The Open Source Paleontologist

ScienceOnline2012 - Parting Thoughts

2012-01-22T11:00:00.000-08:00

My thoughts on Days 2 and 3 of ScienceOnline2012are found elsewhere - here I sum up some other impressions.

Twitter at ScienceOnline
This is the first time I've actively tweeted through an entire meeting, and found it to be a worthwhile addition. It was cool to see what other folks in my sessions were thinking (at times it was like passing notes in class), and also nice to be able to follow the sessions in other rooms. Over 300 active users participated (on and off-site), and over 17,000 tweets discussed the meeting (see this cool summary map)! It's this broad participation that took Twitter from just being a small piece of the meeting to an essential component - an important observation for groups like Society of Vertebrate Paleontology that might want to acknowledge (or even encourage) Twitter.

Some thoughts on the state of blogging
One perception I have after ScienceOnline 2012 is that blogging - as an activity and as a medium of communication - seems to have reached a relatively mature state. Sure, there are incremental advances and changes, but by and large I don't really get the sense that there is much substantively new going on (other than new people joining the blogging fold on occasion). This is somewhat reflected by the blogging-relevant sessions at ScienceOnline2012 - they are much the same kind of stuff you might have seen at ScienceOnline 2010, or 2009, or 2011. Topics like getting students involved in blogging, increasing acceptance of blogging in academia, use of images on blogs, etc., are important but really not much advanced beyond where we were a few years ago. [brief note - this should not be interpreted as me saying that I think things are just OK as they are - in fact, it is a rather sad thing that some of these issues are still issues!]

I don't mean this as a criticism, but just a state of how things are. In fact, stability is partly a good thing in that someone new to the world of blogging can jump in with clear role models, expectations, and pathways to success (whatever success may be). Many of the broad principles have been laid out, and now we're working on refining the details. Some big issues do remain (we can always increase the acceptance of quality blogging for academic career advancement, for instance), but many of these will probably just require the imperceptible cultural shifts that happen over time.

Some thoughts on the state of online science
Perhaps it just reflects my own intellectual trajectory, but it seems like we're approaching some measure of stability for many of the old issues in science communication. Open access - important, but not really novel anymore. Blogging - same thing. Social media - ditto. As all of these trends started, I took a wait-and-see approach before engaging myself. As such, I have missed out on getting in at the very, very beginning of some trends, but have also avoided wasting time with trends that haven't much gone anywhere or have fizzled out (e.g., SecondLife and GoogleWave, to name just two). Based on my attendance at ScienceOnline 2012, the areas to watch include:

Crowdfunding: Small donations can add up to decent funding for a focused project, and present unique outreach opportunities. In a field of shoestring budgets like paleontology, I see crowdfunding as a potentially important new trend.
Article-level metrics and data set archival and citation: I've tied these two topics together because they reflect a major advance beyond the old journal-level metrics like Impact Factor. Neither topic is completely new, but I saw plenty of new tools at ScienceOnline that may move the discussions and usage of these metrics forward. Furthermore, there is still a long way to go for community buy-in.

There may indeed be some major issues to watch in science art or writing that I have missed because I'm not really plugged in to those communities, so please comment if there is something I missed!

ScienceOnline2012 - Day 3

2012-01-21T19:36:00.000-08:00

In Day 3 of ScienceOnline 2012 (my second day), we had a fun mix of split sessions and common gatherings. Areas of interest for me included:

