December 10, 2013
Many thanks to everyone who played pin-the-skull-on-the-carnivore. The answers are down at the bottom of this post, so if you’ve just arrived here and want to take the challenge, go here before you scroll down.
To fill up some space, let me point out how crazy variable the skulls of black bears, Ursus americanus, are.
Here’s the one I helped dig up, missing the occipital region. Note the double inflection in the dorsal outline that separates the forehead from both the snout and top of the head, and the way the nasal bones stick out at a very different angle from the maxilla.
Here’s the skull of a black bear from the La Brea tar pits, in the Page Museum in L.A. I don’t know if this one was female or juvenile or what, but the dorsal margin of the skull is one mostly-smooth curve from occiput almost to incisors, with the nasals scarcely deviating at all. Lest you think these differences were caused by evolutionary change rather than intraspecific variation, similar “roundhead” bear skulls from modern times are here and here and near the bottom of this page.
It’s this variability that first got me thinking about doing the Carnivore Skull Challenge. I saw a couple of photos of skulls of wolverines, and except for having carnassial cheek teeth instead of flatter premolars and molars, the wolverine skulls look like they could fit right into the span of black bear skull variability (in shape; obviously they’re not nearly as big). Then I saw a hyena skull and thought that it wasn’t that far off from a wolverine either. A little more searching for plausible distractors and I was all set.
Here are the answers, by the way:
It’s kind of ironic, then, that the first two people to venture identifications picked out the black bear right away. In the very first comment, Dean got it almost all right except for swapping the seal and the fossa. Dean was also the first to get all of the skulls correctly identified, albeit on his second pass. Markus Bühler (of Cthulhu-sculpting fame) was the first to get them all the first time. Tom Nutter, our own Darren Naish, and microecos Neil also aced the test, although in light of the Page Museum bear skull shown above, I was amused to see Darren’s “D: Bear. Because forehead.” I guess it’s one of those presence-of-forehead-means-bear, absence-of-forehead-does-not-rule-out-bear things that logicians are always going on about.
I was really happy to see people getting the wolverine and hyena mixed up, because they really do look strikingly similar to me. It’s almost like hyena + bear = wolverine.
Brian Engh asked on Facebook when I was going to do one for sauropods. Patience, good sir! It’s on my to-do list.
Something very different, and very unexpected, tomorrow.
December 9, 2013
In this image I have assembled photos of skulls (or casts of skulls) of six extant carnivores. I exclusively used photos from the Skulls Unlimited website because they had all the taxa I wanted, lit about the same and photographed from similar angles. The omission of scale indicators is deliberate.
Your mission, should you choose to accept it, is to match these skulls with the animals they came from. Here are their currently-understood hierarchical relationships, scientific names, and common names (aside: I know this is ugly, is there a way to make nested tables in WordPress?).
- – Herpestoidea
- – - – Eupleridae
- – - – - – Fossa, Cryptoprocta ferox
- – - – Hyaenidae
- – - – - – Brown hyena, Hyaena brunnea
- – Arctoidea
- – - – Ursoidea
- – - – - – American black bear, Ursus americanus
- – - – Musteloidea
- – - – - – European badger, Meles meles
- – - – - – Wolverine, Gulo gulo
- – - – Pinnipedia
- – - – - – Mediterranean monk seal, Monachus monachus
If you accept the challenge, leave your guesses as comments below, but only if you’ve played fair–no checking websites, references, or your own skull collection! Don’t worry about being wrong, I freely admit that I would have flunked this bigtime if anyone else had inflicted it on me. I decided to set up this challenge after I noticed the striking similarity between two of these critters in particular; I’ll tell you which two when I post the reveal in a day or two.
December 6, 2013
Lots of researchers post PDFs of their own papers on their own web-sites. It’s always been so, because even though technically it’s in breach of the copyright transfer agreements that we blithely sign, everyone knows it’s right and proper. Preventing people from making their own work available would be insane, and the publisher that did it would be committing a PR gaffe of huge proportions.
Enter Elsevier, stage left. Bioinformatician Guy Leonard is just one of several people to have mentioned on Twitter this morning that Academia.edu took down their papers in response to a notice from Elsevier. Here’s a screengrab of the notification:
And here is the text (largely so search-engines can index it):
Unfortunately, we had to remove your paper, Resolving the question of trypanosome monophyly: a comparative genomics approach using whole genome data sets with low taxon sampling, due to a take-down notice from Elsevier.
Academia.edu is committed to enabling the transition to a world where there is open access to academic literature. Elsevier takes a different view, and is currently upping the ante in its opposition to academics sharing their own papers online.
Over the last year, more than 13,000 professors have signed a petition voicing displeasure at Elsevier’s business practices at www.thecostofknowledge.com. If you have any comments or thoughts, we would be glad to hear them.
