The Open Source Paleontologist

An Australian Dinosaur Extravaganza

2009-07-03T00:03:00.011-04:00

The 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

The End of the Internet Mailing List? Part III

2009-07-01T23:03:00.007-04:00

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?

My Dissertation - Now Open Access

2009-06-21T10:01:00.005-04:00

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)

The End of the Internet Mailing List? Part II

2009-06-17T00:03:00.003-04:00

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

The End of the Internet Mailing List?

2009-06-14T23:15:00.003-04:00

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

What Place Do Blogs Have in Science?

2009-06-09T00:02:00.002-04:00

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.

Good News for Zotero

2009-06-06T00:26:00.002-04:00

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

How Big (Dead) Mammals Respond(ed) to Global Warming: Paleontology and Our Climate Crisis

2009-06-05T00:44:00.010-04:00

After all of the commotion over "Ida," I'm happy to point out a new, thought-provoking paper in PLoS ONE that perhaps has more relevance to modern humans than any old primate of debated affinity. This new contribution ties two rather cool issues together: charismatic megafauna and global warming. And what might they have to do with each other?

Within the scientific community, our current cycle of climate change ("global warming") is pretty well-supported by numerous lines of evidence. In light of this change, many biologists, conservationists, and policy-makers want to know exactly how this change will affect living things (humans and wildlife alike). Will animals adapt to the new conditions? Will they die out? Will different animals cope in different ways? Models, simulations, and short-term studies are all useful, but only provide one small piece of the puzzle. Short-term studies (by short-term, I mean on the scale of months, years or decades) provide useful ground-truthing for the models, but in matters of conservation and policy, they may come too late for imperiled ecosystems. It's like having your house burn down around you before you can see the smoke.

An oft-overlooked source of data comes from the fossil record. Earth's climate has changed numerous times over the millenia, and by studying previous warming or cooling episodes we may be able to understand our own times. This is where a new study, led by Larisa R. G. DeSantis in collaboration with Robert Feranec and Bruce MacFadden, comes in.

Ice Age Antics
Beginning around 2.58 million years ago, in the late Pliocene, our planet has been in an Ice Age. This ice age is characterized by cooling periods (glacial periods, in which the ice sheets advance) and warming periods (interglacial periods, in which the ice sheets retreat). For the last 10,000 years or so, we've been in an interglacial period (and our present climate change is above and beyond this). As a neat natural experiment, DeSantis and colleagues decided to look at how large animals reacted (in terms of diet, etc.) to the switch from a cool period to a warm period.

Grind Up Fossils in the Name of Science
The team focused on two sites from Florida: one from a glacial period, between 2.0 and 1.6 million years old, and another from an interglacial period, between 1.6 and 1.3 million years old. Using a little drill, the researchers sampled tooth enamel from a variety of Ice Age organisms, including horses, deer, tapirs, elephants, and other herbivorous critters that roamed Florida during that interval. And why grind up fossil specimens? It turns out that you can run the enamel powder through a spectrometer that measures the proportions of various isotopes of carbon and oxygen.

And what do these isotopes tell us? Simply put, you are what you eat. Different plants use different pathways of carbon fixation (C3 and C4 were investigated here). Animals eating lots of C4 plants (primarily "warm season grasses") have one isotopic signature for carbon, and animals eating C3 plants ("cool season grasses," trees, and shrubs) have another. Furthermore, oxygen isotopes are different for arid environments and relatively wet environments. So, by looking at oxygen and carbon isotopes in concert, you can get an idea of the relative aridity of the area as well as the diet of a given animal.

And now the modern tie-in: According to DeSantis and colleagues, many studies and models have concluded that under environmental change, animals tend to try to be pretty consistent in what they eat. In other words, if you start out at a grass-eater, you will try and stay a grass eater. So, mammals don't really do much in response to warming (or cooling). Of course, this has pretty important implications for conservation: once the grass disappears in the face of a changing climate (whatever the cause), our grass-eaters are toast.

The Results
Interestingly, it turns out that different mammals had different stories over the course of the glacial cycle. Based on the isotopic data, the types of plants changed over time, with C3 plants dominating the cooler cycle (as would be expected) and C4 plants predominating in the warm interval. And, many of the same animals are found in both the "warm" and the "cool" study sites. Although some apparently maintained similar diets (e.g., tapirs), most other animals (e.g., deer and horses) showed very different isotopic signatures over time. They were eating different foods. . .thus, these animals were quite adaptable!

What It All Means
A striking implication of the study is that some animals may not be as vulnerable to climate change as previously thought. These Ice Age species changed their ecological niches in the face of climate change. So, if large modern animals can adapt their diets relatively easily, they may be able to escape extinction too. The bottom line still is that previous assumptions of do-or-die dietary stability for large mammals are not valid in all cases. Here we have yet another cool example of how paleontology can provide important information for "real-world" problems!

Parting Thoughts
The paper, posted at PLoS ONE, covers much more than the little bit I've highlighted here. There are some interesting tidbits on changes in rainfall and ecological partitioning, among other things. It's a quick and very accessible read (weighing in at 7 PDF pages, including figures and references), and even this non-geochemist followed the text pretty easily. So, go check it out! As always, you can rate the paper or make comments at the PLoS ONE website.

