Monday, December 26, 2011

New Fossil Species of 2011 - A PLoS ONE Retrospective

What do sauropods, primates, crabs, cats, and crocodiles have in common? They're all animals in the fossil record that had new species named in PLoS ONE this year!

Chela (claw) of Geograpsus severnsi, from Paulay & Starmer, 2011

As 2011 winds down, I'm going to devote two posts to some navel-gazing at paleontology in the online, open access journal PLoS ONE. PLoS ONE really has been a ground-breaking publication, partly responsible for spawning the term "megajournal" as well as inspiring clones from the very publishers who invested some effort over the past few years in downplaying the worth of the PLoS ONE publishing model.

[Note before we continue: Although I do have an "official" volunteer role as one of the academic and section editors for the journal, any opinions in this post are entirely my own.]

Skull of Arenysuchus gascabadiolorum, from Puértolas et al., 2011

In any case, let's start our 2011 retrospective with a look at some of the new taxonomy that appeared this year. 17 new species of extinct organism were named on the "pages" of PLoS ONE this year, but these were not by any means distributed evenly across the tree of life.

Five out of 17 were mammals, only one was a non-vertebrate (a lonely, recently extinct land crab from Hawaii), and three - THREE!!! - were sauropodomorph dinosaurs. What kind of crazy world is this where sauropodomorph taxa outnumber crocodylimorphs, and arthropods? Dinosaurs as a whole did quite well, with seven new non-avian dinosaurs gracing the HTML code of PLoS ONE.

New Fossil Taxa Named in PLoS ONE - 2011
Arenysuchus gascabadiolorum (crocodyliform)
Boutakioutichnium atlasicus (theropod footprint)
Gaudeamus aslius (rodent)
Gaudeamus hylaeus (rodent)
Geograpsus severnsi (crab)
Kawichthys moodiei (chondrichthyan)
Khoratpithecus ayeyarwadyensis (primate)
Leonerasaurus taquetrensis (sauropodomorph)
Leyesaurus marayensis (sauropodomorph)
Linhevenator tani (troodontid)
Lycophocyon hutchisoni (carnivoramorph mammal)
Panthera zdanskyi (felid)
Paravipus didactyloides (theropod footprint)
Pissarrachampsa sera (crocodyliform)
Talos sampsoni (troodontid)
Tapuiasaurus macedoi (sauropod)
Tonsala buchanani (bird)

In 2012, I would love to see the following trends:
  • An expansion in the number of new taxa published in PLoS ONE (assuming that high scientific standards are maintained - no junk taxa, please).
  • Greater diversity in the taxonomic groups represented. Archosaurs are cool and all, but where are the plants? Where are the brachiopods? This will probably just take time, and perhaps a pioneer in each field of study to raise awareness of the journal. I first seriously considered publishing in PLoS ONE because a high-profile dinosaur worker published there, and I suspect other folks in other fields have similar thoughts.
  • More authors taking advantage of the format of PLoS ONE when submitting their new taxonomy. With few or no practical limits on figures (color, size, number) and text, every new description could potentially (and should, with few exceptions) get the monographic treatment. I am happy to say that most authors did just this, but there is always room for improvement!

Skull of Tapuiasaurus macedoi, from Zaher et al., 2011

In the next post: PLoS ONE is now a major force in paleontological publishing. What were the overall trends in 2011? What might the future bring?

Thursday, December 15, 2011

The Paleo Project Challenge

I've been woefully behind in promoting this (and Dave Hone has taken the lead in hosting it this year - thank you, Dave!), but it is time to get on with the 2011 Paleo Project Challenge. Got a nagging little project that just requires a few days of concentrated effort to finish? Quit the excuses, and just get it done! That's the whole point of this. Whether it's research, artwork, a curation project, or whatever, anything is fair game.

Dave Hone has more over at Archosaur Musings. Mike Taylor and Matt Wedel have blogged about their own contribution. What will yours be?

Thursday, December 8, 2011

Hello, Spinops!

In case you haven't yet noticed, there's a new horned dinosaur in town: Spinops sternbergorum, yet another example of the ceratopsians' incredible evolutionary radiation.

Spinops sternbergorum, as envisioned by Dmitry Bogdanov

This animal has special significance for me, because it is the first new dinosaur for which I have been senior author. In a lot of ways, that's a childhood dream coming true!

