Thursday, July 2, 2009

An Australian Dinosaur Extravaganza

ResearchBlogging.orgThe Cretaceous of Gondwana - the formerly connected southern landmasses of Antarctica, Australia, South America, Africa, India, Madagascar, and Arabia - is a sticky problem. The terrestrial fossil record is spotty at best in most locations, and tremendous geographic and temporal gaps remain. As a consequence, there is considerable debate about the sequence of the tectonic breakup of Gondwana and even the very identity and relationships of some of its dinosaurs and other Mesozoic beasts. Once in a great while, some intrepid field paleontologists take a chance and make discoveries that move our knowledge ahead by leaps and bounds. Areas of Gondwana such as Madagascar and Argentina have had fossils rolling out of the Cretaceous hills, doing wonders for paleontological knowledge. Today, a new paper in PLoS ONE has done such a thing for Australia.

Historically, paleontologists working in the Cretaceous of Oz have had to make do with pretty fragmentary material. With the exception of Muttaburrasaurus (a plant eating ornithopod known from reasonably complete skulls and skeletal material) and Minmi (an armored ankylosaur known from a relatively complete skeleton), most of the other named taxa from this time are known only from scrappy elements (e.g., Kakura, a theropod known from an isolated, opalized tibia). This poor fossil record has resulted in some odd, and highly unlikely, claims. For instance, it has been suggested that ceratopsians (otherwise known only from the northern hemisphere) lived in Australia (based on isolated ulnae that admittedly do look rather ceratopsian - although other assignments haven't necessarily been ruled out effectively), and that Allosaurus (a late Jurassic theropod from North America) survived into the early Cretaceous here. When it comes to the meat-eating theropods and the long-necked sauropods, the material is pretty frustrating. Without better specimens, it's virtually impossible to know how Australia's animals compared to those elsewhere!

For this reason, the new paper is so very important. A team of paleontologists from the Queensland Museum and the Australian Age of Dinosaurs Museum of Natural History here describe three completely new dinosaur species. Two are sauropods, the third is a theropod, and all come from the Winton Formation of Queensland. The portion of the Winton Formation hosting the dinosaurs is estimated as late Albian in age (based on fossil pollen, an important criterion in the absence of radiometric dates), or roughly 100 million years old.

The two sauropods belong to a group called titanosaurs. Titanosaurs were the dominant sauropods of the Cretaceous, with a virtually global distribution. Diamantinasaurus matildae (the sauropod at the top in the illustration, charmingly named after "Waltzing Matilda") and Wintonotitan wattsi (bottom) are both known from partial skeletons, whose owners might have measured 50 feet in total length (~14.8 m) when alive. Unfortunately, the phylogenetic position of the two animals is somewhat uncertain. The authors chose to put the animals into two very different datasets for their cladistic analysis (in terms of characters and taxon selection), so it's tough to know where the things actually fall out. It would be informative to merge the two datasets as much as possible and see how that affects tree topology. The incongruent trees also complicate any biogeographic conclusions that might be drawn. Regardless, it looks like Wintonotitan is a relatively basal titanosauriform (what some folks might call "primitive"), and Diamantinasaurus falls out within a group called Lithostratia, close to or within the saltasaurids (many of these animals are well-known for the armor studding their backs).

There is a slim possibility that one or both new species of sauropod are synonymous with Austrosaurus mckillopi, a taxon based on poorly preserved, incomplete vertebrae from a roughly contemporaneous formation. There is some overlap with Wintonotitan, but the vertebrae from the two animals are apparently pretty different. Diamantinasaurus doesn't preserve any vertebrae, so we can't directly compare it with Austrosaurus. But because the type of Austrosaurus is so incomplete, it might be safely ignored as a nomen dubium. I'll leave it to the sauropod experts to decide that!

Our third beast is a theropod (meat-eating dinosaur) named Australovenator wintonensis. It was perhaps a third of the body length of the two sauropods and is represented by a partial skeleton including a complete hindlimb, partial forelimbs, and a portion of the lower jaw. For Australian theropods, this is simply dumbfounding material (remember Kakura, only known from a fragmentary leg bone?). Heck, for theropods anywhere this is pretty darned good. Australovenator falls out as an allosauroid (a pretty common group of predators from the Jurassic and Cretaceous) just outside of carcharodontosaurids. With Australovenator thrown into the mix, allosauroids had a nearly global distribution.