The Citation
DeSantis, L., Feranec, R., & MacFadden, B. (2009). Effects of global warming on ancient mammalian communities and their environments PLoS ONE, 4 (6) DOI: 10.1371/journal.pone.0005750

PalArch Goes Open Access

2009-06-04T10:22:00.003-04:00

Postings have been slow lately, as we enter the busy field season. I have a few comments to respond to, and a few posts in the works. For now, I wanted to point out that the PalArch family of journals has now gone completely open access. Of particular interest for readers of this blog is the PalArch Journal of Vertebrate Paleontology. Congratulations to the journal staff on making this a reality!

Re-posted from a message to the VRTPALEO listserv by Brian Beatty:

Greetings!
The PalArch Foundation is happy to announce that our website (www.palarch.nl) has been revised and updated. The PalArch Foundation supports three peer-reviewed, online journals focusing on Vertebrate Palaeontology, Archaeology of Northwest Europe, and Archaeology of Egypt/Egyptlogy.

These new revisions includes *RSS feeds*, as well as sections for *comments* with each paper, much like one has in a blog format. We hope this will encourage more open discussions of work and lead to collaborations and more rapid developments in our fields of interest.

Though we are still updating some texts and uploading the archive of book reviews, we have FINALLY managed to get the support and organization to have not only the site revised and easier to use, but also the *entire archive of papers available OPEN ACCESS*. PalArch's Journal of Vertebrate Palaeontology can be accessed here: http://www.palarch.nl/category/vertebrate_palaeontology/

More importantly, we have revised the operational plan of the journals to allow us to maximize the utility of being an online journal. That is, instead of publishing issues on a periodical basis, *papers will be published as soon as they are accepted, formatted, and finally approved*. This way we can more rapidly share new information, eliminating much of the logistical delays of publishing and retaining only the delays of critical, thorough peer review.

We hope you will consider submitting papers to PalArch, and take advantage of the open access, archive, and commenting features. PalArch is an entirely volunteer-run journal and a non-profit run by people wanting to get good science published without the financial and political hassles that can occur, and we hope you will participate.

About That Adapid. . .Or, Hype In the Digital Age

2009-05-19T20:41:00.007-04:00

Today's PLoS ONE includes an article on a new primate from the Eocene of Germany, Darwinius masillae. Poor Darwinius has suffered heaps of abuse over her existence (we know the specimen is probably a she, based on the lack of a baculum). She died young, possibly suffocating during a belch of noxious gas from a volcanic lake. She got squashed ("lightly crushed," as her describers euphemistically say) under tons of rock, and then was rudely given a split personality upon her discovery. Each half of Darwinius was sold privately to a different collector, and eventually one half made it as far as a museum in Wyoming. This half received a little bit of creative restoration somewhere in between. The other, more intact half eventually made it to a museum in Norway. But, the fun was only beginning!

Our friend was described by a multi-national team of scientists, who teamed up with the History Channel, BBC, and other outlets to create a media blitz the likes of which the world has never seen before. Not only a peer-reviewed article, but press conferences, book deals, television programs, interviews, and much more.

Why is there such a fuss over such a little specimen (weighing in at approximately a kilogram while alive)?

First off, this is a spectacular fossil. The Messel Beds of Germany have produced truckloads of spectacular specimens with exquisite soft tissue preservation (everything from bats to birds to rodents), but primates are exceedingly, exceedingly rare. Nobody would debate the tremendous scientific value of the find. People are debating the authors' interpretation of the find.

The authors claim that Darwinius is a haplorhine primate. That is, Darwinius (and other members of its clade, the adapoid primates) is more closely related to anthropoid primates (including monkeys of all sorts, apes, humans, etc.) than to strepsirrhine primates (the group including lemurs). It's hard to believe for those of us who study dinosaurs, but this is a ridiculously contentious claim. To put it into context for you dinosaur nerds, this would be similar to someone claiming that Compsognathus is more closely related to birds than Velociraptor. Oh, the humanity!

The claim of Darwinius and other adapoids as a haplorhine is contentious for two reasons: 1) most recent, widely accepted cladistic analyses place adapoids as closer to lemurs (strepsirrhines) than to monkeys (haplorhines); and 2) there is no real cladistic analysis to support the claim made by the present paper. Instead, the authors give a list of characters that they believe to support the assignment to the haplorhine clade. Unfortunately, there is little or no discussion as to what these characters (including absence of a "toilet-claw" and "tooth comb," features found within, but not universally across, lemurs and kin) mean, including the possibility of convergence or mosaic evolution.

So, it appears that some extraordinary claims are made about Darwinius, but the supporting analyses are spartan. Given the wonderful preservation of the skeleton, it should be relatively straight-forward to code this specimen and present a cladistic hypothesis (because this will resolve all questions, right?!). Darwinius is an important fossil. The problem is that the interpretation of this specimen is highly debateable. The authors may very well be correct. . .but the burden of proof is still upon them.

As always with articles in PLoS ONE, the paper is free for everyone. Judging by the blogosphere today, there are some very strong opinions about this specimen - if you have thoughts on the little critter, please post a comment or note over at PLoS ONE!

Further Reading in the Blogosphere
Brian presents an excellent, in-depth analysis of Darwinius over at Laelaps.
Bora provides a nice list of blog coverage over at Blog Around the Clock.
Carl writes another excellent critique at The Loom.