Best of all, it was a lot of fun to work with some respected colleagues. Michael Ryan (ceratopsian expert extraordinaire) and I enjoyed bouncing ideas off of each other (even if we haven't yet reached a consensus on epiparietal homology, as acknowledged in the paper), and Mark Loewen added another ceratopsian voice to the mix. Darren Tanke offered his historical perspective (particularly important for this specimen, which was found in 1916), and Dennis Braman's expertise in palynology was absolutely invaluable. All of us owe a huge debt to Paul Barret's efforts at the Natural History Museum (London), where the type material is held, as well as for his cladistic wizardry. Last but certainly not least, Mark Graham did a bang-up job with preparing the fossil. When I first saw the holotype parietal, it was upside down and embedded in plaster. Mark took this and made it beautiful!

The art was contributed by several different folks. Phil Hurst took some exceptionally high-quality photographs, and Lukas Panzarin rendered the bones with his usual finesse. Our first life restoration of Spinops was undertaken by Dmitry Bogdanov, and it deservedly has been shown widely in the press.

Speaking of art, our representation of Spinops is conservative. We don't know what the frill looked like to the outside of the big spikes, so it is quite possible that there were more than what illustrated. So to the paleoartists out there: make it as spiky as you want! Anything is possible (until we find more fossils that tell us otherwise).

The specimens of Spinops have a long and interesting history, which has been detailed elsewhere. So, I encourage you to check out Brian Switek's write-up at Dinosaur Tracking, an excellent story by John Mangels in Cleveland's Plain Dealer, a story in The Telegraph, the NHM's press page, the Cleveland Museum's press page, or my own museum's web site.

If you're looking for something completely different, check out The Gawker's take on Spinops. It's snarky and quite funny. Many folks have taken some offense at it, but I'm positively delighted to be featured amongst the celebrity gossip - the story is decidedly tongue-in-cheek!

Finally, if you're really interested in digging deeper, check out the original paper, published in Acta Palaeontologia Polonica. It's open access and free to read by anyone!

Citation: Farke, A. A., M. J. Ryan, P. M. Barrett, D. H. Tanke, D. R. Braman, M. A. Loewen, and M. R. Graham. 2011. A new centrosaurine from the Late Cretaceous of Alberta, Canada, and the evolution of parietal ornamentation in horned dinosaurs. Acta Palaeontologica Polonica 56(4):691-702. doi:10.4202/app.2010.0121 [link to the original paper]

Sunday, October 16, 2011

Should we review for any old journal?

It's no secret that academic publishers are able to cut expenses by getting free content, free review, and often free editorial expertise from the scientific community. Web hosting, copy editing, and printing costs remain, of course, so publishers cover these expenses by charging for the content - often by charging subscription and article access fees (directly or indirectly) to the very same researchers who provide their expertise for free. When some commercial publishers are generating impressive profits in spite of the bad economy, many researchers are rightfully perturbed. How should we, as a research community, respond?

Mike Taylor, writing at SV-POW! and Times Higher Education, argues that (among other strategies) scientists should refuse to review manuscripts submitted to non-open publications. To his credit, he has put his money where his mouth is (no surprise to those who know how solid Mike's character is). If done by enough people, this will surely have the desired effect of slowing down the cogs of the big non-open access journals (and making open access [OA] a more appealing alternative). But, what is the collateral damage? Is it worth it? Who would even receive the message?

I argue that, unless carefully constructed, such reviewing boycotts may never be noticed by some of the concerned parties. A typical journal editor will think "oh, Reviewer 1 refused to review. . .on to Reviewer 2." Even if the refusal to review is accompanied by a note explaining the reasoning behind the refusal, only the editor will ever see it (and potentially the publishing admins - who have little vested interest in changing the status quo).

Second, when the pool of qualified reviewers is small to begin with, this could have the consequence of letting some really bad stuff slip into publication. I've reviewed enough papers and read enough literature to know that unless I flag some manuscripts, nobody else will. (Richard has a similar sentiment in his comments at SV-POW!). Despite the schadenfreude of seeing non-OA journals become associated with increasingly substandard work, it would also mean that we're left with a mess to clean up (particularly in the case of "new" species). Profits are reported quarterly, but we have to deal with crummy taxonomy forever.

