I mentioned on Twitter that I’d left a comment on the Scholarly Kitchen that had been blocked in moderation, and several people asked what the comment was.

censored

It was a response to this comment from David Crotty (who as well as being a commenter is also the editor of the Scholarly Kitchen.) We were once more discussing David’s lamentable tendency to beg the question of Sci-Hub’s morality by abusing the term “theft” to mean copyright violation. My comment was as follows:

> Sorry no–a term everyone, at least the court system, agrees upon, is “theft”.

This is simply not true. It’s a crusade that you, for reasons which remain opaque to me, have taken on. Outside of a few lawyers (who, as we all know, routinely use language in completely different ways from civilians), the use of “theft” is widely recognised as an inflammatory misrepresentation.

It’s bad enough that the wildly inappropriate term “piracy” has been so widely adopted. Obfuscating the issue yet further helps literally no-one. Once more: why are you doing this? It’s hard to avoid the conclusion that it’s because you don’t believe you can win an actual argument about copyright infringement, and have to poison the rhetorical well instead.

> If I told you not to use the terms “paywall” or “toll access” because I don’t like them, would you?

What term to do you prefer over “paywall”?

In any case, “paywall” is a purely descriptive term, not an attempt to pre-decide an argument by applying an inapplicable analogy. If instead I referred to paywalls as “fraudwalls” or “embezzlewalls”, then you would certainly have a point in asking me to change my language.

> I think the easiest way to avoid this distracting nonsense is to simply moderate our comments a bit more strictly, and delete any “it’s not theft” response. Those who wish to debate semantics can do so elswhere.

Ah yes — the final solution for those who realise they can’t win an argument.

I suppose this would be as good a conclusion to this thread as any: following up the repeated and deliberate abuse of language with actual censorship has a pleasing narrative consistency; and would of course demonstrate how wrong you are far more effectively than any words you might say.

… or of course you could stop deliberately creating a pointless side-conflict.

I really don’t expect this from you, David.

I honestly can’t see what was so objectionable about this that David decided to censor it; but as I’ve noted elsewhere, it’s his blog, and his prerogative to moderate it how he sees fit. But I really don’t want to see the Scholarly Kitchen being presented as a meeting of minds, or some kind of melting pot, when it’s increasingly clear that it’s actually an advocacy site for legacy publishing — and, more to the point, for legacy publishers.

Again: there’s nothing wrong with advocacy sites. SV-POW! is one itself (among other things), and I am pretty happy about it. But no-one coming to SV-POW! is under any illusions that it’s meant to be meeting-place for all stakeholders in scholarly communication. It’s not that. It’s a place where we express one point of view: our own. (Despite this, no-one coming to SV-POW! has to worry about their comments being censored. The only comments that ever get blocked in moderation are spam and outright personal attacks.)

Of course, wiser heads than mine have realised some time ago what the Scholarly Kitchen is. People like PLOS’s Mike Eisen and the Royal Society’s Stuart Taylor stopped trying to participate some time ago; RLUK’s David Prosser says “I gave up on them quite a while ago. Occasionally read the odd article people point me to, but see no merit in engaging.” Copyright guru Charles Oppenheim writes “It could have been a good place for proper debates, but is now of no use for that”.

It’s a real shame. I think we do need a place where people on all sides of the debate can argue it out on an equal footing. But that simply isn’t possible in a venue where one of the debaters has the power to instantly gag anyone who says something he doesn’t like.

This is of course very far from my first run-in with the Scholarly Kitchen. In fact, nearly four years ago I drafted an SV-POW! post entitled “Why I am really, really, really done with The Scholarly Kitchen”, but concluded it wasn’t constructive and never posted it.

My problem is, like a dog returning to its own vomit, I keep going back in the hope of a constructive dialogue, because I am, as Philip Lord put it, “an incorrigable enthusiast”. It’s true that I retain a completely unrealistic level of optimism. But The Wretched Hive of Scholarly Villainy is slowly fixing that bug.

