Stegotetrabelodon making tracks at Mleisa, © Mauricio Antón

Sweet new paper out today by Bibi et al. in Biology Letters, on some awesome elephant tracks from the United Arab Emirates. I’ve known this was coming for a while, because the second author on the study, Brian Kraatz, has his office about 30 feet down the hall from mine. And I just ran into the lead author, Faysal Bibi, at the Museum fur Naturkunde in Berlin when I was there in December. I knew Faysal when he was an undergrad at Berkeley, and now he’s Dr. Bibi and doing a postdoc in Berlin–how time flies. Congratulations to Faysal, Brian, and the rest of the team on a really cool discovery.

The study is nothing to do with sauropods, but it has a lot of weird connections to SV-POW! Most importantly, the paper is open access, which is both awesome and timely. The life restoration is by the wicked talented Mauricio Antón, who is best known for his paleomammals work but who also restored Brontomerus for National Geographic last year. And some comparative data used in the paper was supplied by SV-POW! favorite and sometime sci-fi author John Hutchinson.

Finally, the elephants that made the tracks were probably Stegotetrabelodon, and although they might not have been full-on Tolkien-by-way-of-Jackson Amphicoelias-sized war-beasts, they were still big four-tusked proboscideans, so I’m calling them oliphaunts. Bibi et al. didn’t find any evidence that the trackmakers were ridden by Haradrim, but they didn’t find any evidence that they weren’t, so that’s how I’m going to imagine them.

Probably not the Mleisa trackmakers. Dammit.

For more stuff, including the paper, the full-res version of the image at top, more sweet images, author bios, and so on, see the press page. There are also nice writeups at Not Exactly Rocket Science and Laelaps. Go check it out.

Reference

Bibi, F., Kraatz, B., Craig, N., Beech, M., Schuster, M., and Hill, A. 2012. Early evidence for complex social structure in Proboscidea from a late Miocene trackway site in the United Arab Emirates. Biology Letters. doi: 10.1098/rsbl.2011.1185

A very quick note to let you all know that my new article is now up at Discover Magazine‘s guest blog, The Crux.  Entitled It’s Not Academic: How Publishers Are Squelching Science Communication, the topic will not be unfamiliar to SV-POW! readers.  But I make an effort to address a new angle every time I write one of these, so this one emphasizes the history of how we got into the current bind and the strange academic culture that perpetuates it.

The goal of articles like this one is not really to reach SV-POW! readers, who are already familiar with most of the issues, but to bring them up before people who otherwise might not think about open access.  So please do go and read it; but really, the most helpful thing you can do is probably to let your friends and colleagues know about it.  The SOPA/PIPA protests were only successful because the word spread.  That is now the challenge for us as we hope to see the RWA defeated and the FRPAA accepted.

Go to It’s Not Academic: How Publishers Are Squelching Science Communication

Let’s look at some animals!

February 20, 2012

An important new paper is out:

R. Kent Sanders and Colleen G. Farmer.  2012.  The pulmonary anatomy of Alligator mississippiensis and Its similarity to the avian respiratory system. The Anatomical Record: Advances in Integrative Anatomy and Evolutionary Biology (advance online publication). doi:10.1002/ar.22427

(It’s paywalled, naturally, but let’s just assume that everyone who reads this blog is affiliated with a big university and has access.)

First of all, congratulations to the authors on doing this properly: publishing a proper paper (sixteen pages) to follow up their big-splash Science paper of just over a year ago.  As Mickey Mortimer has shown, follow-through rates when people publish in Science and Nature are generally not at all good, and it’s always encouraging to see an exception.

Here’s the abstract:

Using gross dissections and computed tomography we studied the lungs of juvenile American alligators (Alligator mississippiensis). Our findings indicate that both the external and internal morphology of the lungs is strikingly similar to the embryonic avian respiratory system (lungs + air sacs). We identified bronchi that we propose are homologous to the avian ventrobronchi (entobronchi), laterobronchi, dorsobronchi (ectobronchi), as well as regions of the lung hypothesized to be homologous to the cervical, interclavicular, anterior thoracic, posterior thoracic, and abdominal air sacs. Furthermore, we suggest that many of the features that alligators and birds share are homologous and that some of these features are important to the aerodynamic valve mechanism and are likely plesiomorphic for Archosauria.

