It's Almost Here. . .

All shall be revealed later this week.

Open Access Publishing and the Paleontologist

Open access publishing provides free and unrestricted access to scientific works. This contrasts with the traditional model of publishing, in which an interested reader either needed to purchase a personal copy of the publication or access to a library with a subscription. The rise of the internet has made open access a reality--and a thorny issue for the paleontologist looking to get published.

In this post, I'll talk about some of the benefits and drawbacks of open access publishing from the perspective of a paleontologist. I'll also discuss how to choose an open access journal.

Kinds of Open Access
Open access comes in many different flavors. From least to most restrictive, they are:

• Open Access Immediately. Your paper is available, for free to the reader, from the instant of publication. Palaeontologia Electronica and PLoS One are widely known examples.
• Open Access After Awhile. The paper is available to paid subscribers for a set length of time (perhaps six months or a year), and then becomes freely available. Journal of Experimental Biology, as one example, uses this method.
  
• Hybrid Access. The article is in a normally closed-access journal, but the author pays a fee to allow open access for all readers. Journal of Systematic Palaeontology allows this option.
  
• Author's Choice Access. The author pays a fee to a closed-access journal for the privilege of posting a PDF of the said article on a personal website. Journal of Vertebrate Paleontology is a well-known example of this mode.
  
• Author's Email Access. The author pays to get a PDF file that they can then distribute (legally) via email only. JVP also allows this mode.

Benefits of Open Access
The most striking benefit of open access is availability--the article is free to download for anyone who has an internet connection. The paper is picked up by Google and other search engines pretty much automatically, and people who are looking for that sort of research will usually find it.

From the author's standpoint, open access publishing is also usually faster than the standard model. Everything is done electronically, including the final publication. There is no lag time to mail the journals out, and some open access journals have a "rolling" publication schedule (meaning that once your article is approved, it's out there). Because many of the journals aren't bound by page constraints, they can place as many articles in a single issue as are available. There's no waiting 14 months for space to be available in the journal (a frighteningly common problem in many journals - if you've published papers, you've probably experienced this at least once).

Finally, the electronic-only mode of many open access journals allows some creativity in presentation. Need to have a movie as Figure 1 in your paper (rather than just a supplement)? Go right ahead (in some cases)!

The Costs of Open Access
Like many "regular" publications, some (but not all) open access journals have page charges. Depending on the journal, these can run up to $3,000 for a single article. A partial list of typical fee schedules is available here (thanks to Dr. Randy Irmis for passing along this link).

What is a poor paleontologist to do? In some cases, universities (that is, if you're based at a university) will partially subsidize the cost. In other cases, the journals (such as PLoS One) may partially or completely waive the open access fee for those with financial need. Finally, you can always find an open access journal with no fees (and they are numerous!). The most ethical of open access journals will not consider ability to pay in making decisions on publication.

A more critical concern, from the standpoint of relatively unestablished authors, is that some in the scientific community don't consider open access journals "real" or as good as their closed access counterparts. Yes, there are some open access journals out there with questionable editorial practices (they are in the minority, fortunately) --but there are also printed journals with loose standards (and these are also in the minority). And, there are many quite excellent open access journals, which are widely cited and recognized as such! So, the "quality" argument doesn't hold a lot of water in my view. Unfortunately, this reality doesn't necessarily hold up to the perception of the search, award, or tenure committee (rightly or wrongly).

Hope for the Future
How does a researcher support open access and circumvent this last concern? As a compromise, I might recommend using open access journals as one part of a publishing portfolio. After all, there are some really good closed-access publications out there (e.g., Journal of Vertebrate Paleontology, etc.) that do well at getting research into the hands (and minds) of the right audience. Some open access journals (Acta Palaeontologica Polonica, PLoS One, etc.) also do a good job at this. Choose the right journal for your paper--and an open access journal if that will get the research to the right people. Out of all the papers I have published, the one that gets cited the most was in Palaeontologia Electronica. I submitted it there on a whim, and have been pleasantly surprised by just how widely read it has been. Finally, just write good papers! A good paper is recognized as one no matter what, regardless of the journal.

Time will be the most important factor in changing attitudes. As open access publishing becomes more common, it will be seen as less freaky by the powers-that-be. And, this is a very, very good thing.

It's Coming. . .

Look for a major research announcement in one week. . .

Welcome, Longhorns!

I hear from a reliable source that your Digital Methods in Paleontology course has this blog listed as a recommended website for some supplemental readings. So, to all of you UT Austin students, welcome! I hope that the content here is at least somewhat useful. . .don't hesitate to post if you have any questions or comments. I (and my readers) are particularly eager to hear if you run across any other good software tools that aren't listed here, or if you have your own feedback on some of the software I've reviewed previously.

