Citation Format Wars

Over at SV-POW!, Mike Taylor recently addressed the issue of how to format in-text citations. Writing in his inimitable style, he makes the case that PLoS ONE is simply doing it all wrong; the majority of commenters there have agreed. I posted a lengthy comment there, but realized that it would be appropriate to revise and republish those thoughts here too.

First off, let's have a quick recap of the issue. When writing a scientific paper (or any paper, for that matter), it is essential to credit the sources of information and ideas. Not only does it allow the reader to learn more about the topic, it's the ethical thing to do. Rather than a simple reference listing at the end of the paper, most scholarly works also reference the relevant works within the text. This is called an in-text citation, and allows the reader to know precisely which information was associated with which author.

Two Worlds
Two styles of in-text citation dominate the scientific literature. The first of these is author-year, which looks something like this: (Farke, 2010). The second is numbered, which looks like this: [1]. This number then refers to a specific bibliographic entry at the end of the paper. Many variants of each style exist.

PLoS ONE uses numbered citations, in common with many other high profile journals (such as Nature), and in marked contrast to most of the paleontological, geological, and anatomical literature (such as Journal of Vertebrate Paleontology, The Anatomical Record, Geology, and others). The SV-PoW! post, of course, argues that the numbered format is vastly inferior to the author-year format. Let's boil the argument down to its essentials, and delve into the pros and cons of both formats in more detail.

Two essential reasons are given for why the author-date format are preferable: 1) ease of reading for authors familiar with the literature; 2) paleontologists don't like it. PLoS ONE thus chose a numbered reference format simply because they wanted to copy the glamour magazines. Do any of these arguments hold up?

Advantages of Author-Year (and disadvantages of Numbered)
Of course, there are some significant advantages to the author-year format. These include:

1. It's easy for readers who are familiar with the literature to know exactly what's being discussed. If I quote from my 2010 JVP paper on ceratopsian sinuses, "Less detailed descriptions have been published for other chasmosaurine and some centrosaurine ceratopsids (e.g., Gilmore, 1917; Lehman, 1990; Sampson, 1995; Sampson et al., 1997)," a long-time ceratopsian worker will know right off the top of her or his head that I'm talking about the Gilmore Brachyceratops monograph, Tom Lehman's paper in the Dinosaur Systematics volume, Scott Sampson's description of the Two Medicine centrosaurines in JVP, and the ZJLS paper with Scott, Michael, and Darren. I see pages from those papers when I close my eyes, and I could almost write the citation for each of them off the top of my head.
2. You don't have to flip back and forth between the main text and the reference list. For the ceratopsian expert described above, there's no need to waste time skipping around the paper (or PDF). It's just easier.
   
3. It helps readers new to the field to become familiar with the major names and papers. See the names "Wedel," "Taylor," "Wilson," "Curry-Rogers," and others often enough, and you probably have a good picture of a few of the major recent workers in sauropods.
   
4. It's easier for authors to keep their references straight. When writing and revising without use of a citation manager, the numbered system can get very unwieldy. If you add a reference in the middle of the paper, you not only have to renumber the entire bibliography after that reference, you also have to change the numbers within the manuscript itself. Miss one, and your readers are going to be grumpy when the number and citation don't match up.
5. It's familiar to the paleontological community. As mentioned above, "It's Got What Paleontologists Crave."
   

Disadvantages of Author-Year (and Advantages of Numbered References)
As you might have guessed, there are some disadvantages, too:

1. The author-year format is helpful only if you are already familiar with the relevant literature. Otherwise, you're still in the game of flipping back and forth to the reference section. Anticipating that most of my readers are savvy to vertebrate paleontology, but not to the latest in tectonics, contrast my above example in point 1 with this example (Najman et al., 1997, Geology 25:535-538): "Why is this so, as crustal thickening and metamorphism are thought to have occurred by this time (Frank et al., 1977; P. Zeitler in Hodges and Silverberg, 1988; Inger and Harris, 1992; Searle, 1996, and references therein; Vanny and Hodges, 1996)?" Although I understand the meaning of the sentence, the names and dates have absolutely no meaning to me, other than to help me find the appropriate citation in the back. I'm not familiar with that literature, so I'm annoyed by the extra text.
   