The main reason I want to post this (apart from the fact that it’s an important finding) is because someone had to blog David Marjanovic’s classic response on the Dinosaur Mailing List (quoted with permission, since David doesn’t have his own blog):

See, this is the kind of thing where I’m totally baffled that it wasn’t figured out a hundred years ago, or 120 or 130.

I suppose the logic that has prevented people from dissecting crocodilian lungs for so long went like this:

1) Crocodilians are reptiles.
2) So, crocodilians have reptile lungs, not mammal lungs or bird lungs.
3) What are reptile lungs like? Let’s dissect the nearest reptile and find out!
4) We’re in Europe, so let’s just take the nearest lacertid, perhaps the nearest “colubrid” and maybe the nearest viperid and cut them open.
5) <snip> <snip>
6) Hooray! We’ve figured out what reptile lungs are like!
7) Textbook describes and illustrates generic non-varanid squamate lung as “reptile lung”.
8) Everyone believes it is known what reptile lungs are like.
9) Everyone believes it is known what crocodilian lungs are like, because crocodilians are reptiles.

Ceterum censeo Reptilia esse nomen delendum.

If you must keep the name, follow Joseph Collins and restrict it to Squamata or Lepidosauria. Otherwise, destroy it. Kill it with fire.

So true.

We could draw a whole lot of conclusions from this analysis, but let’s just concentrate on one: look at animals.  See how they behave.  Then cut them open and see what’s inside.  Don’t assume.  Don’t guess.  Find out.  To quote the splendid motto of the Kirkcaldy Engineering Works, “FACTS, NOT OPINIONS”.

Seriously.  Who’d have though there was a Science paper and an Anatomical Record paper just in cutting open an alligator and having a poke around in there?  Sometimes, science doesn’t progress by paradigm shifts; sometimes it progresses just by looking at things.

Folks, just a short post to let you know that, together with my colleagues in the @access Working Group, I have just launched a new web-site.

One of the problems we have in promoting Open Access is getting non-scholars involved.  So the whole enterprise can feel like an ivory-tower issue, one that just doesn’t affect the great majority of people.  But that’s not true.

The new site is called Who needs access? You need access?.  Its goal is to tell stories of many different kinds of people — teachers, doctors, artists, politicians, entrepreneurs — who need access to research papers.  Some stories are positive ones about how access has helped; others are more negative, about how lack of access has hindered.  We have just three stories on the site as we launch; we want to add more, quickly.  Each story needs to be specific, not too long, and have a human face.

Please check it out, contribute, and tell your friends!

WhoNeedsAccess.org

AN ALIEN IS COMING!

February 19, 2012

Re-posted with permission.

Of course, these these days John is better known for this work on the evolution of musculature on the line to birds, tyrannosaur hindlimb mechanics, and elephant anatomy.  But it seems the world lost a promising novelist.

[Originally posted on Twitter, by John.]

See also: Acaren and the Evil Wizards.

An interesting conversation arose in the comments to Matt’s last post — interesting to me, at least, but then since I wrote much of it, I am biased.  I think it merits promotion to its own post, though.  Paul Graham, among many others, has written about how one of the most important reasons to write about a subject is that the process of doing so helps you work through exactly what you think about it.  And that is certainly what’s happening to me in this series of Open Access posts.

Dramatis personae

Liz Smith: Director of Global Internal Communications at Elsevier
Mike Taylor: me, your co-host here at SV-POW!
Andy Farke: palaeontologist, ceratopsian lover, and PLoS ONE volunteer academic editor

Script

In a long and interesting comment, Liz wrote (among much else):

This is where there seems to be deliberate obtuseness. Sticking a single PDF up online is easy. But there are millions of papers published every year. It takes a hell of a lot of people and resources to make that happen. You can’t just sling it online and hope somebody can find it. The internet doesn’t happen by magic.

