Thursday, January 28, 2010

Where is paleontology?

Last week, many of the leading journals in evolutionary biology - including The American Naturalist, Molecular Ecology, Journal of Evolutionary Biology, Evolution, and a number of others - announced a data archiving policy. In short, this policy states that the data behind the results of a paper should be publicly archived in well-known respositories such as Data Dryad, GenBank, or TreeBASE. Do you notice anything missing in this illustrious list of publications?

Not a single one of those journals explicitly focuses on paleontology. Last time I checked, we paleontologists like to think of ourselves as evolutionary biologists. Time and time again, we lament how we're not allowed a place at "The High Table" of evolutionary thought, and how paleontology is viewed as largely irrelevant by the "people who matter." So why weren't any paleontology publications on this list? Will we see any on the list in the near future?

The article in The American Naturalist gives a good run-down of the arguments for sharing data, so I'll only briefly summarize them here:
  • It allows reproducibility of analyses.
  • It allows others to build upon your work more easily.
  • Papers that release their data may get cited more frequently.
  • The data will be lost to science otherwise.
  • It's the right thing to do.
And to counter some potential objections:
  • This would only request the release of data directly relevant to the study. Not your pages and pages of raw notes. Just that Excel spreadsheet that you already generated on your way to the analysis. Seriously. It's not a lot of extra work, if any.
  • This is not requesting the digitization and distribution of video, CT scan, or similarly large and unwieldy data (although that would be nice in the future).
  • No, it does not mandate the release of locality data, or similarly privileged information.
  • The policy does not require immediate release of the data, if there's a good reason (i.e., another pending publication) to do so. I'm not sure I entirely support this (if you're publishing the analysis, you should publish the data), but I understand it as a necessary compromise to get more individuals on board. I won't let the perfect be the enemy of the good.
Some of the most ground-breaking and high-profile work in paleontology is happening on account of large meta-analyses of data pulled together from the literature - largely thanks to efforts like the Paleobiology Database. This work has real implications for big questions facing our science and our world: Climate change. The pace of evolutionary radiations. The origins of modern biological diversity. These sorts of databases focus primarily on geographic, stratigraphic, and taxonomic data - but think how much more powerful they could be if all of the morphological data ever published were available! Or if the PBDB volunteers didn't always have to transcribe the information from a PDF file. And look at the great strides that molecular biology has made with the ready availability of sequence data on GenBank! This would not have happened with a mentality of data hoarding.

Look. Amateur hour is over. If we want to play in the big leagues, we have to start acting like a real science. Real science is reproducible. Real science is data-driven. Real science involves sharing data. Yes, I know it's hard. It's new. We haven't done things this way before. There are potential problems. Not everyone is adopting it quickly. But if we always wait five years to "see what happens," we paleontologists quite frankly don't deserve a place at the High Table. Let's be leaders, not followers.

Piwowar, H. A., R. S. Day, and D. B. Fridsma. (2007). Sharing detailed research data is associated with increased citation rate. PLoS ONE 2(3):e308, DOI: 10.1371/journal.pone.0000308.
Whitlock, M., McPeek, M., Rausher, M., Rieseberg, L., & Moore, A. (2010). Data archiving. The American Naturalist, 175 (2), 145-146 DOI: 10.1086/650340

For previous posts on data sharing in paleontology, see here and here. Want to get involved? Spread the word. Talk to your local journal editor. Let the people who count know what you think.

Sunday, January 17, 2010

ScienceOnline2010 Report #scio10

I am just freshly back from ScienceOnline2010, where I was graciously invited to talk about the Open Dinosaur Project by Bora Zivkovic (who co-organized the "un-conference" with Anton Zuiker). Simply put, this is one of the best conferences I have attended in a long, long time. So what was it that got me so excited about the event?