Open Access Nerdiness
This paper is a fantastic example of the real benefits of an on-line, open access journal like PLoS ONE. Without page limitations, the authors were allowed to truly monograph the heck out of the bones. Virtually every element is illustrated from multiple angles (with high resolution photos downloadable from the website!) and accompanied by thorough text descriptions and measurements. The editors of most journals would freak out over such a "waste" of precious space - but I have a feeling that future researchers are going to thank the authors for their thoroughness. As a PDF, the paper weighs in at 51 pages - and this doesn't include the supplementary information!

The authors (perhaps at the editors' behest) also make very explicit statements about the nomenclatural availability of the names, a direct result of the Darwinius fallout. Hopefully this will satisfy the requirements ICZN.

On the rather nitpicky side, I would note that the minimal post-processing of the manuscripts employed by PLoS ONE shows up here and there. For instance, the term "phalange" is used as the singular instead of the correct "phalanx" (one of my few pet peeves), among a few other oddities. These are rather minor bones to pick in an otherwise weighty manuscript.

As always, if you have something to say, post a comment here and then go provide your comments, notes, and ratings of the article at the PLoS ONE website.

The Bottom Line
So what's so important about this paper? Well, we finally have good sauropod material from the Cretaceous of Australia, and an excellent theropod specimen to go along with it. No doubt--these specimens are going to be critical for future studies on the evolution and biogeography of both groups, as well as greatly filling in our understanding of Australia's geological past. It is not an exaggeration to say that Australian dinosaur paleontology has taken a quantum leap forward!

Update: Read more about the discovery at the PLoS community blog, the museum website, and SV-POW!. Finally, a paleo discovery that's worth the hype!

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

The Citation
Hocknull, S., White, M., Tischler, T., Cook, A., Calleja, N., Sloan, T., & Elliott, D. (2009). New mid-Cretaceous (Latest Albian) dinosaurs from Winton, Queensland, Australia PLoS ONE, 4 (7) DOI: 10.1371/journal.pone.0006190

Wednesday, July 1, 2009

The End of the Internet Mailing List? Part III

In the previous two posts of this series, I discussed the past, present, and future of the internet mailing list--along with the other new technologies jostling for position in the fray. In this final post of the series, I want to address the role of the blog in scientific discourse. What does it bring to the table? What are its drawbacks?

The Blog
As a case study, let's consider the case of Ida (more properly known as Darwinius masillae). This little primate, announced in the open access publication PLoS ONE and accompanied by a media juggernaut of unprecedented proportions, grabbed the world's attention (including mine). Every corner of the Internet, from the mailing lists to the blogs to the news sites to the home page of Google, was buzzing.

From the nearly the start, people picked up on something unsatisfactory with the story. Whether it was the hype, the conclusions of the paper, or the validity of the name, nearly everyone had an opinion. Within minutes, wonderfully cogent critiques were presented - largely in the blogosphere (see Brian Switek's blog carnival at Laelaps for the cream of the crop). Sure, there was some back-and-forth on VRTPALEO and various other mailing lists, and certainly some (often snide) comments on the social networks, but the blogs were where the real action was!

As a prime example, let's look at the problem of the validity of the name "Darwinius". By the standards of the bean counters at the ICZN, it wasn't valid as originally published! A commenter (among others throughout the Internet) at Carl Zimmer's The Loom really brought the issue front and center, resulting in extensive discussion by a number of professional paleontologists, and two widely read follow-up posts. Perhaps in part due to this widespread exposure, the issue was very, very quickly resolved. Again--some of the mailing lists were discussing this, but the "good stuff" was in the blogosphere.

What is it about blogs that contribute to this phenomenon? To start superficially, blogs are attractive. With just an internet connection and a laptop, pretty much anyone can create a profesionally-appearing, attractive layout with relevant graphics and links. The plain-text mailing lists just don't allow this.

Next, blogs allow a forum for knowledgeable people to speak and be heard. Degreed professionals--such as the guys at SV-POW!--and talented science writers--I'll pick on Brian Switek again as a paleontological example--do a tremendous job of presenting complicated information to the public and professional communities. This sort of commentary and presentation just wouldn't be found at Facebook or a mailing list--it's outside their scopes. Of course, this is a double-edged sword--some bloggers tend towards grandstanding and pandering to the fanbase at the expense of real content. In part, this is a function of the medium--a blog belongs to an individual (or a few individuals), and is in some ways intended to communicate more by decree than by conversation. Whether this is a good thing or not largely depends upon the blog.

This aside, the comment threads are another important part of the blogosphere. As an excellent example, check out the exchange on the recently-published primate Ganlea. Particularly in cases where the threads are of a manageable size, people pay attention. Real discussion is happening there. But, this does tend to fall apart in blogs that are too big. . .

So what is the big difference of a blog's comments from a typical mailing list? The comment threads are more readily accessible to the public - you don't need to access some text-only or subscriber-only archives. The thread of conversation is right there with the conversation starter. And wow, can these comment threads be enlightening!

