My attempt at a fully Engh-ed out brachiosaur
July 26, 2013
Last Sunday I got to hang out with Brian Engh and some of his friends in LA. You may remember Brian from this, this, this, this, and, most notoriously, this. We got to drawing dinosaurs, naturally.
Now, for me to try to draw dinosaurs next to Brian is more than a little intimidating. I really felt the need to bring my A-game. So this is what I came up with. I’m posting it not because I think it is particularly likely* but because the blog has been a little sauropod-lite this summer, and heck, it’s Friday.
* Although frigatebirds and anoles and such might have some things to say about that.
The Royal Society has taken some steps to improving reporting of submit/resubmit/accept times
July 25, 2013
Last October, we published a sequence of posts about misleading review/reject/resubmit practices by Royal Society journals (Dear Royal Society, please stop lying to us about publication times; We will no longer provide peer reviews for Royal Society journals until they adopt honest editorial policies; Biology Letters does trumpet its submission-to-acceptance time; Lying about submission times at other journals?; Discussing Biology Letters with the Royal Society). As noted in the last of these posts, the outcome was that I had what seemed to be a fruitful conversation with Stuart Taylor, Commercial Director of the society.
Then things went quiet for some time.
On 8 May this year, I emailed Stuart to ask what progress there had been. At his request Phil Hurst (Publisher, The Royal Society) emailed me back on 10 May as follows:
Dear Mike
Stuart has asked me to update you on the changes we have made following your conversation last year.
We have reviewed editorial procedures on Biology Letters. Further to this, we now provide Editors with the additional decision option of ‘revise’. This provides a middle way between ‘reject and resubmit’ and ‘accept with minor revisions’. Editors use all three options and it is entirely at their discretion which they select. ‘Revised’ papers retain the original submission date and we account for this in our published acceptance times.
In addition, we now publicise ‘first decision’ times rather than ‘first acceptance’ times on our website. We feel this is more meaningful as it gives prospective authors an indication of the time, irrespective of decision.
The first thing to say is, it’s great to see some progress on this.
The second thing is, I must apologise for my terrible slowness in reporting back. Phil emailed me again on 17 June to remind me to post, and it’s still taken me more than another month.
The third thing is, while this is definitely progress, it doesn’t (yet) fix the problem. That’s for two reasons.
The first problem is that so long as there is a “reject and resubmit” option that does not involve a brand new round of review (like a true resubmission), there is still a loophole by which editors can massage the journals’ figures. Of course, there is nothing wrong with “reject and resubmit” per se, but it does have to result in the resubmission being treated as a brand new submission — it can’t be a fig-leaf for what are actually minor revisions, as in the paper that first made me aware of this practice.
So I would urge the Royal Society either to get rid of the R&R option completely, replacing it with a simple “reject”; or to establish firm, explicit, transparent rules about how such resubmissions are treated.
The second problems is with the reporting. It’s true that the home pages of both Proc. B and Biology Letters do now publicise “Average receipt to first decision time” rather than the misleading old “Average receipt to acceptance time”. This is good news. Proc. B (though for some reason not Biology Letters) even includes a link to an excellent and very explicit page that gives three times (receipt to first decision, receipt to online publication and final decision to online publication) for five journals, and explains exactly what they mean.
Unfortunately, individual articles still include only Received and Accepted dates. You can see examples in recent papers both at Proc. B and at Biology Letters. As far as I can tell, there is no way to determine whether the Received date is for the original submission, or (as I can’t help but suspect) the minor revision that is disguised as a resubmission.
The solution for this is very simple (and was raised when I first talked to Stuart Taylor back in October): just give three dates: Received, Revised and Accepted. Then everything is clear and above board, and there is no scope for anyone to suspect wrongdoing.
Tutorial 15c: The bones of the ornithischian skeleton
July 18, 2013
Readers with long memories might recall that, nearly two years ago, we published annotated skeletal reconstructions of Camarasaurus and of Tyrannosaurus, with all the bones labelled. At the time, I said that I’d like to do an ornithischian, too.
Well, here it is at last, based on Marsh’s (1891) classic reconstruction of Triceratops:
Click through for the full-sized version (2076 by 864 pixels), which — like the other two — you are welcome to print out and hang on your wall as a handy reference, or to use in teaching. (Marsh’s original is out of copyright; I hereby make my modified version available under the CC By 3.0 licence.)
