Thursday, January 27, 2011

Nedoceratops - Random Thoughts

The last two posts here have focused on my most recently published paper, fully describing the skull of the horned dinosaur known as Nedoceratops hatcheri and critiquing the hypothesis that it, along with Torosaurus latus, is simply an older individual of what we call Triceratops. Because I've already talked about the science of the paper, and some collegial interactions, I'm going to spend this final post in the series talking about a few odds-and-ends that just didn't fit anywhere else. Most of these are little windows into the process behind the paper - from writing to review to revision. And we'll start with. . .

Open Source Composition
I'm proud to say that every single step of the authoring process for my paper happened in open source software. I wrote the manuscript in Writer, formatted most of the references in Zotero, did initial image editing (contrast adjustment and background removal) in GIMP, assembled the figures in Inkscape, and submitted the manuscript through the journal website on the browser Firefox, all of which were running on various releases of Ubuntu. Score one for open source software (and open access publishing)!

On Organizing the Paper
I'm under no illusion that everyone (?anyone?) will agree with my conclusion that Nedoceratops is a valid taxon. In fact, I'm quite accepting of the possibility that I may be wrong. But even if this is the case, I still want my paper to be useful. So, I made my best effort to separate data from interpretation in the description section of the paper. Of course, I couldn't be completely successful on this point - after all, I had to compare Nedoceratops with Triceratops and Torosaurus (the most likely candidates for synonymy) - but I like to think that I mostly achieved my goal. If nothing else, I have pretty pictures. And. . .

Speaking of Pictures
My figures went through some pretty drastic changes during the evolution of this paper. In the first round of reviews, it was pointed out that in the text I kept referring to various structures illustrated in the figures, but only a ceratopsian geek could figure out what I was talking about.

For example, we have this lovely sentence:
The narial strut is inclined rostrally towards the dorsal end of the element, and enough original bone surface is preserved to indicate that a posterior internarial flange did not project from the caudal surface of this structure (Figure 4).
My original Figure 4 looked like this:
The photo is relatively pretty, but only a die-hard ceratopsian nerd could locate the narial strut or know where to look for a posterior internarial flange if such a thing even existed in this animal. So, for my next iteration I added some labeling:
Of course, all of the abbreviations are explained in the caption (not shown here). "ns" refers to the narial strut I was talking about above. Finally, the editor mentioned that I should do a better job of indicating the "cpf" (canal at the edge of the premaxillary fossa). It wasn't just at the tip of the arrow, but over a somewhat broader area. Thus, that brings us to version 3:
This, with the extra arrows showing the position of the canal, was the version that appeared in the paper.

If I learned anything from this experience, it was about the importance of good labeling and interpretive drawings for non-expert readers. Most of the labeled interpretive drawings alongside photographs (with the exception of parts B and D in Figure 1) were added at the direct request of the editor. Looking at the end product, this addition was a major improvement to the paper. Of course, I must also admit that having relatively unlimited space in an online journal allows this luxury!

Editorial Ethics
It's probably not a surprise to many of you that I am a volunteer academic editor at PLoS ONE. And those of you who have been paying attention probably noticed that the Nedoceratops paper was just published in that very same journal. This sounds pretty problematic on the face of it.

Thankfully, PLoS ONE has pretty strict editorial controls when one of their own editors submits a paper (in addition to a competing interests policy that covers this and similar situations). My experience as a submitting author was exactly the same as for any other author. Once the "submit" button was pressed, I had to wait just like everyone else. I couldn't control which editors handled it, who reviewed it, or even have a sneak peek at the reviews on-line. In other words, the system functioned exactly as it should.

My authorial feet were held to the fire by Leon Claessens, the handling editor for my submission. Leon, in my opinion, did a very professional job and didn't let me get away with anything (even sending the manuscript back to me a second time for a few last corrections and improvements). The reviewers - Michael Ryan and Peter Dodson - also did their jobs (in my opinion). And, as mentioned in my last post, comments by John Scannella and Jack Horner offered additional constructive feedback.