And now here I am again, like an addict saying “This time it’ll be different, this time I can give it up, for sure.” And this time, I will. Anyone finds me commenting on the Scholarly Kitchen again, do me a favour, come round here and kick my butt. Because it’s stupid of me to keep wasting my time there.

Here is a vertebra that Matt and I saw on our recent travels through Utah:

IMG_2530

IMG_2542

I will explain in a subsequent post where we saw it, who gave us access, where and when it is from, and so on.

For now, I want people’s gut reactions: what is it?

It’s very doubtful that Franz J. Ingelfinger ever intended the rule named in his honour to prevent online preprints — after all, such things didn’t exist when he introduced his no-prior-publication policy at the New England Journal of Medicine in 1969, or even at the time of his death in 1980. Yet the rule lingers on in corrupt form.

zombie_scientist_by_sweetpeachtea14-d5gjcz7

Poor Franz’s name has been associated with the so-called “Ingelfinger Rule“, even as that rule has been extended, distorted and abused to the general detriment of science. His goal was to prevent scientists from going to the press with sensationalised findings before they had been though peer review. But now …

Well, I’ll let Kim E. Barrett, Dean of the Graduate Division and Distinguished Professor of Medicine at UC San Diego, tell you about it:

I just had a student who was not allowed to include one of her published papers in her dissertation, or even a paraphrase of it, because of publisher policies governing dissertations posted online. She had to resort to including only a link.

On the same mailing list, Glenn Hampson offered an optimistic take: “as with so many disputes, poor communication seems to be at the heart of it. So repairing this might be easy.” But Barrett was clear:

The first student I mentioned had multiple interactions with the publisher, and her communications were remarkably clear. They just said no.

Speaking as one whose own dissertation was five published papers bound into a single volume, I have to say that is completely outrageous. At the time of submitting my Ph.D, two chapters were in press, two were in review (subsequently to be published in different journal from the ones that were then reviewing them), and only one had been published. If I’d been labouring under this idiot interpretation of Ingelfinger, my dissertation would have been once chapter long.

 

In a recent blog-post, Kevin Smith tells it like it is: legacy publishers are tightening their grip in an attempt to control scholarly communications. “The same five or six major publishers who dominate the market for scholarly journals are engaged in a race to capture the terms of and platforms for scholarly sharing”, says Smith. “This is a serious threat to academic freedom.”

A fisted hand tightly gripping US Currency.People can legitimately have different ideas about precisely what it is that Elsevier intends to do with SSRN, now that it’s acquired it. But as we discuss the possible outcomes, we need to keep one principle in mind: it’s simply unrealistic to imagine that Elsevier, in controlling Mendeley and SSRN, will do anything other than what is best for Elsevier.

That’s not a criticism, or even a complaint. It’s a statement of what a for-profit corporation does. It’s in it’s nature. There’s no need for us to blame Elsevier for this, any more than we blame a fox when it eats a chicken. That’s what it does.

The appropriate response is simply to prevent any more of this kind of thing happening, by taking control of our own scholarly infrastructure.

The big problem with SSRN is the same as the big problem of Mendeley: being privately owned and for-profit, they owners were always going to be susceptible to a good enough offer. People starting private companies are looking to make money from them, and a corporation that comes along with a big offer is a difficult exit strategy to resist. When we entrusted preprints to SSRN, they were always vulnerable to being taken hostage, in a way that arXiv preprints are not.

Again: I am not blaming private companies’ owners for this. It’s in the nature of what a private company is. I recognise that and accept it. The thing is, I interpret it as damage and want to route around it.

So what is the solution?

bridge

It’s simple. We, the community, need to own our own infrastructure.

One one level, this is easy. We, the community, know how to do it. We have experience of good and bad infrastructure, we know the difference. We have excellent, clearly articulated principles for open scholarly infrastructure. We have top quality software engineers, interaction designers, UI experts and more.

What we don’t have is funding. And that is crippling.