2. Not every reader wants to become an expert on a given subspecialty. Believe it or not, I may not be reading a plate on Indian tectonics (or sauropod vertebrae) because I want to become an expert on said subject. Let's say that I'm chasing the above-mentioned example from Najman because I want to know the context for some fossils I found in a format described in that paper. I just want the bare minimum of info, and I don't care about Frank, or Zeitler, or Hodges, or Silverberg, or Inger, or Harris, or Searle, or Vanny. Sure, maybe I'll chase some of those references for alternate opinions, but once that's done the names will probably never cross my mind again. This leads to the next point. . .
3. The author-year format clutters the text. I'm not the first person to state this, and I'm not the last. By editing my ceratopsian quote above, you now get: "Less detailed descriptions have been published for other chasmosaurine and some centrosaurine ceratopsids [1-4]." Try the same with the Najman quote. Much shorter and more easily readable. A comment on the SV-POW! post by Zen Faulkes gives some more nice supporting opinions.
4. Most of the rest of the scientific world uses numbered citations. I think people are giving Science and Nature a little too much credit for driving the numbered citation game. Yes, they certainly are the most visible journals to those of us in paleo/geo/zoological sciences, but that's a rather myopic view. I did a quick survey of the other 99 percent of the scientific literature, and numbered citations simply dominate. Even arXiv - the epitome of digital presentation with no real standard format - has a vast majority of papers with the [1,2,3] style (in fact, the only counterexamples I found were in a handful of biologically-oriented papers). The medical literature (medically oriented papers are the great majority of PLoS ONE submissions), computing literature, physics literature, etc., most often use numbered citations. Let's face it - paleontologists are not the biggest fish in the sea. It doesn't mean we're wrong or can't change things, just that it's a very uphill battle.

Closing Words
So, I have to say that the arguments for author-year and against numbered references are not as simple as one might hope. Major advantages and disadvantages characterize both formats. In the end, I suspect much of it comes down to "what we were born into." I like the author-year format because that's all I've ever known. My spouse, who is a physicist, surely thinks otherwise, but then again all she has ever known is the numbered format. She also thinks paleontologists are silly because we don't use LaTeX (and good luck getting that instituted, no matter how easy it would make things for us).

Interestingly, I came into this with a strong preference towards the author-year citation format, but after thinking about it I'm not sure that numbered citations are the Great Evil that they have been made out to be. What are your thoughts?

Update: The above-mentioned Zen Faulkes has a post strongly coming down on the side of numbered references. He argues that numbered references decrease overall manuscript length, greatly improve readability, and level the playing field for both readers and cited authors. The last argument is particularly novel, and strikes at the heart of the true purposes of citations. I'm not sure I totally agree, but it's definitely food for thought. [12 January 2011]

(As an interesting side-note, the author-year referencing style may be so common in the paleontological and zoological literature because of a historical accident - the format was apparently invented by a Harvard zoologist, and spread throughout the zoological part of the literature. I suspect the weight of the Harvard name didn't hurt.)

Disclaimer: Although I am a volunteer editor at PLoS ONE, this posting is written strictly as my private opinion.

Thank you to the many commenters at the SV-POW! blog, whose thoughts inspired this post.

Re-Evaluating Ancient Beavers

Beavers are some of the most distinctive (and largest) rodents around today. Two species of the extant beaver, Castor, are found throughout the northern hemisphere, and these animals have an enormous effect on their landscapes. Beavers are perhaps most famous for their dam-building activities, altering the flow of streams and generating valuable wetlands used by other animals. Surely, the impact of this group extends far back in geological time.

Many early beavers were fossorial, or burrowing, with little indication of aquatic tendencies. For instance, the 25 million year old Palaeocastor produced giant spiraled burrows known as "devil's corkscrews." Perhaps the acme of beaver evolution occurred during the Miocene (~23 to 5 million years ago). At least 12 genera lived worldwide; only one of these, Castor, survived to the present day. An obvious question for paleontologists thus concerns the when and where of modern beavers' origins.

Enter Sinocastor. This genus was named in 1934 by famed Chinese paleontologist C.C. Young, for several species recovered in China and Mongolia from rocks deposited during the last 5 or 6 million years. Almost immediately, other authors lumped Sinocastor into Castor, and there Sinocastor has stayed for the most part. Was this a valid opinion, or did such lumping obscure a more interesting paleontological pattern?