And I replied:

Actually, you can and I do. That is exactly how the Internet works. I don’t have to do anything special to make sure my papers are found — Google and other search engines pick them up, just like they do everything. So to pick an example at random, if you search for brachiosaurus re-evaluation, the very first hit will be my self-hosted PDF of my 2009 JVP paper on that subject. [Correction: I now see that it's the third hit; the PDF of the correction is top.] Similarly, search for xenoposeidon pdf and the top hit is — get ready for a shock! — my self-hosted PDF of my 2007 Palaeontology paper on that subject.

So in fact, this is a fine demonstration of just how obsolete much of the work that publishers do has now become — all that indexing, abstracting and aggregation, work that used to be very important, but which is now done much faster, much better, for free, by computers and networks.

Really: what advantages accrue to me in having my Xenoposeidon paper available on Wiley’s site as well as mine? [It's paywalled on their site, so useless to 99% of potential visitors, but ignore that for now. Let's pretend it's freely available.] What else does that get me that Google’s indexing of my self-hosted PDF doesn’t?

Liz is quite rightly taking a break over the weekend, so she’s not yet replied to this; but Andy weighed in with some important points:

To address your final statement, I see three main advantages to having a PDF on a publisher’s site, rather than just a personal web page (this follows some of our Twitter discussion the other day, but I post it here just to have it in an alternative forum):

1) Greater permanence. Personal web pages (even with the best of intentions) have a history of non-permanence; there is no guarantee your site will be around 40 or 50 years from now. Just ask my Geocities page from 1998. Of course, there also is no guarantee that Wiley’s website will be around in 2073 either, but I think it’s safe to say there’s a greater likelihood that it will be around in some incarnation than a personal website.

2) Document security. By putting archiving in the hands of the authors, there is little to prevent them from editing out embarrassing details, or adding in stuff they wanted published but the reviewers told them to take out, or whatever. I’m not saying this is something that most people would do, but it is a risk of not having an “official” copy somewhere.

3) Combating author laziness. You have an excellent track record of making your work available, but most other authors do not, for various reasons.

It is also important to note that none of the above requirements needs a commercial publisher – in fact, they would arguably be better served by taking them out of the commercial sector. My main point is that self-hosting, although a short-term solution for distribution and archival, is not a long-term one.

Finally, just as a minor pedantic note, search results depend greatly on the search engine used. Baidu – probably the most popular search engine in China – doesn’t give your self-hosted PDF anywhere in its three pages of search results (neither does it give Wiley’s version, though).

And now, here is my long reply — the one that, when I’d finished it, made me want to post this as an article:

On permanence, there are a few things to say. One is that with the rate of mergers, web-site “upgrades” and suchlike I am actually far from confident that (say) the Wiley URL for my Xenoposeidon paper will last longer than my own. In fact, let’s make it a challenge! :-) If theirs goes away, you buy me a beer; if mine does, I buy you one! But I admit that, as an IT professional who’s been running a personal website since the 1990s — no Geocities for me! — I am not a typical case.

But the more important point is that it doesn’t matter. The Web doesn’t actually run on permanent addresses, it runs on what gets indexed. If I deleted my Xenoposeidon PDF today and put it up somewhere else — say, directly on SV-POW! — within a few days it would be indexed again, and coming out at or near the top of search-engine results. Librarians and publishers used to have a very important curation role — abstracting and indexing and all that — but the main reason they keep doing these things now is habit.