We can’t build and maintain community-owned infrastructure; and (to a first approximation anyway) no-one is funding it. It’s truly disgraceful that even such a crucial piece of infrastructure of arXiv is constantly struggling for funding. arXiv serves about a million articles per week, and is the primary source of publications in many scientific subfields, yet every year it struggles to bring in the less then a million dollars it costs to run. It’s ridiculous the the Gates Foundation or someone hasn’t come along with a a few tens of millions dollar and set up a long-term endowment to make arXiv secure.

And when even something as proven as arXiv struggles for funding, what chance does anything else have?

The problem seems to be this: funders have a blind spot when it comes to funding infrastructure. That’s why we have no UK national repository; it’s why there is no longer an independent subject repository for social sciences; it’s why the two main preprint archives for bio-medicine (PeerJ Preprints and BioRxiv) are privately owned, and potentially vulnerable to the offer-you-can’t-refuse from Elsevier or one of the other legacy publishers in the oligopoly(*).

BlindSpot_DSC_5842_H2

When you think about funders — RCUK, Wellcome, NIH, Gates, all of them — they are great at funding research; and terrible at funding the infrastructure that allows it to have actual benefit. Most funders even seem to have specific policies that they won’t fund infrastructure; those that don’t, simply lack a way to apply for infrastructure funding. It’s a horribly short-sighted approach, and we’re seeing its inevitable fruit in Elsevier’s accumulation of infrastructure.

We’ll look back at funding bodies in 10 or 20 years and say their single biggest mistake was failing to see the need to fund infrastructure.

Please, funders. Fix this. Make whatever changes you need to make, to ensure the the scholarly community owns and controls its own preprint archives, subject repositories, aggregators, text-mining tools, citation graphs, metrics tools and what have you. We’ve already seen what happens when we cede control of the scholarly record to corporations: spiralling prices, poor quality product, arbitrary barriers, and the retardation of all progress. Let’s not make the same mistake again with infrastructure.

 

 


(*) Actually, I don’t believe PeerJ’s owners would sell their preprint server to Elsevier for any amount of money — and the same may be true of the BioRxiv for all I know, I’ve never spoken with the owners. But who can tell what might happen?

Another day, another puff-piece from academic publishers about how awesome they are. This time, the Publisher’s Association somehow suckered the Guardian into giving them a credible-looking platform for their party political broadcast, Think academic publishers are greedy? Do your research. I have to give the PA credit for coming up with about the most patronising title possible.

Yes, I did my research. Guess what? Academic publishers are greedy.

Greedy-diner

(The article doesn’t say it’s by the Publishers Association, by the way. It’s credited to Stephen Lotinga, who LinkedIn tells us is Chief Executive of The Publishers Assocation, but the article doesn’t declare that.)

Oh boy do I get tired of constantly rebutting the same old bs. from publishers. And it really is the same bs. They’re not even taking the trouble to invent new bs., just churning out the same nonsense each time — for example, equating their massive profits with investment in improvements.

Of course, what they actually can do with those massive profits is hire full-timers whose actual job is to churn out such propaganda. Whereas I have to rebut in my spare time — in between day-job and academic work. As though I didn’t have real work to do.

Here are responses to just some of the nonsense in the Guardian‘s piece.

The academic publishing market is worth £4.4bn to the UK economy.

No it’s not: it has revenue of £4.4bn, which is not at all the same thing. Meanwhile, it’s exerting an enormous drag on academic and commercial research, retarding medical progress, reducing access to the arts and humanities, and overall doing the equivalent of far more than £4.4bn damage to the economy.

Publishers invest heavily in scholarly communication, for example, including the technology-intensive digital platforms upon which authors, reviewers, editors and readers conduct their work.

In other words, they invest in their own assets. Whoop-de-doo. Name me any organisation that doesn’t do this. And remember, those massive 32%-42% profits are what’s left after this investment.

Publishers offer value to research institutions by providing data-driven metrics and analytics that inform their research management activities. This investment allows for rigorous peer review

What? What? This seems to be saying that publishers’ selling their own usage stats back to them somehow makes peer-review possible. But that can’t be what it’s saying, can it? Because that would not merely be wrong, it would be completely incoherent. It’s like claiming that publishers’ ability to format headings in Helvetica is what makes it possible for researchers to sequence DNA.