Fortunately, the exquisitely-preserved type (first described) specimen for Sinocastor anderssoni was recently restudied by a team of paleontologists from Canada and the United States. Led by Natalia Rybczynski of the Canadian Museum of Nature, the paper describing their findings appeared this week in the open access journal PLoS ONE.

The authors of the new paper used geometric morphometrics, a type of shape analysis, to see just how similar the skull of Sinocastor (at right) was to modern and recently extinct Castor. For additional comparison, the early European beaver Steneofiber castorinus was also thrown into the mix. Points on the various skulls were digitized from photographs and run through computer programs that calculated the similarity between the specimens.

In the end, the skull of Sinocastor fell well outside the anatomical range for modern and even most extinct beavers. Rather substantial shape differences distinguish Sinocastor from Castor; for instance, the snout is shorter and the braincase broader in Sinocastor. Although genera are always somewhat subjective, Rybczynski and colleagues argue that the major differences between Sinocastor and the species of Castor warrants the retention of Sinocastor as its own genus.

Based on several other lines of evidence (including tooth anatomy), it is suggested that Sinocastor may be the sister taxon (closest relative) to modern beavers. In concert with dated fossils, this means that the common ancestor of these two kinds of beaver may have originated in eastern Asia and then spread westward into Europe and eastward into North America. The arrival of modern beavers on that landscape must have had massive ecological consequences - only more investigation of the fossil record will tell!

Stayed tuned: Tomorrow, an interview with Josh Samuels, one of the paper's authors!

Citation
Rybczynski, N., Ross, E., Samuels, J., & Korth, W. (2010). Re-evaluation of Sinocastor (Rodentia: Castoridae) with implications on the origin of modern beavers PLoS ONE, 5 (11) DOI: 10.1371/journal.pone.0013990

Full disclosure: I am an academic editor at PLoS ONE, the journal at which the paper described here was published.
Image credits: Image at top from Wikimedia Commons (by Steve); fossil skull modified from Figure 14 in Rybczynski et al., 2010.

Have You Accepted the Paleo Project Challenge?

A little over three weeks ago, Dave Hone and I kicked off the 2010 Paleo Project Challenge. Basically, it is an opportunity to finish off those nagging projects (whether they be manuscripts, artwork, blog posts, fossils to prep, or whatever) by the end of the year, or else face public shame. Lazy individuals that we are, we know that unless we make a public commitment to finish some projects, they will never get done!

So far, a number of individuals have accepted the challenge. It's not too late to join in - just post in the comments section. Remember. . .the goal is to finish the project by December 31. Everyone is watching!

Participants in the Paleo Project Challenge
Brian Beatty - paper on meningeal ossification in cetaceans
Andrea Cau - describe new theropod remains from north Africa
Andy Farke - finish paper for ODP; finish paper on ceratopsian anatomy
Nick Gardner - paper piggybacked with one of Casey's
Casey Holliday - either a new croc species description or paper related to frontoparietal fossae
Dave Hone - the necks paper
Heinrich Mallison - finish Plateosaurus CAE paper; sauropod rearing paper; sauropodomorph rapid locomotion paper
Jordan Mallon - Anchiceratops manuscript
Anthony Maltese - sharks scavenging on mosasaur paper; Niobrara ammonite paper
Patty Ralrick - paper on subfossil mass mortality site
Manabu Sakamoto - finish Pachyrhinosaurus drawing; finish and submit theropod bite force paper
Mike Taylor - finally finish the Archbishop sauropod description
Bruce Woolatt - 1/10 scale Quetzalcoatlus northropi flesh restoration
Anonymous - find job; paper for Paleobiology; prep alligator fossil
Jay - finish sauropod description

The 2010 Paleo Project Challenge

Everyone has an unfinished project. Most of us have at least a half dozen. Those partly finished manuscripts, paintings, data sets, and preparation projects. Oh, we started out with good intentions. Maybe we even poured a productive week into it. But then, the honeymoon glow faded. Something else got in the way. The field season, or teaching duties, or another more pressing project, or a grant deadline, or just plain old life circumstances, interrupted us.

Luckily, all of that work doesn't have to go to waste. Why not finish up that project? What are you waiting for? Heck, what am I waiting for?