Third, the journals are not the ones hurt most directly by review boycotts; it is the authors. The journal will almost always find someone else to review the paper (with a delay as these reviewers are recruited); and if not, the manuscript will be returned for lack of qualified reviewers (with a delay as the paper is prepared for submission elsewhere). Rightly or wrongly, publications are a primary currency of academia. If getting that publication delayed means my friend or colleague doesn't get a job, or a grant, or tenure, I have hurt them, not just the profits of the journal.

There are some constructive alternatives, fortunately - given a choice, I would say #2 and #3 have the most utility and best balance intended and unintended consequences.

1) Refuse to review the paper, but fully explain why in a letter submitted directly and separately to the editor, journal, and authors. This way everyone gets the message - not just a select few.

2) Review the paper, but include a message with the review (perhaps both in the review text and in a direct letter to the authors) on the shame of the work being locked behind a paywall. Make the authors think twice about whether or not the intended audience will ever see the paper.

3) Submit your own work to open access journals, cite work in open access journals, and encourage your colleagues to do the same.

I sympathize with the sentiment that we academics shouldn't be propping up the questionable practices of some publishers, but we also need to avoid shooting ourselves (and our colleagues) in the foot as a result.

Update: Mike Taylor has posted a response to this post at SV-POW!

Thursday, September 15, 2011

Paleontology Journals - Cheers and Jeers

In my previous post, I introduced a compilation of data concerning various journals relevant to paleontologists. The data, which are freely available in Google Spreadsheet, Excel and HTML form, detail costs to readers, costs to authors, and more. In this post, I want to outline my personal opinions on the journals that I surveyed. Which have good policies for authors and readers, and which need some work? The answers may surprise you; they certainly surprised me. Some of the best-known journals in the field are not necessarily the best for those who need to use them.

A disclaimer: The opinions presented here are my own and do not represent any organization with which I am associated. Any critical comments are directed at the publishing practices of the journals, not the quality of the science or the efforts of the volunteer editors, authors, and reviewers. If I have made an error in compiling a journal information, I will happily correct it upon notification and verification. I have published in, and in some cases will continue to publish in, some of the journals of which I am critical. Although I personally would like to publish only in open access, non-profit journals, the realities of a career in science make that difficult at times.

Cheers to:
  • Journals that promote open access. Even with a delay, open access allows an increased readership (and hopefully increased citation) of articles. Although critics of OA often imply that scientific papers are just too complex for the lay public to understand, in a field like paleontology the lay public is a major consumer of our primary literature. So, cheers to journals like PLoS ONE, Palaeontologia Electronica, and Proceedings B, who practice and promote open access. Even some commercially-published journals (e.g., The Anatomical Record) deserve special mention for their OA efforts.
  • Journals with reasonable download fees. Although every journal would be free and open access in an ideal world, it does cost money to run a publication. I salute those journals of various sizes and business models that keep their per-article download charges at $15 or less; this includes Canadian Journal of Earth Sciences, Journal of Paleontology, Paleobiology, PNAS, and Science. Here's your next challenge, journals: lower the price to $5. I would predict that this is the tipping point in the balance between price and convenience for many readers of the paleontology literature.
Jeers to:
  • Journals that charge ridiculous fees for per-article downloads. I'm especially looking at you, Journal of Vertebrate Paleontology. $41 for a PDF of a one page taxonomic note?! Not even Cretaceous Research, owned and published by the oft-maligned Elsevier, charges that much ($37.95). Somehow or another, Journal of Paleontology only charges $12 per article. I realize that different journals have different goals and revenue streams, but it is absolutely unseemly that a society journal like JVP charges that much for its articles. One wonders how many potential purchases (and thus society revenue) are lost in the face of the fee.
  • Journals that only allow authors to publish the pre-peer reviewed version of a manuscript. Journal of Morphology and The Anatomical Record get this dubious honor. I can understand asking authors to delay posting the unformatted manuscript or to refrain from posting the published PDF (to allow the journal to recoup some revenue), but it makes no sense to prevent entirely the authors from posting the peer-reviewed, unformatted version. Given the sometimes substantial changes introduced during peer review (which is done by volunteers, and nearly always coordinated by volunteer editors), posting of an unreviewed manuscript has too much potential for making the author as well as the journal look bad. The Journal of Morphology is a particularly egregious offender. I feel a little bad listing The Anatomical Record in this category, because they do have default OA after one year.
  • Journals that lock supplementary information behind paywalls. Erecting paywalls for supplementary information may, in some cases, keep the data out of sight of legal readers. Someone who has only a paper reprint or PDF of the printed work legally obtained from the author, or a hard copy in the journal library, cannot access supplementary data. Keep in mind that most journals only minimally format the data, if at all, for publication, so there is no real value added by the publisher beyond posting it on the server. Prime offenders in this category include Journal of Vertebrate Paleontology, Canadian Journal of Earth Sciences, Historical Biology, and Cretaceous Research.
Top contenders in various categories:
  • Most reader friendly. Criteria: Cost of download, time to OA. Top picks: Acta Palaeontologica Polonica, Palaeontologia Electronica, PLoS ONE, PalArch's JVP. Runners up: PNAS, Science.
  • Least reader friendly. Criteria: cost of download, availability of supplementary information, availability of open access and/or author versions. Bottom picks: Journal of Vertebrate Paleontology, Historical Biology, Cretaceous Research.
  • Most author friendly. Criteria: OA fee and/or fee waiver, maintenance of author rights, impact factor. Top picks: Acta Palaeontologica Polonica, Palaeontologia Electronica. Good bets: PLoS ONE, PalArch's JVP.
  • Best all-around journals: These journals balance needs of the author and reader, using the criteria above. In this case, Acta Palaeontologica Polonica and Palaeontologia Electronica are at the top of the list.
  • Best Glamour Magazine: Science, by a long-shot. With the high impact factor that authors crave, and the low download fee and eventual open access that readers love, this journal has the entire package. PNAS is a very close runner-up.
*I would note that PaleoBios may be making some additional changes to propel themselves into the "best all-around journal" category; details will be added when available.
**I would also note that by "readers", I am referring to all possible readers, not just those with society memberships or at institutions with well-stocked electronic libraries.

