Friday, July 24, 2009

A Few Quick Peeks Before Fieldwork Hiatus

Sorry for the massive delay in posting - as many of my readers probably experience, summer is a busy time for fieldwork, catching up on research projects, and the like. In the morning, I'm heading into the field for the next three weeks. Upon my return, you can look forward to the following posts:
  • A full review of the Asus Eee PC 901 as an option for field paleontologists. I bought one a few months ago as an ultra-light travel laptop as well as a machine for the field. Its extended battery life (up to 8 hours under the most ideal conditions, allegedly) is particularly intriguing to me. . .will it hold up to the hype?
  • A look at how to use ImageJ for basic measurements from digital photographs, including lengths and angles.
  • More open source journal goodness, with a focus on one or two publications in particular.
  • And, much more!
And finally, a link. . ."Does publication in top-tier journals affect reviewer behavior?" This study, published recently in PLoS ONE, asks an interesting question with direct relevance to all of us who publish.

And another link. . .an interesting piece of free software called paleoPhylo was just published in the latest issue of Paleobiology. It slices! It dices! It draws temporally-calibrated phylogenies using R!

See all of you in a few weeks.

Wednesday, July 15, 2009

JVP's Big Switch - A Good Thing or Not?

Journal of Vertebrate Paleontology, as many readers of this blog know, is the flagship publication of the Society of Vertebrate Paleontology. Like the journals of many other small societies, JVP is a high-quality, largely volunteer effort. With the growth of SVP, the journal has grown too - from 422 published pages during its first year (1981) to 1,245 pages during 2008. This sort of expansion is not without its problems - how do you fit the increasing number of scientifically worthy submissions within the fixed-page format of a relatively expensive publication medium? Massive backlogs are bound to happen (and have, apparently). One option is to drastically increase the rejection rate of previously worthy papers - not necessarily a healthy option for the journal or the society as a whole (particularly for students and others not in the inner circles). Another tactic is to increase the number of pages per year, or the number of issues. For a society-funded journal, this is a very expensive proposition.

So, the Society of Vertebrate Paleontology has taken a compromise position - partnering with commercial publishing house Taylor & Francis Group. At the face of it, this seems to be a win-win situation. . .the number of issues will be bumped up to six issues per year, which will decrease the journal's backlog and allow more high-quality papers to be published. The society retains editorial control, gets a bunch of free color pages every year (no small chunk of cash saved here!), and will get a memoir issue every year too (also a major bonus - these things are very, very expensive to produce). Taylor & Francis also has an open access option for many of their journals (although it is unknown yet if JVP will have this available), which may be a step forward from the previously no-open-access-option of JVP.

This all seems like a Good Thing. So, why am I hesitant to completely cheer on the switch? My caution lies entirely with all of the uncertainties behind a switch to a big commercial publisher. The T&F Group seems to have much more restrictive policies on PDF distribution, for instance. . .in my quick look through their present journals, I didn't see any evidence for any journal that authors are allowed to purchase a PDF for a reasonable price that would legally allow posting of a copy on a personal or institutional website (as JVP presently does--something I really like about the journal). At best, authors get the concession of a free PDF for emailing purposes only. . .and only for up to 50 colleagues. There are days when I like to think more than 50 people might be interested in my research, but perhaps this is a fantasy. My hope is that something better has been negotiated for the society, but it is presently too early to tell. Furthermore, non-members of the society at non-subscribing institutions can look forward to paying $37/article (regardless of page count!) for PDF access. This is a step ahead of the previous situation (no easy way to get a PDF short of writing the author, assuming their contact information is still valid and the author is still alive), but a debatable improvement nonetheless.

Other questions abound. What will happen to copyright (previously assigned to the society)? T&F is no Elsevier (thank goodness!), but what are the options for the society if the publisher engages in unethical publishing practices or overpriced bundling schemes?

All we have to go on right now is the press release. I am sure that many more details will be unveiled in the months leading up to the formal handover to Taylor & Francis. Some of my fears will be unfounded (I hope), and other unforeseen issues may rear their heads. At the very least, I will be keeping a close eye on further developments. If you publish in JVP or are thinking about doing so, and care about authors' rights, I encourage you to remain vigilant too.

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?