Students as Messengers of Science: This discussion focused on how to engage high school and college students in science blogging. There are no easy solutions, but there were some tips to get them started. In particular, planning is key. What is the goal? Who are the potential readers?
Why the Resistance to Science Blogging? This session was pretty much as advertised. Unfortunately, there was little new here - yes, there are downsides to putting yourself out there on a blog, but for the most part it seems like it will just take slow attrition of the skeptics to normalize blogging for non-blogging scientists. Same issues as in 2011, 2010, 2009. . .but little in the way of new solutions. One good piece of advice, though: should we put blogging activity on our CV, and if so how? In many cases, there are impactful ways to describe this activity - online outreach editor, web editor, etc. These or similar terms can be honest, accurate descriptors that are more positive for those who might be instinctively averse to the word "blog."
Raising Money for Your Science and Journalism with Crowd Funding: This session filled in many of the details related to yesterday's demo - and was quite interesting. One clear worry is that crowd funding in science could be hijacked by "stodgy" forces that try to impose NSF-style limitations on the crowdfunding community (e.g., layers of vetting by experts, etc. - in fact, I think the odds are quite good that someone will un-ironically submit an NSF proposal in the near future to put together a service to validate and serve as a clearinghouse for crowdfunding science). This could have the chilling effect of squeezing out small players in favor of big institutions that are already comparatively well-funded. Vigilance is required - and the situation will doubtlessly change rapidly over the next few years. Either way, it has cool potential.
CyberScreen Science Film Festival: Again, what the label says. I'm hoping to find a link to a list of the films - there were some really excellent ones.
Closing Plenary Panel on Scientist/Journalist Relations: This isn't a new topic (see here for one recent post), and is getting a little tiresome for many. Lots of discussion, little movement from either side. My thought is that the real problem is not with the journalists or scientists at ScienceOnline, but the reporters who aren't science specialists, or who just copy press releases, or who throw stuff together without contacting relevant scientists.

Next. . .parting thoughts.

ScienceOnline2012 - Day 2

2012-01-20T20:24:00.000-08:00

ScienceOnline is really one of those unique experiences - explicitly set up as an "UnConference," it encourages freewheeling input from all attendees, bursting the bounds of conventional presentations. In fact there really aren't presentations in the conventional sense. The presenter is only a facilitator; everyone else is encouraged to join in the conversation. As such, it is both a disconcerting and intensely rewarding experience.

In my second trip to one of these unconferences (see here for my report on the last trip), ScienceOnline 2012 has proven to be worth every instant of invested time. It's been enjoyable to meet the faces behind the websites, interact with science media types (both bloggers and "conventional" reporters), and learn about the current trends in doing science in the internet age.

Work scheduling meant I had to miss the first day of the conference (disappointing, as there were some good sessions), but I was happy to drop in Day 2. Some highlights of the sessions included:

Saying howdy to the infamous Bora Zivkovic - a tireless promoter for science on the internet, and arguably one of the most influential individuals out there in the new science communication landscape (Bora is the reason why I'm involved with PLoS ONE!).
Seeing a presentation from the talented high school students behind Extreme Biology Blog. It's tough to balance the demands of being a high school student and being a blogger - but blogging can clearly be a good component of the curriculum.
Learning about FigShare.com - a newly revamped way to share all sorts of data (not just figures!). This looks to have some great potential, especially once the long-term archiving is worked out (which seems to be on the near horizon)
Learning about ROMEO, a clearinghouse for summaries of publisher policies - a great place to find out whether you can post a copy of your paper on your own site, for instance.
ORCID is an upcoming service to assign unique identifiers to researchers. Launching later this year.
Annotum is a WordPress plug-in to allow writing, peer-review, editing, and publication of scientific papers.
SciFund is a way to crowdfund research projects. But, it's not just about collecting dollars - the most successful fundraisers made a solid outreach connection with the public.
I really enjoyed visiting with some of the other paleontologists here. It is nice to see other paleo folks on the ScienceOnline bandwagon, but also a little distressing how out of touch many of our colleagues are with the world of online outreach!

One interesting observation is the slight change in feel of the conference from 2010. Back then, scienceblogs.com was the reigning champion of science communication - and to be honest, parts of the 2010 banquet felt like a string of in-jokes between a handful of bloggers. As the landscape has shifted, it feels as if things are a little more inclusive. All in all, a good thing! ScienceOnline2012 is a little bigger, but it has retained all of the charm and good qualities that made ScienceOnline2010 a useful, fun experience. Kudos to the organizers and presenters!