So Now What?
Vote with your manuscript submissions. Submit only to journals whose policies benefit you. Encourage journals with non-friendly policies to change them. Although it may be tough to change strictly for-profit journals, we may be able to make a difference with society publications. Speak up. Blog about it. Talk to your colleagues. Ask the hard questions of the people who make the decisions. Make a noise at the annual meetings. Let's even the publishing playing field!

Update: Heinrich Mallison posted a nice response to the selection of Palaeontologia Electronica as one of the "best all-around journals" for paleontology, over at their official blog.

What are your thoughts? Weigh in with your own nominations for best/worst, or any additional opinions, in the comment section!

Thursday, September 8, 2011

Paleontology Journals - Policies, Costs, and Accessibility

When preparing to submit a paper for publication, journal choice is critical. Numerous factors play into the decision (distribution, audience, accessibility, and cost, just to name a few), as has been outlined in wonderful detail elsewhere. As I advance in my own research career, publisher behavior has become more important to me. Does the publisher of the journal to which I am submitting my manuscript conduct its business in a manner consistent with my own personal ethics? Who will have access to my research, and how much will it cost them? This is a tough question to sort out, and in reality there are no perfect players. However, in order to make this decision just a little easier, I assembled data about a number of journals relevant to my own research program.

The full data are posted on a freely-accessible Google spreadsheet, and this post explains each of the categories I recorded. Although I have a personal bias towards open access, I have attempted to present the data in the spreadsheet without commentary. Every person will have his or her own opinion about which factors matter most to him or her. In a follow-up post, I will provide my own opinions on which journals are "best". For now, please make up your own mind.