Tataouinea hannibalis and its crazy pneumatic pelvis
July 16, 2013
Here is Tataouinea, named by Fanti et al. (2013) last week — the first sauropod to be named after a locality from Star Wars (though, sadly, that is accidental — the etymology refers to the Tataouine Governatorate of Tunisia).
Fanti et al. (2013: figure 3) T. hannibalis selected elements and reconstruction. (a) Sacral neural arches 1-3, right lateral view; (b) sacral neural spine 4, right lateral view; (c) sacral neural spine 5, right lateral view; (d) caudal vertebra 2 and fragment of caudal 1 postzygapophyses, left lateral view; (e) caudal vertebra 1, left lateral view; (f) sacral centrum 1, ventral view; (g) sacral centra 2-5, ventral view; (h–j) caudal vertebra 3, anterior (h), left lateral (i), posterior (j) views; (k) left ilium, lateral view; (l) right ischium, medial view; and (m) skeletal reconstruction of T. hannibalis. Missing elements based on other nigersaurines. Scale bar: 10 cm (a-l), 1 m (m). a, acetabulum; f, fossa; hr, hyposphenal ridge; ip, ischial peduncle; ll, lateral lamina; pf, pneumatic foramen; pl, pleurocoel; poz, postzygapophysis; pp, pubic peduncle; psdf, prezygospinodiapophyseal foramen; sdl, spinodiapophyseal lamina; spol, spinopostzygapophyseal lamina; spzl, spinoprezygapophyseal lamina; sr, sacral rib; tp, transverse process. The asterisk indicates the fossa bounded by the spzl and the sdl.
No doubt Matt willl have much more to say about this animal, and especially its pneumatic features. I just thought it was time for a picture-of-the-week post.
UPDATE: Matt here, just a few quick thoughts (I’m in the middle of my summer anatomy lectures so they will be less extensive than this animal deserves). First, it’s awesome to see so much pneumaticity, and in elements that have not previously been reported as pneumatic in sauropods. The authors make a good case that we’re looking at actual pneumaticity here, for example in the pelvic elements, and not something else. So that’s cool.
What’s even cooler is that we’re seeing this in a diplodocoid: Tataouinea is a rebbachisaurid. We’ve seen extreme pneumaticity in saltasaurines, and now we’ve got a parallel evolution of this character complex in diplodocoids. That’s cool by itself, and it’s further evidence that the underlying generating mechanism–the air sacs and their diverticula–were all in place long before they started leaving traces on the skeleton. The case for a birdlike lung-air sac system in sauropods, in saurischians, and in ornithodirans generally only keeps getting stronger. That is, we’re seeing more evidence not just that air sacs were there, but that they were bird-like in their layout, e.g., pneumatization of the pectoral girdle by clavicular air sacs, in both saltasaurines and theropods (avian and otherwise), and now extensive pelvic pneumatization (i.e., going beyond what we’ve seen previously in saltasaurines) by abdominal air sacs in rebbachisaurids and theropods (and pterosaurs, can’t forget about them). Happy times.
Reference
Fanti, Federico, Andrea Cau, Mohsen Hassine and Michela Contessi. 9 July 2013. A new sauropod dinosaur from the Early Cretaceous of Tunisia with extreme avian-like pneumatization. Nature Communications 4:2080. doi:10.1038/ncomms3080
Pacific Rim, a large-animal anatomist’s dream come true
July 13, 2013
Anyone else see these images and really, REALLY want to go dissect one of these bad boys?
From the moment I saw this in the trailer, I was thinking: “WANT!”
Click to embiggen, and check out the heavy equipment being used to cart off the soft tissue.
Tutorial 16: giving good talks (in four parts)
July 12, 2013
As the conference season heaves into view again, I thought it was worth gathering all four parts of the old Tutorial 16 (“giving good talks”) into one place, so it’s easy to link to. So here they are:
- Part 1: Planning: finding a narrative
- Make us care about your project.
- Tell us a story.
- You won’t be able to talk about everything you’ve done this year.
- Omit much that is relevant.
- Pick a single narrative.
- Ruthlessly prune.
- Find a structure that begins at the beginning, tells a single coherent story from beginning to end, and then stops.
- Part 2: The slides: presenting your information to be understood
- Make yourself understood.
- The slides for a conference talk are science, not art.
- Don’t “frame” your content.
- Whatever you’re showing us, let us see it.
- Use as little text as possible.
- Use big fonts.
- Use high contrast between the text and background.
- No vertical writing.
- Avoid elaborate fonts.
- Pick a single font.