  • Meeting new people. Coming into the event, I had met precisely three of the 251 other attendees in person before, and wouldn't say I knew any of them particularly well. Some folks I knew from cyberspace (either through blogs, or PLoS-related functions), but there is something entirely different about in-person interactions. Even better were the unexpected and unplanned meetings - bumping into someone completely new who had wonderfully convergent interests, or a stimulating viewpoint, or was just plain interesting. All in all, it was a tremendously friendly bunch.
  • The civility and positivity. When I (a major proponent of open access) can sit down over a beer and have a really enjoyable, wide-ranging chat with an employee of Elsevier, that's pretty cool. This friendly tenor was by-and-large a hallmark of the meeting. For instance, I was enormously impressed by Pete Binfield's presentation on article level metrics [full disclosure: I'm a section editor at PLoS ONE - Pete is the guy at the helm of the journal]. It wasn't a rant against impact factors, or how PLoS ONE's article level metrics are going to put all of the commercial publishers out of business. His presentation was a factual overview of the plus's and minuses, some genuine recognition of the good things other companies are doing, and an open invitation for others to join the article level metric club. Why can't some segments of the blogosphere be more like this?
  • Seeing the cutting edge. For better or worse, paleontology is a conservative discipline in many respects. This is not to say that every other discipline is lightyears ahead (they're not - scientists of all sorts have tremendous cultural and institutional inertia), but simply that the innovations aren't necessarily happening in our field. I was incredibly energized by the discussions of improving public outreach over the internet, open notebook science, open access publishing, and much more. Some of the concepts will fade into oblivion, some will be superseded by unforeseen technology, and some will become the dominant way of doing things within a few short years. It's going to be very fun to look back, 10 years from now, and remember when issue X or technique Y seemed so new and fresh.
  • The openness of the conference. Nearly every session was YouTubed (videos to go up soon), blogged, livestreamed, and tweeted. The more I see how effective this format is, the more I like it. Yes, yes, I know that it's just not possible for "real" science conferences. . . .But why not?
  • The librarians. Yes, really. Prior to this, I knew librarians as the people who put books back on the shelves and sometimes process an interlibrary loan. During this meeting, I learned that if we want any hope of saving our data (not just our published papers), the librarians will be key in making it happen. If you're looking for some readable and interesting blogs, I would recommend checking out Confessions of a Science Librarian, Christina's LIS Rant, and The Book of Trogool. I got to hang out with both of their authors, and they're really cool people.
  • The Shiny Digital Future isn't just for, or being engineered by, white male nerds under the age of 30. Readily identifiable asocial weirdos were pretty darned scarce, and I was impressed by the number of people past the first few years of their career. We were all geeks, but I think many of us (?some of us?) could pass as normal if you ran into us at the supermarket.
In the afterglow of the conference, the wheels in my brain are turning in multiple directions. This is a sign of a great event, and a sure indication that you'll be seeing more blog posts (and projects) inspired by my weekend here.

Tuesday, January 12, 2010

Paleo Paper Challenge: The Final Round-Up

Well. . .January 1, 2010 has faded into memory, and with it the 2009 Paleo Paper Challenge (PPC). For those of you who need a brief reminder, the PPC (sponsored by me and Dave Hone) was a chance for all of us who have partly-finished papers to give them the final push out the door. We had 22 individuals from around the world accept the challenge, and everyone made a pretty solid effort.

Now some folks expressed disappointment that they weren't able to complete everything they had hoped for. Personally, I only had a 50 percent success rate. But, as Dave said elsewhere, that wasn't really the point. As long as some work got done, that's what really counts. And if a paper got submitted - even better!

So, congratulations to all of our participants! I've included preliminary results below - if there is something I should update, either drop me an email or else leave a note in the comments. Here's looking forward to the PPC 2010. . .stay tuned for details, probably in September.

Results of the Paleo Paper Challenge
Brian Beatty
Calvert Formation terrestrial mammals review with Ralph Eshelman
Final status: Unknown

Tor Bertin:

Statistical analysis of evolution of sauropod body size, involving a mystery specimen
Final status: Unknown
Spinosauridae review
Final status: In progress

Lisa Buckley

Papers to be decided
Final status: Unknown

Andrea Cau:
Description of metriorhynchid from northern Italy
Final status: Major Progress

Andy Farke:
Myledaphus paper
Final status: Failure to launch
Final dissertation chapter
Final status: Revised and resubmitted

John Foster:
Morrison critter paper
Final status: Unknown

Francisco Gasco:
Master's thesis
Final status: Some progress

Mike Habib:
Pterosaur flight range
Final status: Some progress
Pterosaur aquaflyer paper
Final status: Submitted and accepted

Penny Higgins:
Bulk isotopic ratios from tooth enamel and general interpretation of environment
Final status: Major progress

Casey Holliday:
Articular cartilage paper
Final status: Major progress, almost ready for submission

Thomas Holtz:
Tyrannosaur heterochrony/paleoecology
Final status: Unknown

Dave Hone:
Unspecified papers
Final status: Two papers submitted, one still awaiting launch

ReBecca Hunt:
Mygatt-Moore taphonomy paper
Final status: Unknown

Nick Gardner:
Unspecified paper with Mickey Mortimer
Final status: Unknown

Chris Note and Ari Grossman:
Dinosaur ecomorphology
Final status: Unknown

Bill Parker:
Revueltosaurus manuscript
Final status: Unknown

Heinrich Mallison:
sauropods rearing
Final status: Minor progress
sauropodomorph rapid locomotion
Final status: Minor progress

Anthony Maltese:
Unspecified paper
Final status: One in press, one with a co-author, another with major progress

Mark Mancini:
Redondosaurus cranial description (with Axel Hungerbuehler)
Final status: Unknown

Eric Snively:
Chicken electromyography and implications for big theropod neck muscles
Final status: Submitted
Atlas of gekkotan lizards of the Paris Basin
Final status: Some progress
Artiodactyl vs. Stegoceras head-strike mechanics
Final status: Some progress

Mike Taylor:
The Archbishop description
Final status: Major progress

Matt Wedel:
Final dissertation chapter
Final status: Unknown

Adam Yates:
Early sauropodomorph pneumaticity
Final status: Unknown
Rauisuchians of the Elliot Formation
Final status: Unknown

Thursday, January 7, 2010

For All You Pterosaur Fans

Dave Hone has asked me to pass on his announcement of the launch of This new web page is a collaborative effort by a number of pterosaur experts to provide a gateway to accurate, scientifically-based information on this fascinating clade. It looks great, both in terms of content and some eye-popping artwork, so I strongly recommend checking it out!