One thing I really like about PLoS ONE is that my competing interest - as an editor at the journal - is stated up-front in the paper. Although it's somewhat scary seeing it there, I think such notices are certainly appropriate.

Final Thoughts
It's nice to finally have this paper out there - these ideas have been floating around in my head for awhile, and I've always had a secret desire to be the person to describe Nedoceratops. I'm relatively pleased with the final product (of course, there are always one or two typos that slip through, and why couldn't some of the figures in the PDF have been bigger?), and look forward to the discussion that this paper generates. Thank you to all who helped out (see the acknowledgments for a comprehensive list)!

Wednesday, January 26, 2011

Nedoceratops - Fun with Science

In my last post, I mentioned that I have had more fun with my recent project on Nedoceratops than anything else I've done lately. Just as a refresher, this paper described an oft-neglected horned dinosaur skull known as Nedoceratops hatcheri, and presented counter-evidence to a hypothesis (published by John Scannella and Jack Horner) that Nedoceratops, Triceratops, and Torosaurus were all the same animal. This all sounds kinda boring and academic, so where's the fun in that?

As a scientist in a small field like vertebrate paleontology, it can be awkward when you disagree with a colleague. I've heard third-hand accounts of shouting matches at scientific conferences, and have occasionally seen very heated discussions during the Q&A time at presentations. Thankfully, this sort of behavior is pretty rare. Yet, I was a little worried about what might happen when I publicly presented a counter-argument to Scannella and Horner's hypothesis.
My nightmare of a confrontation with John Scannella (left) at SVP. Maybe there wouldn't be fists involved, but at a minimum a wrestling match. He's in better shape than I am, so I would be in trouble.

Of course, I was less concerned about a shouting match, and more focused on not being a jerk in print. I've known both John Scannella and Jack Horner for a number of years, and wanted to stay on at least semi-cordial terms with them. Of course I was going to disagree with them (based on my interpretations of the available data), but I wanted to do so in a way that was fair, collegial, and honest.

So, I did something that some people might consider stupid. I sent John and Jack a copy of my unpublished, unaccepted, in-review manuscript. At the very least, I figured it was only fair that I should give them a heads-up that I would be presenting counter-arguments to their hypothesis about Triceratops and Torosaurus. More importantly, I wanted to make sure that I was representing their work fairly and accurately.

This initiated a lengthy and wide-ranging email conversation. Although I had done a decent job of representing most of their points, there were a few areas where I had inadvertently set up a straw man. I fixed those as best I could. In some (thankfully minor) areas, I needed to update information or account for some specimens I had neglected. For instance, I had grossly understated the amount of variation in the frills of various adult Triceratops (something that has only been adequately documented thanks to John's Ph.D. work). With their honest feedback, I was able to craft a much-improved version of my manuscript. It is not just a smarmy platitude to state that I genuinely appreciate their input.

Of course, I won't claim that Scannella and Horner find my counter-arguments (that Torosaurus and Triceratops are different animals) entirely convincing. And, my current opinion on the matter is not unchangeable. John and I had a nice long chat at the SVP meeting this year, comparing notes and talking about our future research plans. He has some really cool data (some of which he has presented at SVP and other conferences), and I look forward to seeing it in print. Undoubtedly, we will both modify our interpretations as new data are published.

Now why am I finding this to be so enjoyable? It's the joy of discovery, the entertainment of questioning long-held ideas (especially my own), and the pursuit of new data. After all, science shouldn't be about scoring rhetorical points, but working towards an accurate view of our world. I know beyond a doubt that we all are playing on the same team. My dialog with John (and Jack) has been engaging, challenging, and stimulating in a unique way. I've learned more about Triceratops in the past six months than I had in the past six years (to be ultra-nerdy, for instance, some specimens lack the mid-line epiparietal - neat!!!). It's just darned fun to be working on a research problem like this!

