How do you read the literature? Thoughts on academic maturation

How much should you trust the scientific literature? Reflecting on my own academic maturation, as well as observing on-line discussions of dinosaur paleontology for over 15 years (yikes, I'm getting old!), I have concluded that most of us pass through three stages: 1) Credulity; 2) Cynicism; and 3) Maturity.

Credulity
This is inevitably one's first stop on the journey through the scientific literature: accepting everything that's published at face value. Credulity is also paired with the assumption that the most recent publication must be the most conclusive. For instance, let's say Dr. X described a new species in 2001. Dr. Y published a new paper in 2010, saying that the new species is invalid. Dr. Y must be correct, because she had the last word, right?

Another symptom of this stage is fanboy(girl)-ism. Anything published by Dr. Glamour is the bee's knees (it's widely featured in the news media, so it must be true)! Wow, Dr. Glamour published a new theory on the dinosaur extinction - it will revolutionize the science! Any nay-sayers are just jealous, or afraid of change.

I hit this stage during high school and college.

Cynicism
Suddenly, everything comes crashing down. You talk to another paleontologist, who tells you that Dr. Glamour's work isn't actually that highly regarded. Maybe he has a reputation for massaging his data just a little too much, or conveniently omits contradictory evidence in his papers. Then you find out that Dr. Z has just published a paper saying that Dr. X was actually correct in the first place, and Dr. Y's synonymization was a little too hasty. Your obvious conclusion: the scientific literature is untrustworthy. Everything ever written is a steaming pile of unreliable ramblings.

Most people don't go through a full-blown case of cynicism, of course. Usually we just get an incomplete case. Everything written by Dr. Glamour (but only some of the stuff by Dr. Y) is untrustworthy, etc. A related syndrome focuses on the methodology; a paper is considered horrible because it used or didn't use a particular technique.

I hit this stage between the end of my undergrad and the early to middle parts of my graduate career.

Maturity
Most of us reach this stage only after a lengthy amount of time in the field (or the end of our graduate student career). Our BS detectors are honed to an appropriate level, and we accept that many of the papers out there aren't half-bad, and a minor mistake or two isn't enough to relegate research to the dustbin.

For my part, I still occasionally waver between cynicism and maturity; I might cast an exceptionally suspicious eye on research coming from certain researchers or using certain techniques (even if it's not necessarily warranted). Maybe I even have a little credulity at first, if it's a technique or area of science I'm not yet completely familiar with. At the same time, having been around the block a few times as a scientist, I am a little more understanding when it comes to the perceived shortcomings of a paper. As long as the basic science is still good, live and let live. A paper can have a fantastic morphological description, but a pretty weak discussion. With a little practice reading the literature, it's becoming easier and easier to pick up on the high and low points of a publication.

Summing it up
We all relate to the academic literature in different ways, depending on our life experience, scientific goals, and "academic maturity." It's up to us - with the help of trusted friends and colleagues - to continually work to improve our own approaches.

Welcome, Seitaad!

I am pleased to announce the publication in PLoS ONE of Seitaad ruessi, a new sauropodomorph dinosaur from the Lower Jurassic Navajo Sandstone of southern Utah. Sauropodomorphs are (mostly) herbivorous dinosaurs that lived from the Triassic all the way until the end of the Cretaceous. Although most people know the giant quadrupedal sauropodomorphs like Brachiosaurus and Apatosaurus ("Brontosaurus"), many of the early sauropodomorphs were bipeds smaller than humans. Seitaad fits in the latter category. For reasons explained below, this is a really cool little animal and a truly rare find.

I have a personal connection to this fossil on two levels. First, the authors of the article, Joe Sertich (at left, pictured with the specimen) and Mark Loewen, are good friends and colleagues of mine. So, I was really excited when they told me that they wanted to submit their manuscript to PLoS ONE (full disclosure: I am an editor there; for obvious reasons, someone else handled their submission). I'll confess that I did little to discourage them. Congratulations, Joe and Mark, on a great paper!

Second, I was one of the lucky people who got to carry the block containing Seitaad from its original resting place, way back in 2005. This thing was heavy! It took a crew of 12 people (8 carrying at a time, and 4 resting for rotation back in) to haul it out. After several years of preparation and study, the new animal is finally named!