Reference
Franzen, J., Gingerich, P., Habersetzer, J., Hurum, J., von Koenigswald, W., & Smith, B. (2009). Complete Primate Skeleton from the Middle Eocene of Messel in Germany: Morphology and Paleobiology PLoS ONE, 4 (5) DOI: 10.1371/journal.pone.0005723

Image at top from the original article at PLoS ONE (Franzen et al., 2009).

Book Review: Charles R. Knight, Autobiography of an Artist

2009-05-17T10:34:00.006-04:00

Charles R. Knight was one of the most influential paleontological artists of the 20th (and latest 19th) century. His iconic paintings of Tyrannosaurus, Brontosaurus, woolly rhinos, and other prehistoric animals have influenced the direction of scientific thought, inspired movies and toys, and motivated paleontologists for decades. Every paleontologist, whether consciously or not, owes a debt of gratitude to Knight and his work.

I was particularly thrilled to receive a copy of Knight's autobiography for my birthday recently. This slim paperback, largely written by the author himself, is a fascinating glimpse into one of paleontology's vivid imaginations.

The story opens in Knight's childhood, with his earliest recollections of visits to the newly-founded American Museum of Natural History, among other memories. He details his early loss of vision in one eye, a sometimes strained relationship with his stepmother, and an early trip across the Atlantic to visit his father's family. The prose offers a window into a lost (but not necessarily simpler) time, as we see the stirrings of an interest in natural history.

The next phase of the book covers Knight's initial training in art, from sketches to stained glass. A parade of characters passes by at this and other points in the book, from the obscure, to the eccentric, to the famous. We learn about Knight's first wildlife art, and then his near-chance meeting with paleontologist Jacob Wortman. So began a paleo-art career that was to span decades.

The rest of the book largely functions as a travelogue, with occasional vignettes of paleontological characters. Most fascinating for me, as a dinosaur paleontologist, were the pages devoted to Knight's collaboration with Edward Drinker Cope. Knight describes in detail the faded glory of Cope's home at 2102 Pine Street, packed to the brim with papers and bones. Curiously, despite the tremendous influence that Cope had upon Knight's early art, the men only knew each other for a few months before Cope's death.

Perhaps because Knight wrote the book as an autobiography rather than a paleontological treatise, the reader gets only the briefest glimpse into Knight's imagination and thoughts on prehistory. The book is focused on people and places, rather than on the fossils. Some readers may be disappointed by this, but I found the format quite engaging from start to finish. Judicious editing by Jim Ottaviani helps the book flow along quickly--the manuscript was left unfinished by Knight, so I am sure it took a little bit of work to whip the text into shape.

The book is greatly augmented by a few pages of text from some notables--forewords by Ray Bradbury and Ray Harryhausen, and afterwords by a number of paleontologists from the American Museum of Natural History. Illustrations by Mark Schultz bring to life many of the distinctive characters (including what is probably the earliest description of a "crazy snake guy"). Finally, memories from Charles Knight's granddaughter, Rhoda Knight Kalt, add a unique perspective and a fitting tribute. If you're looking for an enjoyable read in the field this summer, make sure to pack this book!

Charles R. Knight, Autobiography of an Artist, by Charles R. Knight (with forewords, introductions, and afterwords by a number of other folks), 112 pages, published by G. T. Labs, Ann Arbor, Michigan.

Open Access Dissertations in Physical Anthropology

2009-05-15T09:51:00.003-04:00

My colleague Biren Patel (who is doing some awesome research on primate locomotion and functional morphology) passed on this link to open access dissertations in physical anthropology and paleoanthropology, hosted by the Paleoanthropology Society. A number of very nice dissertations from major centers of anthropological research are posted here, some that have been published formally and others that have not. We paleontologists would do well to heed more closely the world of physical anthropology - oftentimes the "hot new techniques" presented at SVP have long been old news in the anthropology world. Furthermore, a number of our anthropological colleagues are asking the exact same questions we are! It pays to keep up on their literature.

The Paleoanthropology Society also hosts an on-line, open access journal called (oddly enough) PaleoAnthropology. Go check it out!

The True Cost of Journal Subscriptions

2009-05-06T23:00:00.004-04:00

Most of us paleontologists have a handful of journals to which we personally subscribe, usually associated with society memberships. In other cases, we rely upon our institution's library, other local libraries, or the goodwill of colleagues to get access. In these days of tight budgets, many libraries are eyeing journal cuts. But, one might say, "I only pay $100 a year in membership dues--surely the institutions can't be that strapped for cash!" The key thing, though, is that institutional and individual subscriptions are entirely different animals.

To some extent, it is easy to legitimize a higher cost for an institutional subscription. An inexpensive journal is a perk of society membership, for instance--and this low cost is subsidized in part by library subscription fees. Additionally, the journal publishers might have a much slimmer amount of income per printed page for institutional subscriptions (because many, many people would be utilizing the same copy). So, to keep things running smoothly, it's necessary to charge a little more to an institution.