Regular readers of this blog may remember that Dave Hone and I instituted the "Paleo Paper Challenge" (PPC) last year, in an effort to shame all of us into cleaning our (figurative) research plate. We had pretty remarkable success - although not everyone (including ourselves) were able to finish everything we wanted to, most folks made some major progress. Some papers even made it into publication, in venues like Journal of Vertebrate Paleontology and PLoS ONE. Not too shabby.

Not wanting to rest on our laurels, it's time to kick things off for 2010. This year, Dave and I want to pursue a "bigger tent" approach. Why limit the PPC to just academic research? Let's open it up to all paleo enthusiasts! Preparators, artists, researchers, bloggers. . .after all, paleontology does not survive on publication alone. Thus, we are happy to kick off:

The Paleo Project Challenge
Do you have a paper that just needs the finishing touches before it heads off to publication? Is there some half-prepped fossil sitting in a cabinet in the lab? Have you started and finished a big blog post half a dozen times, but never pulled the trigger? Is that masterpiece rendering of a live Tylosaurus still sitting on the easel? Stop sitting around, and finish it!

Here are the rules:
1) Indicate your willingness to participate in the Paleo Project Challenge (PPC) in the blog comment section. You should at a minimum indicate the category it falls under (paper, blog, art, or whatever), and the project (if you can - we totally understand the need for secrecy in some cases!).
2) Do the work! You have until December 31, 2010. Remember, we're all watching.
3) Once you're done, celebrate!

You can read more about it from Dave's perspective here. Now, let's get to work!

My Commitments
1) Write up the ODP results.
2) Finish a long-running paper on ceratopsian anatomy.

What are you going to do? Chime in below in the comments section!

Two articles of note

First, congratulations to Chris Brochu and colleagues on their paper describing a new species of "horned" crocodile from Olduvai Gorge in Kenya. This probably was an animal that preyed on our earliest human ancestors, as evidenced by a variety of hominid bones from the area with crocodile bite marks. Consequently, this animal has been given the name Crocodylus anthropophagus ("human-eating crocodile"). The paper is freely viewable at PLoS ONE, as a regular web page, XML file, or PDF, and you can also download high resolution versions of the figures. Have a question or comment on the paper? Head on over to the website and get yourself heard! (full disclosure: I am an editor at PLoS ONE)

The second paper of interest concerns the issue of data sharing, which I covered a few weeks back. Following up on a statement published in The American Naturalist, the editors of Evolution have issued their statement (institutional subscription or payment required, sorry) supporting mandatory archival of most data for papers published within the journal. This isn't a huge surprise (they were listed in the earlier article as a supporter), but it's still nice to see something in print. Thanks to Randy Irmis for the notice!

Citations
Brochu CA, Njau J, Blumenschine RJ, Densmore LD (2010) A new horned crocodile from the Plio-Pleistocene hominid sites at Olduvai Gorge, Tanzania. PLoS ONE 5(2): e9333. doi:10.1371/journal.pone.0009333

Rausher MD, McPeek MA, Moore AJ, Rieseberg L, Whitlock MC (2010) Data archiving. Evolution 64: 603-604. doi:10.1111/j.1558-5646.2009.00940.x

Four-Winged, Psychedelic Dinosaurs

When many of us think of viewing things under a "black light," we either think of those psychedelic posters from the 1960s or else the displays of fluorescent minerals that nearly every science museum has. It's also virtually mandatory to have a scene involving the use of "black light" in the popular CSI television programs - many bodily fluids show up nice and pretty under these conditions. "Black light," more properly known as "ultraviolet (UV) spectrum light", is just outside the visible light spectrum for us humans (past violet, hence the name). And, through some neat tricks of physics, many objects will brightly fluoresce under intense UV light when they wouldn't look like anything special under your standard sunlight or incandescent light bulb.

Oddly enough, many fossils fluoresce under UV light (certain minerals in fossils, including phosphates, are behind this phenomenon). Thus, this technique has been used to look for otherwise hidden features of some exceptionally well-preserved fossils. Historically, it's been the domain of invertebrate paleontologists (looking at crustaceans from the Jurassic of Germany, for instance), but vertebrate paleontologists have used the technique to identify forged fossils (like Archaeoraptor), study Archaeopteryx, and much more. What might be a very subtle or invisible structure under regular light (such as a feather shaft, or antenna, or soft tissue outlines) sometimes shines nicely under UV light.