I queried one of Seitaad's authors, Mark Loewen, for his thoughts on the find (Joe Sertich is out of the country, so wasn't able to contribute). Here's what Mark had to say.

Briefly, what is the most significant aspect of the new find reported in PLoS ONE?
Seitaad is the first dinosaur discovered from the Navajo Sandstone of Utah and one of the oldest known dinosaurs from Utah. The Navajo Sandstone is a dominant rock unit exposed all over the west. . .and is hiked by thousands of people every year. Fossils in this formation are extremely rare. Prior to its discovery our entire view of the fauna of the Navajo consisted of a partial tritylodont, three chunks of crocodylomorphs, parts of a small theropod, [and] two fragmentary sauropodomorphs. Seitaad is the most complete fossil from the Navajo and through comparisons with taxa across the world gives a much better picture of the largest herbivore in the sand seas of western North America at the same time that large true sauropods had evolved in other parts of the world.

How did you choose the name that you did?
Seitaad was found by Joe Pachak [pictured at left, with the specimen], a local archaeologist and artist from Bluff, Utah while hiking Comb Ridge to document petroglyphs and pictographs. He reported the specimen to the BLM, who alerted us at the Utah Museum of Natural History. We went down to check it out, and immediately started to excavate the specimen. With a crew of 12, including Andy Farke, we hauled out the jackets and began preparing them at the UMNH.

The area around Comb Ridge is covered with numerous archaeological sites and cliff dwellings from the ancestral Puebloan (Anasazi) culture. In fact, Seitaad was located directly below a dwelling called the Eagles Nest. The people who lived in the area at the time would have recognized the white bones of Seitaad eroding out of the cliff if they had seen them. A nearby cliff dwelling has a slab with a dinosaur track incorporated into the window sill. I’m confident that the person who [put] this stone into the window had awareness and appreciation for the fossils preserved in the Four Corners region.

"Seitaad" is derived from Seit’aad, a sand-desert monster from the Navajo (Diné) creation legend that swallowed its victims in sand dunes. The skeleton of Seitaad had been "swallowed" by a fossilized sand dune. The [species name] "ruessi" is derived from Everett Ruess, the famous young artist, poet, historian, and explorer who disappeared in southern Utah in 1934. Ruess is celebrated for his love of the region, its people, and for his free-spirited and adventurous lifestyle. Everett Ruess loved the red rock country of Utah and spent a lot of time exploring the Navajo Formation, so we thought it was fitting to honor him in the taxonomic name.

Why did you choose PLoS ONE as a venue for your research?
We chose to submit to PLoS ONE for several reasons. The open-access format of PLoS ONE and rapid turn-around were major factors. Another factor was the opportunity to reach a broader audience and the rising impact and recognition of PLoS ONE within the paleontology academic community. Another consideration was the lack of limits to figures and unrestricted use of color. The unlimited use of color became a concern during the preparation of our manuscript, when it became clear that black and white photos were not revealing proper contrast between white bones of Seitaad and the pink sandstone of the Navajo Formation.

Is there anything about this find that didn't make it into the scientific paper?
When we first saw photos of the skeleton in the cliff wall we thought it was a pterosaur. The v-shaped ischia looked like dentaries. It wasn’t until UMNH preparators got into the block that we changed our identification to theropod. Then when we got to the hand, we know from the thumb claw that it was a sauropodomorph.

Mark Loewen with the skeleton of Seitaad ruessi

***************

Check out the original article for free at the PLoS ONE website. As always, you can leave comments or rate the article there.

Citation
Sertich, J.J.W., & Loewen, M. (2010). A New Basal Sauropodomorph Dinosaur from the Lower Jurassic Navajo Sandstone of Southern Utah PLoS ONE, 5 (3) DOI: 10.1371/journal.pone.0009789

Other Readings
The paper is all over the news and blogosphere; check out Dave Hone and ReBecca Hunt's blogs for more.

Image Credits: Mark Loewen and Utah Museum of Natural History

DeepDyve Reviewed

Many of the recent posts on this blog have dealt with issues of access to the scholarly literature for those outside the library systems of large research institutions. A digital divide is developing in academia, largely due to the expensive costs of institutional subscriptions and pay-per-download distribution schemes of commercial and non-profit publishers alike.

