Science - Now With Open Access Archives

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?

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

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

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.

Bone-ing Up on Allometry

Allometric scaling - roughly defined, when different parts of an organism grow at different rates - is an important factor in biology. In part, allometry describes how babies have relatively larger heads than adults (we exhibit negative allometry in this trait, because our skulls don't grow as quickly as the rest of the body) or how some crabs have gigantic claws (an example of positive allometry, in which the claw grows much faster than the rest of the body). Allometry (and its counterpart isometry, in which proportions don't change at all) can be examined on an intraspecific level, such as the example in humans, or on an interspecific level.

It's not cute - it's allometric!
Toronja Azul, Chihuahua Puppy, 5 August 2007 via Wikimedia Commons, Creative Commons Attribution 2.0

For paleontologists and biologists, allometry and isometry are particularly interesting when it comes to understanding groups with large ranges in body size. When you grow a Tyrannosaurus from an Eoraptor-like ancestor, what has to change in order to support the body mass? Sometimes it's postural - big animals tend to have more "columnar" posture (with the supporting legs straight beneath the body) and small animals tend to have more "flexed" posture. In other cases, it's allometric - big animals might tend to have relatively thicker bones than small animals. Sometimes, it might even be both. And sometimes, none of these comfortable patterns seem to fit perfectly.

Looking at Cats
Regardless of the patterns (and often because of them), scaling studies of limb bones have attracted a lot of ink over the years. A recent contribution, authored by Michael Doube and colleagues, appeared the other week in the open access journal PLoS ONE. Their paper, entitled "Three-dimensional geometric analysis of felid limb bone allometry," takes a novel peek at how different limb bones scale within cats. Cats are a particularly interesting study subject, because they span a range of adult body masses - from as little as 3 kg in the domesticated cat to 306 kg in the largest tiger.

Domesticated cat (left) and lion skeletons, scaled to roughly the same height at the shoulders.

Limb bone allometry in its own right is an interesting, but rather conventional, topic. Most studies are content to take some linear measurements, or perhaps a cross-section or two, for a range of species. Doube and colleagues did something unique - they examined the three-dimensional properties of entire limb bones, as well as two-dimensional properties in series along the entire bone, using CT scans coupled with custom-written software macros.

The macros (which are one of the really cool things about this paper, and a big reason for why I'm highlighting it here) calculate a variety of cross-sectional properties automatically from CT scan data. Previous macros (such as the very useful MomentMacroJ) required a human operator to do things one slice at a time. Believe me, this can take forever for a limb bone data set of 200 CT slices. The authors of the paper in question were able to quickly and efficiently assemble data sets for a variety of measurements from a variety of limb bones for a variety of felid species - over 16,000 CT slices in total! So, this allowed compilation of a database for measurements throughout the bone - not just at the boring old mid-shaft. Furthermore, they calculated joint geometries (through a sphere-fitting routine, to approximate surface area of certain joints) as well as moments of inertia for entire bones.

This data set allowed the authors to get one of the the most complete pictures of limb bone properties ever assembled. In general, cross-sectional properties at mid-shaft (a standard location for measurement) did not differ significantly from isometry (i.e., big cat bones look the same as little cat bones). Of course, a larger sample might achieve statistical significance at P less than 0.05 (results are suggestive, but don't differ significantly from isometry). Interestingly, joint surfaces and moments of inertia tend to scale with positive allometry. In other words, big cats have relatively bigger joints and beefier bones (a more thorough and accurate explanation of moments of inertia is beyond the scope of this post) than do small cats.

So why are these results interesting? Well, it appears that cats "get big" differently from other animals. Whereas comparably sized mammals tend to change from flexed limb postures to more columnar limb postures as body size increases, cats apparently maintain a relatively flexed posture across their size range. Instead, cats compensate for the change in body mass by beefing up their bones. Skeletal and postural responses to increased body size are pretty darned diverse, and there is no "one size-fits-all" solution. It will be very interesting to see broader applications of this methodology.

Open Source Solutions
The authors used ImageJ, an open source image processing system (detailed in a previous post here) for much of their data collection. The macro they wrote and used is also freely available with their paper--so feel free to try it out with your own data. Their massive datafiles were collated with MySQL, and the statistical analysis was conducted within R, using the SMATR package for regression analysis. So, it was an open source project from start to finish! As the cherry on top of the cake, publication in PLoS ONE means that the paper is easily and freely accessible to all. I've already made a few notes on the paper, with quick and gracious responses from one of the authors. If you have anything to add to the discussion, don't be shy!

Further Reading
If you're interested in more open source solutions to these sorts of problems, check out lead author Michael Doube's web page. He's got lots of macros, pretty pictures, and other goodies for enjoyment and download.

The Citation
Doube, M., Wiktorowicz-Conroy, A., Christiansen, P., Hutchinson, J., & Shefelbine, S. (2009). Three-dimensional geometric analysis of felid limb bone allometry. PLoS ONE, 4 (3) DOI: 10.1371/journal.pone.0004742

Lizard Skulls! (the update)

In a previous post, I noted a really nifty collection of digital lizard skulls available thanks to the efforts of Nick Gardner, writer of "why I hate theropods" and a student in the Casey Holliday lab. Well, it turns out that I jumped the gun just a little bit (thanks for nothing, Facebook!). . .the complete director's cut of the page is now available, and is highlighted in a posting here. Congratulations on a really great resource!