcher to publish work effectively and allow readers access to that work?
That is really two ——quite separate questions that may have completely different answers: 1, what business model will allow a researcher to publish work effectively?; and 2, what business model will allow readers access to that work? If you are an “A”, you’ll care most about the second question; if you’re a “C” you’ll care about the first question; and if you’re a “B” you might still be thinking about the business model mentioned at the start of the question.
It’s fruitless to expect “A”s, “B”c and “C”s to agree on an answer to a question when each group is hearing a different question.
Here’s another example:
The real story here is that the rights and desires of academics are being represented by organizations that do not reflect their needs, and that perhaps do not even understanding them. There is a form of fundamentalism that dictates to academics that this is what you need; just let us lead the way and we will make things right for you.
This statement suggests a “C” mindset: that the rights and desires of researchers are paramount. But if the organisations in question are “A”s (as for example you’d expect the Alliance for Taxpayer Access or RCUK to be), then this complaint is a non-issue. Of course they don’t reflect researchers’ desires — that’s not what they’re there for. They reflect the needs of broader society (which are often aligned with those of researchers, but by no means always).
That’s not a bug. That’s a feature.
And similarly:
I would suggest that there is nothing fundamentally wrong with a subscription model.
This may be true for “B”s (who might prefer the subscription model because they think it yields the most revenue) and for “C”s (who might want to place their work in a specific paywalled journal that is well regarded in their field). But it’s much less likely for “A”s, who see great public benefit in free access, and conversely great harm in arbitrary barriers.
So there you go. Fundamentals.
We may never know how flexible sauropod necks were
November 8, 2018
The more I look at the problem of how flexible sauropod necks were, the more I think we’re going to struggle to ever know their range of motion It’s just too dependent on soft tissue that doesn’t fossilise. Consider for example the difference between horse necks (above) and camel necks (below).
The skeletons of both consist of vertebrae that are pronouncedly opisthocoelous (convex in front and concave behind), so you might think their necks would be similarly flexible.
But the balls of horse cevicals are deeply embedded in their corresponding sockets, while those of camels have so much cartilage around and between them that the tip of the ball doesn’t even reach the rim of the socket. As a result of this (and maybe other factors), camel necks are far more flexible than those of horses.
Which do sauropod necks resemble? We don’t currently know, and we may never know. It will help if someone gets a good handle on osteological correlates of intervertebral cartilage.
[This post is recycled and expanded from a comment that I left on a Tetrapod Zoology post, but since Tet Zoo ate that comment it’s just as well I kept a copy.]
Will we ever find the biggest dinosaur?
June 12, 2015
I was contacted recently by David Goldenberg (dgoldenberg@gmail.com), a journalist who’s putting together a piece on the biggest dinosaurs. He asked me a few questions, and since I’d taken the time to write answers I thought I may as well post them here.
1) Do you think that we will ever know what the largest dinosaur (by mass) was?
In principle, we can never know that we’ve found the largest dinosaur. All we can know (and we probably can’t really know even this, as we’ll see below) is that we’ve found the largest so far. If we were dealing with animals where there’s a good sample size, there would be statistical techniques that we could use to figure out the likely size-range. But most giant dinosaur species are known only a handful of specimens — sometimes only a single one. How big did Puertasaurus get? We can’t possibly say: the best we can do is estimate how big the one known specimen of Puertasaurus was.
That said, we can sort of get a feel for size classes. There are quite a few sauropods that seem to come in at around 30-40 tonnes — Brachiosaurus, Giraffatitan, Supersaurus, Dreadnoughtus — which suggests there might be some kind of a limit there. But there are bigger titanosaurs (Argentinosaurus, Puertasaurus, Futalognkosaurus) which show that if the barrier exists at all, it’s a “soft” one. And of course the tantalising hints of super-giant sauropods.
There are at least three of these: Amphicoelias fragillimus, a diplodocid known from a drawing of a vertebral arch which has since been lost or destroyed, which could well have massed 100 tonnes. Bruhathkayosaurus, a giant titanosaur known from a two-meter tibia, since destroyed, which could conceivably have massed twice that; and the Broome Sandstone track-maker, known only from footprints, which might have been somewhere in between.