Thus, Beijing paleontologist Dave Hone and colleagues applied the UV light technique to some of the spectacular fossils coming out of the Cretaceous-aged beds of China. In particular, they were interested in a little critter called Microraptor. A dromaeosaur (part of the same group including Velociraptor), Microraptor is relatively well-known as the "four-winged dinosaur." Spectacular fossils with feather impressions show the standard pair of bird-like wings on the arms and a second set of wings on the hind limbs. This suggests to some researchers that birds went through a four-winged flight phase early in their evolution, and the two-winged flight with which we are familiar only happened later.

Cast of the type specimen of Microraptor gui, from the Wikimedia Commons, reproduced under a Creative Commons Attribution-Share Alike 2.5 Generic license.

Although the fossil looks spectacular, many paleontologists speculated that appearances might be deceiving. Were the feathers on the legs actually in place, near their life position? Or had they gotten moved around from somewhere else on the body? A pale halo of sediment (probably from the decomposition process) obscured the contact of the feathers with the bones, so the issue remained unresolved. Either way, it had major implications for avian evolution.

Hone and colleagues wondered if the full anatomy was obscured under visible light. So, they turned a UV light source against the specimen. It turns out that the feather structures fluoresce quite nicely - and can be traced right through the "halo" and up to the very edge of the leg bones. So, the feathers really are in place. Problem solved! [image, showing full skeleton, modified from Figure 2 in Hone et al. 2010]

Now that we're more confident that Microraptor really was four-winged (and not just an accident of fossilization), the conversation can move forward. And, this is a great rallying cry for other researchers - who knows what structures we might discover with UV light!

Close-up of hind legs of Microraptor under UV light, with arrows indicating feathers. The yellow stripes leading up to the leg bones are portions of the feathers visible only under UV. Modified from Figure 3 in Hone et al. 2010

Read the full paper in the freely-available, open access journal PLoS ONE (full disclosure: I was the editor who handled this manuscript). You can post comments or ratings for the article there, too! In the blogosphere, check out Dave Hone's posting on his article and this follow-up, Adam Yates' write-up, as well as ReBecca Hunt's interview with Dave.

Citation

D. W. E. Hone, H. Tischlinger, X. Xu, & F. Zhang (2010) The extent of the preserved feathers on the four-winged dinosaur Microraptor gui under ultraviolet light PLoS ONE 5 (2) : 10.1371/journal.pone.0009223

Paleo Paper Challenge: The Final Round-Up

Well. . .January 1, 2010 has faded into memory, and with it the 2009 Paleo Paper Challenge (PPC). For those of you who need a brief reminder, the PPC (sponsored by me and Dave Hone) was a chance for all of us who have partly-finished papers to give them the final push out the door. We had 22 individuals from around the world accept the challenge, and everyone made a pretty solid effort.

Now some folks expressed disappointment that they weren't able to complete everything they had hoped for. Personally, I only had a 50 percent success rate. But, as Dave said elsewhere, that wasn't really the point. As long as some work got done, that's what really counts. And if a paper got submitted - even better!

So, congratulations to all of our participants! I've included preliminary results below - if there is something I should update, either drop me an email or else leave a note in the comments. Here's looking forward to the PPC 2010. . .stay tuned for details, probably in September.

Results of the Paleo Paper Challenge

Brian Beatty
Calvert Formation terrestrial mammals review with Ralph Eshelman
Final status: Unknown

Tor Bertin:
Statistical analysis of evolution of sauropod body size, involving a mystery specimen
Final status: Unknown
Spinosauridae review
Final status: In progress

Lisa Buckley
Papers to be decided
Final status: Unknown

Andrea Cau:
Description of metriorhynchid from northern Italy
Final status: Major Progress

Andy Farke:
Myledaphus paper
Final status: Failure to launch
Final dissertation chapter
Final status: Revised and resubmitted

John Foster:
Morrison critter paper
Final status: Unknown

Francisco Gasco:
Master's thesis
Final status: Some progress

Mike Habib:
Pterosaur flight range
Final status: Some progress
Pterosaur aquaflyer paper
Final status: Submitted and accepted

Penny Higgins:
Bulk isotopic ratios from tooth enamel and general interpretation of environment
Final status: Major progress

