Sunday, June 21, 2009

My Dissertation - Now Open Access

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

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

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

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

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

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

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

The appropriate citation for the dissertation is:

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

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

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

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

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

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

Tuesday, June 16, 2009

The End of the Internet Mailing List? Part II

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

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

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

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

Thoughts? Alternative Perspectives?

Coming up. . .Blogging and the Paleontological Community

Sunday, June 14, 2009

The End of the Internet Mailing List?

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

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

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

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

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

Coming Up. . .Shifting Sands of Communication

Monday, June 8, 2009

What Place Do Blogs Have in Science?

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

Friday, June 5, 2009

Good News for Zotero

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

Thursday, June 4, 2009

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

ResearchBlogging.orgAfter 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

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:
The PalArch Foundation is happy to announce that our website ( 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:

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.