Can It Last?
I would argue that the real on-line conversation about science has moved to the blogs. But is this sustainable? Only time will tell. Just two years ago, there was only a fraction of the number of blogs we have today. As the medium expands, it is getting tougher and tougher to keep on top of things. I predict that we're going to see more niche blogs developing, too. With so many good "general paleontology" blogs out there, it's going to be more appealing to specialize in topics like the Triassic, or sauropod vertebrae, or aquatic amniotes. We may very well see a fragmentation of the blog audience as a consequence, with a few heavy hitters getting consistent widespread pageviews, and everyone else catering to a more niche audience. Who knows what the future will bring?

Sunday, June 21, 2009

My Dissertation - Now Open Access

ProQuest's UMI Dissertation Publishing is pretty much the distributor of dissertations and theses in the US and Canada (beyond an author posting the work on his or her personal website, or an ILL to the relevant academic library). ProQuest/UMI offer the service of permanently archiving and making your work searchable and accessible - and readers pay $36 for a PDF or $43 for an unbound print copy. To be fair, I personally consider this a reasonable price for documents the size of a dissertation (considering that Elsevier and kin charge roughly the same for the PDF of a 2-page paper from a second-rate journal), and the authors do see a (small) royalty check for any sales (and I do know folks who have gotten such royalties - good luck getting Elsevier or other commercial publishers to ever agree to any author royalties, ever!).

On the other hand, I realize that $36 is a deterrant for those casually or even non-casually interested in a piece of research (no matter how relevant it might be). So. . .open access seems to be the best way to go, in terms of ensuring a wide audience. This then leaves us two options: 1) post a PDF on a personal website; or 2) take advantage of open access through ProQuest (or both 1&2).

For long-term accessibility, I decided that #2 would be a good way to go. Sure, I'll post it on my own website (as I work on designing this), but it also made sense to make it available through as many sources as possible. Lots of folks use the ProQuest search engine (at least I do, whenever I want to check up on a dissertation), and this could very well be the main way interested parties find my dissertation document.

So, when submitting all of the paperwork before graduation last spring, I signed on the dotted line and wrote the little check (right now, it is $65 for their standard processing fee, which everyone pays, and an extra $95 for the open access fee*) to make my work open access, through PQDT Open. This meant that my work would be indexed in their database, made searchable through Google, and that nobody (me or ProQuest or UMI) would be earning any more money off of the document (but how many people were going to buy it in the first place, right?).

PQDT Open also offers an "author embargo" option, in which you can delay full dissemination of the dissertation for a specified length of time (six months, one year, or two years, I believe). I chose to delay by a year, in order to allow me a little lead time to get most of the chapters through the review process and into press. I was 2/3 successful for my three big chapters, and the third big chapter is now in review. Would I do it this way again (i.e., delayed access), or allow immediate access? I'm not sure. I see costs and benefits to both ways.

So, this is just a long way of announcing that my 2008 dissertation on cranial pneumaticity and ceratopsid sinuses is now available permanently and free of charge as a PDF through ProQuest, right here.

I should also give a big shout-out to Matt Wedel (aka Dr. Vector), for first getting me thinking about the issue.

The appropriate citation for the dissertation is:

Farke, A. A. 2008. Function and evolution of the cranial sinuses in bovid mammals and ceratopsian dinosaurs. Ph.D. dissertation, Stony Brook University, Stony Brook, New York, 226 pp. (available for download here)

The component chapters (with the exception of the introduction, conclusions, and occasional small sections of the other chapters) are either published or wending their way through the publication process. Relevant citations include:

Farke, A. A. 2008. Frontal sinuses and head-butting in goats: a finite element analysis. Journal of Experimental Biology 211:3085-3094. (PDF and full text now freely available here; see here and here for my blog posts about the article)

Farke, A. A. In press. Evolution and functional morphology of the frontal sinuses in Bovidae (Mammalia: Artiodactyla), and implications for the evolution of cranial pneumaticity. Zoological Journal of the Linnean Society. (Should hopefully be up on EarlyView shortly - I am happy to send a PDF of the final draft to anyone who is so interested)

Farke, A. A. In review. Evolution, homology, and function of the supracranial sinuses in ceratopsian dinosaurs. (Look to this blog for further updates)

(*note - I updated this post to reflect the open access fees current as of fall 2008)

Tuesday, June 16, 2009

The End of the Internet Mailing List? Part II

In my previous post, I outlined the (in my opinion) glory days and slow change (some might even say decline) of email-based lists such as the Dinosaur Mailing List. That post ended with a question - what happened?

