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A few bits and pieces about the PLOS Collection on sauropod gigantism that launched yesterday.

2013-10-29-SauropodEbook1-thumb

First, there’s a nice write-up of one of our papers (Wedel and Taylor 2013b on pneumaticity in sauropod tails) in the Huffington Post today. It’s the work of PLOS blogger Brad Balukjian, a former student of Matt’s from Berkeley days. The introduction added by the PLOS blogs manager is one of those where you keep wanting to interrupt, “Well, actually it’s not quite like that …” but the post itself, once it kicks in, is good. Go read it.

Brad also has a guest-post on Discover magazine’s Crux blog: How Brachiosaurus (and Brethren) Became So Gigantic. He gives an overview of the sauropod gigantism collection as a whole. Well worth a read to get your bearings on the issue of sauropod gigantism in general, and the new collection in particular.

PLOS’s own community blog EveryONE also has its own brief introduction to the collection.

And PLOS and PeerJ editor Andy Farke, recently in these pages because of his sensational juvenile Parasaurolophus paper, contributes his own overview of the collection, How Big? How Tall? And…How Did It Happen?

Finally, if you’re at SVP, go and pick up your free copy of the collection. Matt was somehow under the impression that the PLOS USB drives with the sauropod gigantism collection would be distributed with the conference packet when people registered. In fact, people have to go by the PLOS table in the exhibitor area (booth 4 in the San Diego ballroom) to pick them up. There are plenty of them, but apparently a lot of people don’t know that they can get them.

References

This is an exciting day: the new PLOS Collection on sauropod gigantism is published to coincide with the start of this year’s SVP meeting! Like all PLOS papers, the contents are free to the world: free to read and to re-use. (What is a Collection? It’s like an edited volume, but free online instead of printed on paper.)

There are fourteen papers in the new Collection, encompassing neck posture (yay!), nutrition (finally putting to bed the Nourishing Vomit Of Eucamerotus hypothesis), locomotion, physiology and evolutionary ecology. Lots for every sauropod-lover to enjoy.

x

Taylor and Wedel (2013c: Figure 12). CT slices from fifth cervical vertebrae of Sauroposeidon. X-ray scout image and three posterior-view CT slices through the C5/C6 intervertebral joint in Sauroposeidon OMNH 53062. In the bottom half of figure, structures from C6 are traced in red and those from C5 are traced in blue. Note that the condyle of C6 is centered in the cotyle of C5 and that the right zygapophyses are in articulation.

Matt and I are particularly excited that we have two papers in this collection: Taylor and Wedel (2013c) on intervertebral cartilage in necks, and Wedel and Taylor (2013b) on pneumaticity in the tails of (particularly) Giraffatitan and Apatosaurus. So we have both ends of the animal covered. It also represents a long-overdue notch on our bed-post: for all our pro-PLOS rhetoric, this is the first time either of has had a paper published in a PLOS journal.

Wedel and Taylor (2013b: Figure 4). Giraffatitan brancai tail MB.R.5000 (‘Fund no’) in right lateral view. Dark blue vertebrae have pneumatic fossae on both sides, light blue vertebrae have pneumatic fossae only on the right side, and white vertebrae have no pneumatic fossae on either side. The first caudal vertebra (hatched) was not recovered and is reconstructed in plaster.

It’s a bit of a statistical anomaly that after a decade of collaboration in which there was never a Taylor & Wedel or Wedel & Taylor paper, suddenly we have five of them out in a single year (including the Barosaurus preprint, which we expect to eventually wind up as Taylor and Wedel 2014). Sorry about the alphabet soup.

Since Matt is away at SVP this week, I’ll be blogging mostly about the Taylor and Wedel paper this week. When Matt returns to civilian life, the stage should be clear for him to blog about pneumatic caudals.

Happy days!

References

It shouldn’t come as a huge surprise to regular readers that PeerJ is Matt’s and my favourite journal. Reasons include its super-fast turnaround, beautiful formatting that doesn’t look like a facsimile of 1980s printed journals, and its responsiveness to authors and readers. But the top reason is undoubtedly its openness: not only are the article open access, but the peer-review process is also (optionally) open, and of course PeerJ preprints are inherently open science.

During open access week, PeerJ now publishes this paper (Farke et al. 2013), describing the most open-access dinosaur in the world.