Any one of those, we might write off and say it’s too good to be true — all three stories are pretty vague as to evidence and require a lot of guesswork in the inferences. But the fact that we have all three of these makes me feel pretty certain that there were indeed sauropods out there in the 100-200 tonne range (i.e. the size of big whales). I only hope we find solid, verifiable, curated evidence for them some time soon.
2) What bones do you need to have before you can make an accurate measurement?
You can’t ever make an accurate measurement. Consider even a really well represented, essentially complete specimen such as MB.R.2181 (previously known as HM S II), the giant mounted skeleton in the Museum für Naturkunde Berlin. Peer-reviewed published estimates of the mass of that one individual have varied between 13,618 and 78,258 kg — a factor of 5.75. Even if you discard these obvious outlier estimates, recent and credible estimates vary from 23,337 to 38,000 kg, which is still a factor of 1.63.
And this is not completely crazy. Two humans with essentially identical skeletons can weigh 70 and 114 kg, after all. Soft tissue is essentially impossible to predict.
3) What do you make of the fact that so many different species have been given the title? Is that the fault of the media or scientists or what?
A big part of is that it depends on what you count. That Berlin brachiosaur is the biggest dinosaur known from an essentially complete skeleton, so Giraffatitan is a legitimate holder of the crown. (Confusing matters further, it used to be thought to be a species of Brachiosaurus). But there were definitely bigger sauropods than that — just not known from such complete specimens. Argentinosaurus was certainly bigger, for example. But there’s no way to put a meaningful whole-body mass estimate on it.
But yes, there is also an understandable tendency towards sensationalism, both from scientists and the press. There have been plenty of new discoveries that can legitimately be described as “could be the biggest yet”.
Copyright from the lens of reality
May 7, 2015
This post is a response to Copyright from the lens of a lawyer (and poet), posted a couple of days ago by Elsevier’s General Counsel, Mark Seeley. Yes, I am a slave to SIWOTI syndrome. No, I shouldn’t be wasting my time responding to this. Yes, I ought to be working on that exciting new manuscript that we SV-POW!er Rangers have up and running. But but but … I can’t just let this go.
Copyright from the lens of a lawyer (and poet) is a defence of Elsevier’s practice of having copyright encumber scientific publishing. I tried to read it in the name of fairness. It didn’t go well. The very first sentence is wrong:
It is often said that copyright law is about a balance of interests and communities, creators and users, and ultimately society as a whole.
No. Copyright is not a balance between competing interests; it’s a bargain that society makes. We, the people, give up some rights in exchange for incentivising creative people to make new work, because that new work is of value to society. To quote the US constitution’s helpful clause, copyrights exist “To promote the Progress of Science and useful Arts” — not for authors, but for wider society. And certainly not of publishers who coerce authors to donate copyright!
(To be fair to Seeley, he did hedge by writing “It is often said that copyright law is about a balance”. That is technically true. It is often said; it’s just wrong.)
Well, that’s three paragraphs on the first sentence of Elsevier’s defence of copyright. I suppose I’d better move on.
The STM journal publishing sector is constantly adjusting to find the right balance between researcher needs and the journal business model, as refracted through copyright.
Wrong wrong wrong. We don’t look for a balance between researchers needs (i.e. science) and the journal business model. Journals are there to serve science. That’s what they’re for.
Then we have the quote from Mark Fischer:
I submit that society benefits when the best creative spirits can be full-time creators and not part-timers doing whatever else (other than writing, composing, painting, etc.) they have to do to pay the rent.
This may be true. But it is totally irrelevant to scholarly copyright. That should hardly need pointing out, but here it is for those hard of thinking. Scholars make no money from the copyright in the work they do, because (under the Elsevier model) they hand that copyright over to the publisher. Their living comes in the form of grants and salaries, not royalties.
Ready for the next one?