What Happened to Mailing Lists?
In short, the Internet matured. 10 or 15 years ago, mailing lists were really the only game in town (aside from a handful of themed chat rooms). If you were a dinosaur fan, you joined the Dinosaur Mailing List. Today, you can choose between the DML, various internet forums, social networks, and blogs. Simultaneously, the user community has exploded. Literally hundreds--and perhaps even thousands--of folks follow, comment, and create paleo content on the web every day. The conversation has not only moved, it has expanded into a variety of niches.

In the rest of this post, and the next post, I'll focus on two technologies in particular: social networking and blogs.

Social Networking and the Paleontologist
Over the past year or two, I have found that I get much of my informal news and gossip from Facebook. In fact, Facebook is the primary method of communication that I have with some colleagues, even above email. Facebook is quick, easy, and allows for real-time chat. Over the past few weeks, I learned nearly immediately who had SVP abstracts accepted and rejected, and often get up-to-the-minute reports of manuscript acceptances, fieldwork successes (and failures), and other details from status postings. At its best, Facebook provides a level of casual (sometimes too casual) interaction with many of my far-flung colleagues on a daily basis - a finger on the pulse of the community. The informal nature of Facebook and similar sites mean that, for now, it probably won't replace mailing lists for announcement of new papers or serious discussion. But, social networking sites certainly offer a fun and informative way to keep in touch with other paleo types.

Thoughts? Alternative Perspectives?

Coming up. . .Blogging and the Paleontological Community

Sunday, June 14, 2009

The End of the Internet Mailing List?

No doubt, the internet has changed the way we do paleontology. Email allows faster collaborations among workers at widespread institutions, and sometimes continents. Open access journals and PDFs from "closed access" publications allow virtually instantaneous distribution of peer reviewed research. And, internet mailing lists, forums, social networking sites, and blogs allow a whole new dimension of discussion and dissemination of research results.

The role of the latter venues has had no small level of controversy, ever since their beginnings. Some professionals grumbled over the way any person with an internet connection could flood mailing lists with intellectual garbage. In relatively rare cases, this has happened. Some avocational and non-degreed paleontologists grumbled over real and perceived slights from the "Ivory Tower." This too on occasion has happened, but rather rarely (despite frequent accusations from some quarters). Despite these misgivings, the new modes of scientific communication and discourse are here to stay. But, like all new technologies, the situation is evolving rapidly.

As someone who remembers the days before the Internet, and during the early days of Internet access (for me, beginning around 1997 when the first connections were available at my school), it has been very interesting to follow (and participate in) the trends on-line. In this series of posts, I'll be addressing the past, present, and future of informal electronic communication. This is part of a broader discussion that has been happening throughout the blogosphere recently, particularly at SVP-POW!

The Glory Days of the Internet Mailing List
One of the earliest thrills in my initial exploration of the internet was something called the "Dinosaur Mailing List." Here was a fantastic place where seemingly unfettered discussion of all things dinosaurian took place. New discoveries - including the first inklings of amazing feathered(!) theropods from China - were announced on a seemingly daily basis. Reports from SVP filtered out, and were eagerly read by those of us who couldn't attend the meetings. Acknowledged experts--such as Tom Holtz, Jim Farlow, Darren Tanke, and Ralph Chapman--rubbed elbows and shared discussions with neophytes, fans, and future paleontologists alike. The DML was the place to be for anyone interested in dinosaur paleontology, at any level. You just had to sign up, in order to receive a steady stream of interesting and insightful communications direct to your email inbox.

In the 12 years that I have belonged to the DML, something has changed. The change has been subtle, slow, and creeping, but it has certainly been happening. Fewer professionals are making fewer postings (although many still follow the list). I find myself skipping or deleting 95 percent of the list's messages. Although there are some delightful exceptions, less real scientific discussion is happening here (beyond the perennial topics of the origins of bird flight and theropod systematics). I have seen similar shifts on other mailing lists and internet forums that I belong to, so it is not limited strictly to the DML, nor is it the fault of the hard-working moderaters. What, then, has happened?

Coming Up. . .Shifting Sands of Communication

Monday, June 8, 2009

What Place Do Blogs Have in Science?

While I'm currently on vacation, I've also been thinking hard about a "major" upcoming post on the role of blogs in scientific discourse. Through a very fortuitous bit of serendipity, SV-POW! has a stimulating post and discussion going on about aspects of this very topic. Check it out, and look back here next week for my own contribution to the fray.

Friday, June 5, 2009

Good News for Zotero

The lawsuit by Thomson Reuters against Zotero, the free bibliographic plug-in for Firefox, has been dismissed. Read more about it here.