Thus, I was very excited to hear about the launch of DeepDyve. This website essentially offers a rental service for scholarly publications. Search a database, find an article, and view it on the website's Flash viewer. The prices are quite reasonable - 99 cents per article for the Basic Plan, $9.99/month to get 20 rentals a month on the Silver Plan, and $19.99/month to get unlimited rentals on the Gold Plan. I decided to test out a free trial of the Gold Plan and see if DeepDyve was right for me.

Promotional literature promised "30 million articles from thousands of authoritative journals," so I was expecting good things. Landing on DeepDyve's simple, attractive home page, I sat down to run my first queries.

Unfortunately, the hype hasn't yet caught up with the reality of scholarly publishing. A search for "Triceratops" launched from the web site's home page generated over 84,000 hits. . .most of which were completely irrelevant medical literature ("Median and Radial Nerve Compression About the Elbow" popped up on the first page, for instance). Using the site's advanced search filters, I was able to trim the results down to 71 articles. Of these articles, 8 were listed as "free" (they were already available through open access journals) and 61 only offered a preview of the abstract. A scant 2 articles were available for rental (from the journals Annual Review of Earth and Planetary Sciences and Annual Review of Ecology and Systematics).

Why such a poor showing? It comes down to the fact that many of the societies and publishers that own or license our publications haven't yet reached an agreement with DeepDyve to allow rental of relevant articles. Thus, papers from heavy hitters like Journal of Vertebrate Paleontology and Paleobiology simply aren't available.

The rental plan also may turn some people off (although I don't think it is a complete deal breaker). In short, you can't download a PDF - all you can do is look at the file within the provided viewer. This is useful for those times when the article turns out to be irrelevant. But, it may ultimately prove unsatisfactory for those inevitable moments when you want to be able to access literature away from an internet connection (and we all have those times!). And, it seems somewhat unsettling to pay for content that you don't actually get to keep (unlike services such as iTunes).

I want to like DeepDyve. . .I really do! It promises to open up swaths of the scholarly literature that were previously unavailable. But, right now DeepDyve is shackled by the limited availability of publications (at least for us paleontologists). There is very little value-added over a standard Google search. Perhaps the future has big things in store. . .I'll be keeping an eye on the situation!

For additional commentary on DeepDyve, and some responses from the company, check out this post at the Scholarly Kitchen.

Dinosaur Running and Endothermy in PLoS ONE

On a personal note, I have recently stepped up as "Section Editor" for paleontology at PLoS ONE. This means that I'll be coordinating the editorial flow for most paleo-themed papers that come the journal's way.

One of the real joys of editing for a major journal like PLoS ONE is getting a "sneak peak" at some pretty nifty research. Today, Herman Pontzer, Vivian Allen, and John Hutchinson have a new paper that should be of interest to this blog's general audience [full disclosure: I was the academic editor for this contribution]. As always, papers at PLoS ONE are free to download, comment upon, and rate.

The abstract and citation are copied below; for more info, check out the press release or Ed Yong's excellent blog post on the topic.

The bipedal and presumably endothermic Velociraptor. From the original by Matt Martyniuk, licensed under a Creative Commons Attribution ShareAlike 3.0 license.

Citation: Pontzer H, Allen V, Hutchinson JR (2009) Biomechanics of running indicates endothermy in bipedal dinosaurs. PLoS ONE 4(11): e7783. doi:10.1371/journal.pone.0007783

Abstract
Background
One of the great unresolved controversies in paleobiology is whether extinct dinosaurs were endothermic, ectothermic, or some combination thereof, and when endothermy first evolved in the lineage leading to birds. Although it is well established that high, sustained growth rates and, presumably, high activity levels are ancestral for dinosaurs and pterosaurs (clade Ornithodira), other independent lines of evidence for high metabolic rates, locomotor costs, or endothermy are needed. For example, some studies have suggested that, because large dinosaurs may have been homeothermic due to their size alone and could have had heat loss problems, ectothermy would be a more plausible metabolic strategy for such animals.

Methodology/Principal Findings
Here we describe two new biomechanical approaches for reconstructing the metabolic rate of 14 extinct bipedal dinosauriforms during walking and running. These methods, well validated for extant animals, indicate that during walking and slow running the metabolic rate of at least the larger extinct dinosaurs exceeded the maximum aerobic capabilities of modern ectotherms, falling instead within the range of modern birds and mammals. Estimated metabolic rates for smaller dinosaurs are more ambiguous, but generally approach or exceed the ectotherm boundary.