FarkeEtAl2013-parasaurolophus-fig4

It’s a baby Parasaurolophus, but despite being a stinkin’ ornithopod it’s a fascinating specimen for a lot of reasons. For one thing, it’s the most complete known Parasaurolophus. For another, its young age enables new insights into hadrosaur ontogeny. It’s really nicely preserved, with soft-tissue preservation of both the skin and the beak. The most important aspect of the preservation may be that C-scanning shows the cranial airways clearly:

FarkeEtAl2013-parasaurolophus-fig9

This makes it possible for the new specimen to show us the ontogenetic trajectory of Parasaurolophus — specifically to see how its distinctive tubular crest grew.

FarkeEtAl2013-parasaurolophus-fig11

But none of this goodness is the reason that we at SV-POW! Towers are excited about this paper. The special sauce is the ground-breaking degree of openness in how the specimen is presented. Not only is the paper itself open access (and the 28 beautiful illustrations correspondingly open, and available in high-resolution versions). But best of all, CT scan data, surface models and segmentation data are freely available on FigShare. That’s all the 3d data that the team produced: everything they used in writing the paper is free for us all. We can use it to verify or falsify their conclusions; we can use it to make new mechanical models; we can use it to make replicas of the bones on 3d printers. In short: we can do science on this specimen, to a degree that’s never been possible with any previously published dinosaur.

This is great, and it shows a generosity of spirit from Andy Farke and his co-authors.

But more than that: I think it’s a great career move. Not so long ago, I might have answered the question “should we release our data?” with a snarky answer: “it depends on why you have a science career: to advance science, or to advance your career”. I don’t see it that way any more. By giving away their data, Farke’s team are certainly not precluding using it themselves as the basis for more papers — and if others use it in their work, then Farke et al. will get cited more. Everyone wins.

Open it up, folks. Do work worthy of giants, and then let others stand freely on your shoulders. They won’t weigh you down; if anything, they’ll lift you up.

References

Farke, Andrew A., Derek J. Chok, Annisa Herrero, Brandon Scolieri, and Sarah Werning. 2013. Ontogeny in the tube-crested dinosaur Parasaurolophus (Hadrosauridae) and heterochrony in hadrosaurids. PeerJ 1:e182. http://dx.doi.org/10.7717/peerj.182

My hobby:

October 17, 2013

oh crap im part furry

Fear and Loathing dinosaur tail 2

Relic cover

polar dinosaur babies

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.

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:

  1. Those that make the teller look good.
  2. Those that make the teller look bad.
  3. Those that make someone else look good.
  4. 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.

I’m gathering all seven parts of Tutorial 19 (“Open Access definitions and clarifications”) in one place for easy reference. Here they are:

And see also this more recent post:

Enjoy!

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?

DiChristina’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 to 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?

moo-2011-flamingo-neck

But not “funny ha-ha”. More like, “funny how that neck is clearly impossible.” I mean, really.

This is another shot from the Museum of Osteology in Oklahoma City. A few hundred more posts like this and I’ll be done.

For more flamingo-related weirdness, check out Casey Holliday’s work (with Ryan Ridgely, Amy Balanoff, and Larry Witmer) on the wacky blood vessels in flamingo heads. Unfortunately, Holliday et al. found no evidence of the antigravity generators that are obviously present in flamingoes somewhere. So there’s more work to be done here.

Kinda makes me sad, to ponder all of the sweet soft-tissue adaptations that extinct organisms must have had, that we will probably never know (enough) about. At least we have freaks like this around to remind us.

The LSE Impact blog has a new post, Berlin 11 satellite conference encourages students and early stage researchers to influence shift towards Open Access. Thinking about this,  Jon Tennant (@Protohedgehog) just tweeted this important idea:

Would be nice to see a breakdown of OA vs non-OA publications based on career-stage of first author. Might be a wake-up call.

It would be very useful. It makes me think of Zen Faulkes’s important 2011 blog-post, What have you done lately that needed tenure?. We should be seeing the big push towards open access coming from senior academics who are established in their roles don’t need to scrabble around for jobs like early-career researchers. Yet my impression is that in fact early-career researchers are doing a lot of the pro-open heavy lifting.

Is that impression true?

We should find out.

Here’s one possible experimental design: take a random sample of 100 Ph.D students, 100 post-docs, 100 early-career researchers in tenure-track jobs and 100 tenured researchers. For each of them, analyse their last ten years of publications and determine what proportion are paywalled, what proportion are free to read (e,g, on arXiv or in an all-rights-reserved IR), and what proportion are true (BOAI-compliant) open access.