- Stick to standard fonts.
- You might want to avoid Ariel.
- Do not use MS Comic Sans Serif.
- Use a consistent colour palette.
- Avoid putting important information at the bottom.
- Avoid hatching.
- Skip the fancy slide transitions.
- Draw highlighting marks on your slides.
- Show us specimens!
- Part 3: Rehearsal: honing the story and how it’s told
- Fit into the time.
- Become fluent in delivery.
- Maintain flow and momentum.
- Decide what to cut.
- Get feedback.
- Part 4: Delivery: telling the story
- Speak up!
- Slow down!
- Don’t panic!
Also, some addenda written later:
- Addendum 1: give a talk that holds attention!
- Love your taxon.
- Show us pictures of your taxon.
- Engage with the audience.
- Tell a story.
- Talks are not papers.
- Addendum 2: giving talks: what to leave out
- Don’t start by saying the title.
- Don’t introduce yourself.
- Don’t reiterate your conclusions at the end.
- Don’t say “thanks for listening”.
- Don’t read the acknowledgements out loud.
- Don’t say “I’ll be happy to take questions”.
- Addendum 3: giving talks: some more positive thoughts
- Offer lots of jump-back-on points.
- Anticipate possible objections and meet them in advance.
- Do the work to make it worth the audience’s while.
- Efficiently introduce a taxon and make it interesting before launching into details.
Why Robin Osborne makes no sense
July 9, 2013
Robin Osborne, professor of ancient history at King’s College, Cambridge, had an article in the Guardian yesterday entitled “Why open access makes no sense“. It was described by Peter Coles as “a spectacularly insular and arrogant argument”, by Peter Webster as an “Amazingly wrong-headed piece” and by Glyn Moody as “easily the most arrogant & dim-witted article I’ve ever read on OA”.
Here’s my response (posted as a comment on the original article):
—
At a time when the world as a whole is waking up to the open-access imperative, it breaks my heart to read this fusty, elitist, reactionary piece, in which Professor Osborne ends up arguing strongly for his own irrelevance. What a tragic lack of vision, and of ambition.
There is still a discussion to be had over what routes to take to universal open access, how quickly to move, and what other collateral changes need to be made (such as changing how research is evaluated for the purposes of job-searches and promotion). But Osborne’s entitled bleat is no part of that discussion. He has opted out.
The fundamental argument for providing open access to academic research is that research that is funded by the tax-payer should be available to the tax-payer.
That is not the fundamental argument for providing open access (although it’s certainly a compelling secondary one). The fundamental argument is that the job of a researcher is to create new knowledge and understanding; and that it’s insane to then take that new knowledge and understanding and lock it up where only a tiny proportion of the population can benefit from it. That’s true whether the research is funded publicly or by a private charity.
The problem is that the two situations are quite different. In the first case [academic research], I propose both the research questions and the dataset to which I apply them. In the second [commercial research] the company commissioning the work supplies the questions.
Osborne’s position here seem to be that because he is more privileged than a commercial researcher in one respect (being allowed to choose the subject of his research) he should also be more privileged in another (being allowed to choose to restrict his results to an elite). How can such an attitude be explained? I find it quite baffling. Why would allowing researchers to choose their own subjects mean that funders would be happy to allow the results to be hidden from the world?
Publishing research is a pedagogical exercise, a way of teaching others
Yes. Which is precisely why there is no justification for withholding it from those others.
At the end of the day the paper published in a Gold open access journal becomes less widely read. […] UK scholars who are obliged to publish in Gold open access journals will end up publishing in journals that are less international and, for all that access to them is cost-free, are less accessed in fact. UK research published through Gold open access will end up being ignored.
As a simple matter of statistics, this is flatly incorrect. Open-access papers are read, and cited, significantly more than paywalled papers. The meta-analysis of Swan (2010) surveyed 31 previous studies of the open-access citation advantage, showing that 27 of them found advantages of between 45% are 600%. I did a rough-and-ready calculation on the final table of that report, averaging the citation advantages given for each of ten academic fields (using the midpoints of ranges when given), and found that on average open-access articles are cited 176% more often — that is, 2.76 times as often — as non-open.
There can be no such thing as free access to academic research. Academic research is not something to which free access is possible.
… because saying it twice makes it more true.
Like it or not, the primary beneficiary of research funding is the researcher, who has managed to deepen their understanding by working on a particular dataset.
