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 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 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!
November 19, 2013
In lieu of the sauropod neck cartilage post that I will get around to writing someday, here are some photos of animals London and I saw at the Arizona-Sonora Desert Museum this Sunday morning.
In chronological order:
Mountain lion, Puma concolor
Black bear, Ursus americanus, which taxon has also graced these pages (and my desk) with its mortal remains.
Bobcats, Lynx rufus. These two play-fought for a while. Watching them was the highlight of the morning, and maybe the highlight of the whole trip.
Gray fox, Urocyon cinereoargenteus. This guy just paused here for a moment, but I am super happy with the chiaroscuro effect.
Javelina, Pecari tajacu. Sunday evening we saw a couple of wild javelinas alongside one of the roads on the west side of Tucson–only the second time I’ve seen them in the wild.
Coyote, Canis latrans. Now these guys I see all the time–on my own street, even, some mornings.
Great Horned Owl, Bubo virginianus. This one flew right over our heads during the Raptor Free Flight demonstration. I tried to get photos of it on the wing but it was too darned fast. Most impressive: however big they look in pictures, they look a heck of a lot bigger–and scarier–swooping two feet over your head.
Mexican Wolf, Canis lupus baileyi
And, okay, here’s a sauropod, or part of a sauropod: a mounted cast of the forelimb of Sonorasaurus thompsoni. Nine-year-old Homo sapiens for scale.
So, pretty outstanding place, and I highly recommend going. But, like every other printed or digital source I found, I recommend getting there first thing in the morning to see all the animals while they are out and about. London and I walked out of the big “critter loops” at 10:30 and the Mexican wolf was the only animal still roaming around.
November 10, 2013
That’s me on top of the Giraffatitan, Matt to the right, and Darren swinging from its wattle.
October 17, 2013
convincing genetic engineers that everyone would look better if they had sauropod tails.
If you have no idea what I’m on about, go check out XKCD.
October 16, 2013
If the internet has any underlying monomyth, or universally shared common ground, or absolute rule, it is this:
People love to see the underdog win.
This rule has a corollary:
When you try to censor someone, they automatically become the underdog.
I say “try to censor” someone, because on the internet that is remarkably difficult to achieve. I’m not going to argue that the attention paid to the range of stories told on the internet is fairly distributed–being published is not the same as being read, and people seem to prefer cat pictures to reading about genocide. But it’s awfully hard to shut someone up, and any attempt to do so may backfire spectacularly.
If you work for an organization of any size, or have amassed any considerable power, reputation, or influence personally, you need to keep that at the forefront of your mind in every interaction you ever have with anyone, anywhere, ever. The reason for this constant attention is to keep you from becoming the overdog and thereby making an ass of yourself (and your organization, if you belong to one). Go read about the Streisand Effect and think proactively about how to keep that from happening to you.
Now, for the purposes of this tutorial I am going to arbitrarily sort the full range of possible messages into four bins:
- Those that make the teller look good.
- Those that make the teller look bad.
- Those that make someone else look good.
- Those that make someone else look bad.
Two and three are dead easy and often go hand in hand. If you want to spread messages of that type, all you have to do is find someone with less power, reputation, or influence–a prospective underdog, in other words–and be a jerk to them, thus turning them into an actual underdog. Coercion, threats, employment termination–these are all pretty good and may eventually pay off. But if you really want to look like a complete tit, and make the other party an instant hero, you gotta go for censorship. Out here in bitspace, it is the ne plus ultra of suicidal moves. It’s like Chuck Norris winding up for a roundhouse kick to someone’s face, only somehow his foot misses the other person’s face and hits him right in the junk instead. We will click and tap on that until they pry the mice and touchscreens from our cold, dead hands.
The first one–positive messages about yourself–is tricky. You can’t just go around telling people that you’re awesome. Anyone with any sense will suspect advertising. The only sure-fire method I know of is to do good work where people can see it. One thing you will just have to accept is that reputations are slow-growing but fast-burning. So, again, try to avoid burning yours down.
The last one–making someone else look bad–is also surprisingly tricky. If you just broadcast negatives to the world, that will probably backfire. At the very least, people start thinking of you as a negative force rather than a positive one. If the person you want to make look bad has ever lied or falsified data or oppressed anyone, use that. If they’ve ever tried to censor someone, or are actively trying to censor you, rejoice, they’ve done most of the work for you.
The upside of that last one is that, provided you’re not actively nasty, it is hard for others to hurt your reputation. If they just spew vitriol, it will probably backfire. If they lie about you, it will definitely backfire. About the only way to really trash your reputation is through your own actions. Your fate is in your own hands.
So, this is transparently a meditation on the DNLee/Biology Online/Scientific American story.
I would really like to know the backstory. Did someone at Biology Online contact SciAm and ask them to take down DNLee’s post? If so, well, geez, that was stupid. Why does anyone ever expect this to work anymore? I mean, the actual event from which the Streisand Effect got its name happened a decade ago, which may seem short in human terms but is an eternity online (it’s two-thirds of the lifespan to date of Google, for example).