Conclusions/Significance
Our results support the hypothesis that endothermy was widespread in at least larger non-avian dinosaurs. It was plausibly ancestral for all dinosauriforms (perhaps Ornithodira), but this is perhaps more strongly indicated by high growth rates than by locomotor costs. The polarity of the evolution of endothermy indicates that rapid growth, insulation, erect postures, and perhaps aerobic power predated advanced “avian” lung structure and high locomotor costs.

Buying PDFs: Truth and Consequences

On-line journals are great. You get immediate access to the latest research and can download a fully searchable PDF for later use. Journal digitization has revolutionized the pace of science communication and increased the reach of formerly obscure journals. Through the wonders of the Internet, anyone can get access! Right?

Not so fast. On-line journals offer full benefits only to those whose institution has a subscription. If you don't have a subscription, you're out of luck. . .mostly. Thankfully, it is possible to buy PDFs of individual articles. Right?

Not so fast. It is indeed possible to buy PDFs of articles from most journals. . .if you can cough up the money to do so. Let's face it. PDFs are expensive. Ridiculously so. A three page note from Journal of Vertebrate Paleontology might cost nearly $30! A six page paper from Geology runs $25. [end of this post] Is it really worth it?

Big Problems
I won't pretend that journal sales don't support professional societies I care about. I won't pretend that publishers shouldn't get compensated for their services. I won't pretend that everything is going to turn open access tomorrow.

But, I'm not shy about saying that the current system stinks. No matter how you slice it, $30 for a PDF article is unaffordable for a typical consumer of paleontological publications. The new membership rates for the Society of Vertebrate Paleontology, which include electronic access to Journal of Vertebrate Paleontology, cost $115 for e-journal only. Assuming around 120 articles per year (a rough count for JVP in 2008), this works out to a little less than $1 per article (and remember that this assumes that 100 percent of membership dues go to the journal subscription - certainly not the case). Why is there a 3,000 percent markup for non-members? Wouldn't journals be able to get by with, perhaps, a 500 percent markup over the member rate? [IMPORTANT NOTE: I am not intending to single out JVP and SVP exclusively; nearly all journal publishers are guilty of this problem. . .it just so happens that JVP is the example most relevant to most readers here]

Let's put it another way. At the current costs of PDF articles, buying every single article in the journal would cost an individual around $3,600 per year.

And let's look at it from yet another angle. Institutional paper subscriptions to JVP are $270/year for US institutions (pre-Taylor & Francis switch; we don't yet know what the cost will be post-switch). This works out to an average of$2.25/article. . .for a format that is much more expensive to deliver than an electronic document!

And one last angle. . .the Mesozoic Birds: Above the Heads of Dinosaurs edited volume, which is a beautifully produced and scientifically important work, includes 20 articles, ships in hard cover and retails for $100 new. This works out to $5/article within the book. Contrast this with $30 or more for a single digital file.

Commenting in a recent thread here at the OSP, a librarian noted that libraries are paying between $2-$4 per PDF article when bought in bundles from for-profit publishers like Elsevier (which, incidentally, continues to post profits in the midst of the recession). Although it is certainly fair to have volume discounts (although the pricing schemes and the bundled journals are often rather dubious in practice), it is of dubious benefit to science to charge such a disproportionate rate to private individuals who are just trying to do some science.

Do these pricing schemes serve science? Do these pricing schemes serve the interests of the authors, who just want their work to be read?

Commonly Suggested "Solutions"
When the issue of paying for individual PDFs is brought up, there are often a number of "solutions" proposed. I put the word in quotes because, as explained below, none of these is fool-proof.

Why not write the author for a PDF?
In some cases, this is a good workaround. But it's never a perfect workaround. Sometimes authors are unresponsive, have changed email addresses, retired, or passed into the fossil record. In this case, the researcher in need of the paper is out of luck.

Why not post a PDF request to VRTPALEO or the DML?
In some cases, this is a workaround. . .one need only look at mailing list archives to see that this is a common strategy. But, PDF requests unfortunately carry a small annoyance factor for many list subscribers. Sometimes no one responds. Finally, PDF sharing by anyone other than the author is generally illegal in the eyes of the publishers and societies (but let's not pretend it doesn't happen).