No matter how this whole issue shakes out, I think there is one thing we can all agree on right now. Horned dinosaurs are AWESOME!

John Scannella and I, with our favorite dinosaur

Coming Up: A few final thoughts on the process behind this paper.

Tuesday, January 25, 2011

Nedoceratops - A Full Description at Last
Every group of animals has at least one notable yet neglected specimen. In horned dinosaurs, a particular example is a large skull at the Smithsonian discovered in Wyoming during the closing years of the 19th century. Unfortunately, this specimen has suffered a twisted and sometimes tragic history.
The skull of Nedoceratops hatcheri, modified from Farke 2011

The collector of the fossil, John Bell Hatcher, wrote a paper about the specimen, but died before he could publish it. So, the task fell upon Yale's Richard Lull, who gave this nearly complete skull the name of Diceratops hatcheri. It looked much like a Triceratops (the famous three-horned face), but differed from the standard "Trike" in having a tiny nose horn, several holes in the frill, and a handful of other characteristics. Later on, other scientists decided that these differences were probably just the result of individual variation, injury, or other illness. So, Diceratops became just another Triceratops to most workers (a 1986 paper by John Ostrom and Peter Wellnhofer was influential in this regard). Still, there wasn't unanimity in that thought - Cathy Forster, for one, published the opinion (in 1996) that Diceratops was indeed distinct from Triceratops.

Nedoceratops hatcheri, as restored by Nobu Tamura.

In 2000, the skull (which was on exhibit at the Smithsonian) was damaged when some rowdy museum visitors crashed through a barricade and broke the snout. Fortunately, the museum's preparators were able to fix it. As if to add insult to injury, it turned out that the name Diceratops wasn't unique. A German entomologist (coincidentally named Förster) had applied the name to an insect way back in 1868, so a new name had to be found for the dinosaur. Unfortunately, this didn't happen in the most organized way. Two researchers independently published the replacement names of Diceratus (in 2008) and Nedoceratops (in 2007). The second one, although less elegant (in my opinion), had priority because it was published first.

But wait - there's more! The story of Nedoceratops took an interesting twist last year, when John Scannella and Jack Horner suggested that it represented a life stage of Triceratops, halfway through its transformation into Torosaurus (see the figure below). This was not an evolutionary transformation, of course, but ontogenetic (one that happened as an individual animal got older). So, our three animals - Triceratops, Nedoceratops, and Torosaurus - were all just the same thing! Such revelations happen frequently in paleontology. For instance, the duck-billed dinosaur Procheneosaurus turned out to be young Corythosaurus, Lambeosaurus, Hypacrosaurus, and the like. But, not all horned dinosaur experts are convinced that this was what was going on with Nedoceratops and Torosaurus.

From left, life restorations of Triceratops, Nedoceratops, and Torosaurus (all modified after originals by Nobu Tamura). The arrows indicate the relative age of each animal, as proposed by Scannella and Horner. If they all are the same thing, Triceratops is the "young" life stage, and Torosaurus is the "old" life stage, with Nedoceratops being a transitional form. The big question: are these the same animal, or different species?

Named, renamed, renamed again, broken, pieced together, and declared invalid, Nedoceratops has had a checkered past. Yet, the skull has never received a fair treatment in the scientific literature. I'm not just talking about people's opinions of the specimen. Instead, I'm talking about a full description.

Descriptions - detailed accounts of a specimen's characteristics - are the data upon which much of paleontology relies. But, the skull of Nedoceratops was never fully described. A few paragraphs have been written about it here or there, but it turns out that many aspects of these were inaccurate or incomplete. Given the controversy over this skull, an accurate and complete description of the animal was particularly important. So, I set out to fix the situation. In my recent PLoS ONE paper, I published the first comprehensive description and illustration of Nedoceratops hatcheri.