Casey Holliday:
Articular cartilage paper
Final status: Major progress, almost ready for submission

Thomas Holtz:
Tyrannosaur heterochrony/paleoecology
Final status: Unknown

Dave Hone:
Unspecified papers
Final status: Two papers submitted, one still awaiting launch

ReBecca Hunt:
Mygatt-Moore taphonomy paper
Final status: Unknown

Nick Gardner:
Unspecified paper with Mickey Mortimer
Final status: Unknown

Chris Note and Ari Grossman:
Dinosaur ecomorphology
Final status: Unknown

Bill Parker:
Revueltosaurus manuscript
Final status: Unknown

Heinrich Mallison:
sauropods rearing
Final status: Minor progress
sauropodomorph rapid locomotion
Final status: Minor progress

Anthony Maltese:
Unspecified paper
Final status: One in press, one with a co-author, another with major progress

Mark Mancini:
Redondosaurus cranial description (with Axel Hungerbuehler)
Final status: Unknown

Eric Snively:
Chicken electromyography and implications for big theropod neck muscles
Final status: Submitted
Atlas of gekkotan lizards of the Paris Basin
Final status: Some progress
Artiodactyl vs. Stegoceras head-strike mechanics
Final status: Some progress

Mike Taylor:
The Archbishop description
Final status: Major progress

Matt Wedel:
Final dissertation chapter
Final status: Unknown

Adam Yates:
Early sauropodomorph pneumaticity
Final status: Unknown
Rauisuchians of the Elliot Formation
Final status: Unknown

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.

The Award-Winning Open Source Paleontologist

I was pleasantly surprised to learn earlier today that last week's post about pachycephalosaur ontogeny was awarded "Blog Pick of the Month" for October by everyONE, the PLoS ONE community blog. Thanks!

On a related note, check out the following video from UC Berkeley, with a great summary of the research published last week in PLoS ONE:

A Happy Family of Pachycephalosaurus

Distinguishing the skulls of juveniles and adults of the same species, and sometimes different species, can be a prickly thing in the fossil record. The result is that paleontology is littered with juvenile fossils that have been considered adults at some time or another. The crested duck-billed dinosaur Corythosaurus has also been known under names like Procheneosaurus, the famous Monoclonius is actually a juvenile of adult Centrosaurus, Styracosaurus, and kin, and the debate still continues on whether Nanotyrannus is a juvenile Tyrannosaurus.

Yesterday in the open access journal PLoS ONE, paleontologists Jack Horner and Mark Goodwin published a long-awaited paper positing synonymy for a trio of iconic (and melodiously-named) dinosaurs. The bone-headed dinosaurs Pachycephalosaurus, Stygimoloch, and Dracorex are all one and the same animal, according to their work. The latter two are juvenile stages, whereas Pachycephalosaurus represents a full adult.

Skulls of Pachycephalosaurus (top), Stygimoloch (middle; the front of the skull is missing), and Dracorex (bottom; the skull is crushed from top to bottom). In particular, note the changes in skull size and similarities in spike placement. Modified after the original in Horner and Goodwin 2009.

How is this possible? The animals look so different, right? Pachycephalosaurus has this big bowling ball on top of its head, which the other two lack. Stygimoloch has a uniquely-shaped, narrow dome, and Dracorex has a completely flat head. Furthermore, Pachycephalosaurus lacks the elongated spikes that make the other two look so fearsome.

Well, it turns out that this can all be attributed to ontogenetic changes (i.e., change as the animals get older). Horner and Goodwin assemble multiple lines of evidence for this hypothesis.

First, the skulls of Dracorex, Stygimoloch, and Pachycephalosaurus form a size gradation from smallest to largest--exactly what one would expect for a growth series. By itself, this is not irrefutable proof, of course--it could just be that Dracorex had a small adult size compared to Pachycephalosaurus.

Second, many of the knobs and bumps on the skulls can be matched up one for one between individuals of the various specimens. Alternatively, one would also expect that closely related (but different) species might have similar patterns of bumps. As Horner and Goodwin admit, there is some variation between individuals of the different "species"--but, the authors also note that this sort of variation is entirely expected and occurs even within undisputed adult Pachycephalosaurus.