Your first reading assignment (if I'm reading the syllabus correctly) is found here. . .it gives some good background info on the blog. If you're completely bored, I would strongly recommend this post as a logical follow-up. Despite the name of this blog, I am not an open source zealot, and the referenced post gives some of the pros and cons of using open source software. Don't know what open source software is, exactly? This page is as good as any for a succinct introduction to the concept.

Good luck in the coming semester, and enjoy the class!

Workshop for the Digital Paleontologist

If you're a grad student interested in using mathematical techniques in your paleontological research, this workshop is for you! John Alroy and colleagues are presenting the fifth annual Paleobiology Database Summer Course in Analytical Paleobiology, hosted at the campus for the University of California's National Center for Ecological Analysis and Synthesis in Santa Barbara.

The rest of this post is taken directly from the announcement to the VRTPALEO list by John Alroy. I never had the chance to participate in this workshop (field season and all, and then I was too old of a grad student), but wish I had!

About the course
Since 2005 the Paleobiology Database has conducted a five-week intensive course in analytical paleobiology at the University of California's National Center for Ecological Analysis and Synthesis in Santa Barbara. In 2009 the course is scheduled to run from 30 June to 4 August, following NAPC. It will be supported primarily by the Paleontological Society with additional contributions from NESCent, the Palaeontological Association, and the Society of Vertebrate Paleontology.

Topics will include community paleoecology, quantitative biochronology, diversity curves, speciation and extinction, phylogenetics, phenotypic evolution, and morphometrics. Both simulation modelling and data analysis methods will be employed. The course will combine lectures and labs. Students will be given hands-on instruction in programming using R and trained in other analytical software. In addition to the course coordinator, each week a new instructor will be present. The instructors are expected to be John Alroy, Gene Hunt, Tom Olszewski, Pete Wagner, and Mark Webster.

There is no fee for registration, and students will be housed for free in apartments on the UCSB campus. Students are urged to apply for travel funds from their home institutions. If such funds are not available, travel expenses may be reimbursed for up to $400 if coming from the United States, $600 if coming from Western Europe, or $800 if coming from other countries. Students are responsible for meal expenses. There are no other charges of any kind, and no other major expenses are likely.

How to apply
Participating students should be in the early stages of their own research in any area related to paleontology. They should have a background in basic statistics, and preferably also programming. The ability to understand rapidly spoken English is essential. The course is open to undergraduates and advanced graduate students, but first or second year graduate students are particularly encouraged to apply. We also strongly encourage applications from women, minorities, and international students. Applications from professionals who have completed their studies will be considered, but strong preference will be given to students.

Applications should be submitted in PDF format to John Alroy (alroy@nceas.ucsb.edu). The review process will begin on 15 February 2009, and applications received by midnight Pacific time on that day will receive priority. Applications should consist of a one page statement. Do not include separate documents such as a curriculum vitae. No form needs to be filled out.

The statement should include a brief description of current research plans, a list of degrees earned stating the year of graduation in each case, a brief list of relevant classes taken, and an account of the student's previous use of statistics and programming. Students who do not employ English as a primary language should describe their experiences learning and speaking it. Applicants are encouraged to explain why the topics addressed by the course are of special interest to them, and which of these subjects are taught at their home institutions.

Applications must be accompanied by a recommendation letter, also in PDF format, written by the student's academic advisor and e-mailed separately. Obtaining a recommendation from anyone who is not an advisor must be explained. It is important that the recommendation give details about the applicant's personal character and abilities, not just credentials and descriptions of research projects. Recommendation letters also must be received by the end of the due date.

The Death of the Kinetic Dinosaur Skull?

Cranial kinesis, in which moveable joints within the skull allow flexion and expansion during feeding, is well-documented in birds, snakes, many lizards, bony fish, and sharks. And of course, many readers of this blog know that lots of dinosaurs had cranial kinesis too. It allowed Tyrannosaurus to munch on big prey items and Edmontosaurus to chew its way through the Cretaceous landscape (see here for a nifty animation of how this should occur). Right?

Maybe not, after all. Casey Holliday and Larry Witmer just published their paper critically evaluating the evidence, "Cranial kinesis in dinosaurs: intracranial joints, protractor muscles, and their significance for cranial evolution in diapsids," in Journal of Vertebrate Paleontology. Irrefutable demonstration of cranial kinesis requires observation of living animals--and we just can't do that in dinosaurs. So, paleontologists look at the bony evidence in order to document skull function in non-avian dinosaurs (from here on out I'll just call them "dinosaurs"--yes, yes, I know that birds are dinosaurs too, but I don't want to weigh this post down too much).