Unfortunately, the problem results when subscription rates increase at a rate exceeding institutional budgets. The fact of the matter is that some journals are just ridiculously expensive for a library to purchase! Just how ridiculously expensive, you might ask? Let's consider the case of the journal Palaeoworld. In 2008, the journal had a total of 264 published pages, and an annual institutional subscription cost of $532. This comes to a cost per printed page of $2.02--no wonder most institutions can't afford it!

You are probably thinking to yourself that I've chosen a ridiculous example--and to some extent I have. Palaeoworld is a relatively small journal targeting a limited audience. Let's look at a "better known" journal--Palaeogeography, Palaeoclimatology, Palaeoecology. They regularly publish high-impact, groundbreaking research--to the tune of $1.02 per page. The venerable Cretaceous Research costs $1.09 per page!

Then, there are the cases that are so egregiously expensive that it simply boggles the mind. Consider Journal of Morphology. It's not strictly a paleontology journal, but it frequently publishes paleontology-related content--and its reputation is pretty solid. In fact, I've even published there. Yet, a yearly institutional subscription costs $6,031!!! That works out to a staggering $3.89 per page.

Are there any reasonably-priced journals for institutions? Fortunately, there are some, if you dig around a little. Kudos to the folks at Journal of Vertebrate Paleontology, with a price per page of 22 cents. And let's hear it for Acta Palaeontologica Polonica, barely tipping the scales at 13 cents per page. As opposed to the examples above, these are society or labor-of-love journals published through relatively small publishing houses. Yet, even the for-profit journal Nature manages 42 cents per page for institutional subscriptions. In my mind, these are all perfectly reasonable costs.

Some savvy publishers have figured out a very slick way to seemingly lower the price--"bundling" packages of electronically-accessed journals together for a group discount. This is somewhat admirable in modestly reducing the overall price per page (for the short term), but it also means that you get stuck with supporting journals of very, very dubious scientific quality. See this news release from Cornell about why it's not a good economic idea in the long-run, too (and a quick internet search will turn up many other examples).

I think that the concept of commercial journal publication is not inherently bad--there are a number of good-quality journals run by such companies. It's just that they're so blatantly overcharging for access to this content! A journal clocking in at $2/page is not sustainable in the long-run. Although I have a strong preference for open access (which someone has to pay for somewhere along the line), I also recognize that some very good closed-access journals provide a valuable service (and see delayed open access as a viable compromise).

So, I challenge you publishing readers (and myself) to weigh all of the factors before submitting that next research paper. What is the impact factor? How respected is the journal? And, will people be able to afford to read it? Let's publish responsibly.

Methodological Notes--I grabbed the most recent available annual, instutional subscription prices from publishers' websites, with rates for US institutions in US dollars whenever possible. I then counted up the total number of pages published in 2008, and divided this by the subscription rate to come up with a value for dollars/page.

Get the Goat Head Paper for Free!

2009-05-06T00:28:00.003-04:00

I am happy to announce that one of the papers resulting from my dissertation research, on head-butting in goats, is now freely available for download. You can get the paper in HTML or PDF form. For a previous blog post on the topic, check here. Journal of Experimental Biology is one of the progressive mainstream journals that opens up their archives after six months. . .it is a high-profile publication (impact factor in 2007, for what it's worth, of 2.972), and there are a lot of really cool papers in there (beyond mine, of course). Go check it out!

Reference
Farke AA (2008) Frontal sinuses and head-butting in goats: a finite element analysis. Journal of Experimental Biology 211: 3085-3094. doi:10.1242/jeb.019042

Albatross vs. Pterosaur

2009-04-29T22:26:00.008-04:00

Today, there was a paper tangentially related to pterosaurs in the open access journal PLoS ONE. A team of investigators wired up albatrosses and petrels with accelerometers, in order to measure the percentage of time these animals spent flapping their wings and soaring. They found two main styles of wing flapping (as inferred from the accelerometer measurements): 1) high frequency flapping during take-off; and 2) low-frequency flapping during soaring. Interestingly, the frequencies scale with body mass in such a way that a maximum possible body size for the albatross-like body plan that still allows flight is extrapolated to a body mass of 41 kg and wingspan of 5.1 m (with the requisite error bars, of course).

The authors then go on to discuss the implications for pterosaur paleobiology, essentially suggesting that albatross-style soaring was physically impossible for pterosaurs such as Quetzlcoatlus (assuming that it also had albatross-style wings). Frustratingly, there is little discussion of the alternative possibilities of wing shape in pterosaurs, among other things. Furthermore, the underlying data for the analysis only focus on four species of birds with limited morphological diversity. As suggested by the authors of the current paper, data on thermal-soaring birds such as condors (which have a decidedly un-albatross-like form) are sorely needed.

So, kudos to Sato et al. for collecting some interesting morphological data. This sort of information is invaluable for verifying and refining existing models of vertebrate flight. However, the relevance of the data to pterosaurs should probably be reviewed by someone who knows the group better than I do - so if you're one of those people, hop (or soar) on over to PLoS ONE and comment on the article!

Reference
Sato, K., Sakamoto, K., Watanuki, Y., Takahashi, A., Katsumata, N., Bost, C., & Weimerskirch, H. (2009). Scaling of soaring seabirds and implications for flight abilities of giant pterosaurs. PLoS ONE, 4 (4) DOI: 10.1371/journal.pone.0005400

Tyrannosaurus rex, The Tyrant King--Reviewed

2009-04-29T01:04:00.003-04:00

For those who are interested, I have a book review of Tyrannosaurus rex, The Tyrant King, (edited by Peter Larson and Ken Carpenter), in the latest issue of the on-line, open access journal Palaeontologia Electronica. Go check it out (both the book and the review), and let me know what you think!