New Fossil Species of 2011 - A PLoS ONE Retrospective

2011-12-26T11:29:00.000-08:00

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?

The Paleo Project Challenge

2011-12-15T13:26:00.001-08:00

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?

Hello, Spinops!

2011-12-08T11:30:00.000-08:00

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]

Observations on SVP

2011-11-06T10:22:00.001-08:00

Should we review for any old journal?

2011-10-16T07:19:00.000-07:00

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!

Paleontology Journals - Cheers and Jeers

2011-09-15T07:00:00.000-07:00

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!

Paleontology Journals - Policies, Costs, and Accessibility

2011-09-08T20:34:00.000-07:00

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.

Categories

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?

The OSP on Twitter

2011-09-07T06:00:00.000-07:00

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.

How do you read the literature? Thoughts on academic maturation

2011-09-02T06:30:00.000-07:00

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

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

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

I hit this stage during high school and college.

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

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

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

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

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

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

How to Inspire a Future Paleontologist

2011-06-28T09:30:00.000-07:00

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

Life After Death At Yellowstone: An Interview with Josh Miller

2011-04-08T10:30:00.000-07:00

In 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!

Citation

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.

Life After Death at Yellowstone

2011-04-03T21:56:00.000-07:00

Taphonomy - 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]

Citation
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.

Building Momentum for Open Data in Paleontology

2011-03-28T14:30:00.000-07:00

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.

Data Archival and the JVP

2011-02-22T19:07:00.001-08:00

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]

Nedoceratops - Random Thoughts

2011-01-27T15:30:00.000-08:00

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 OpenOffice.org 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)!

Nedoceratops - Fun with Science

2011-01-26T17:30:00.000-08:00

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.

Nedoceratops - A Full Description at Last

2011-01-25T20:30:00.000-08:00

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!

Citations

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.

Paleo Project Challenge 2010: The Final Reckoning

2011-01-11T06:32:00.000-08:00

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
DeinonychusDinosaur - 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]
Jason - 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

Citation Format Wars

2011-01-09T08:12:00.000-08:00

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:

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.
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.
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.
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.
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:

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.
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. . .
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.
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.

Last Day of the Paleo Project Challenge!

2010-12-31T10:09:00.000-08:00

As 2010 draws to a close, so does the 2010 Paleo Project Challenge (PPC). It sounds like some folks are doing well, others haven't made much progress, and others have made some. We'll have the final check-in next week!

Common Mistakes in Scientific Writing [or, A Pedant's Paradise]

2010-12-26T13:06:00.000-08:00

In scientific writing, proper terminology is everything. I learned early on that many of my favorite turns of phrase were technically incorrect - and I have been working to improve my writing and editing ever since. Below, I've included some of my "favorite" stylistic oddities. . .hopefully this is useful for at least a few readers! This may be old hat for some of you - in that case, please post a comment with your own grammatical grumblings.

"Outcrops" as a verb

Despite rampant misuse, there is no verb form of "outcrop."

Incorrect: "The Barstow Formation outcrops in southern California."

Correct: "The Barstow Formation crops out in southern California."

"Monophyletic clade"

A clade is, by definition, monophyletic. So, save your space and only use one of the two words!

Incorrect: "Dinosauria is a monophyletic clade."

Correct 1: "Dinosauria is monophyletic."

Correct 2: "Dinosauria is a clade."

"Data is. . ."

The word "data" is plural; "datum" is the singular. You're bucking against popular culture, but think of how delightfully smug you can feel whenever you use the words correctly.

Incorrect: "The data is overwhelming."

Correct 1: "The data are overwhelming."

Correct 2: "The datum is overwhelming, which is odd because it's only a single measurement."