Humans and other mammals fuse up their skulls pretty tightly--any open sutures between bones are so tightly interlocked that movement is effectively nil. Many other animals leave open sutures (often in the form of ball-and-socket joints)--and this is where kinesis takes place. Paleontologists have documented these open joints in dinosaur skulls, and used this as evidence of kinesis during feeding.

But, the story isn't quite that simple. Open joints are necessary for kinesis--but they aren't sufficient. And this is the core of Holliday and Witmer's argument. They lay out four criteria, present in modern tetrapods with cranial kinesis:

1. A synovial basal joint. A synovial joint is basically a joint between bones with a fluid-filled cavity between them - a good example might be your jaw joint. The basal joint is between the pterygoid (a bone of the palate) and the basipterygoid process of the braincase. Pretty much all dinosaurs have this--and so do many modern reptiles and birds with both kinetic and akinetic skulls.
   
2. A synovial otic joint. The otic joint is between the squamosal (a bone of the skull roof) and the quadrate (a bone of the jaw joint). Again, pretty much all dinosaurs, and many kinetic and akinetic modern animals, have a potentially mobile otic joint.
3. Protractor musculature. These muscles attach to the bones of the basal and otic joints (and you need to move those bones for kinesis), but the muscles are present even in modern taxa with akinetic skulls (e.g., the tuatara). These protractors apparently varied in size across dinosaurs.
4. Kinetically permissive linkages. This is a fancy way of saying that the skull is set up to allow movement (aside from the otic or basal joints). In modern animals, this takes the form of thin and flexible bones (as in the snout of some birds), missing bones (as in the loss of stabilizing cheek bones in lizards), and the addition of extra synovial joints, among other things. All modern animals with kinetic skulls have these--and dinosaurs lack them, in Holliday and Witmer's view.
   

All modern animals with kinetic skulls do fulfill all four criteria. Many dinosaurs possess two or three of these criteria, but none possess the whole shebang. Even the dinosaurs with the most supposed kinesis--such as T. rex--only fill criteria 1-3. Many of the supposed "extra" open joints in the skulls of animals such as Tyrannosaurus are of the sorts seen in modern animals with akinetic skulls. No major amounts of movement probably occurred here in T. rex, then. So, the conclusion is that dinosaurs as a whole just weren't capable of cranial kinesis.

At this point, I also want to mention the fact that a few other folks have started to question the kinetic skull idea, particularly for hadrosaurs. Robin Cuthbertson, Natalia Rybczynski, and others have all recently discussed this at SVP and in other venues. For a recent publication by these folks (including Holliday as a co-author), see their paper at Palaeontologia Electronica.

So why leave open sutures? Allowance of cranial growth probably played an important role. Maybe open sutures were helpful for absorbing shocks to the skull during feeding. This paper opens up a lot of interesting questions--and many of the answers will be found only with further study of modern animals.

Casey M. Holliday, Lawrence M. Witmer (2008). Cranial Kinesis in Dinosaurs: Intracranial Joints, Protractor Muscles, and Their Significance for Cranial Evolution and Function in Diapsids Journal of Vertebrate Paleontology, 28 (4), 1073-1088 DOI: 10.1671/0272-4634-28.4.1073

Casey has made the paper available as a PDF on his web page, along with high resolution versions of some of the figures.

R in the NY Times

I've detailed, R, that wonderful piece of statistical software in a previous post, but an article in today's NY Times gives some nice additional background to the whole project. Check it out if you want to know "the rest of the story." There's also a delightfully snarky quote from a spokesperson for SAS, the chief commercial rival to R.

“I think it addresses a niche market for high-end data analysts that want free, readily available code," said Anne H. Milley, director of technology product marketing at SAS. She adds, “We have customers who build engines for aircraft. I am happy they are not using freeware when I get on a jet.”

Because everyone knows that commercial software is always reliable. Personally, I don't care what software an engineer uses to design a jet. Just as long as the software and the engineer both know what they're doing. The same goes for the software (a mix of commercial, open source, and free closed-source programs) I use in my own research--I'm not a complete open source zealot (all my FEA analyses are on commercial software, because I still haven't found an open source alternative that doesn't require a computer science degree), but if I can get the job done for free, the price is right!

Thanks to Denim and Tweed for pointing me towards this link.