Just supposing this strange assertion is true (which I don’t at all accept), I’m left wondering what Osborne thinks the actual purpose of his research is. On what basis does he think our taxes should pay him to investigate questions which (as he himself reminds us) he has chosen as being of interest to him? Does he honestly believe that the state owes him not just a living, but a living doing the work that he chooses on the subject that he chooses with no benefit accruing to anyone but him?
No, it won’t do. We fund research so that we can all be enriched by the new knowledge, not just an entited elite. Open access is not just an economic necessity, it’s a moral imperative.
We’ve covered rodent teeth here a few times before (one, two)–more than is probably right, for a blog ostensibly about sauropod vertebrae. Sherlock Holmes said, “Life is a great chain, the nature of which can be determined by the discovery of a single link.” I’d amend that to, “Life is a great tree, the inherent fascination of which flows through every tiny twig.”
Back when we started SV-POW!, Mike predicted that the technical niche blog was the wave of the future. That prediction does seem to be coming true, albeit more slowly than I thought it would. Nevertheless, if you are susceptible to the inherent fascination of rodent teeth, get yourself over to Ian Corfe’s Tetrapod Teeth & Tales for more geeky goodness.
Now, in a move that will possibly enrage one segment of the audience but hopefully delight another, I am going to forge even further away from the ostensible raison d’être of the blog and talk about monsters. Specifically Cthulhu–in my experience, in the Venn diagram of life, the “interested in paleo” and “interested in Lovecraft” circles overlap almost entirely. Over at my everything-except-paleontology-and-astronomy blog, I’ve been thinking about Lovecraftiana and wrestling with what a Cthulhu idol, such as those described in Lovecraft’s stories, ought to look like. If you’d like to contribute, get on over there and leave a comment. If you send* me a picture (drawing, painting, 3D render, photo of sculpture, whatever) or leave a link, I’ll include it in an upcoming post. Cthulhu fhtagn!
* Send to mathew.wedel@gmail.com, please include Cthulhu in the subject line.
A loophole in PLOS’s use of the CC By licence
July 3, 2013
Christopher W. Schadt tells a distasteful story over on his blog, about how a PLOS ONE paper that he was a co-author on was republished as part of a non-PLOS printed volume that retails for $100. The editors and publishers of this volume neither asked the authors’ permission to do this (which is fair enough, it was published as CC By), nor even took the elementary courtesy of informing them. Worse, the reprinted copy in the book doesn’t have a reference to the original version in PLOS ONE.
It’s clear the editors of this book have (to put it mildly) been rather rude here. But what they’ve done is possibly legal and in accordance with the terms under which the article was originally published. The CC By licence requires attribution, and sure enough the work is attributed to the correct authors.
But does CC By require that the original publication also be credited? Not exactly. The terms of the licence say that the work can be reused subject to this condition:
Attribution — You must attribute the work in the manner specified by the author or licensor (but not in any way that suggests that they endorse you or your use of the work).
So the author could specify (and PLOS should probably specify in the published form of their articles) that the manner in which the work should be attributed requires not only authorship to be recognised but also the original publication in PLOS to be cited.
But the current PLOS wording on this is unfortunately a mess. Schadt’s article, like all PLOS ONE articles, says:
Copyright: © 2010 Reganold et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
This is probably intended to say that attribution must mention both author and source (i.e. citation of original publication). But what this wording actually does, wrongly, is state that this is what the CC BY licence intrinsically requires.
So PLOS have a bit of work to do to tidy this up. And they are not alone in this. PeerJ uses the exact same form of words, and BMC says something a bit different (“… provided the original work is properly cited”) which us also open to misinterpretation.
All three of these publishers, and probably many others using CC By, need to tighten their wording so that they don’t claim that CC By requires a full citation, but stipulate that in their use of CC By, providing a citation is part of what constitutes proper attribution.
Had PLOS ONE done that, then the reprinted version of the Reganold et al. paper would have been clearly not covered by the CC By licencing option, and so would have constituted copyright violation plain and simple. As it is, they’re clearly guilty but have some wiggle-room. (To be fair, representatives of the production company and publisher have been quick to apologise on Schadt’s blog.)
Museum of Osteology: Tegu skull
July 3, 2013
Another shot from my visit last month to the Museum of Osteology in Oklahoma City: the business end of a tegu (Tupinambis). Lots of cool stuff in this pic: heterodont dentition, wacky sclerotic ossicles, and some sweet neurovascular foramina along the maxilla. Someone should knock out a shrink-wrapped life restoration, a la All Todays.