"e.g." and "i.e."

"E.g." is an abbreviation from the Latin "exempli gratia", basically translating as "for example." "I.e." is the abbreviated form of the Latin "id est", translating as "that is." The meaning for the former should be pretty clear; the latter is used when one wishes to provide further clarification of a point.

Incorrect 1: "Many dinosaurs are found in the Hell Creek Formation (i.e., Triceratops and Tyrannosaurus)."

Correct 1: "Many dinosaurs are found in the Hell Creek Formation (e.g., Triceratops and Tyrannosaurus).

Incorrect 2: "Bird skeletons are pneumatized; e.g., they are filled with air sacs."

Correct 2: "Bird skeletons are pneumatized; i.e., they are filled with air sacs."

Lower/Upper vs. Early/Late

Unless you have had a solid introduction to geology (and even then, it's easy to forget), most people probably don't know that there is a major nitpicky difference between Upper Cretaceous and Late Cretaceous. The Upper/Lower designation refers to lithostratigraphic divisions of rocks; they are not the same as the geochronologic ages of the rocks. In other words - Upper Cretaceous refers to a physical lump of sedimentary rocks; Late Cretaceous refers to the age of these rocks. Whenever I try to figure out which word to use, I concentrate on whether I'm talking about time (Early/Late) or position in the rock column (Lower/Upper).

Incorrect 1: These Early Cretaceous rocks are full of fossils.

Correct 1: These Lower Cretaceous rocks are full of fossils.

Incorrect 2: Tyrannosaurus is Upper Cretaceous in age.

Correct 2: Tyrannosaurus is Late Cretaceous in age.

Want some more? The style guide for Journal of Vertebrate Paleontology (available in PDF format) has lots more great hints and tips!

Back to the Late Jurassic, With Chris Noto

2010-12-13T08:43:00.000-08:00

If you ask the average person to imagine the Age of Dinosaurs, odds are quite good that they might envision a scene from the Morrison Formation. This Late Jurassic-aged (156 - 147 million year old) rock unit of the western United States has given us such dinosaur greats as Stegosaurus, Apatosaurus, Allosaurus, and more. Many of these animals are known from exquisitely-preserved, complete skeletons - and thus their anatomy has been described in pretty ridiculous detail. The functional morphology (how these animals moved, breathed, ate, and fought) has also gotten a lot of attention. But, this only tells us about the individual lives of the organisms. To really understand their world, we need to think bigger.

Chris Noto, my friend and academic brother (we had the same Ph.D. advisor), has devoted his scientific career to a big-picture understanding of dinosaur ecology. He has a special place in his heart for the dinosaurs of the Morrison Formation, and has been chipping away at their ecology for quite awhile now. Thus, it was really exciting to see his recent co-authored paper in PLoS ONE, about that very topic. Also of note was that this paper served as Chris's contribution to the 2009 Paleo Project Challenge!

Chris was kind enough to offer a little behind-the-scenes look at his project and the research results. I hope you'll find it enlightening!

How did you get the idea for your project?
Well, this involves going back a ways. I have always been fascinated by extinct organisms, particularly what they were like as living, breathing individuals in their environment. As an undergraduate at the University of Chicago I had the privilege of working with two really great scientists: Paul Sereno and Fred Ziegler. Paul is a well known paleontologist who has worked all over the world. Fred’s work was responsible for many of the paleogeographic and paleoclimate maps used today. Working with Paul got me thinking about how dinosaurs varied over space and time; working with Fred introduced me to global climate patterns and changes in continental arrangement.

Once I got to graduate school at Stony Brook University I was taught the fundamentals of ecological theory. I started formulating an idea for looking at variation in dinosaur communities (the collection of all the different types of organisms that live in an area) and how those differences may be related to climate, but wasn’t sure how to approach it. Enter my good friend (and coauthor) Ari Grossman, who suggested applying this method, called Ecological Structure Analysis, commonly used in the study of fossil mammals. After some discussion on the appropriate way to adapt this method to the type of information available for dinosaur fossils, we agreed to work together on this project.