Third, specimens of Stygimoloch, both in CT scans and physically cut specimens, show an open suture between the two frontal bones of the dome. Pachycephalosaurus domes are completely fused up. Open sutures are often strong indications that an animal is still growing--and, it's particularly intriguing that a small "species" has them but a large "species" doesn't!

Finally, microscopic examination of the bones in two of the three "species" (Stygimoloch and Pachycephalosaurus; there weren't any Dracorex available for cutting up) shows that Stygimoloch was still growing (and thus not a full adult)--but Pachycephalosaurus specimens weren't growing much at all (and therefore were probably full adults).

Any one of these lines of evidence might be interesting, but not completely convincing. Taken together, however, they make a pretty compelling case that Dracorex and Stygimoloch are juvenile Pachycephalosaurus. Because Pachycephalosaurus was named first, the first two become junior synonyms. It's a shame, because they're such cool names!

As for duckbilled dinosaurs, horned dinosaurs, and even modern crested birds like the cassowary, the story in the pachycephalosaurs suggests that weird ornaments on the skull were something that happened only as the animals approached full size. The domes practically appeared overnight! The teenage years must have been a real headache for these dinosaurs.

Thanks to the wonders of open access, the article is freely available for all to read. Additionally, it is worth taking advantage of the rating and comment features at PLoS ONE [disclaimer: I am a section editor for that journal]. . .few other scientific publications allow the readers to annotate the papers directly!

Citation
Horner, J., & Goodwin, M. (2009). Extreme cranial ontogeny in the Upper Cretaceous dinosaur Pachycephalosaurus. PLoS ONE, 4 (10) DOI: 10.1371/journal.pone.0007626

The Paleo Paper Challenge

Dave Hone of Archosaur Musings and I were recently chatting online and were lamenting the inevitable problem of ‘the unfinished paper’. Most researchers have a project or two (or anything up to 20) that were started and then kind of stalled for various reasons – uncooperative co-authors, being unable to find the elusive essential paper, other projects taking priority, or just general malaise. It’s left as a few pages of notes, or unreferenced, without figures or a key analysis complete or whatever. It’s good science and publishable, it’s just not done. Without a good incentive to get them finished off (like a rival group) or them getting out of date (the stuff is interesting but not ground breaking and will not revolutionize the field when it comes out, but it’s not old either) these things can last for ever. Sometimes, all the manuscript needs is one day of solid work to kick the thing out the door!

Both of us have these kinds of papers knocking around and we are far from the only ones. As such with SVP around the corner we decided to issue the Paleo Paper Challenge (or Palaeo Paper Challenge, if you're so inclined). If you have a palaeo paper that really needs to be finished off then we challenge you to sign up here and get it done this year. If so, simply leave a note in the comment thread and we’ll total them all up in a few days and create a register of those taking part (so you can’t back out!). There is no need to let everyone know exactly what it is you are working on (if people want to keep things private, that’s fine) but of course juicy details will be welcome. Dave and I will also both be canvassing at SVP, and if you want to encourage others to join, do please mention this on your own blogs etc.

This should serve as both self-motivation to get the project done and a nice little race to see who can finish first and get their paper(s) submitted or in print. The real challenge of course is simply to get it done, so we are setting January 1, 2010, as your ‘official’ deadline – if you are joining the challenge you’ll have about three months to get it done. There are hundreds if not thousands of these papers languishing on hard drives so let’s try and get a few of them out there!

[NOTE: This post was largely written by Dave. . .I've modified it slightly for posting here. Perhaps this laziness is why I have so many half-finished papers sitting on my hard drive right now.]

The Big (and Crazy) Announcement

A few months ago, Matt Wedel (of SV-POW! fame) lamented the lack of measurements in most contemporary scientific papers. As a real numberhead, his post resonated with me. It got me thinking. Despite the shortcomings of some papers, there are a lot of measurements out there in the literature already. With measurements, you can do science. Potentially some really cool science. But how could I collect all of these data? This could take years!

The gears in my brain started turning. One idea led to another. A plan was forming. Something crazy. Deeply, insanely crazy.

So what happened next? I teamed up with SV-POW's Matt Wedel and Mike Taylor to create a research project in dinosaur paleontology that anyone can participate in. The Open Dinosaur Project. We (yes, "we" includes you) will comb through the literature (which, thanks to a number of open access publications and archives, is quite data-rich) and pull out measurements for further analysis. The process - from data collection to analysis to publication - will be completely open. Every step of the way will be blogged. And. . .all contributors are invited to join us as co-authors. The project: look at the evolution of the limbs in ornithischian dinosaurs.