The Academia.edu Team
(Kudos to the Academia.edu team, by the way, for saying it like it is: “upping the ante in its opposition to academics sharing their own papers online”. It would have been easy for them to give no opinion on this. Much better that they’ve nailed their colours to the mast.)
I was going to comment on Elsevier’s exceedingly short-sighted and mean-spirited manoeuvre, but happily the Twittersphere is on it already. Here are a few thoughts:
- David Winter wrote: Added value! Subs fees pay for lawyers to stop you sharing your work with colleagues…
- Rich FitzJohn speculated: I wonder what their long game is here; petty harassment like that makes me way less inclined to publish in an Elsevier journal.
- To which Rafael Maia responded: so silly…is it really worth it? its like they are proudly embracing being the dicks of academic publishing
- But Dr. Wrasse was more forthright.
This doesn’t directly affect me, of course, since I’ve had the good fortune not to have published in an Elsevier journal. But it’s another horrible example of how organisations that call themselves “publishers” do the exact opposite of publishing. The good people I know at Elsevier — people like Tom Reller, Alicia Wise and The Other Mike Taylor — must be completely baffled, and very frustrated, by this kind of thing.
Every time they start to persuade me that maybe – maybe – somewhere in the cold heart of legacy publishers, there lurks some real will to make a transition to actually serving the scholarly community, they do something like this. It’s like a sickness with them.
Do scholarly publishers really need to be reminded that “publish” means “make public”? Yes. Yes, they do. Apparently. Remember how I called legacy publishers “enemies of science” back at the start of 2012? Yup. Still true. And, astonishingly, as Rafael Maia noted, Elsevier seem determined to lead the way.
Have they learned nothing? Will they never?
November 26, 2013
Reading the Government’s comments on the recent BIS hearing on open access, I see this:
As a result of the Finch Group’s work, a programme devised by publishers, through the Publishers Licensing Society, and without funding from Government, will culminate in a Public Library Initiative. A technical pilot was successfully started on 9 September 2013
Following the link provided, I read:
The Report recommended that the existing proposal to make the majority of journals available for free to walk-in users at public libraries throughout the UK should be supported and pursued vigorously.
I’m completely, completely baffled by this. The idea that people should get in a car and drive to a special magic building in order to read papers that their own computers are perfectly capable of downloading is so utterly wrong-headed I struggle to find words for it. It’s a nineteenth-century solution to a twentieth-century problem. In 2013.
Who thought this was a good idea?
And what were they smoking at the time?
I can tell you now that the take-up for this misbegotten initiative will be zero. Because although it’s a painful waste of time to negotiate the paywalls erected by those corporations we laughably call “publishers”, this “solution” will be more of a waste of time still. (Not to mention a waste of petrol).
I can only assume that was always the intention of the barrier-based publishers on the Finch committee that came up with this initiative: to deliver a stillborn access initiative that they can point to and say “See, no-one wants open access”. Meanwhile, everyone will be over on Twitter using #icanhazpdf and other such 21st-century workarounds.
November 22, 2013
As a nice little perk–presumably for being early adopters and users of PeerJ–Mike and I each have been given a small number of referral codes, which will allow other folks to publish in PeerJ for free, as long as the papers are submitted by March 1, 2014. Here’s the scoop, straight from the monkey’s mouth:
If you have colleagues who would like to publish at PeerJ, then we want to give them the opportunity to try us out for free. Therefore, as a Published PeerJ Author, we are providing you with 5 unique ‘Referral Codes’ (which expire on March 1st) to distribute to your colleagues. Each code entitles the recipient to an entirely FREE PeerJ publication. They simply need to quote your referral code in the “Notes to Staff” field, when they submit to PeerJ, and as a result they will be able to publish that article for free (assuming it passes peer-review). Please disseminate these codes to colleagues who you feel will use them, but please make sure that they realize that this code is only valid for submissions made before March 1st, 2014.
Note that this is alongside the current promo wherein, if you post a preprint to PeerJ PrePrints (which is a smashing way of getting fast feedback, or at least it was for us), that manuscript can be published in PeerJ for free, as long as it is formally submitted before January 1, 2014. So if you can get the lead out before the end of the year and don’t have an allergy to fast feedback, you don’t actually need one of these codes.
So. If you’re not a PeerJ member but you have a manuscript that you’d like to send to PeerJ before the first of next March, let us know and we’ll hook you up with a referral code. If you’re fairly sure you will use one but aren’t ready to ship yet, let me know and I’ll set one aside for you, with the proviso that I can give it away if we’re getting close to the deadline and you’re not realistically going to make it.