What was the most challenging part of writing the manuscript?
Like many papers, this one languished half done for many years. This was a side project of ours, and unfortunately our dissertation research had to come first. Every time I started working on it again I would realize that the data needed to be changed or updated, and this would sometimes change the results and our interpretation. I am a stickler for details and want to make sure all the data are as accurate as possible. But this project was simply too cool to let go. Once I graduated I decided to finish this manuscript as a first priority. It actually didn’t take too long after that once I put my mind to it; in the end I think that the paper was all the better for it. I learned a lot in the meantime, which contributed to making it a stronger manuscript. The hardest part by far though was actually submitting it to PLoS ONE for consideration. No one likes to be rejected, especially after putting so much work into a project! But this is the way the peer-review system works.

I noticed that you used the program PAST for your statistical analyses - how did you decide on that program? Were there any particular challenges to using this software?
I was attracted to PAST because it could perform the analyses I needed to do without a lot of unnecessary complication. Best of all, it was free, and I was a poor graduate student at the time. Most commercial statistics programs are expensive and difficult to use. PAST has a relatively simple interface and the results are easy to interpret, which is important. The major challenge with using PAST is in data management. If the data are not arranged in exactly the right way the analysis will not work correctly. Therefore it requires arranging the data first in a program like Microsoft Excel, and then copying and pasting it into PAST.

What was the most interesting thing you learned while doing your research?
First of all, I wasn’t sure what to expect when I started doing this research. No one has looked for large-scale patterns like this in dinosaurs before. One interesting thing I learned is that such patterns exist in the fossil record and are preserved over the immense spans of time between when these communities existed and when they were recovered. The most exciting result for me has to be the fact that the proportion of different “ecomorphs”, such as high-browsing herbivores vs. low-browsing herbivores or bipeds vs. quadrupeds, varies with climate. So, we can draw a connection between the climate, environment, and adaptations of organisms living in an area (see figure below). This is no surprise for any ecologist working today, but has not been shown in a terrestrial ecosystem as ancient as the Jurassic (~155 million years ago). This opens up new areas of research into the role climate change plays on the structure of ecosystems over time.

Cartoon showing variation of environment and dinosaur ecomorphs. Drier conditions are on the left, where very large herbivores dominated among relatively sparse plant life. Communities under seasonal conditions are towards the center, and include a greater diversity of feeding modes among increased ground cover. To the right are moister conditions, where smaller herbivores are more prevalent within a more densely vegetated environment. Green=high browser, orange=intermediate browser, blue=low browser, red=ground forager. After Noto and Grossman 2010.

Thanks, Chris! For more about his research, check out his web site.

[Disclaimer: Although I am an editor at PLoS ONE, I had no role in the handling of this paper]

Citation
Noto, C., & Grossman, A. (2010). Broad-scale patterns of Late Jurassic dinosaur paleoecology PLoS ONE, 5 (9) DOI: 10.1371/journal.pone.0012553

The Curse of the Nonexistent Dinosaurs

2010-12-09T20:00:00.000-08:00

You all probably remember Darwinius, that little extinct primate that caused such a huge fuss last year (the image at left is from the original paper). In addition to the massive hyperbole surrounding the specimen (much of which has now been tempered by additional analyses from other researchers), an early issue concerned the validity of the name Darwinius itself.

Scientific names for new animals, living or extinct, are governed by a set of rules from the International Commission on Zoological Nomenclature (ICZN). This body - which has no real authority, other than that granted it by us scientists - is by its nature a rather conservative entity. This isn't necessarily a bad thing, particularly because stability in our naming system is so critically important. When I say Kosmoceratops richardsoni, everyone else should know I'm talking about. But, this conservatism also means that the ICZN has been very, very slow to react to electronic publishing. Right now, names published in electronic-only form are not valid! A paper version, even if it is otherwise identical to the electronic version, must be created (although the ICZN is working to change this).