Thus was born The Open Dinosaur Project. Consider this your invitation to join us. Read more about it at the project blog!

Big News on the Way

Research of catastrophic proportions. Another piece of the Shiny Digital Future. An unholy union between members of SV-POW! and The Open Source Paleontologist. Bigger than Ida. A cast of dozens. . .hundreds. . .thousands! Visit here on Tuesday morning to find out what the hyperbole is all about!

Get the Goat Head Paper for Free!

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

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

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

Two Items

First, congratulations to Dr. Mark Loewen, who successfully completed his dissertation defense on Tuesday afternoon. His dissertation focused on variation in Allosaurus, and was truly an epic piece of work.

Second, check out this paper that just came out in PLoS ONE. The paper covers some interesting aspects of limb bone allometry (shape changes with size), and provides open source macros for ImageJ, so you could do similar analyses on your own dataset. In the next day or two, I should have more to say, but for the time being check out the link. . .as always, the papers are free to download, and please take advantage of the commenting/note-making/rating features on the PLoS website.

Doube M, Conroy AW, Christiansen P, Hutchinson JR, Shefelbine S (2009) Three-Dimensional Geometric Analysis of Felid Limb Bone Allometry. PLoS ONE 4(3): e4742. doi:10.1371/journal.pone.0004742

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

New Paleo Paper in PLoS ONE

If you haven't seen already, the past two weeks have been great for paleontology on the pages of PLoS ONE, a high-profile open access journal. Phil Gingerich and colleagues have just published a paper on Maiacetus, a new fossil whale from Pakistan. Other bloggers have done a much more thorough job than I could of presenting the work and its importance for understanding whale evolution, so I'll just link to them and the original article.

It is good to see more paleo papers taking the open access route!

Gingerich PD, ul-Haq M, von Koenigswald W, Sanders WJ, Smith BH, Zalmout IS. (2009) New Protocetid Whale from the Middle Eocene of Pakistan: Birth on Land, Precocial Development, and Sexual Dimorphism. PLoS ONE 4(2): e4366. doi:10.1371/journal.pone.0004366

Read about it at Laelaps, Not Exactly Rocket Science, A Blog Around the Clock, The Loom, and elsewhere.

The Open Source Triceratops Paper

Wow! The past few days have been a real whirlwind. As mentioned in my last post, our long-awaited paper (well, long-awaited by my co-authors and me) on Triceratops horn use and paleopathology was unleashed by PLoS ONE on Tuesday evening. We've received some wonderful feedback through this blog and email, and are very ready to move on to the next research project.

Because this blog focuses partly on open access and open source software, I wanted to write briefly about how these issues factored into our research. This is one of the most "open" projects I've attempted to date, from start to finish. Here are the details:

• The data collection and statistical analysis were completed in OpenOffice.org Calc, with the calculations based on a spreadsheet file I found (and tested against known examples) from somewhere on the internet (but can't remember where, now!). R will also do the appropriate calculations, but I stuck with the spreadsheet because my data files were so small and straight-forward.
  
• The manuscript was written in OpenOffice.org Writer, but my co-authors and I batted it back and forth in Word format (because Darren and Ewan are using the latter program). We had no problems with this strategy, and the format conversions were a snap for the relatively simple documents we were using.
• The bibliography was compiled and formatted using Zotero. Zotero even has a readily available style file for PLoS, so this made my life very easy.
  
• The figures were edited for contrast and brightness in GIMP (no other manipulation was performed on the images) and assembled in Inkscape.
• The journal, PLoS ONE, was selected because of its high profile, high impact, and open access. Thanks to the open access policy, our article is readable by anyone who wishes to see it. I hope that the broader exposure will facilitate debate and further research on the topic--only time will tell. If I have any future articles of potentially broad interest, PLoS ONE will definitely be on my list of candidate journals.
• The popularization of the article was initiated by PLoS ONE, with follow-ups by numerous journalists and bloggers. Thanks to the wonders of the internet, many of the articles are available for free. And, I am happy to say, most of them are pretty well-done.