  • Title: self explanatory
  • Publisher / Distributor: This category indicates which organization distributes the journal; this may be the same as the sponsor of the journal, or the work may be contracted to an outside organization.
  • Publisher Status: Is the publisher a non-profit or for-profit entity? Some non-profit organizations publish their journals with a for-profit publisher, and some journals are purely non-profit or for-profit.
  • Sponsor: As alluded to above, some journals are ultimately coordinated by a scientific society. I understand that some scientific societies receive a portion of the profits from the for-profit publishers, so a journal published by a for-profit entity may not always be a net loss for scientific funding. However, I would caution that no data are available on what percentage of revenue actually reverts to societies.
  • OA (Open Access) Default: Some journals automatically post all articles as open access (either immediately or with a delay; indicated as "Yes" on the spreadsheet). Others have open access options only if the authors pay an extra fee (indicated as "No" on the spreadsheet).
  • Time to OA: Some OA journals (e.g., PNAS) have closed access for a set period of time (usually one year), and then automatically open the archives.
  • OA Fee & OA Fee Waiver: Most journals, even those that are not entirely OA, require a fee for open access. The fee varies from free (e.g., Acta Palaeontologica Polonica) to $3,250 (Historical Biology). In some cases (e.g., PLoS ONE) a fee waiver is available. For delayed OA journals (e.g., PNAS), the fee allows immediate OA posting of the article, rather than free OA after a set amount of time.
  • Download Fee: Delayed OA or non-OA journals require that non-subscribers (or those who do not have institutional access) pay a per-article charge. Within paleontology-focused journals, the cheapest is Journal of Paleontology ($12), and the most expensive are Journal of Vertebrate Paleontology and Historical Biology ($41).
  • Free Supplementary Data: Increasingly, authors rely on supplementary data to publish and disseminate the measurements, cladistic tables, etc., supporting their papers. Most journals allow non-subscribers to access supplementary data; others (e.g., JVP and Cretaceous Research) require purchase of the entire article (even if the user already has obtained a legal copy as a physical reprint or PDF from the author).
  • IF: The "Impact Factor", the most "standard" (if opaque) form of which is calculated by Thomson Reuters, is a measure of the extent to which the articles within a journal are cited. Although this metric is often criticized, it is still an important consideration for many authors, and is thus included here.
  • Primarily Paleo?: In assembling this list, not all of the included journals are strictly paleontology-focused (e.g., Proceedings B, Nature). However, because they frequently include paleontology content, I felt it useful to include them.
  • Author Rights: Publishers vary greatly in the rights that are left in the hands of the authors. Although copyright issues are certainly important (i.e., whether the copyright remains with the author, or is transferred to a commercial publisher or professional society), here I focused on what the authors are allowed to do with their own work in the context of a personal (or institutional) web page. In some cases, the authors may post the final published PDF; in others, the authors may only post the unformatted text. In the most restrictive case (as mandated by the journal Geology), authors are not allowed to post any version of the article.
All information was drawn from the official web pages for the various journals; any errors are unintentional but possible, due either to my own misinterpretation or updated journal policies. If you find any mistakes, please let me know, and I will do my best to correct them. This list is not intended to be exhaustive by any means; instead, it focuses on the journals of most personal interest.

See the Data:
To view the spreadsheet, you can see the freely-available Google Spreadsheet, or an Excel spreadsheet, or this web page.

Coming up: Which journals do I think deserve applause for their policies?

Wednesday, September 7, 2011

The OSP on Twitter

For the past few months, I have begun to switch much of my regular on-line communication to Twitter. Like this blog, my Twitter feed (@andyfarke) covers open access issues, recent paleontological discoveries, and the like. I am a bit of a late adopter, but have to say that I'm generally finding it quite useful. If you're not a Twitterhead, you can read the most recent posts in the blog sidebar.

Upcoming post: A survey of open access policies, OA fees, data availability, and the like for many major paleontological journals.

Friday, September 2, 2011

How do you read the literature? Thoughts on academic maturation

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

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

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

I hit this stage during high school and college.

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

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

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

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

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

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

Tuesday, June 28, 2011

How to Inspire a Future Paleontologist

I was sorting through some files today, and found this. Back when I was 10 years old, I knew I wanted to devote my life to paleontology, and paleontology research would be even better. So, I started writing letters to researchers I had read about in books and magazines. Some didn't respond (everyone is busy, so I can't fault them too much), and some sent really nice replies. It's those replies that propelled me into a serious career as a paleontologist. Thank you, to those who wrote back.
Little did I know that I would be visiting those collections as a researcher, only 10 years later

Friday, April 8, 2011

Life After Death At Yellowstone: An Interview with Josh Miller

ResearchBlogging.orgIn my last post, I introduced a ground-breaking study recently published in PLoS ONE, that shows how we can infer long-term trends in animal populations just from their bones. This work has big implications for ecology, conservation, and public policy, and is also a really neat piece of science. For this post, I talked to the author of the study, Josh Miller, about his work and some of the tidbits that didn't make it into the paper.