If someone at SciAm did it unilaterally to protect their valued financial partner, it was doubly stupid, because not only did the censorship act itself fail, but now people like me are wondering if Biology Online asked for that “protection”. In other words, people are now suspecting Biology Online of something they might not have even done (although what they did do–what their employee did on their behalf, which amounts to the same thing–was bad enough).
So all in all the affair is like a tutorial on how to royally cock things up on the internet. And in fact it continues to be–Mariette DiChristina’s “apology” is a classic non-apology, that uses a torrent of words to say very little. Her self-contradictory tweets are much more revealing, despite being under 140 characters each. And in fact her loudest message is the complete lack of communication with DNLee before she pulled the post. So meaning scales inversely with message length for DiChristina–not a great quality in an Editor-In-Chief. And, OMG does she need to learn about the Asoh defense.
In the end, the whole thing just saddens me. I’m sad that SciAm made the wrong call immediately and reflexively. It says to me that they don’t care about transparency or integrity. They may say otherwise, but they are belied by their actions.
I’m sad that, having not even known that Biology Online exists, my perception of them now starts from a position of, “Oh, the ones that called that science writer a whore.” (If you’re a BO fan, please don’t write in to tell me how wonderful BO actually is; doing so is just admitting that you didn’t read this post.)
I’m sad that this happened to DNLee. I hope that going forward her reputation is determined by the quality of her work and the integrity of her actions, and not by words and circumstances inflicted on her by others.
… I wonder if I could make it as a corporate consultant if I put on a suit, walked into rooms full of pointy-haired bosses, and just explained the Streisand Effect and the Asoh Defense as if they were novel insights. I’ll bet I could make a killing.
October 14, 2013
In what is by now a much-reported story, @DNLee, who writes the Urban Scientist blog on the Scientific American blog network, was invited by Biology Online to write a guest-post for their blog. On being told this was a non-paying gig, she politely declined: “Thank you very much for your reply. But I will have to decline your offer. Have a great day.” To which Biology Online’s blog editor Ofek replied “Are you an urban scientist or an urban whore?”
So far, so horrible. I had never heard of Biology Online before this, and won’t be seeking them out. You can add my name of the long list of people who certainly won’t be writing free content for them.
It’s what happened next that bothers me.
DNLee posted on her blog about what happened — rather a restrained post, which took the opportunity to discuss the wider implications rather than cursing out the perpetrator.
And Scientific American deleted the post.
They just deleted it.
This bothers me much more than the original incident, because I had no idea who Biology Online are, but thought I knew what Scientific American was. Looks like I didn’t. All I know for sure about them now is that they’re a company that accepts advertising revenue from Biology Online. Just saying.
Not a word was said to DNLee about this censorship by the people running the network. The post just vanished, bam. If you follow the link, it currently says “You have reached this page due to an error”. Yes. An error on the part of the blog-network management.
(This, by the way, is one of the reasons I don’t expect Sauropod Vertebra Picture of the Week ever to join one of these networks. I will not tolerate someone else making a decision to take down one of my posts.)
What makes this much worse is that Scientific American‘s Editor in Chief Mariette DiChristina has flat-out lied about this incident at least once. First she tweeted “@sciam is a publication for discovering science. The post was not appropriate for this area & was therefore removed.” Then after a day of silence, she blogged “we could not quickly verify the facts of the blog post and consequently for legal reasons we had to remove the post“.
So which was it, SciAm? Did you censor the post because it was off-topic? Or because of a perceived legal threat? Or, since we know at least one of these mutually contradictory claims isn’t true, maybe neither of them is, and you removed it avoid inconveniencing a sponsor?
DoChristina’s blog-post is a classic nonpoplogy. It says nothing about the original slur that gave rise to all this, and it doesn’t apologise of DNLee for censoring her perfectly reasonable blog-post. What it does do is blame the victim by implying that DNLee’s post is somehow illegal. (You can judge for yourself whether it is by reading one of the many mirrors.)
Then there’s this: “for legal reasons we had to remove the post”. What legal reasons? When did the SciAm legal team get involved in this? (Did they at all? I am sceptical.) Have you actually been threatened by Biology Online? (Again, I have my doubts.) Even if a threat has been received, it’s at best cowardly of SciAm to cave so immediately, and grotesquely unprofessional not even to bother notifying DNLee.
So SciAm are digging themselves deeper and deeper into this hole. Even their usually prolific and reliable blog editor @BoraZ has gone uncharacteristically quiet — I can only hope because he, too, is being silenced, rather than because he’s complicit.
There are only two ways for the SciAm blogging network to get out of this with some shreds of their reputation intact. They need to either show clearly that DNLee was lying about Biology Online, in which case they would merely have mismanaged this incident; or they need to reinstate her post and apologise properly. ”Properly” means “We screwed up because of our cowardice, please forgive us”, not “We’re sorry if some people were offended by our decision to do this thing that we’re going to keep claiming was OK”. Because it wasn’t.
Right then, SciAm. Where now?