Why not join the society, and then you get all of the articles as part of your membership?
Again, this is a solution in some cases. If you are a paleontological enthusiast or professional who loves (or needs) to follow every bit of the literature, you should probably join the Society of Vertebrate Paleontology and/or the Palaeontological Association and/or the Paleontological Society.

But, let's be realistic. Nobody can afford to join every society to get access to all society publications. In some cases, it's just not necessary. Consider this hypothetical situation. You're a population biologist working for a small nature preserve who wants a little background on the evolutionary history of the coyote. You do a search on Google, and find a citation to Journal of American Paleontology with an abstract that details ecological shifts by coyotes during the Ice Age using isotopic analysis. You click on the link, and. . .paywall! The Society of American Paleontology wants $30 for a five page article. Is it really worth your time and money (as a population biologist) to join a society of paleontology, when you are already stretching your budget to cover dues for two more relevant societies? If the charter for the American Paleontological Society says that they are to promote and advance the science of paleontology, is the society really living up to this mandate? If the society wants to foster cross-discipline appreciation for the relevance of the field, is this happening if the research is not easily accessible? Are the authors who contribute to the journal being well-served by having their research so restricted?

Finally, some journals just aren't sponsored by societies. There is no solution in this case, other than to pay a few hundred dollars per year.

Most of the other journals charge $30 for a PDF!
This is not a solution (or even a "solution"), but an excuse. During the business meeting for a scholarly society to which I belong, I raised a concern about the prices that the society's journal was charging for individual PDFs. Can you guess the answer that I received? I remember something my mother often said to me. . ."If everyone else jumped off a cliff, would you too?" Exorbitant PDF costs may be the norm, but that doesn't mean it's the ethical thing to do (especially for a non-profit society whose stated mission includes phrases like "advance the science" and "serve the common interests").

What Needs to Change?
Science (yes, that's the reason why most research is published) is not being served by the current pricing schemes. Alleged solutions for those beyond the boundaries of the pay-wall are not comprehensive, and again do not serve the interests of science.

PDFs of individual articles need to cost less. There is no way to legitimize charging $25, $30, or more for something that costs less to produce than a printed journal, particularly when it prices out to up to a 3,000 percent markup. The current pricing scheme restricts the readership of articles and creates a hierarchy of have- and have-not researchers, in a time when the Internet is supposed to fix these problems for academia. Also, let's not forget that the research behind these articles is often heavily subsidized by public tax dollars. . .

I would suggest that $5, or maybe $10 in exceptional circumstances (e.g., a 50 page monograph) is a cost that I would be willing to pay for a PDF. I would also submit that many journals would see increased PDF sales (particularly for popular topics, such as dinosaurs) if the price was set at something mere mortals could afford to pay.

Is There a Solution?
Right now, it sounds like I'm doing a lot of complaining and not a lot of problem solving. Well. . .yes. This post is partly a rant. Unless people are aware of the problem, nothing will ever happen.

So what can we do? Here are a few suggestions:

• Ask journals and professional societies to consider the implications of pricing schemes for PDFs. Speak out to the people who matter. Let them know how you feel, and how it affects you.
  
• Don't pay the ridiculous charges. Find low-cost, legal alternatives (e.g., writing to the author or interlibrary loans) whenever possible.
• Submit your work only to journals with researcher-friendly publishing policies.
• If you are an author, do everything you (legally) can to get your work out there for free. If the journal allows you to post a PDF, do so. Respond promptly to PDF requests from other individuals.
  

What are your thoughts?

Addendum 1: As if by magic, this post at The Scholarly Kitchen appeared at nearly the same instant as I hit the "publish" button on this post. I haven't followed up on the service (which essentially offers cheap rental access to articles from various scientific publishers), but will certainly be looking into it.

Addendum 2: Matt over at Protichnoctem has a nice post with more on the issue of buying PDFs. Go check it out!