If we get more takers than codes, we’ll figure out some fair way of choosing who gets a code, probably randomly. I will be strongly biased toward people without big paychecks* or institutional support, like grad students and postdocs. (If you’re an undergrad, you can already publish in PeerJ for free, at least for the duration of the pilot program.) So if you’re a grad student or postdoc with a serious plan to get published, speak up and you’ll go to the head of the line. So if you let us know why getting a code would benefit you, you’re more likely to get one.
* I know in academia none of us think we have big paychecks, but compared to most grad students and postdocs, those of us with steady full-time employment are living the dream. I’m trying to reach the folks for whom the $99 lifetime membership fee would be a genuine impediment.
As is apparently the usual thing now when I’m writing about PeerJ and don’t have any images of my own queued up, I’ve borrowed images from Brant Bassam’s astoundingly cool BrantWorks.com to spice up this post. Explicit permission to reproduce the images with credit can be found on this page, which is coincidentally where these images themselves are from. Get on over there and prepare to lose some time looking at sweet stuff.
Update! Five more Golden Tickets available!
As noted in the comment below, Heinrich Mallison also has five PeerJ vouchers to distribute to deserving causes. So if Matt and I run out, the options are still open. Feel free to contact Heinrich directly or to go through us if you prefer.
November 21, 2013
Well, folks, I’m back from Berlin. And what an extraordinary couple of days it was. There were in fact three days of open-access talks, though I was only able to be there for the first two. Day one was the satellite conference, aimed at early-career researchers; days two and three were the much larger main conference, attended mostly by heavy hitters: senior librarians, university administrators, a sprinkling of politicians, and of course some researchers and publishers.
It was my privilege to speak at both satellite and main conferences. This post is really just to advertise those talks. Why am I doing this? Because I’m convinced that they’re by far the most important talks I’ve ever given. It’s great fun to talk about Barosaurus at SVPCA, or about intervertebral cartilage in Bonn, but if someone says to me that that work doesn’t really matter in a cosmic sense, I’ll be hard put to find reasons why they’re wrong. But open access has profound and immediate consequences for health, industry, education, third-world development, and more fields than I can list.
So here are the talks.
Satellite meeting talk
First up, at the satellite conference, my subject was: Towards universal Open Access: what we can do about it, and who should do it. My goal here was to help researchers see what practical steps they can take right now towards the open-access goal that we all aspire to. I covered six areas:
- Publish our own work open access (whether Gold or Green)
- Review for Open Access journals
- Edit for Open Access journals
- Advocate Open Access policies
- Deprecate journal rank
- Talk about Open Access
Along the way, we talked about the open-access citation advantage, the (mostly non-) problem of article processing charges, the complete non-problem of “predatory open-access publishers”, the acceptable length of Green-OA embargoes (zero), the SV-POW! decision tree, publishers’ lack of control over what you do before you sign the copyright transfer, the inability of impact factor to predict citation count (post to come), the childishness of evaluating individuals by journal rank, and the knotty problem of who should take responsibility for fixing our current broken system.
Here are a few tweets that went out as I was giving this talk: “a blistering, fantastic presentation“, “Can we get a twitter round of applause … Absolutely BRILLIANT presentation“, “TOTALLY BRILLIANT“, “This is why we HAVE to record these conferences. Not recording that presentation would be a crime“, “It was AWESOME!“, and finally my favourites: “making you not just know #openaccess , but feel it” and “Mike’s talks at the #Berlin11 conference was 1of the most emotional 1′s I have ever seen!“
I actually don’t know whether it’s going to be possible for people who missed the live stream to watch this talk. That was the plan, but I heard a rumour that the recording went wrong. If a video does becomes available, I’ll let you know. In the mean time, you can at least get the slides [PowerPoint or exported PDF]. They are CC By.
Main meeting talk
In the main conference, I used my slot to remind us all that Open Access is about sharing, unity and sanity, not about money. Because I was addressing a more senior audience that necessarily has to think more about practicalities, finances, ways and means, I wanted to take the opportunity to remember that those are not the issues that gave birth to Open Access; rather, it started out as an unabashedly idealistic movement (as reading any of the three great declarations will show you). I don’t want us to walk away from that high-ground and be reduced to thinking only about practicalities, important though they are.
Publishers and their associates often say — rightly, as far as they go — that “Scientific and technical publishing is a business“. But no-one goes into it because of they money they can make. Everyone involved in doing or publishing research surely got into that business because their eyes were on a higher prize. So the burden of my talk was that publishing research is a mission; that far from “getting rid of the idealists“, we should cherish them; and that we should encourage rather the curb our own idealistic tendencies.
Perhaps the most satisfying part of the whole conference was giving this talk — you might almost call it a preach — and watching the nodding agreement spread across the audience. Folks, we’re about a great work. Let’s not forget that. Let’s not sell ourselves short.