Yellowstone NP gets a lot of visitors, and you surely must have had some interactions with them during your fieldwork. How did they react to what you were doing?
JM: I work in areas that are generally well off trail and in places most Yellowstone visitors just don't see. Over the years, there are have been very few times when tourists actually ever saw my teams conducting our bone work. Most of the time, conversation with the public occur in the evenings back at camp. We generally use the public campgrounds for our homebases and my research will often come up in conversation with tourists. When folks learn what my teams and I are up to, they are always very interested and ask lots of questions. Our National Parks are an important resource, and I think people like to be reminded of their biological and scientific value. At the same time, I think it gives folks a way of looking at Yellowstone in a new and exciting way. I know lots of people who talk to us one day and keep an eye out for bones the next.

Miller studying bone survey data sheets on Northern Range, Yellowstone National Park. Photo by Scott Rose.

You looked at hundreds of bones during your survey. Was there any particular specimen that stuck out in your mind? What about it was interesting?
JM: I looked at over 20,000 bones during my work in Yellowstone. And you are right, there are a few that really stand out. Some of the most memorable bones are those of animals with severe bone maladies. In some individuals we found severe arthritis or broken bones that didn’t heal properly. Other memorable bones include rare and unusual species. One of the most exciting finds was the skull of a mountain lion. We just stumbled upon on it one afternoon walking from one transect to another. This beautiful rounded huge cat skull just lying in the grass staring up at us –a rare and amazing site.

This paper focused on bones from large animals, but surely there are a lot of small animal bones out there too - rodents, bats, rabbits, etc. Do you think they would show a similar correlation over time between abundance in life and death? Or are the taphonomic effects too different between large and small animals to expect the same pattern?
JM: Stay tuned! I kept careful attention to the bones of the small mammals we found. My bone survey teams were amazingly good at finding bones of all shapes and sizes (from bison skulls to limb bones of squirrels). One of the challenges, unfortunately, is the lack of high-quality data on the living populations in Yellowstone. One thing I'll say at the moment, however, is that the record of small-bones is surprisingly rich and diverse on the Yellowstone landscapes.

I see that you used the open source stats program R to do your data analysis. Was this something you picked up just for your dissertation work? Why did you choose R over some of the other commercial packages that are out there?
JM: I was introduced to R during the early days of my graduate work. R is a very powerful statistics language, in part, because of the large community of scientists and academics that use R and contribute to its ever-expanding utility. Another reason I use R is that I can completely control all aspects of the analysis. In canned programs, much of the analysis sits under a black box and uncovering exactly how the data were analyzed can be very difficult. But most of all, R just fits how I do science.

Thank you for your time, Josh!

Miller, J. (2011). Ghosts of Yellowstone: Multi-Decadal Histories of Wildlife Populations Captured by Bones on a Modern Landscape PLoS ONE, 6 (3) DOI: 10.1371/journal.pone.0018057

Note: I'm an academic editor at PLoS ONE, but had no role in the handling of this paper.

Sunday, April 3, 2011

Life After Death at Yellowstone

ResearchBlogging.orgTaphonomy - the study of what happens to an organism after it dies - is integral to reconstructing the past. Perhaps the most important lessons come in inferring ecological interactions. Did that group of animals live and die together, or were they jumbled long after death? Were all of those shark teeth with the plesiosaur bones from a feeding frenzy, or just a fluke of currents? How closely does a set of fossils represent the relative abundance of the different species during their lifetime? Such examples are numerous, and thus we commonly think of taphonomy as a study in deep time. This is certainly true, but also certainly incomplete. In fact, some of the most ground-breaking taphonomic work has been done in contemporary ecosystems. Kay Behrensmeyer, for instance, has spent decades studying bone accumulations in Kenya, and a 1927 work by Johannes Weigelt (complete with photos of dead cattle) is still considered a classic.

A new study by paleontologist and taphonomist Josh Miller, just published in PLoS ONE, shows some of the great insights that can arise from looking at taphonomy in modern settings. Josh and his field assistants trekked through Yellowstone National Park (one of the western USA's oldest and best-known parks), cataloging the identity and physical condition of every animal bone sitting out on the surface (an elk skeleton from the project is shown at right; photo courtesy of and copyright Josh Miller). Using these data, Josh found that you can actually infer the major ups and downs of animal populations from their old bones. This is quite exciting, not just from a gee-whiz factor, but because it may be possible to infer population trends for areas where historical surveys are absent or spotty. Such data are important not only for ecologists, but for informed public policy. It sounds magical, so how was the study done?