The Journal List
The Anatomical Record (Wiley): $29.95
Bulletin of the Geological Society of America (GSA): $25 (GSA website)
Bulletin of the Geological Society of America (GSA): $32 (Geoscience World website)
Cretaceous Research (Elsevier): $31.50
Geology (GSA): $25 (GSA website)
Geology (GSA): $32 (Geoscience World website)
Ichnos (Taylor & Francis): $37
Journal of Experimental Biology (The Company of Biologists): $10
Journal of Morphology (Wiley): $29.95
Journal of Paleontology (Paleontological Society): $12 (BioOne website)
Journal of Paleontology (Paleontological Society): $15 (Geoscience World website)
Journal of Vertebrate Paleontology (SVP): $30 (BioOne website)
Nature (Nature Publishing Group): $32
Palaeogeography, Palaeoclimatology, Palaeoecology (Elsevier): $31.50
Paleobiology (Paleontological Society): $12 (BioOne website)
Paleobiology (Paleontological Society): $15 (Geoscience World website)
Palaeontology (Wiley): $29.95
Proceedings of the National Academy of Sciences (NASUSA): $10 ($25/full journal access for seven days)
Science (AAAS): $15

Albatross vs. Pterosaur

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

Keeping On Top of the Literature

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!

Finding that PDF

Unfortunately, not everyone has access to a massive research library (or in some cases, any research library at all). Yet, the literature is an essential part of any paleontologist's repertoire. In this post, I'll briefly review some options out there for locating free or low-cost scientific publications on the web.

• Google Search: Sometimes, all it takes is a quick Google search to find a paper. For instance, say I'm looking for Marsh's old paper on characters of Odontornithes. I type "Characters of the Odontornithes, with notice of a new allied genus" into the old Google search box, and what do you know? It gives me a link to Matt Wedel's archive of O.C. Marsh papers! Sometimes, of course, you might have to try a few variants on a search before you hit on the right PDF. Often, when I'm doing initial research on a topic, I'll type in "[taxon or topic name here] pdf". You never know what you might find! For instance, typing "Triceratops PDF" gave me a link to several very relevant papers. Google Scholar also works pretty well in this regard (and will often filter out most of the non-scholarly stuff).
• Google Books: I have had some real success, particularly with older works, on this search engine. I strongly recommend setting the search settings to only find books with "full view," if you're not interested in just snippets of text. Once the recent settlement with publishers gets worked out, I think we can expect some really good things in terms of low-cost access to out-of-print but in-copyright publications.
  
• Scribd: This website offers browsable documents for a surprising number of paleontological papers, although you must be a registered user (free) to download PDFs.
• Journal Archives: Many museum publications, such as Fieldiana and all of the AMNH publications, are available online. It's always worth checking out museum web pages to see if their old publications are out there. A number of journals also have freely available archives. 'Nuff said.
  
• Author's Web Page: More and more scientists have PDFs of their papers on their web page - so, it's always worth a quick search to see what's available.
  
• Writing the Author: If you can't find the PDF for a recently published article through other means, send an email to the author. As I mentioned in a previous post, it's a great ego boost for those of us who write scientific papers!

Of course, these suggestions probably aren't news to some of the more experienced paleontologists out there - but I do hope this is useful for those just beginning in the field. What other sites do you find particularly useful for this sort of background research?

Disclaimer: It is entirely up to the user to be aware of any copyright restrictions that may apply to the download or use of any of the resources addressed here.

Update: Dave Hone has posted a really nice continuation of this theme over at his blog.

Crouching Theropod, Hidden Dragon

Fossil footprints (falling in the general category of "ichnofossils") reveal a wealth of information about dinosaur biology, such as speed, posture, and behavior. These traces are particularly useful when offering information independent from, but consistent with, hypotheses derived from purely anatomical studies.

Today, a new paper in the open access journal PLoS ONE presents an unusual set of theropod (meat-eating dinosaur) ichnofossils from the Early Jurassic-aged Moenave Formation of southwestern Utah. The tracks are preserved within the St. George Dinosaur Discovery Site at Johnson Farm, a massive facility housing thousands of footprints (for additional scientific publications and background on the site, refer to this page). But, if there are thousands of footprints known at the site (in addition to the thousands known from other sites throughout the world), what makes the fossils featured in the paper so special?

Theropods were bipedal animals, and known ichnofossils typically only preserve evidence of the hindlimb. But, one specimen in particular at the St. George locality preserves impressions of the hind feet, forefeet, and the rear end of a lazy carnivore. A resting trace!

Artist's conception of the St. George trackmaker at rest. Note in particular the resting posture and the orientation of the hands. From Milner et al. 2009; painting by Heather Kyoht Luterman.