The alternatives to a copyright-based market for published works and other creative works are based on near-medieval concepts of patronage, government subsidy […]
Woah! Governments subsidising research and publication is “near-medieval”? And there we were thinking it was by far the most widespread model. Silly us. We were all near-medieval all this time.
Someone please tell me this is a joke.
Moving swiftly on …
Loud advocates for “copyright reform” suggest that the copyright industries have too much power […] My comparatively contrarian view is that this ignores the enormous creative efforts and societal benefits that arise from authoring and producing the original creative work in the first place: works that identify and enable key scientific discoveries, medical treatments, profound insights, and emotionally powerful narratives and musical experiences.
Wait, wait. Are we now saying that … uh, the only reason we get scientific discoveries and medical treatment because … er … because of copyright? Is that it? That can’t be it. Can it?
Copyright has no role in enabling this. None.
In fact, it’s worse than that. The only role of copyright in modern scholarly publishing is to prevent societal benefits arising from scientific and medical research.
The article then wanders off into an (admittedly interesting) history of Seeley’s background as a poet, and as a publisher of literary magazines. The conclusion of this section is:
Of course creators and scientists want visibility […] At the very least, they’d like to see some benefit and support from their work. Copyright law is a way of helping make that happen.
This article continues to baffle. The argument, if you want to dignify it with that name, seems to be:
- poets like copyright
- => we copyright other people’s science
- => … profit!
Well, that was incoherent. But never mind: finally we come to part of the article that makes sense:
- There is the “idea-expression” dichotomy — that copyright protects expression but not the fundamental ideas expressed in a copyright work.
This is correct, of course. That shouldn’t be cause for comment, coming from a copyright lawyer, but the point needs to be made because the last time an Elsevier lawyer blogged, she confused plagiarism with copyright violation. So in that respect, this new blog is a step forward.
But then the article takes a sudden left turn:
The question of the appropriateness of copyright, or “authors’ rights,” in the academic field, particularly with respect to research journal articles, is sometimes controversial. In a way quite similar to poets, avant-garde literary writers and, for that matter, legal scholars, research academics do not rely directly on income from their journal article publishing.
Er, wait, what? So you admit that scholarly authors do not benefit from copyright in their articles? We all agree, then, do we? Then … what was the first half of the article supposed to be about?
And in light of this, what on earth are we to make of this:
There is sometimes a simplistic “repugnance” about the core publishing concept that journal publishers request rights from authors and in return sell or license those rights to journal subscribers or article purchasers.
Seeley got that much right! (Apart from the mystifyingly snide use of “simplistic” and the inexplicable scare-quotes.) The question is why he considers this remotely surprising. Why would anyone not find such a system repugnant? (That was a rhetorical question, but here’s the answer anyway: because they make a massive profit from it. That is the only reason.)
Well, we’re into the final stretch. The last paragraph
Some of the criticism of the involvement of commercial publishing and academic research is simply prejudice, in my view;
Yes. Some of us are irrationally prejudiced against a system where, having laboriously created new knowledge, it’s then locked up behind a paywall. It’s like the irrational prejudice some coal-miners have against the idea of the coal they dig up being immediately buried again.
And finally, this:
Some members of the academic community […] base their criticism on idealism.
Isn’t that odd? I have never understood why some people consider “idealism” to be a criticism. I accept it as high praise. People who are not idealists have nothing to base their pragmatism on. They are pragmatic, sure, but to what end?
So what are we left with? What is Seeley’s article actually about? It’s very hard to pick out a coherent thread. If there is one, it seems to be this: copyright is helpful for some artists, so it follows that scholarly authors should donate their copyright to for-profit publishers. That is a consequence that, to my mind, does not follow particularly naturally from the hypothesis.
Open-access megajournals reduce the peer-review burden
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.
Interview with Open Access Nigeria
October 22, 2014
Last night, I did a Twitter interview with Open Access Nigeria (@OpenAccessNG). To make it easy to follow in real time, I created a list whose only members were me and OA Nigeria. But because Twitter lists posts in reverse order, and because each individual tweet is encumbered with so much chrome, it’s rather an awkward way to read a sustained argument.