And that’s because of the wonderful loosely coupled nature of the Internet. Back when people first started posting research papers on the web, there were no search engines — CERN, famously, maintained a list of all the world’s web-sites. Search engines and crawlers as we know them today were never part of the original vision of the web: they were invented and put together from spare parts. And that is the glory of the open web. The people at Yahoo and AltaVista and Google didn’t need anyone’s permission to start crawling and indexing — they didn’t need to sign up to someone’s Developer Partnership Program and sign a non-disclosure form before they were allowed to see the API documentation, and then apply for an API Key that is good for up to 100 accesses per day. All these encumberances apply when you try to access data in publishers’ silos (trust me: my day-job employers have just spent literally months trying to suck the information out of Elsevier that is necessary to use their crappy 2001-era SOAP-based web services to search metadata. Not even content.) And this is why I can’t get remotely excited about things like ScienceDirect and Scopus. Walled gardens can give us some specific functionality, sure, but they will always be limited by what the vendor thinks of, and what the vendor can turn a profit on. Whereas if you just shove things up on the open web, anyone can do anything with them.

With that said, your point about document security is well made — we do need some system for preventing people from tampering with versions of record. Perhaps something along the lines of the DOI register maintaining an MD5 checksum of the version-of-record PDF?

You are also right that not all authors will bother to post their PDFs — though frankly, heaven alone knows why not, when it takes five minutes to do something that will triple the accessibility of work you’ve spent a year on. This seems like an argument for repositories (whether institutional or subject-based) and mandatory deposition — e.g. as a condition of a grant.

Is that the same as the Green OA route? No, I want to see version-of-record PDFs reposited, not accepted manuscripts — for precisely the anti-tampering reason you mention above, among other reasons. Green OA is much, much better than nothing. But it’s not the real thing.

Finally: if Baidu lists neither my self-hosted Xenoposeidon PDF or Wiley’s version anywhere in its first three pages of search results, then it is Just Plain Broken. I can’t worry about the existence of broken tools. Someone will make a better one and knock it off its perch, just like Google did to AltaVista.

And there, for the moment, matters stand.  I’m sure that Liz and Andy, and hopefully others, will have more to say.

One of the things I like about this is the way that a discussion that was originally about publisher behaviour mutated into one on the nature of the Open Web — really, where we ended up is nothing to do with Open Access per se.  The bottom line is that free systems (and here I mean free-as-in-freedom, not zero-cost) don’t just open up more opportunities than proprietary ones, they open up more kinds of opportunities, including all kinds of ideas that the original group never even thought of.

And that, really — bringing it all back to where we started — is why I care about Open Access.  Full, BOAI-compliant, Open Access.  Not just so that people can read papers at zero cost (important though that is), but so that we and a million other groups around the world can use them to build things that we haven’t even thought of yet — things as far advanced beyond the current state of the art as Google is over CERN’s old static list of web-sites.

Barrier-based publishers have been shouting and stomping around a lot recently.  Kind of like a Vogon guard.  But we’re trying to see the situation from their point of view.

FORD: Arthur, try and understand his problem! Here he is, poor lad, his entire life’s work is stamping around, throwing people off spaceships –
GUARD: And shouting.
FORD looks up and pats the GUARD on the arm reassuringly.
FORD: And shouting, sure, and he doesn’t even know why he’s doing it!
ARTHUR nods sympathetically.
GUARD: Well … now that you put it like that, I suppose …
FORD: Good lad!
GUARD: But all right, then, what’s the alternative?
FORD: Well … stop doing it, of course!  Tell them you’re not going to do it any more.
FORD looks at ARTHUR for help, who stares back blankly.
GUARD: Eerrrrrrrrrrrrmmmm…erm, well, that doesn’t sound great to me.

– Douglas Adams, The Hitch-Hiker’s Guide to the Galaxy.

As we point out the many ways in which current academic publishing practices are exploitative, we are sometimes told, as in Jeff Miller’s comment: “I believe that it is the critics’ responsibility to step-up and offer alternatives.”

Here’s the thing.  The alternative we want from barrier-based publishers is that they stop being Vogon guards.  We’re not interested in helping them find better ways to be barrier-based publishers, because that whole model is obsolete, destructive, inimical to the connected world we now live in and completely unacceptable in the 21st Century.  Reducing prices a bit would be nice, yes; but nowhere near the revolution that the world actually needs.

Resistance! Is! Useless!