At risk of boring you readers with endless details, I'll just mention a few minor points. For instance, it turns out that many of the early drawings of the specimen were inaccurate (missing bone was shown as present, for instance). I was able to correct these errors, and talk about areas of the skull that were well-preserved but never discussed in the literature before. My paper also includes detailed and never-before-published photographs of the skull in various views, which I hope will be useful for folks who can't see the skull first-hand.

Finally, and probably of the broadest interest, I go out on a limb and say that Nedoceratops hatcheri is a unique species - not the same as Triceratops or Torosaurus. In my opinion (and it is but an opinion), there are just too many features that are different between these animals, and few features can be chalked up to injury or growth changes. Will this opinion stand the test of time? Maybe, maybe not. My opinion on the validity of Nedoceratops is probably the most tentative conclusion I've ever published, so my feelings won't be terribly hurt if I turn out to be wrong (although of course, I'd rather be right).

And what about the idea of Triceratops being a junior version of Torosaurus? I argue that Torosaurus and Triceratops are indeed distinct species, not just old and young versions of the same animal. Why is this?
  • Triceratops and Torosaurus have vastly different numbers of bony bumps - called epiparietals and episquamosals - on the edges of their frills. If Torosaurus is the younger version of Triceratops, this means that Triceratops added a bunch of these bumps to the frill during growth. Yet, there is no good evidence that any other horned dinosaur did this.
  • Triceratops has a solid frill, and Torosaurus has big holes in its frill. In all other horned dinosaurs we know (such as Protoceratops and Centrosaurus), if adults have holes, the young ones have holes. Thus, it doesn't make a lot of sense that Triceratops/Torosaurus would only add these holes when it got really big. [of course, I will admit that just because something doesn't make sense doesn't mean it couldn't happen - just that it is much less likely]
  • It was previously claimed that there were no good examples of "young" Torosaurus. But, a skull at Yale (collected by Hatcher, the same person who discovered the Nedoceratops skull) fits all of the characteristics of a young animal. Its skull sutures are all open, or unfused, and the bone has a smooth texture typical of young dinosaurs. In my mind, this is probably the best evidence that Torosaurus is not a grown-up Triceratops.
Undoubtedly, many other paleontologists will have something to say about these issues. Some will agree, some will disagree, some will show parts of my paper are incorrect, and others will present more supporting data (at least I hope, on all counts). I suspect the next few years will feature much, much more discussion on these fascinating horned dinosaurs!

Coming Up: It is safe to say that I have had more fun with this project than with anything else I've done recently. Why is that? In part, it's been due to some very stimulating discussions with John Scannella and Jack Horner, who recently published the "Toroceratops" hypothesis. See my next post for more!

Farke, AA (2011) Anatomy and taxonomic status of the chasmosaurine ceratopsid Nedoceratops hatcheri from the Upper Cretaceous Lance Formation of Wyoming, U.S.A. PLoS ONE, 6 (1) DOI: 10.1371/journal.pone.0016196

Forster CA (1996) Species resolution in Triceratops: cladistic and morphometric approaches. J Vertebr Paleontol 16: 259–270.

Förster A (1869) Synopsis der Familien und Gattungen der Ichneumonen. Verhandlungen des Naturhistorischen Vereins der Preussischen Rheinlande und Westfalens 25: 135–221.

Hatcher JB (1905) Two new Ceratopsia from the Laramie of Converse County, Wyoming. Am J Sci, series 4 20: 413–422.

Mateus O (2008) Two ornithischian dinosaurs renamed: Microceratops Bohlin, 1953 and Diceratops Lull, 1905. J Paleontol 82: 423.

Ostrom JH, Wellnhofer P (1986) The Munich specimen of Triceratops with a revision of the genus. Zitteliana 14: 111–158.

Scannella JB, Horner JH (2010) Torosaurus Marsh, 1891, is Triceratops Marsh, 1889 (Ceratopsidae: Chasmosaurinae): synonymy through ontogeny. J Vertebr Paleontol 30: 1157–1168.