It also pays for the development of technology of that ensures articles are discoverable, shareable and able to be accessed in underserved regions.

One interpretation of this statement is that it’s simply a lie. I will adopt the other, more charitable interpretation: that it’s a typo for “Publishers pay for the development of technology that prevents articles from being shareable and able to be accessed”.

Oh, and that technology that makes articles discoverable? It’s called Google, and publishers had and have absolutely nothing to do with it. (Except, of course when they use the robots.txt standard to prevent search engines from indexing articles.)

Many small publishers partner with larger groups in order to take advantage of their scale and reach, thereby reducing costs for members and authors. Such diversity leads to competition.

No, no. Follow carefully. Consolidation of small publishers into larger groups leads to less competition. Which of course is exactly what the big publishers want.

The fact that [the individual researcher] wants to submit … is the result of the good work of publishers to maintain the system in which that can take place.

No it isn’t, it’s the result of the monopoly that the publishers hold on the brands that researchers think (rightly or wrongly) they need on their CV.

Nobody submits to the Journal of Vertebrate Paleontology because it’s published by Taylor and Francis; people submit to it because it’s the journal of the Society of Vertebrate Paleontology.

And so it goes on …

creationism

The Gish Gallop

Reading and responding to all this inanity had a strangely familiar feel to it. After a while, I realised what I was seeing was the technique known as the Gish Gallop, after the prominent creationist Duane Gish. The technique involves “spewing so much bs. in such a short span on that your opponent can’t address let alone counter all of it”.

It’s a very effective tactic. It’s very easy to do, and very difficult to counter. The Publishers’ Association can stand there all day and reel off idiot claims (“publishers’ metrics enable peer review”). They take a single sentence to say, but it’s terribly easy to get suckered into writing multiple paragraphs rebutting them. They waste our time and energy in exchange for very little of their own.

In short, the Gish Gallop is a great way to conduct an argument — provided that you care only about “winning” the argument and have no regard at all for what is actually true.

 

As regular readers will know, Matt and I have recently spent ten glorious days travelling the dinosaur museums of Utah, in a once-in-a-lifetime event that we have been calling the Sauropocalypse. In that time, we visited seven different museums and — this is the truth — had an absolutely fantastic time in all of them. One of the big reasons is of course the quality of their collections and galleries. But equally important is the welcome we got from our hosts at each of these places, and the help they all generously and cheerfully gave us.

Here’s where we visited, in chronological order, with a word of thanks to each host.

1. BYU Museum of Paleontology, Provo

IMG_3392

Mike compares Jensen’s sculpture of the big Supersaurus cervical BYU 9024 with the actual fossil.

At the amazing BYU — where we spent three full days, as it has almost certainly the largest collection of sauropod fossils anywhere in the world — our host was Brooks Britt. (Matt’s mentioned Brooks previously on this blog, as one of the most formative influences on his career: the person who put him onto pneumaticity.)

Brooks set us free in his collections and gallery with no restrictions. He had specimens fork-lifted down from high shelves for us, gave us a pallet lifter so we could move them around at will, and generally did everything he could to make our stay productive. He also took us out to lunch, twice: once at a cheap but delicious taco place, and once at a Brazilian eat-all-you-want barbecue place where I could happily have spent the entire afternoon.

2. The Prehistoric Museum, Price

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Matt inspects the beautifully preserved and prepared anterior cervicals of a Camarasaurus in the main gallery.

Our host at Price was occasional SV-POW! commenter Ken Carpenter, who also arranged for us to give a pair of talks at the museum in the evening. (Mine: Why giraffes have short necks. Matt’s: Why elephants are so small.) Ken gave us free reign to get in among the exhibits, and we took full advantage to make a potentially important discovery (to be discussed in a future post).

Ken also took us to see the CEUM collections, and invited us to take on a huge descriptive project, working on the PR2 brachiosaur. Sadly, that project is just too big for either of us. But there are individual elements within the PR2 collection that are of interest, and no doubt we’ll be posting more about those, too.