An alternative approach would be to randomly sample 1000 open-access papers (from PLOS and BMC journals, for example), and 1000 paywalled papers (from Elsevier and Springer, say) and find the career-stage of their authors. I’m not sure which approach would be better?

Who is going to do this?

I think it would be a nice, tractable first project for someone who wants to get into academic research but hasn’t previously published. It would be hugely useful, and I’m guessing widely cited. Does anyone fancy it?

Update

Georg Walther has started a hackpad about this nascent project. Since Jon “Protohedgehog” Tennant has now tweeted about it, I assume it’s OK to publicise. If you’re interested, feel free to leap in!

Suppose, hypothetically, that you worked for an organisation whose nominal goal is the advancement of science, but which has mutated into a highly profitable subscription-based publisher. And suppose you wanted to construct a study that showed the alternative — open-access publishing — is inferior.

What would you do?

You might decide that a good way to test publishers is by sending them an obviously flawed paper and seeing whether their peer-review weeds it out.

But you wouldn’t want to risk showing up subscription publishers. So the first thing you’d do is decide up front not to send your flawed paper to any subscription journals. You might justify this by saying something like “the turnaround time for traditional journals is usually months and sometimes more than a year. How could I ever pull off a representative sample?“.

Next, you’d need to choose a set of open-access journals to send it to. At this point, you would carefully avoid consulting the membership list of the Open Access Scholarly Publishers Association, since that list has specific criteria and members have to adhere to a code of conduct. You don’t want the good open-access journals — they won’t give you the result you want.

Instead, you would draw your list of publishers from the much broader Directory of Open Access Journals, since that started out as a catalogue rather than a whitelist. (That’s changing, and journals are now being cut from the list faster than they’re being added, but lots of old entries are still in place.)

Then, to help remove many of the publishers that are in the game only to advance research, you’d trim out all the journals that don’t levy an article processing charge.

But the resulting list might still have an inconveniently high proportion of quality journals. So you would bring down the quality by adding in known-bad publishers from Beall’s list of predatory open-access publishers.

Having established your sample, you’d then send the fake papers, wait for the journals’ responses, and gather your results.

To make sure you get a good, impressive result that will have a lot of “impact”, you might find it necessary to discard some inconvenient data points, omitting from the results some open-access journals that rejected the paper.

Now you have your results, it’s time to spin them. Use sweeping, unsupported generalisations like “Most of the players are murky. The identity and location of the journals’ editors, as well as the financial workings of their publishers, are often purposefully obscured.”

Suppose you have a quote from the scientist whose experiences triggered the whole project, and he said something inconvenient like “If [you] had targeted traditional, subscription-based journals, I strongly suspect you would get the same result”. Just rewrite it to say “if you had targeted the bottom tier of traditional, subscription-based journals”.

Now you have the results you want — but how will you ever get through through peer-review, when your bias is so obvious? Simple: don’t submit your article for peer-review at all. Classify it as journalism, so you don’t need to go through review, nor to get ethical approval for the enormous amount of editors’ and reviewers’ time you’ve wasted — but publish it in a journal that’s known internationally for peer-reviewed research, so that uncritical journalists will leap to your favoured conclusion.

Last but not least, write a press-release that casts the whole study as being about the “Wild West” of Open-Access Publishing.

Everyone reading this will, I am sure, have recognised that I’m talking about  John Bohannon’s “sting operation” in Science. Bohannon has a Ph.D. in molecular biology from Oxford University, so we would hope he’d know what actual science looks like, and that this study is not it.

Of course, the problem is that he does know what science looks like, and he’s made the “sting” operation look like it. It has that sciencey quality. It discusses methods. It has supplementary information. It talks a lot about peer-review, that staple of science. But none of that makes it science. It’s a maze of preordained outcomes, multiple levels of biased selection, cherry-picked data and spin-ridden conclusions. What it shows is: predatory journals are predatory. That’s not news.

Speculating about motives is always error-prone, of course, but it it’s hard not to think that Science‘s goal in all this was to discredit open-access publishing — just as legacy publishers have been doing ever since they realised OA was real competition. If that was their goal, it’s misfired badly. It’s Science‘s credibility that’s been compromised.

Update (9 October)

Akbar Khan points out yet more problems with Bohannon’s work: mistakes in attributing where given journals were listed, DOAJ or Beall’s list. As a result, the sample may be more, or less, biased than Bohannon reported.