The latest issue of PE also features articles on Jurassic ammonites, ?Paleocene dinosaurs, and special photography techniques, along with book reviews (including one by Laelaps blogger Brian Switek) and an editorial.

Reference
Farke, A. A. 2009. Review of Larson, Peter L., and Carpenter, K., eds. Tyrannosaurus rex, The Tyrant
King. Palaeontologia Electronica 12, Issue 1, R2:2 pp.

Open Access Paleontology Journals - Community Opinions

2009-04-28T23:28:00.007-04:00

We're almost to the end of the series on the 2009 Open Access Paleontology Journal Rankings (see other posts in the series here, here, and here)! Citations and number of papers are all well-and-good, but one thing that's often omitted in journal comparisons is community opinion. In other words, what do paleontologists think of this or that journal? Have they even heard of the journal?

In order to see how open access journals have fared within the paleontology community, I ran an informal survey. It provided a list of open access journals in paleontology, and asked respondents to rank each publication as "excellent," "good," "fair," "poor," or "I've never heard of it." This survey was advertised on this blog, Facebook, the Dinosaur Mailing List, VRTPALEO Mailing List, and Laelaps. Ninety-two people responded, but not everyone answered every question. I have no idea (for the most part) who filled out the survey, but given the scope of advertising and the bits of feedback I received, I suspect respondents were primarily professional paleontologists and students of paleontology. Given the distribution of results, I have no reason to suspect poll crashing, but would also caution that this is not a scientifically sampled survey, either.

The results were then tallied, and an average rating was assigned to each. An excellent counted as 1 point, good as 2, fair as 3, poor as 4, and "never heard of it" as 5 points. So, here's the list from highest to lowest rating; the results are presented as "Journal Name, Average Score, (# Excellent Ratings, # Good Ratings, # Fair Ratings, # Poor Ratings, # Never Heard of It, Total Responses)." Journals with immediate open access are listed in bold.

Community Opinions of Open Access Paleontological Journals, 2009

Proceedings of the National Academy of Sciences, 1.45 (53, 19, 7, 1, 0; 80 total)
Proceedings of the Royal Society B, 1.52 (59, 20, 3, 1, 4; 87 total)
Bulletin of the American Museum of Natural History, 1.56 (53, 28, 5, 0, 3; 89 total)
American Museum Novitates, 1.57 (51, 33, 3, 0, 3; 90 total)
Acta Palaeontologica Polonica, 1.64 (51, 30, 6, 0, 4; 91 total)
PLoS ONE, 1.79 (44, 27, 8, 3, 4; 86 total)
Palaeontologia Electronica, 1.94 (30, 38, 16, 0, 3; 87 total)
PLoS Biology, 1.99 (36, 32, 4, 2, 9; 83 total)
Biology Letters, 2.36 (23, 33, 11, 1, 13; 81 total)
Smithsonian Contributions to Paleobiology, 2.58 (18, 32, 11, 4, 15; 80 total)
Bulletin of the Museum of Comparative Zoology, 2.62 (19, 28, 17, 1, 17; 82 total)
Paläontologische Zeitschrift, 2.64 (17, 30, 20, 3, 15; 85 total)
Ameghiniana, 2.87 (12, 27, 23, 4, 18; 84 total)
Contributions in Science from the Natural History Museum of Los Angeles County, 2.92 (14, 27, 15, 6, 21; 83 total)
Vertebrata PalAsiatica, 3.01 (10, 22, 26, 9, 17; 84 total)
Geodiversitas, 3.08 (9, 29, 17, 4, 25; 84 total)
Contributions from the Museum of Paleontology, 3.31 (11, 20, 14, 3, 32; 80 total)
Revue de Paléobiologie, 3.48 (5, 23, 15, 3, 34; 80 total)
PalArch, 3.55 (4, 13, 28, 9, 29; 83 total)
Palaeodiversity, 3.71 (3, 22, 13, 3, 42; 83 total)
Memoir of the Fukui Prefectural Dinosaur Museum, 3.94 (3, 8, 19, 10, 39; 79 total)
The Open Paleontology Journal, 4.01 (4, 14, 9, 5, 50; 82 total)
Journal of Paleontological Techniques, 4.04 (5, 7, 14, 8, 46; 80 total)
Geologica Acta, 4.05 (1, 13, 15, 2, 48; 79 total)
Estudios Geológicos, 4.12 (1, 12, 14, 5, 51; 83 total)
Coloquios de Paleontología, 4.24 (2, 8, 14, 3, 56; 83 total)
Geogaceta, 4.43 (0, 7, 10, 5, 59; 81 total)
Natura Nascosta, 4.49 (0, 6, 8, 7, 60; 81 total)
Joannea - Geologie und Paläontologie, 4.51 (2, 5, 5, 7, 62; 81 total)

Notes
A low rating does not necessarily mean a journal for which paleontologists have a low opinion. In at least some cases (e.g., Palaeodiversity), low scores result largely from poor "brand recognition." As the crop of new journals matures, and as the internet allows broader distribution of work, this situation is likely to change.