So here is a transcript of those tweets, only lightly edited. They are in bold; I am in regular font. Enjoy!
—
So @MikeTaylor Good evening and welcome. Twitterville wants to meet you briefly. Who is Mike Taylor?
In real life, I’m a computer programmer with Index Data, a tiny software house that does a lot of open-source programming. But I’m also a researching scientist — a vertebrate palaeontologist, working on sauropods: the biggest and best of the dinosaurs. Somehow I fit that second career into my evenings and weekends, thanks to a very understanding wife (Hi, Fiona!) …
As of a few years ago, I publish all my dinosaur research open access, and I regret ever having let any of my work go behind paywalls. You can find all my papers online, and read much more about them on the blog that I co-write with Matt Wedel. That blog is called Sauropod Vertebra Picture of the Week, or SV-POW! for short, and it is itself open access (CC By)
Sorry for the long answer, I will try to be more concise with the next question!
Ok @MikeTaylor That’s just great! There’s been so much noise around twitter, the orange colour featuring prominently. What’s that about?
Actually, to be honest, I’m not really up to speed with open-access week (which I think is what the orange is all about). I found a while back that I just can’t be properly on Twitter, otherwise it eats all my time. So these days, rather selfishly, I mostly only use Twitter to say things and get into conversations, rather than to monitor the zeitgeist.
That said, orange got established as the colour of open access a long time ago, and is enshrined in the logo:
In the end I suppose open-access week doesn’t hit my buttons too strongly because I am trying to lead a whole open-access life.
… uh, but thanks for inviting me to do this interview, anyway! :-)
You’re welcome @MikeTaylor. So what is open access?
Open Access, or OA, is the term describing a concept so simple and obvious and naturally right that you’d hardly think it needs a name. It just means making the results of research freely available on the Internet for anyone to read, remix and otherwise use.
You might reasonably ask, why is there any other kind of published research other than open access? And the only answer is, historical inertia. For reasons that seemed to make some kind of sense at the time, the whole research ecosystem has got itself locked into this crazy equilibrium where most published research is locked up where almost no-one can see it, and where even the tiny proportion of people who can read published works aren’t allowed to make much use of them.
So to answer the question: the open-access movement is an attempt to undo this damage, and to make the research world sane.
Are there factors perpetuating this inertia you talked about?
Oh, so many factors perpetuting the inertia. Let me list a few …
- Old-school researchers who grew up when it was hard to find papers, and don’t see why young whippersnappers should have it easier
- Old-school publishers who have got used to making profits of 30-40% turnover (they get content donated to them, then charge subscriptions)
- University administrators who make hiring/promotion/tenure decisions based on which old-school journals a researcher’s papers are in.
- Feeble politicians who think it’s important to keep the publishing sector profitable, even at the expense of crippling research.
I’m sure there are plenty of others who I’ve overlooked for the moment. I always say regarding this that there’s plenty of blame to go round.
(This, by the way, is why I called the current situation an equilibrium. It’s stable. Won’t fix itself, and needs to be disturbed.)
So these publishers who put scholarly articles behind paywalls online, do they pay the researchers for publishing their work?
HAHAHAHAHAHAHAHAHAHA!
Oh, sorry, please excuse me while I wipe the tears of mirth from my eyes. An academic publisher? Paying an author? Hahahahaha! No.
Not only do academic publishers never pay authors, in many cases they also levy page charges — that is, they charge the authors. So they get paid once by the author, in page-charges, then again by all the libraries that subscribe to read the paywalled papers. Which of course is why, even with their gross inefficiencies, they’re able to make these 30-40% profit margins.
So @MikeTaylor why do many researchers continue to take their work to these restricted access publishers and what can we do about it?
There are a few reasons that play into this together …
Part of it is just habit, especially among more senior researchers who’ve been using the same journals for 20 or 30 years.