So the whole question about Elsevier, for me at least, comes down to this.  Can they stop being Vogon guards?  Can they find a business model that isn’t based on stamping around, throwing people off spaceships and shouting?  We know that there are viable non-Vogon business models out there, because PLoS is doing very nicely.

But because PLoS isn’t taking in enough money to cream off 36% of all revenue as profit, it seems likely that Elsevier’s response is going to be “Eerrrrrrrrrrrrmmmm…erm, well, that doesn’t sound great to me.”  Especially as the evidence suggests that Elsevier can’t compete on a level playing-field with the likes of PLoS anyway.

I hope I’m wrong, and that the big publishers can save themselves.  But if they can’t, well, we have an increasing number of alternatives.  [That's seven links, not one.]

Post Script

A couple of people have complained that we’re writing too much about Open Access recently and not enough about sauropods.  I am sympathetic to that; no-one could wish more than I do that publishing would just sort itself out and we could get back to doing what we love best.  But until that happens, anyone who wants to read more about the ongoing scholarly revolution might find it useful to read my Twitter feed (@SauropodMike).  You don’t need an account to see it.

… and that’s why we’re angry.

(Note: exact percentages are made up.  But based on a true story.)

 

In a comment on the last post, an Elsevier employee wrote:

Elsevier’s support for the Research Works Act comes down to a question of preferring voluntary partnerships to promote access to research, rather than being subjected to inflexible government mandates like the NIH policy, which seek to dictate how journal articles or accepted manuscripts are disseminated without involving publishers.

While we do appreciate that you’re trying to engage us here, you’re going to have to show a little more effort than just parroting the company line. To be frank, this is a load of crap.

First off, if the NIH pays for the research, the NIH should have a say in how the results of that research are disseminated. We don’t have to talk in oblique terms about what “involving publishers” means, because everyone’s motives are perfectly transparent and known to everyone else. The NIH wants the research results available to everyone who wants them with a minimum of hassle and ideally at no cost to the user, which is understandable since the NIH has already paid for it once. The researchers want the research results available to everyone who wants them with a minimum of hassle and ideally at no cost. And the readers want the research results available to everyone who wants them with a minimum of hassle and ideally at no cost. The publishers–and let’s be specific here and note that we’re really talking about corporate for-profit publishers–want to maximize their profits by selling the research community’s results back to them with just enough “added value” to justify their claim of ownership of those results, and to do that by maximizing costs (whether hassle is something they deliberately set about to create or just a stupid side-effect of the roadblocks set up to restrict access is an open question).

So the corporate for-profit publishers’ motives are directly opposed to everyone else’s: those who pay for the research, those who carry it out, and those who consume it.

What’s going on here is that those latter three groups are (very belatedly) realizing that it’s completely bogus to have all of their desires thwarted by the one player in the game who gives the least and charges the most.

Alternatively I could just cite Cameron Neylon’s wonderful observation that, “Publishers never really did have a business model, they had a public subsidy.”

Also: “voluntary partnerships to promote access to research” my ass. How does Elsevier expect to continue making such immense profits if the other “partners” are in the relationship voluntarily? In any case, all this talk about “promoting access to research” is more folderol. If you want people to have access to research, you just give them access (it’s not hard). If your corporation can’t find a way to do that and satisfy shareholders, boo-hoo. To riff on a great phrase by Tom Holtz, “Sorry if that makes some people feel bad, but I’m not in the ‘make the corporate parasites fattening at the public teat feel good’ business; I’m one of the researchers you’ve been screwing.”

I’ll also note that Elsevier and the other corporate for-profit publishers have had a LOT of opportunities to cultivate goodwill among researchers, and not taken them. For starters–and I am not the first or even the thousandth person to mention this–why not charge a reasonable download fee of, say, $1-5 per paper, instead of $30-50? We all know it’s an outrageous ripoff, but no-one is making any moves to change it. Putting together fake journals full of paid ads masquerading as papers doesn’t look so good either. But surely paying off Congresspeople to sponsor a bill that most funding agencies, researchers, and readers–you know, the groups you’re allegedly trying to engage in conversation–view as actively evil has been the biggest misstep.