Friday, January 1, 2010

2009: Open Access Hits Paleontology

2009 will go down as the year when open access publication really, truly made its mark in the field of vertebrate paleontology. Last year, more than ever before, open access journals featured some of the most high-profile, and in many cases even the highest quality quality, research out there.

No small amount of credit goes to the journal PLoS ONE (full disclosure: I am a section editor for that publication). From Ida to T. rex, from Ice Age extinctions to good mother whales, PLoS ONE articles made a splash.

I would be completely remiss if I did not lead off with "Ida," the exquisitely preserved primate specimen from Messel, Germany (image from the original paper). Announced with an unprecedented media fanfare, the little creature more formally known as Darwinius masillae set off a firestorm [see this blog carnival at Laelaps for a great summary]. Some questions--quite fairly, in my opinion--centered around the perception that the media blitz was just a little too big and too coordinated with the publication (although less attention was paid to this aspect of a similarly coordinated event by another major journal later in the year). There were also some concerns--rightfully so--that claims made in the popular press overplayed the discovery more than a little. At the dawn of 2010, the working consensus is that Darwinius is likely closer to lemurs than to humans, despite highly publicized claims to the contrary. Furthermore, issues were quickly raised about the validity of the name--the ICZN currently doesn't recognize electronic-only publications as valid. Although this problem isn't unique to Darwinius or even PLoS ONE (see virtually every major journal that issues electronic preprints, from Science to Proceedings B), the "Ida" escapade did bring such concerns roiling to the surface. Thankfully, the problem was quickly addressed. Perhaps the biggest lesson from Ida is that the Internet is a force to be reckoned with. The great majority of the debate on this specimen--from the ethics, to the science, to the validity of the name--happened in the blogosphere. I predict that this trend of bloggy discussion will only continue.

Dinosaurs of the Winton Formation of Australia, including Wintonotitan (left), Diamantinasaurus (middle), and Australoraptor (right). This and the above images are modified from the originals by T. Tischler, under a Creative Commons Attribution license.

On a much less controversial note, several papers clearly showed how awesome the electronic publication medium can be. A paper on three new dinosaurs from the Cretaceous of Australia--in many ways, a far more earth-shaking discovery for paleontology than any old primate--took full advantage of unlimited length and high resolution figures. This wasn't a four-page teaser with three tiny figures and 80 pages of on-line supplementary information. Hocknull and colleagues produced an honest-to-goodness monograph! This sort of extensive treatment wasn't the exclusive domain of PLoS ONE - Sereno and Larsson published a 143 page, open access, electronic monograph on crocs from the Cretaceous of Africa in ZooKeys. As more paleontologists realize the benefits of electronic publication (relatively low or no page charges, high resolution images, rapid and broad distribution), I predict that we'll see more of these monographic treatments in the open access literature.

PLoS ONE also pioneered a more transparent form of "impact factors" this year. With their article-level metrics, it is now possible to find out how many downloads a single paper garnered, and when. For instance, there have been nearly 8,000 views of my January 2009 paper on Triceratops horn use co-authored with Ewan Wolff and Darren Tanke; Darwinius has racked up nearly 75,000 views since May. I would wager this is a good deal more than either paper would have garnered on a pay-per-view website. In combination with article-level citation indices (10 citations so far for the Darwinius article, according to CrossRef), these new, individualized impact factors represent a massive step forward from the journal-level, irreproducible impact factor sold by Thompson-Reuters. In another prediction, I expect that more journals will begin to adopt these new measures of article "impact." It is more transparent and, quite frankly, more relevant for many applications.

On a personal note, I am proud of the achievements of the Open Dinosaur Project. Launched in September 2009, the ODP crowd sources data collection for a project studying the evolution of limbs in ornithischian dinosaurs. Furthermore, all aspects of the project--from data collection to analysis to publication--are being blogged. If all goes well, 2010 should witness the first publication of a major paper from the project.

So what will 2010 bring? As described above, we're going to see the blogosphere continue its rise as an important factor in scientific discourse. Open access publishing will continue to expand, and a public archive of NSF-funded publications may well become a reality. Overhyped specimens will appear in both the open- and closed-access literature, and new methods of skullduggery will keep us all busy. In short, business as usual! I look forward to the surprises and new technologies that 2010 has in store for all of us.