The main session was unfortunately not livecast, and to the best of my knowledge, there were never any plans to record it. But as with my satellite talk, you can at least get the slides [PowerPoint or exported PDF]. They are CC By.
Since I made the slides available for download immediately after the talks (three days ago for the satellite meeting, two days ago for the main meeting), I’ve been surprised and delighted to see the download numbers — currently standing at 641 for the satallite talk and 939 for the main talk. The tweet announcing the main talk has also been retweeted 34 times and favourited 26 times. I hope that shows that I struck a chord.
I have an informal invitation to deliver the main-session talk next year to an Italian university, which I’ll be pleased to do once we’re able to sort out the details. I’m not sure whether more invitations are likely to be forthcoming, but I’ll mention them here if they do materialise.
I’d like to finish by thanking my employer, Index Data. As most of you know, I am not a career academic: I work on sauropods in my spare time (and advocate open access in my spare spare time), earning my living as a computer programmer. By the time the invitations to speak at the Berlin conferences came in, I’d already booked up my annual leave allowance, so I had to ask for permission to take unpaid days for the conference. Instead, Index Data gave me two more paid days — because they, like me, believe in the importance of open access.
This is all the more laudable since, if anything, universal open access will harm our business. A significant part of what we build is authentication mechanisms to allow people (legitimate) access to paywalled resources. Once everything is open, no-one will need to pay us to do that. It’s greatly to Index Data’s credit that, despite this, they want to help us push on towards a goal that will benefit society as a whole.
- Taylor, Michael P. Monday 18 November 2013. Towards universal Open Access: what we can do about it, and who should do it. Berlin 11 Satellite Conference for students and early-career researchers. [Slides PPT] [Slides PDF]
- Taylor, Michael P. Tuesday 19 November 2013. Open Access is about sharing, unity and sanity, not about money. Berlin 11 Open Access Conference: 10th Anniversary of the Berlin Declaration. [Slides PPT] [Slides PDF]
November 19, 2013
Yesterday I was at the Berlin 11 satellite conference for students and early-career researchers. It was a privilege to be part of a stellar line-up of speakers, including the likes of SPARC’s Heather Joseph, PLOS’s Cameron Neylon, and eLIFE’s Mark Patterson. But even more than these, there were two people who impressed me so much that I had to give in to my fannish tendencies and have photos taken with them. Here they are.
This is Jack Andraka, who at the age of fifteen invented a new test for pancreatic cancer that is 168 times faster, 1/26000 as expensive and 400 times more sensitive than the current diagnostic tests, and only takes five minutes to run. Of course he’s grown up a bit since then — he’s sixteen now.
Right at the moment Jack’s not getting much science done because he’s sprinting from meeting to meeting. He came to us in Berlin literally straight from an audience with the Pope. He’s met Barack Obama in the oval office. And one of the main burdens of his talk is that he’s not such an outlier as he appears: there are lots of other brilliant kids out there who are capable of doing similarly groundbreaking work — if only they could get access to the published papers they need. (Jack was lucky: his parents are indulgent, and spent thousands of dollars on paywalled papers for him.)
Someone on Twitter noted that every single photo of Jack seems to show him, and the people he’s with, in thumbs-up pose. It’s true: and that is his infectious positivity at work. It’s energising as well as inspiring to be around him.
(Read Jack’s guest post at PLOS on Why Science Journal Paywalls Have to Go)
Here’s the other photo:
This is Bernard Rentier, who is rector of the University of Liège. To put it bluntly, he is the boss of the whole darned university — an academic of the very senior variety that I never meet; and of the vintage that, to put it kindly, can have a tendency to be rather conservative in approach, and cautious about open access.
With Bernard, not a bit of it. He has instituted a superb open-access policy at Liège — one that is now being taken up a model for the whole of Belgium. Whenever members of the Liège faculty apply for anything — office space, promotions, grants, tenure — their case is evaluated by taking into account only publications that have been deposited in the university’s open-access repository, ORBi.
Needless to say, the compliance rate is superb — essentially 100% since the policy came in. As a result, Liège’s work is more widely used, cited, reused, replicated, rebutted and generally put to work. The world benefits, and the university benefits.
Bernard is a spectacular example of someone in a position of great power using that power for good. Meanwhile, at the other end of scale, Jack is someone who — one would have thought — had no power at all. But in part because of work made available through the influence of people like Bernard, it turned out he had the power to make a medical breakthrough.
I came away from the satellite meeting very excited — in fact, by nearly all the presentations and discussions, but most especially by the range represented by Jack and Bernard. People at both ends of their careers; both of them not only promoting open access, but also doing wonderful things with it.
There’s no case against open access, and there never has been. But shifting the inertia of long-established traditions and protocols requires enormous activation energy. With advocates like Jack and Bernard, we’re generating that energy.
Onward and upward!