But what’s more pernicious is the tendency of academics — and even worse, academic administrators — to evaluate research not by its inherent quality, but by the prestige of the journal that publishes it. It’s just horrifyingly easy for administrators to say “He got three papers out that year, but they were in journals with low Impact Factors.”
Which is wrong-headed on so many levels.
First of all, they should be looking at the work itself, and making an assessment of how well it was done: rigour, clarity, reproducibility. But it’s much easier just to count citations, and say “Oh, this has been cited 50 times, it must be good!” But of course papers are not always cited because they’re good. Sometimes they’re cited precisely because they’re so bad! For example, no doubt the profoundly flawed Arsenic Life paper has been cited many times — by people pointing out its numerous problems.
But wait, it’s much worse than that! Lazy or impatient administrators won’t count how many times a paper has been cited. Instead they will use a surrogate: the Impact Factor (IF), which is a measure not of papers but of journals.
Roughly, the IF measures the average number of citations received by papers that are published in the journal. So at best it’s a measure of journal quality (and a terrible measure of that, too, but let’s not get into that). The real damage is done when the IF is used to evaluate not journals, but the papers that appear in them.
And because that’s so widespread, researchers are often desperate to get their work into journals that have high IFs, even if they’re not OA. So we have an idiot situation where a selfish, rational researcher is best able to advance her career by doing the worst thing for science.
(And BTW, counter-intuitively, the number of citations an individual paper receives is NOT correlated significantly with the journal’s IF. Bjorn Brembs has discussed this extensively, and also shows that IF is correlated with retraction rate. So in many respects the high-IF journals are actually the worst ones you can possibly publish your work in. Yet people feel obliged to.)
*pant* *pant* *pant* OK, I had better stop answering this question, and move on to the next. Sorry to go on so long. (But really! :-) )
This is actually all so enlightening. You just criticised Citation Index along with Impact Factor but OA advocates tend to hold up a higher Citation Index as a reason to publish Open Access. What do you think regarding this?
I think that’s realpolitik. To be honest, I am also kind of pleased that the PLOS journals have pretty good Impact Factors: not because I think the IFs mean anything, but because they make those journals attractive to old-school researchers.
In the same way, it is a well-established fact that open-access articles tend to be cited more than paywalled ones — a lot more, in fact. So in trying to bring people across into the OA world, it makes sense to use helpful facts like these. But they’re not where the focus is.
But the last thing to say about this is that even though raw citation-count is a bad measure of a paper’s quality, it is at least badly measuring the right thing. Evaluating a paper by its journal’s IF is like judging someone by the label of their clothes
So @MikeTaylor Institutions need to stop evaluating research papers based on where they are published? Do you know of any doing it right?
I’m afraid I really don’t know. I’m not privy to how individual institution do things.
All I know is, in some countries (e.g. France) abuse of IF is much more strongly institutionalised. It’s tough for French researchers
What are the various ways researchers can make their work available for free online?
Brilliant, very practical question! There are three main answers. (Sorry, this might go on a bit …)
First, you can post your papers on preprint servers. The best known one is arXiv, which now accepts papers from quite a broad subject range. For example, a preprint of one of the papers I co-wrote with Matt Wedel is freely available on arXiv. There are various preprint servers, including arXiv for physical sciences, bioRxiv, PeerJ Preprints, and SSRN (Social Science Research Network).
You can put your work on a preprint server whatever your subsequent plans are for it — even if (for some reason) it’s going to a paywall. There are only a very few journals left that follow the “Ingelfinger rule” and refuse to publish papers that have been preprinted.
So preprints are option #1. Number 2 is Gold Open Access: publishing in an open-access journal such as PLOS ONE, a BMC journal or eLife. As a matter of principle, I now publish all my own work in open-access journals, and I know lots of other people who do the same — ranging from amateurs like me, via early-career researchers like Erin McKiernan, to lab-leading senior researchers like Michael Eisen.