Ukrainsky AS (2007) A new replacement name for Diceratops Lull, 1905 (Reptilia: Ornithischia: Ceratopsidae). Zoosystematica Rossica 16: 292.

Tuesday, January 11, 2011

Paleo Project Challenge 2010: The Final Reckoning

Okay, folks. . .you've had three months and plenty of reminders and warnings. With that, the 2010 Paleo Project Challenge has drawn to a close. It's time to put down your pencils and hand in your tests.

What's that, you say?

You're not quite finished?

Well, here's your chance to bask in the abject humiliation of not finishing a project by the agreed upon deadline (don't worry, I'm feeling the warm glow, too). Or, if you're Dave Hone (my partner in founding and publicizing the PPC) and many of the rest of you, you can bask in the glory of advancing science. Or at the very least, not doing it any major harm.

I purposefully set my sights quite high for this one. Just like last year, I hit one square on (in fact, the reviews just came back!), and the other is going to need some work. My New Year's Resolution: don't let it be hanging around this time next year.

Below, I've given an updated list for the PPC. Those folks who are finished are marked in a congratulatory blue. The rest. . .are so close! If you completed your entry for the PPC (or didn't), drop a line in the comments, so I can mark it here! I'll be updating this entry for the next seven days.

Participants in the Paleo Project Challenge
Andy the Micropaleontologist - submit foram macroevolution paper; write draft of clade shape paper
Anonymous - find job; paper for Paleobiology; prep alligator fossil
Brian Beatty - paper on meningeal ossification in cetaceans
Robert Boessenecker
- finished first draft of master's thesis
Martin Brazeau -
finish redescription Ptomacanthus anglicus and include updated matrix
Andrea Cau
- describe new theropod remains from north Africa
John Conway
- finish Heterodontosaurus painting
- restoration of Dryptosaurus [finished]
Andy Farke
- finish paper for ODP [started!]; finish paper on ceratopsian anatomy [finished!]
Nick Gardner
- submitted grant for Youngina part II
Casey Holliday
- either a new croc species description or paper related to frontoparietal fossae [sent to coauthors]
Dave Hone - the necks paper [finished]
- finish descriptions for Katian graptolite systematic paper.
David Maas
- Illustrating Mallison's Kentrosaurus [so close!]
Heinrich Mallison - finish Plateosaurus CAE paper; sauropod rearing paper; sauropodomorph rapid locomotion paper
Jay - finished sauropod description
Jordan Mallon - Anchiceratops manuscript
Anthony Maltese - sharks scavenging on mosasaur paper; Niobrara ammonite paper
Eric Morschauser - finished theropod description
Paleochick - Cloverly paleobotany paper
Patty Ralrick - wrote paper on subfossil mass mortality site
Julie Reizner - submit Einiosaurus histology paper
Manabu Sakamoto - finish Pachyrhinosaurus drawing; finish and submit theropod bite force paper
John Scanlon - write up Oligocene lizards from Riversleigh; process and sort samples from Miocene microsite
Leo Sham - illustrate Raptorex; write cosmetic surgery review paper
Mark Spencer - finish paper critiquing model-based approaches to phylogeny reconstruction
Brian Switek - finished book proposal; polish and submit paper on Alabamornis; paper on Thoracosaurus specimen
David Tana - sign up for GRE; submit 9 pieces to Art Evolved time capsules; overhaul blog
Darren Tanke - finished biography of Oscar Erdman; finished paper on first helicopter lift of a dinosaur specimen; finished extended abstract on Hope Johnson
Mike Taylor - finally finish the Archbishop sauropod description
Matt van Rooijen - finish up Tarbosaurus bite pattern illustrations
Bruce Woolatt - 1/10 scale Quetzalcoatlus northropi flesh restoration

Sunday, January 9, 2011

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.