The journals Revista Brasileira de Paleontologia, Science, and Journal of Paleontological Sciences were inadvertently omitted from the poll.

Final Thoughts
In hindsight, there are a few more things I'm curious about. How do major closed access journals such as JVP stack up against their open access brethern? Who responded to the survey, and how do different types of paleontologists (students, early career and late career professionals, etc.) consider open access journals versus their closed access counterparts? What are general attitudes amongst paleontologists towards open access?

Coming Up. . .A Final Post With Raw Scores

Open Access Paleontology Rankings - Part III

2009-04-27T22:54:00.005-04:00

This post continues the series on the 2009 Open Access Paleontology Journal Rankings. Previously, I posted the rankings for Immediate Open Access Journals for General Submission and All Immediate Open Access Journals (including those museum publications with more restrictive submission requirements). Here, I'll release the final set of rankings, including both immediate open access and delayed open access journals. A number of notable journals (such as Science) now allow open access after a period of one year, so it only seemed fair to address them too.

As always, the ratings are based on a combination of journal citations, recent citations, number of articles, and community opinion (outlined previously). At the end of this series, I will post the raw data underlying the ratings.

Don't Forget The Caveats
Remember, these rankings are only one method for measuring the efficacy, quality, and impact of a journal, and you will probably disagree with one or more of the placements on the list. Especially for relatively young journals, rankings may change rapidly in the coming years.

Top Open Access Journals for Paleontology 2009
(General Results, Immediate and Delayed OA)

*not included in the community ranking survey

Note
It should be noted that some very fine journals (e.g., PaleoBios) have open access archives for older issues (five years or older), but these publications were not included on the general list. I made the somewhat arbitrary decision to exclude journals with lag times of greater than one year.

Up Next. . .Community Rankings of Journals

Open Access Paleontology Rankings - Part II

2009-04-26T10:34:00.004-04:00

This post continues the series on the 2009 Open Access Paleontology Journal Rankings. Previously, I posted the rankings for Immediate Open Access Journals for General Submission. Here, I'll release the general results for Immediate Open Access Journals. As mentioned previously, this category includes both journals to which anyone can submit a manuscript, as well as those with more restrictive authorship requirements. This latter category includes several museum publications, such as American Museum Novitates [see their submission policies here]. For journals such as these, authors usually must be an employee or research associate of the publishing institution, or receive special invitation. Journals with delayed open access (such as Science) are not included on the present list.

As always, the ratings are based on a combination of journal citations, recent citations, number of articles, and community opinion (outlined in my previous post). At the end of this series, I will post the raw data underlying the ratings.

Yet Again With the Caveats
Remember, these rankings are only one method for measuring the efficacy, quality, and impact of a journal, and you will probably disagree with one or more of the placements on the list. Especially for relatively young journals, rankings may change rapidly in the coming years.

Top Immediate Open Access Journals for Paleontology 2009
(General Results)

*not included in the community ranking survey

Notes
In some cases, relative ranks of journals may differ in this list from the previous category. This is because journals are ranked relative to all entries in a single category. For instance, PLoS ONE and PLoS Biology were tied in the last list, but are separated in the present one. Let's consider the number of article citations - relative to all immediate open access journals, PLoS ONE is ranked fifteenth and PLoS Biology is ranked second. When we exclude museum journals, the ratings move to ninth and second, respectively. When you add up all the rankings, little changes like this can jostle a journal's position; such behavior is particularly common near the top of the list. Later, I'll be releasing the underlying data and you can see for yourself.

Up Next. . .All Open Access Journals

Open Access Paleontology Rankings - Part I

2009-04-26T01:03:00.006-04:00

Over the next few days, I'll be posting results of the 2009 Open Access Paleontology Journal Rankings. These results will be divided into several categories, including:

Immediate Open Access Journals for General Submission (journals to which anyone can submit [excluding most museum publications with more exclusive author criteria], and which provide open access immediately upon publication)
Immediate Open Access Journals (same as above, with museum publications included)
All Open Access Journals (includes those journals with delayed open access)
Community Ranked Open Access Journals (journals as ranked by the opinions from the survey)

In this post, I'll just be covering Immediate Open Access Journals for General Submission. As described above, this includes only journals with immediate open access (versus open access after a set delay) and excludes those with restrictive authorship criteria (e.g., museum publications which usually require employment, association, or invitation to submit). The ratings are based on a combination of journal citations, recent citations, and community opinion (outlined in my previous post). At the end of this series, I will post the raw data underlying the ratings.

Again With the Caveats
Remember, these rankings are only one method for measuring the efficacy, quality, and impact of a journal, and you will probably disagree with one or more of the placements on the list. Especially for relatively young journals, rankings may change rapidly in the coming years.

Top Immediate Open Access Journals for Paleontology 2009
(General Submission)

*not included in the community ranking survey

Notes
While compiling the results, I noted that sometimes community opinions of a journal varied from the rankings by sheer number of articles or citations. This will be highlighted in a future post. So, if you're worried because your favorite journal is lower than you thought, or your least favorite journal is higher than you thought, you'll probably be interested to see those results.