Yet, even resting traces aren't completely unheard of for theropod dinosaurs. The really interesting thing here is that the specimen preserves relatively unambiguous impressions of the hand posture. The animal was resting with its hands turned inward, and the outer surfaces of the fingers and wrist (rather than the palms) touching the substrate.

Why does this matter? Well, it all has to do with reconstructions of forelimb mobility and posture. Old reconstructions of theropod dinosaurs showed them walking around with palms down (think of an alligator dragged upright); later work has strongly suggested that the palms faced inward, more like birds.

Traditional restoration of two theropods, by Charles R. Knight. Note the palm-down, rather than palm-in, posture of the hands.

So, the new St. George tracks are the first good ichno-evidence of forelimb posture in theropod dinosaurs. Furthermore, and perhaps most importantly, it suggests that this posture evolved pretty early on, in some of the first theropod dinosaurs.

As the authors note, anatomical reconstructions of forearm movement have primarily focused on more "derived" theropods (animals from the Late Jurassic and beyond). It would be really, really nice to get additional studies on the anatomical structures of the forelimb in animals like Dilophosaurus and Coelophysis (Ken Carpenter did get a good start on this a few years back; see his 2002 paper, "Forelimb biomechanics of nonavian theropod dinosaurs in predation." Senckenbergiana Lethaea 82: 59-76). Also, paleontologists will want to be on the lookout for similar traces. Is the specimen described here typical, or an individual anomaly? The authors reviewed other alleged resting traces from theropods, but considered that most of them were either misidentified or too poorly preserved to offer usable information. Finally, does resting posture of the forelimbs necessarily reflect what the animals were doing the other 99 percent of the time?

Congratulations to the authors on a stimulating paper. If you have an opinion on this research, don't just post it in the blog's comment section (although please do that, too). Head over the the PLoS ONE website, and register your own comments, notes, and ratings on the article!

The Reference
Andrew R. C. Milner, Jerald D. Harris, Martin G. Lockley, James I. Kirkland, Neffra A. Matthews (2009). Bird-Like Anatomy, Posture, and Behavior Revealed by an Early Jurassic Theropod Dinosaur Resting Trace. PLoS ONE, 4 (3) DOI: 10.1371/journal.pone.0004591

Using the Comment, Note, and Rating Features at PLoS One

In my previous post, I highlighted some new articles from the online, open access journal PLoS ONE, and noted that the commenting feature at this journal is relatively unused for most articles. Some interesting discussion ensued on why this might be (among other issues). . .Mike Keesey suggested that maybe folks just aren't used to commenting in this format. Well then, let's do something about it!

Your Assignment:

• If you haven't already, create a user account on the PLoS website. This will allow you to post notes, make comments, and rate articles.
• Read an article that interests you on PLoS ONE (consider it part of your academic duty to keep on top of the recent literature), and make a substantive comment or note about something in the article. If you don't feel like making a specific comment (or if the article is so incredibly good as to not need comment), just rate the article.
• Feel good about contributing to a scientific discussion!
  

How It Works
Notes are for comments on specific portions of an article. For instance, maybe you think a particular sentence is well said, or relates to a very specific point that you have in mind. In this case, a note is most appropriate.

Comments are for more general thoughts on a paper--is there something particularly good, bad, or ugly? Might you have suggestions for an interesting follow-up study? Is there just something you're wondering about that you'd like the author(s) to answer?

Finally, ratings are a chance to tell folks what you really think about the paper. PLoS has three categories in which you rate an article--insight, reliability, and style. These categories are unfortunately vague in their names, but the PLoS website provides a succinct explanation of what is meant by each. Essentially, the categories rate the "importance" or "thought-provokingness" of an article, solidness of the conclusions, and technical execution and presentation of the whole package.

My First Notes, Comments, and Ratings
To check out an example, see another new paper in vertebrate paleontology published by Bates et. al:

Bates KT, Manning PL, Hodgetts D, Sellers WI (2009) Estimating Mass Properties of Dinosaurs Using Laser Imaging and 3D Computer Modelling. PLoS ONE 4(2): e4532. doi:10.1371/journal.pone.0004532

I just finished some notes, comments, and a rating of the article. (no, I did not do this just for the purpose of the blog--the topic genuinely interests me!) It's easy! Science marches on.

What are you waiting for? Go try it for yourself!

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.