Based on other studies (in combination with radiometric dating), it's known that bones in excellent condition usually came from animals that died only recently, whereas bones in crummy condition are from animals that died longer ago. By using the condition of the bones as a proxy for time since death, Josh estimated how long the various bones of various animals had been around. Then, based on the bone ages, he estimated the relative population of each type of animal a given number of years ago. We have very good wildlife census data for Yellowstone, and it turns out that estimates from the bones match the "real" values quite nicely. Boom years for animals (such as elk) mean lots of bones going into the system, bust years mean few bones, and these trends shows up in bone surveys.

You can read all about it at PLoS ONE, or here, here, and here. I recently talked to Josh to get a few behind-the-scenes tidbits. Stay tuned for the interview later today! [update: now posted here]

Miller, J. (2011). Ghosts of Yellowstone: Multi-Decadal Histories of Wildlife Populations Captured by Bones on a Modern Landscape PLoS ONE, 6 (3) DOI: 10.1371/journal.pone.0018057

Note: I'm an academic editor at PLoS ONE, but had no role in the handling of this paper.

Monday, March 28, 2011

Building Momentum for Open Data in Paleontology

Thanks to a variety of "real world" concerns and deadlines, I've been a little sparse on the blog for the past few weeks. But, that doesn't mean that important things haven't been happening elsewhere in the realm of digital paleontology. If you haven't already, take a look at and consider adding your signature to "An Open Letter in Support of Palaeontological Digital Data Archiving." Kudos to the folks who got the ball rolling on this effort! As paleontology becomes more data driven, and as more of those data are digitized, we need to get our act together as a community now.

Tuesday, February 22, 2011

Data Archival and the JVP

It finally happened - Journal of Vertebrate Paleontology has taken a few more tentative steps into the 21st century! Both in an editorial in the most recent issue (note: full text is paywalled), as well as in an updated version of the instructions to authors, the journal has announced a formal data archiving policy.

What does this mean?
Quoting from the JVP's new instructions to authors, "all data files needed to replicate phylogenetic or statistical analyses published in the journal should be made accessible via the JVP website as online supplementary material." In other words, if you analyzed numbers of any sort, you need to show your source data. This includes cladistic matrices (publication of these is already standard practice) as well as measurements or other data used in statistical analyses. Additional kinds of data - for instance, extraneous measurements unrelated to the study, raw field notes, or raw CT scans - are not included in this proposal (even if it's good scientific practice to make sure this information is available for posterity).