So back to Darwinius. . .when the name was initially published, it was only in electronic form, and thus not "real" in the eyes of the ICZN. Vigilant eyes noted this, and the problem was rapidly broadcast in the blogosphere. Some wags suggested naming Darwinius out from under the authors, but thankfully cooler heads prevailed. PLoS ONE, the journal in which Darwinius was published, was able to produce a paper copy of the article in order to satisfy the ICZN. It took a few days, but finally Darwinius was "real"!

Thankfully, PLoS ONE learned its lesson. Their publication policies (full disclosure: I am an editor there) have been revised to accommodate the needs of the ICZN, and all is happy now. Or is it?

It turns out that other journals haven't necessarily learned this tough lesson. Time and again, scientific names invalid in the eyes of the ICZN are being published by some pretty major journals. This "zombie nomenclature" walks among us, even today. Here are just two examples.

Raptorex (image by Nobu Tamura)

On September 17, 2009, Science posted a preprint of a paper naming a new small tyrannosaur, Raptorex kriegsteini. As near as I can tell, this name existed only in electronic form at the time, and thus was not yet valid in the eyes of the ICZN. Raptorex was very well publicized (and rightfully so - it's a neat specimen), yet no paper edition appeared until October 16, 2009 - a month later. For four weeks, the name Raptorex was in taxonomic limbo.

Koreaceratops (image by Nobu Tamura)

This early horned dinosaur is hot off the digital presses. As you can probably guess, it hails from South Korea, and the authors hypothesize that it may have been aquatic. Koreaceratops appeared on November 17, 2010, as an online preprint at Naturwissenschaften, and some media attention started popping up earlier this week. Yet. . .the name is not yet valid in the eyes of the ICZN! Until Koreaceratops appears on the printed pages of that journal, the name has no real weight. Hopefully this will get resolved soon!

Cryptovenator (image by Charles R. Knight)

Dinosaurs (and Darwinius) aren't the only organisms afflicted by digital naming issues. On September 16, 2010, the genus Cryptovenator appeared on the website for Acta Palaeontologica Polonica, as a new kind of early synapsid (closely related to the fin-backed Dimetrodon, depicted at right). It hasn't yet appeared in print - so remains "undead" according to the ICZN.

Some Thoughts

The rise of online pre-prints is a Good Thing. It speeds the flow of scientific information in a way that just wasn't possible before. Yet, it also creates a bit of a headache for authors. The window of time between pre-printing and real-printing is a dangerous place for a new scientific name. Although the threat is slight, there is nothing to stop someone from accidentally or intentionally "scooping" the rightful authors. As near as I can tell, the proposed ICZN rules won't do anything to fix the situation, either.

So, what solutions are there?

Don't publish pre-prints of papers with nomenclatural acts. This is the simplest solution in some ways, but also produces the undesirable effect of slowing down scientific communication. Canadian Journal of Earth Sciences has adopted this strategy (hat-tip to Hans-Dieter Sues for the reminder on this one).
Petition the ICZN to give priority to the first appearance of the name in the first widely disseminated pre-print of a paper. This would be a nightmare on multiple levels - an addendum to the Code could take years, and how would one decide which version of a paper containing a name is the authoritative one?
Continue to publish pre-prints, assume that all is going to be well, and worry about it when something bad happens (taxonomic scooping, perhaps?). Highly undesirable, but basically the course of action that we're on now.
Expunge the names from the paper in its pre-print form (suggested by Martin Brazeau at another venue). This does solve the problem, but it requires someone to go through the paper and remove all mentions of the taxon. Despite all of the talk from commercial publishers about "value added", I suspect it's either the unpaid editorial volunteers or unpaid authors who would get stuck doing this. Removing names is not so tough in the text, but figures (such as phylogenies) would be a bear. Also, we're left with multiple versions of the same paper floating around.