Unlike the widely-known Science Citation Index, these rankings include very new journals as well as more established journals. Thus, some rankings may change in the coming years are the new kids on the block accumulate more citations, more papers, and more exposure. Still, it is very interesting to note how some quite new journals (such as PLoS ONE) still have a high position within the list.

It is interesting to note how truly global this list is - a healthy mix of journals from South America, Europe, Asia, and North America round out the top 10. What does this mean, if anything, for the future of paleontology?

Up Next. . .All Immediate Open Access Journals

About the Ratings

2009-04-25T01:11:00.003-04:00

In a series of posts over the next several days, I will be releasing the long-awaited(?) rankings of open access journals. This post will provide some background on the journals, the ratings, and my methodology.

What Are Open Access Journals?
If you are not familiar with the concept of open access publication, I recommend checking out my post, "Open Access Publishing and the Paleontologist."

Why Rate Journals?
Lots of open access journals are out there now--but not all are made equally. Some are widely read, others are ignored. Some publish high impact articles of general interest, and others are more focused in their scope. How is one to decide which publication to follow or submit research to? I've developed these ratings primarily as a service to those of us who are looking for open access journals in which to publish. Rankings that incorporate citation counts, numbers of articles published, and community opinion may be useful as one part of this decision-making progress.

How Were the Journals Chosen?
Basically, I combed the internet, dredged up my own knowledge of the literature, used the list on SV-POW!, and incorporated comments from readers. I have quite probably omitted one or two journals by accident, and I can assure you that this was unintentional. I adopted four criteria for selecting journals:

The journal must regularly publish articles on the topic of paleontology (a single article every two years is not sufficient).
Entire issues must be open access, not just selected articles.
The journal must be active, with at least one issue in 2008 (exceptions may be made for irregular museum publications that are not intended to be released on a set schedule).
The journal may have either immediate or delayed open access (a year is the cut-off point).

How Were the Journals Rated?
Journals were evaluated in five general areas:

Number of journal hits. This was calculated by searching for all articles within a given journal on Google Scholar, and recording the number of hits. [example]
Number of paleontology hits. This was calculated by searching for all articles within a given journal on Google Scholar that included the words "paleontology" or "fossil," and recording the number of hits. [example]
Number of article citations. This was calculated by searching for all articles within a given journal on Google Scholar that included the words "paleontology" or "fossil," and recording the number of citations for the top 10 search results. [example]
Number of citations of recent articles. This was calculated by searching for all articles within a given journal on Google Scholar that included the words "paleontology" or "fossil," published in 2007 or 2008, and recording the number of citations for the top 10 search results. [example]
Community rating. A survey was posted with a list of all journals, and respondents were invited to rate each journal as "excellent," "good," "fair," "poor," or "never heard of it." A notice of the survey was posted on this blog, Facebook, the Dinosaur Mailing List, VRTPALEO Mailing List, and Laelaps. Each journal was then given an overall rating, by weighting the number of responses in each category.

The journals were ranked in each category, and then an overall ranking incorporating all categories was calculated.

A Disclaimer
These are informal ratings, compiled in a manner that is probably non-scientific and flawed in one or more ways. No ranking system is perfect! Regardless of any imperfections, I think that these rankings may provide some useful information. Just take it with a grain of salt.

Coming up next. . .rankings for Immediate Open Access Only Journals.

Science - Now With Open Access Archives

2009-04-24T00:36:00.005-04:00

Another high profile journal has made its first steps towards open access! I learned earlier today that Science now has free access to its archives, for articles older than one year and published on or after January 1997. Registration (free) is required, but this is quick and relatively painless.

Unfortunately, it is too late to add Science to the survey, but it will be included in other ranking methods. If you haven't already, don't forget to fill out the open access journal poll! It closes Friday night, 23 April.

[Note: I also learned that the journal has actually had open archives for since 2001 - wow, am I out of the loop!]

What Are the Best Open Access Journals for Paleontologists?

2009-04-18T11:52:00.005-04:00

The number of open access journals available for paleontologists is growing rapidly (see both my previous post as well as a more comprehensive post over at SV-POW!). When it comes time to submit something for publication, the options can be quite disconcerting. What journal will best get that paper out there? Search engines are great for finding specific papers on a specific topic, but it's nice to know that the casual journal reader might also happen across your paper. So, which journals do my colleagues pay attention to? Which journals do my colleagues respect most?

Although inherently flawed in some respects, ranking systems provide a first pass at trying to evaluate publications. So, I've been working on developing a rudimentary ranking system for today's open access paleontology journals. And, I'd like your help! I'll be incorporating citation counts, page rankings, and other metrics, but would also like to consider reader opinion. So, I have developed a highly unscientific survey as part of this effort. Please take a few minutes to fill in your opinions.

As a preview, the survey provides a list of open access journals in paleontology, and asks you to rank them as "excellent," "good," "fair," "poor," or "I've never heard of it." The form will be open until next Friday evening at 11:45 (Pacific time). Results will be published here soon thereafter.

Coming Up, After Your Hard Work on the Poll: The Top Open Access Journals for Paleontology 2009.