There are two potential downsides to publishing in an OA journal. One, we already discussed: the OA journals in your field may not be be the most prestigious, so depending on how stupid your administrators are you could be penalised for using an OA journal, even though your work gets cited more than it would have done in a paywalled journal.
The other potential reason some people might want to avoid using an OA journal is because of Article Processing Charges (APC). Because OA publishers have no subscription revenue, one common business model is to charge authors an APC for publishing services instead. APCs can vary wildly, from $0 up to $5000 in the most extreme case (a not-very-open journal run by the AAAS), so they can be offputting.
There are three things to say about APCs.
First, remember that lots of paywalled journals demand page charges, which can cost more!
But second, please know that more than half of all OA journals actually charge no APC at all. They run on different models. For example in my own field, Acta Palaeontologica Polonica and Palaeontologia Electronica are well respected OA journals that charge no APC.
And the third thing is APC waivers. These are very common. Most OA publishers have it as a stated goal that no-one should be prevented from publishing with them by lack of funds for APCs. So for example PLOS will nearly always give a waiver when requested. Likewise Ubiquity, and others.
So there are lots of ways to have your work appear in an OA journal without paying for it to be there.
Anyway, all that was about the second way to make your work open access. #1 was preprints, #2 is “Gold OA” in OA journals …
And #3 is “Green OA”, which means publishing in a paywalled journal, but depositing a copy of the paper in an open repository. The details of how this works can be a bit complicated: different paywall-based publishers allow you to do different things, e.g. it’s common to say “you can deposit your peer-reviewed, accepted but unformatted manuscript, but only after 12 months“.
Opinions vary as to how fair or enforceable such rules are. Some OA advocates prefer Green. Others (including me) prefer Gold. Both are good.
See this SV-POW! post on the practicalities of negotiating Green OA if you’re publishing behind a paywall.
So to summarise:
- Deposit preprints
- Publish in an OA journal (getting a fee waiver if needed)
- Deposit postprints
I’ve written absolutely shedloads on these subjects over the last few years, including this introductory batch. If you only read one of my pieces about OA, make it this one: The parable of the farmers & the Teleporting Duplicator.
Last question – Do restricted access publishers pay remuneration to peer reviewers?
I know of no publisher that pays peer reviewers. But actually I am happy with that. Peer-review is a service to the community. As soon as you encumber it with direct financial incentives, things get more complicated and there’s more potential for Conflict of interest. What I do is, I only perform peer-reviews for open-access journals. And I am happy to put that time/effort in knowing the world will benefit.
And so we bring this edition to a close. We say a big thanks to our special guest @MikeTaylor who’s been totally awesome and instructive.
Thanks, it’s been a privilege.
Does anyone want a project? How can we understand sauropod neck cartilage better?
September 27, 2014
A couple of times now, I’ve pitched in an abstract for a Masters project looking at neck cartilage, hoping someone at Bristol will work on it with me co-supervising, but so far no-one’s bitten. Here’s how I’ve been describing it:
Understanding posture and motion in the necks of sauropods: the crucial role of cartilage in intervertebral joints
The sauropod dinosaurs were an order of magnitude bigger than any other terrestrial animal. Much sauropod research has concentrated on their long necks, which were crucial to their success (e.g. Sander et al. 2010). One approach to understanding neck function tries to determine neutral posture and range of motion by modelling the cervical vertebrae as a mechanical system (e.g. Stevens and Parrish 1999).
The raw material of such studies is fossilised vertebrae, but these are problematic for several reasons. The invariable incompleteness and distortion of sauropod neck fossils causes fundamental difficulties; but even given perfect fossils, the lack of preserved cartilage means that the bones are not shaped or sized as they were in life.
Ignoring cartilage has dramatic consequences for neutral posture, range of motion and even length of necks: pilot studies (Cobley 2011, Taylor 2011) found that intact bird necks are 8–12% longer than articulated sequences of their dry bones, and that figure is as high as 24% for a juvenile giraffe neck. A turkey neck postzygapophysis was 26% longer when cartilage was included than after being stripped down to naked bone.