3. Dinosaur National Monument, Jensen

IMG_2603

Matt looms ominously over an Apatosaurus cervical in ventral view — or is it Camarasaurus?

Matt has already paid tribute to Dan Chure, our host up on the wall, who came in on his day off just to help us. An extraordinary host at an astonishing venue.

4. Utah Field House of Natural History, Vernal

IMG_2719

Diplodocus butt. Wedel for scale. He likes big butts and he cannot lie.

Here, we were hosted by Mary Beth Bottomley. She went beyond the call of duty in not only allowing us access to the prep room and collections, but helping us to take apart the shelving in collections so we could get better photos of a big, difficult-to-move specimen. Mary Beth was particularly interested in what we were working on, and will (I hope) now be a regular reader of this blog.

5. Dinosaur Journey, Fruita

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Mike, astonished by a particularly extreme apatosaur cervical. But then aren’t they all extreme?

We were, inadvertently, sensationally rude to our host, Julia McHugh. She’d arranged to take us for lunch, but Matt was so obsessed with the transit of Mercury across the sun that he completely forgot, and sent me off to get salads from Subway instead. (Note that I am making the point here that Matt forgot this arrangement. I make no comment on my own recall.) As a result, we cheated ourselves out of a BBQ lunch.

But Julia was great about it, and once again we were given free reign in collections. Matt and I were each able to make valuable observations, one for an already-in-progress paper and one for a new one.

6. Natural History Museum of Utah, Salt Lake City

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Barosaurus, an Allosaurus adult and several juveniles, and Mike.

Here, our host was Carrie Levitt. She welcomed us to the museum, gave us a tour of collections, left us to it, and … we spent almost the entire day in the public gallery instead! I did get a couple of nice photos of the holotype skulls of Kosmoceratops and Diabloceratops, but the truth is that the public gallery was so awesome, it just sucked us in.

But Carrie was great about it. Rather than resenting our having wasted her time in the collections orientation, she was just glad that we got useful observations out of the museum. (And we did. Matt and I can sometimes get so wrapped up in individual vertebrae that we forget they’re part of whole animals. The many fine mounted dinosaur skeletons at UMNH helped to redress this failing.)

7. North American Museum of Ancient Life, Thanksgiving Point

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Matt is attacked by a Utahraptor, but is all like “Am I bovvered?”. To be honest, I suspect he was all dinosaured out by this point.

On our last day — I had to be at the airport by 6pm — we went to NAMAL, We’d not been able to make contact with staff ahead of time, as Matt’s old contact seems to be no longer at the museum. But as we walked past the prep lab near the museum entrance, we saw some beautiful Barosaurus cervicals. As we stood gawping, Rick Hunter, inside the lab, recognised Matt and invited us in.

With no prior notice at all, Rick dropped what he was doing to help us out as we inspected their gorgeous material. That’s been really helpful as we’ve firmed up our ideas on what Barosaurus is. (And I hope we’ve helped them get a better handle on the serial positions of their vertebrae, too.)

In summary, pretty much everyone we met in Utah was super-helpful and super-nice. That also includes John and ReBecca Foster, who put us up for the night in Moab, the night before we went to Arches National Park. The people are one of three reasons why Utah is now my favourite US state. (The others are the sauropods, naturally, and the landscapes.)

Museum folks of Utah, we salute you!

UPDATE 19 May 2016

I belatedly realized that I caused some confusion in the original version of this post. This will hopefully sort things out:

NAMAL Barosaurus cervical with features labeled

The ventrolateral processes (1) are nothing new. As Ken Carpenter pointed out in a comment, Hatcher noted them back in 1901 in his monograph on Diplodocus carnegii. These are the features I describe below as being, “huge in Barosaurus, big in Diplodocus, small in Apatosaurus, and nonexistent in Haplocanthosaurus, Camarasaurus, and the brachiosaurids, at least from what I’ve seen.” To clarify: occasionally in camarasaurs and frequently in brachiosaurs you can trace a ridge along the ventrolateral margin of the centrum from the parapophysis to the cotyle. But these ridges are basically just the ‘corners’ of the centrum, leftover by the lateral and ventral waisting of the centrum – they do not project beyond the margin of the cotyle. In contrast, what I’ve been calling the ventrolateral flanges in diplodocids do project beyond the margins of the cotyle – they are additive structures, not just architectural leftovers. They also don’t vary much, other than to be more pronounced in more posterior cervicals.