Click Here to Take Survey

Open Access Journals in Paleontology

2009-04-17T01:27:00.009-04:00

As part of a larger upcoming post (by the weekend, I hope), I am compiling a list of open access journals that regularly publish articles in paleontology. So far, the journals have been selected using the following criteria:

1) The journal must regularly publish articles on the topic of paleontology (a single article every two years is not sufficient).
2) Entire issues must be open access, not just selected articles.
3) The journal must be active, with at least one issue in 2008 (exceptions may be made for irregular museum publications that are not intended to be released on a set schedule).
4) The journal may have either immediate or delayed open access (a year is the cut-off point).

Here's what I have so far. . .any suggestions for additions or corrections? At this point, I am not making statements one way or another on the quality of the journals. . .just assembling a list!

Acta Palaeontologica Polonica
Ameghiniana
American Journal of Science
American Museum Novitates
Biology Letters
Bulletin of the American Museum of Natural History
Bulletin of the Museum of Comparative Zoology
Coloquios de Paleontología
Contributions from the Museum of Paleontology
Contributions in Science from the Natural History Museum of Los Angeles County
Estudios Geológicos
Geodiversitas
Geogaceta
Geologica Acta
Joannea - Geologie und Paläontologie
Journal of Paleontological Techniques
Memoir of the Fukui Prefectural Dinosaur Museum
Natura Nascosta
Palaeodiversity
Palaeontologia Electronica
Paläontologische Zeitschrift
PalArch
PLoS Biology
PLoS ONE
Proceedings of the National Academy of Sciences
Proceedings of the Royal Society B
Revue de Paléobiologie
Smithsonian Contributions to Paleobiology
The Open Paleontology Journal
Vertebrata PalAsiatica

Keeping On Top of the Literature

2009-04-04T10:43:00.004-04:00

With more journals accessible than ever before, drinking from the stream of knowledge is more like chugging from the fire hydrant of information. Jerry Harris lists over 300 journals that publish vertebrate paleontology-relevant content. . .and the number is increasing all the time! With papers ranging from the obscure to the earth-shaking, it's both an overwhelming and important task to keep on top of the literature.

Fortunately, the same resources that create this flood of information also offer some life rafts to stay afloat. In this post, I'll cover a few tips, tricks, and tools that I use to stay "in the know" on paleontology.

Journal Subscriptions. If you're a paleontologist (avocational, professional, or otherwise) or paleontological enthusiast, you should be subscribing to one or two of the major journals in the field as part of your professional memberships (e.g., Society of Vertebrate Paleontology, Palaeontological Association, Paleontological Society). These will get you the earliest and easiest access to many of the most important articles in the field. Warning: Rant Ahead! Look - if you're seriously interested in paleontology, you need to join one of these societies. Not only do you get to support organizations that are doing good things in the name of paleontology, but you get journal access (print and/or online) as part of the package deal. And, they're really, truly not that expensive. I was a poor student once myself (and am still not what would be considered rich), but let's get real, folks. A student membership for SVP costs only $70 a year. Yes, I know that's real money. . .but it's also not much more than that copy of Halo 3 that you bought, or that history textbook you'll never read, that cable TV subscription you don't need, or the amount you spent on beer (or bottled water, or soda, or coffee, or energy drinks, or whatever your overpriced beverage of choice is) last month. An associate membership in SVP is but $50 (online access to the journal only, but a viable option for those folks who aren't students and/or don't think they will attend one of the annual meetings), and full membership is $140. Seriously - in most cases (and I recognize that there are some exceptions based on personal circumstances - you folks know who you are), there are no excuses for not joining at least one professional society. Start saving your pennies now, because it's an investment in your future as a paleontologist. (ok, my rant is over)
Paleontology Mailing Lists. One of the few (in my opinion) remaining uses for the Dinosaur Mailing List is publication alerts posted by some generous members (in particular, Jerry Harris). These alerts often scrape together valuable papers from obscure or hard-to-find journals. The downside with subscribing is that you also get a blizzard of emails on how T. rex could best a pack of Spinosaurus, PDF requests, and the inevitable "that species name isn't spelled correctly" postings.
Journal Web Pages. Most journals (at least, journals worth their salt) have web pages with listings of current content. So, you can always just browse on over, and see what this month's articles bring. Of course, this gets really old if there are more than about three journals to keep track of, and it's easy to forget. So, how about trying. . .
Journal RSS Feeds. Some journals, such as Palaeontology, have RSS feeds available. These can be really handy, but again overwhelming if you really want to check on a whole host of journals. So, this brings us to. . .
Journal Content Alerts. This is my personal favorite method for keeping updated on the latest and greatest papers. Many publishers and journal bundlers (including Wiley, Evilsevier, BioOne, PLoS, and others) allow you to sign up for free content alerts. So, when a new issue is published, you get a little email with a listing of every article in there. It's kinda like the old-fashioned technique of going to the journal stacks and thumbing through all of the recent issues, except you can do it in your pajamas without funny looks from librarians. As an added bonus, you often can set up searches for alerts whenever a topic of interest, like "dinosaur," shows up in any journal across the publisher's collection. This sometimes results in irrelevant papers (childhood education articles come up frequently), but it also might get you interesting hits from journals that you might not follow otherwise (e.g., respiratory physiology). I've set up a dedicated email account (thanks, Gmail!) just for this purpose.

So, it's easier than ever to be up-to-date on happenings in the journals. And, it isn't always impossible to get copies of these papers, either. The better you know the literature, the better your research will be!