We do not yet know how much articular cartilage sauropods had in their necks, nor even what kind of intervertebral joints they had: crocodilians have fibrocartilaginous discs like those of mammals, while birds have synovial joints, so the extant phylogenetic bracket is uninformative.
The project will involve dissection and measurement of bird and crocodilian necks, documenting the extent and shape of articular cartilage, identifying osteological correlates of fibrocartilaginous and synovial joints, and applying this data to sauropods to determine the nature of their neck joints and length of their necks, to reconstruct the lost cartilage, and to determine its effect on neutral pose and range of motion.
Following completion, we anticipate publication of the project.
References
Cobley, Matthew J. 2011. The flexibility and musculature of the ostrich neck: implications for the feeding ecology and reconstruction of the Sauropoda (Dinosauria: Saurischia). MSc Thesis, Department of Earth Sciences, University of Bristol. vi+64 pages.
Sander, P. Martin, Andreas Christian, Marcus Clauss, Regina Fechner, Carole T. Gee, Eva-Maria Griebeler, Hanns-Christian Gunga, Jürgen Hummel, Heinrich Mallison, Steven F. Perry, Holger Preuschoft, Oliver W. M. Rauhut, Kristian Remes, Thomas Tütken, Oliver Wings and Ulrich Witzel. 2010. Biology of the sauropod dinosaurs: the evolution of gigantism. Biological Reviews 86:117–155. doi:10.1111/j.1469-185X.2010.00137.x
Stevens, Kent A., and J. Michael Parrish. 1999. Neck Posture and Feeding Habits of Two Jurassic Sauropod Dinosaurs. Science 284:798–800. doi:10.1126/science.284.5415.798
Taylor, Michael P., and Mathew J. Wedel. 2011. Sauropod necks: how much do we really know?. p. 20 in Richard Forrest (ed.), Abstracts of Presentations, 59th Annual Symposium of Vertebrae Palaeontology and Comparative Anatomy, Lyme Regis, Dorset, UK, September 12th–17th 2011. 37 pp. http://www.miketaylor.org.uk/dino/pubs/svpca2011/TaylorWedel2011-what-do-we-really-know.ppt
(Obviously some part of this have since been covered by my and Matt’s first cartilage paper, but plenty has not.)
I now think there are two reasons no-one’s taken up this project: first, because I wrote it as very focussed only on the question of what type of joint was present, whereas there are plenty of related issues to be investigated along the way; and second, because I wrote it as a quest to discover a specific treasure (an osteological correlate), with the implication that if there’s no treasure to be found then the project will have been a failure.
But I do think there is still plenty of important work to be done in this area, and that there’s lots of important information to be got out of comparative dissection of extant critters.
If anyone out there fancies working in this area, I’d be delighted. I’d also be happy to offer whatever advice and help I could.
Update (18 October 2014)
Somehow I’d forgotten, when I wrote this post, that I’d previously written a more detailed post about the discs-in-sauropod-necks problem. If you’re interested in the problem, you should read that.
Work on what you love
January 15, 2013
[Neuroscientist and open-science advocate Erin C. McKiernan invited readers of her blog to vote on which of four candidate projects she should work on next. Today she posted the results, and I couldn’t help but comment. This is what I said, lightly edited.]
You should work on what you want to.
Time spent on any project other than the one that’s burning in your hindbrain will feel painful, awkward and boring, and probably be unproductive. That’s true even if the project you’re working on is the one that your colleagues, or Internet voters, think sounds most interesting, or the one that would be most advantageous to your career.
Whereas when you work on what you love at that moment, you’ll enjoy it more, you’ll work harder, you’ll concentrate better, you’ll be more productive. And if you’re anything like me, by the time you’re done (or probably before) your passion will have have involuntarily switched back to one of the other projects, or a completely new one. So switch to that when it happens, and you can always be working on what you love.
(Exception: when a project is close to finished, sometimes you just have to take a deep breath, put up with a few boring days or week, and shove it over the finishing line.)
Sauropod Vertebra Picture of the Week 