What thoughts do you have on the matter? Is it really an issue? Or am I making a mountain out of a molehill? Speak up in the comments section!

Disclaimer: Mention of the "invalid" names above is not, not, not an invitation for paleontological wannabes, ethical miscreants, or rabblerousers to wreak havoc on paleontological nomenclature. Although I hesitate to draw attention to particular instances, I feel that without some concrete examples, my arguments would be less effective. Furthermore, the names are already out there in some very widely read venues! Leave the names for the authors; the situation is not their fault.

Update December 31 2010: Bill Parker over at Chinleana has a great post relevant to this issue.

Paleo Project Challenge: 27 Days to Go!

2010-12-04T06:29:00.000-08:00

We're now about three months into the 2010 Paleo Project Challenge (PPC), an annual "contest" co-sponsored by Dave Hone's Archosaur Musings and The Open Source Paleontologist. As a quick recap, this event is for anyone (vocational or avocational paleontologist, researchers, preparators, artists, etc.) who has that nagging project that just needs a final kick in the pants. In exchange for signing up, we list your name publicly as an extra bit of. . .incentive. . .to finish the project.

So, how have you done? Out of my two goals, I got one (the paper on anatomy of a certain ceratopsian) submitted this past week, and the other one (for the ODP) is moving along nicely. I'm not sure if the latter will make the December 31 deadline imposed by the PPC, but significant progress is still happening. And that's the point of this whole Challenge, isn't it?!

In case you need your memory jogged, the participants are listed below. Tell us how you're doing in the comments! If you finished a project and I missed you, let me know and I'll update your status.

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 - finish 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
DeinonychusDinosaur - restoration of Dryptosaurus [finished]
Andy Farke - finish paper for ODP; finish paper on ceratopsian anatomy [finished!]
Nick Gardner - submit grant for Youngina part II
Casey Holliday - either a new croc species description or paper related to frontoparietal fossae
Dave Hone - the necks paper [finished]
Jason - finish descriptions for Katian graptolite systematic paper.
David Maas - Illustrating Mallison's Kentrosaurus
Heinrich Mallison - finish Plateosaurus CAE paper; sauropod rearing paper; sauropodomorph rapid locomotion paper
Jay - finish sauropod description
Jordan Mallon - Anchiceratops manuscript
Anthony Maltese - sharks scavenging on mosasaur paper; Niobrara ammonite paper
Paleochick - Cloverly paleobotany paper
Patty Ralrick - 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 - finish 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 - finish biography of Oscar Erdman [finished]; finish paper on first helicopter lift of a dinosaur specimen; finish 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

Youngina, Undergrad Research, and Nick Gardner

2010-11-26T08:25:00.000-08:00

Last week, the online, open access journal Palaeontologia Electronica published a new issue, with a fantastic spectrum of papers. Much discussion has ensued on the blogosphere. For one, PE is unusual among paleontological journals in having its own blog (would that other major paleo journals follow suit!). A series of posts has detailed many of the articles in the current issue. Furthermore, Mike Taylor over at SV-POW! blogged about figures and the online journal, with a focus on PE. Not to be left off the bandwagon, here's my own contribution to the blogstorm.

Among other fantastic papers in the latest PE, Nick Gardner, Casey Holliday, and Robin O'Keefe have published their description of the braincase of Youngina. Youngina is an early diapsid (the group including crocodiles, dinosaurs, birds, lizards, snakes, and probably turtles), which was very lizard-like in appearance during life (its skull is pictured at left, modified after Gardner et al. 2010). It lived in South Africa during the Permian, and has been a key animal for understanding the early evolution of diapsids. Despite some excellent fossil material, the braincase of Youngina has never been completely described. This could provide important information for figuring out more precisely how Youngina is related to other early diapsids. Thus, Gardner and colleagues turned to CT scanning to see all of the details hidden behind the rock in a specimen of Youngina housed at the American Museum of Natural History.