The irregular ventral ridges (2) are a totally different thing. They’re on or near the sagittal midline of the centrum, usually restricted to the anteroposterior middle of the ventral centrum (so, about halfway between the condyle and the cotyle), and as my preferred term implies, highly variable among individuals and even among vertebrae in a series.

Hope that helps! (Original post starts below.)

– – – – – – – – – – – – – – – – – – – – –

2005-07-29 BYU 16918 Diplodocus left lateral

Back in 2005 I visited BYU while I was working on my dissertation. Back then I noted ventral ridges in a few diplodocine cervical vertebrae. (I hesitate to call such flimsy things ‘keels’.)

Up above is BYU 16918, a mid-to-posterior cervical vertebra of Diplodocus from the famous Dry Mesa Quarry. Here it is again in posterior view:

2005-07-29 BYU 16918 Diplodocus posterior view labeled

The things I have labeled VLF here are ventrolateral flanges, which are huge in Barosaurus, big in Diplodocus, small in Apatosaurus, and nonexistent in Haplocanthosaurus, Camarasaurus, and the brachiosaurids, at least from what I’ve seen. See this post for details. I know that the left VLF here looks like a second ridge, but the cotyle is broken off in such a way that we’re seeing the fossa just dorsal to the VLF margin. The ridge itself is skewed to the right, which could be natural or a result of taphonomy – as you can see from the photo at the top of the post, this vert has seen better days.

Here’s another Dry Mesa vert, BYU 11617, this time an anterior cervical of Barosaurus and in left lateral view:

2005-07-29 BYU 11617 Barosaurus left lateral

Again in right lateral view – on this side you can see the fossa in the VLF more clearly:

2005-07-29 BYU 11617 Barosaurus right lateral

And here’s the ventral view showing the ridge:

2005-07-29 BYU 11617 Barosaurus ventral view labeled

I noted these things in my notebook back when, filed them under, “Huh. How about that?” and went on with life.

Then last week Mike and I were at the North American Museum of Ancient Life in Lehi, Utah, and we saw this super-nice Barosaurus cervical on display in the prep lab (left ventro-lateral view). Check out the monster ventrolateral flanges, and the ridges between them at about mid-centrum.

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Here’s another view, a more square-on ventral this time:

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We owe a big thank you to Rick Hunter, who let us into the prep lab at the North American Museum of Ancient Life to see the Barosaurus material up close.

So what’s the deal with these ridges? I assume that they’re caused by pneumatic diverticula remodeling the ventral surface of the centrum. We know that such diverticula were down there because there are actual foramina on the ventral centrum in Supersaurus, many apatosaurines (Lovelace et al., 2008), many brachiosaurids, and probably loads of other things that haven’t been checked. Oddly enough, I’ve never seen the ridges in any of those other taxa. It seems that you get foramina or ridges, but not both. I have no idea what’s up with that – to paraphrase Neal Stephenson, Barosaurus cervicals are confections of air and marketing, and you’d think that if any sauropod would have straight-up foramina down there, it would be Barosaurus. But Barosaurus gets ridges and clunky old Apatosaurus gets foramina (sometimes, not all the time).

It’s a sick world, I tell you.

Reference

  • Lovelace, D. M., Hartman, S. A., & Wahl, W. R. (2007). Morphology of a specimen of Supersaurus (Dinosauria, Sauropoda) from the Morrison Formation of Wyoming, and a re-evaluation of diplodocid phylogeny. Arquivos do Museu Nacional, Rio de Janeiro 65(4):527-544.
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