So, what do I want Elsevier to do? I want it to do what Mike suggested–throw its support behind the FRPAA–and then restructure itself as an open-access publisher. That will probably mean saying goodbye to 30+% annual profit margins, but hey, wake up. If PLoS ONE can offer no length limits, no full color figure limits, and full BOAI-compliant open access for $1350, charging $3000 for an inferior product is the definition of a broken business model.

Such a restructuring is probably impossible for Elsevier, given its corporate mandate to maximize profits for shareholders, and if so, I’ll settle for it just dying. Karma’s a bitch. I signed the declaration of independence, so Elsevier’s already dead to me anyway.

Note that I’m speaking here of the corporation dying, not its constituent humans. Although there must be a few real worms in there to have conceived all of the shenanigans that Elsevier has perpetrated recently, I’m sure that the vast majority of Elsevier employees are honest people of good conscience. If you’re one of them, what I’d like you, personally, to do is either agitate for change from within, if you can pursue that course wholeheartedly, or go work somewhere else. Elsevier isn’t the only publisher in the world. There’s a reason why some people won’t work for the tobacco industry or companies that make land mines: their consciences won’t let them.

If, on the other hand, you choose to not only identify with Elsevier but to try to defend the practices that got it into this mess, don’t be surprised if you don’t get much sympathy from the people your corporation is currently screwing and actively seeking to screw even harder in the future, and don’t complain if we call BS on your arguments and fire back with our own.

The Elsevier boycott at The Cost Of Knowledge is the most visible sign of the recent uprising against exploitative publishing practices, but it’s far from the only one.  Anyone who’s been keeping an eye on the developing shift in attitudes will hardly have been able to miss:

No-one organised all this.  There is no Open Access Mastermind stroking a long-haired white cat behind the scenes, manipulating his minion into a co-ordinated assault on non-open scientific publishing.  What we’re seeing is a spontaneous response — catalysed by the Research Works Act, yes, but not caused by it.  The roots run much deeper.  The discontent being expressed now is only the first rumblings of a seismic event that’s been building up for a long time.  People who have spend the last decade thinking “this sucks, but what’s the point on complaining?” have started to speak.

And there are encouraging moments when it seems that the publishers are truly starting to Get It.  Elsevier’s most recent formal response to the boycott says:

We pay close attention to the voices of the research community we serve, including those who have responded to an online petition that is putting forward some serious negative judgments about Elsevier. Being criticized by even one researcher, let alone all the signatories of the petition, is difficult for a company whose reason for being is to serve the research community.
[...]
The depth of feeling among some in the research community is real and something we take very seriously. We’re listening to all the concerns expressed and redoubling our substantial efforts to make our contributions to that community better, more transparent, and more valuable to all our partners and friends in the research community.

This is encouraging stuff.  And reading it has made me realise that there is a real window of opportunity here for Elsevier to radically reposition themselves.

Because the problem is that the big chunk in the middle of the statement that I quoted above — the part that I replaced with an ellipsis — is all justification for the current business model and current behaviour.

But Elsevier don’t have to do this.

At a stroke, they can sweep away the researcher hostility that has built up against them over the last month.  They can completely reverse the perception that they are the worst of all the big-money publishers.  How?  It’s simple?

Elsevier should repudiate the RWA and throw themselves behind the Federal Research Public Access Act.

Yes, really.  Why not?  Just imagine the impact of a press release right now:

We pay close attention to the voices of the research community we serve, including those who have responded to an online petition that is putting forward some serious negative judgments about Elsevier.  We realise we have seriously misjudged what authors want and need from us, and that by supporting the Research Works Act we were not acting in accordance with the partnership we so value with authors.  Accordingly, we hereby withdraw our support for the RWA, and instead support the FRPAA.

Wouldn’t that be huge?

Wouldn’t it totally change the game overnight?

I know it’s hard to turn a supertanker on a sixpence, but I suspect it can be done if the will is there.

Can they do it?

Will they?

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