Why is this a good thing?
  • Data archival allows others to build upon previous work more easily. For instance, let's say I publish a statistical analysis of molar size in the early horses Mesohippus bairdi and Mesohippus westoni. Maybe there is another worker out there who wants to look at variation in some other Mesohippus species. If my dataset is available, it is much easier for another research to quickly advance beyond my work (assuming they trust my data, of course - see below).
  • Data archival allows new and unexpected uses for data (thus increasing citations). My p-values and arithmetic means of Mesohippus teeth are interesting, but not that useful outside the context of my paper. If I publish the raw data, though, other individuals can use these data (and cite my paper) in all other sorts of contexts. Maybe someone wants to throw the data in her study of horse tooth evolution (hey, it's another citation!). Maybe someone else is interested in Oligocene herbivore ecology as evidenced in molar properties (and there's another citation!).
  • Data archival ensures transparency. Everyone makes statistical or analytical mistakes. Unfortunately, these mistakes may render the results of a paper highly suspect at best, or worthless at worst. With the availability of raw data, it is much easier for someone to reproduce a study or correct misuse of statistics. (as a case study from my own work, I discovered that nearly all paleopathology studies in the literature were using incorrect statistical assumptions - and a reanalysis of the data forced some new interpretations!) Additionally, taxonomy frequently changes, meaning that previous categories applied in an analysis are hopelessly outdated. Not so, if you can go back to the author's original data, make a few corrections, and rerun the analysis!
  • Publicly funded research deserves to be public. So much of paleontology research is funded by government grants, or conducted on company time. It is not a good use of our limited resources to keep data locked up after the original study has been published. This is somewhat analogous to writing an NSF grant to collect fossils for one's personal collection. Why should data be any different?
Answers to some common objections
  • "I have other plans for the data." Some researchers want a monopoly on their data. They have this fear in the back of their head that someone is going to go out and do exactly the same next step study planned by the original researcher. I have several responses to this. First. . .really? Second, I would remind authors that it is bad science (perhaps even unethical) to publish research results that are not transparent to scrutiny. Third, I would remind authors that they are never obligated to publish all of the tangential data. If you are publishing a paper on dentary lengths in hadrosaurs, you don't have to release the data on predentary dimensions too! Finally, I would remind authors that this is just a lame excuse to put off their own follow-up research. We all know the stories of this or that researcher who has sat on a dataset for years. Science is not being helped by keeping those data secret.
  • "Interested researchers can just contact the authors." As an example of why this is a bad idea, please refer to the work of Leonard Radinsky. He published a number of wonderful morphometric studies of fossil mammals, clearly based on hundreds of measurements. But, he also passed away in 1985. Unless you have a Ouija board that actually works, it's highly unlikely that anyone will be able to exactly reproduce the results in his oft-cited "Ontogeny and phylogeny in horse evolution." Authors leave academia, pass away, or lose their data sheets all of the time. It's a pipe dream to assume that "data are available upon request." [to be fair to Radinsky, his paper did not indicate that the data were available - I just chose it as one prime example where the data are probably irrecoverable]
  • "It just encourages lazy research by data miners, because you should never trust anyone else's research data." There is a grain of truth in this - inter-observer error may creep into measurements, and maybe a certain author likes to measure plaster reconstructions. But once again, this is just a lame excuse for lazy research by the person who is objecting to data transparency! After all, if you can't trust the data, you can't trust the paper, so what's the point in publishing? It's a slippery slope. The benefits far outweigh the drawbacks.
  • "It's just more work for the authors." This too falls into the "lame excuse" category. If you've already gone to the trouble to put together an Excel spreadsheet for your statistical analysis, you can spend an extra 10 seconds transferring those data to the manuscript submission system. If it takes you longer than that, you may want to reconsider your data management practices.
Recommendations for JVP
I have just a handful of recommendations for the editors at JVP, based on my own experience as both a data user and a data generator. Some of these suggestions may already be incorporated, and others may be planned. Others may be impractical at this time. Either way, I think it is helpful to consider the following:
  • Make sure the data files are in a usable format. Historically, supplemental information at JVP has been launched as PDF files (with some NEXUS files). This is great for casual reading, but horrible for analysis. Just try copying 3,382 measurements from a PDF table into an Excel spreadsheet, and you'll see what I mean. This does not mean you need to choose a single format - why not have the data in PDF, Excel, and raw text? Multiple formats ensure maximum usability of the data across multiple platforms (as well as flexibility in the face of future software upgrades).
  • Consider a data embargo for reluctant authors. Many journals allow a six month or (maximum) one year embargo on supplemental data, to allow authors the chance to finish up any outside projects. Although I philosophically disagree with this option, I see its utility. And, it is an appropriate compromise between protecting author rights and protecting scientific integrity.
  • Consider partnering with DRYAD or a similar data repository. A number of other evolutionary societies are doing this - why shouldn't SVP be a part of this?
  • Solicit society input. The members of SVP and the authors of JVP probably have some great thoughts on what they would like to see in data archival. Why not solicit input from the community to find out what the community needs? This will only solidify ownership of the data archival efforts by paleontologists!
  • Check out a recent publication on this very topic. Michael Whitlock recently published a great review article [paywall] on best practices in data archival - many of the points mentioned above are contained there. (thanks to Randy Irmis for passing the link along)
The Last Word
All in all, I am pleased to see JVP take these steps. Congratulations to the editors of the journal, for taking this stand for good science!

More Reading
Berta, A., and Barrett, P. M. 2011. Editorial. Journal of Vertebrate Paleontology 31: 1. doi:10.1080/02724634.2011.546742 [paywall]

JVP Instructions to Authors [link to pdf]

Whitlock, M. C. 2011. Data archiving in ecology and evolution: best practices. Trends in Ecology & Evolution 26: 61-65. doi:10.1016/j.tree.2010.11.006. [paywall]

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