Others (including Nick, Casey, and the PE blog) have blogged about some major aspects of the new paper. So, I wanted to focus on a different angle altogether: undergraduate research. Nick is a senior at Marshall University and has been active in research nearly from the beginning. The fact that he already has a first-authored publication (and a second-authored one) is going to serve him very well in applications to graduate school (and beyond!). Given Nick's successes so far, I thought I would ask him about his thoughts on undergrad research (along with some other OSP-relevant parts of the project).

It's pretty unusual for an undergrad to have lead authorship on a major project like this. How did you get started working on this paper?
I've always wanted to participate in doing research since I was younger. Casey [Holliday] gave me my first opportunities, assisting him in his lab working on lizard and croc head anatomy. Somewhere midway along that, Robin [O'Keefe] brought up redescribing Youngina, and I sort of just fell into it. The braincase project was mostly something I worked on during last summer after I got an institutional research fellowship for undergrads.

I see that you used the Amira software package in order to generate the reconstructions of Youngina's anatomy. Were there any particular challenges to working with this program, or the particular dataset?
I went with Amira because that's what I was trained on. There were some issues in getting the data to load properly at first, so I ended up having to get help from Witmer Lab to fix some issues with the individual slice files. The other big issue was the data was flipped along the sagittal plane, so that had to be corrected before I could do any real work on it. But that was a pretty easy fix for Ryan [Ridgeley; research associate at Witmer Lab]. The big issue was just loading it up on a computer where the data could be managed. It's a really big data set.

What, if anything, was the most fun part of the project?
The most fun for me was in segmenting. It was pretty amazing to sit and work on virtually digging out something that no one had ever seen before. Every day was more exciting, to see new bits of it come together. The braincase is mostly hidden by matrix in the holotype, and no one had ever seen what an articulated and almost entirely complete braincase of Youngina looked like.

What advice would you give to other undergraduate students who want to get involved with research at an early stage?
Find out what's available to you at your university, talk to professors who do research, and just get involved. Be careful, though, while doing research. Something I struggle with is maintaining balance between grades, work and research. It's best if you can get into a situation where you're paid for helping out as a research assistant. But when you're trying to juggle all three, that's where it gets tough.

Thanks, Nick! And to all of the OSP readers, don't forget to check out his wonderfully-titled blog, "why I hate theropods."

Citation
Gardner, N.M., Holliday, C.M. , and O’Keefe, F.R. 2010. The braincase of Youngina capensis (Reptilia, Dipsida): new insights from high-resolution CT scanning of the holotype. Palaeontologia Electronica Vol. 13, Issue 3; 19A:16p. [link]

Welcome, Hippodraco and Iguanacolossus!

2010-11-22T20:46:00.000-08:00

Iguanodonts certainly have been a fertile ground for study lately - for a short summary, check out Darren Naish's excellent posts here, here, and here. Although the European iguandonts (such as the classic Iguanodon) get much of the attention, their North American cousins were also apparently pretty speciose.

Today, a new study headlined by the University of Pennsylvania's Andrew McDonald names two genera and species from the Early Cretaceous-aged Cedar Mountain Formation of Utah - Iguanacolossus fortis and Hippodraco scutodens (pictured below). [full disclosure: I was the academic editor at PLoS ONE who handled this manuscript]

Hippodraco scutodens (left) and Iguanacolossus fortis (right); modified from original artwork by Lukas Panzarin, in McDonald et al. 2010. Scale bar equals 1 m.

Each animal is known from a rather nice partial skeleton, allowing relatively confident phylogenetic placement of the two animals. McDonald and colleagues did a fantastic job describing and illustrating both taxa; all of the known elements are shown in some detail, which will be a huge help for other researchers who may not have easy access to the original material in Salt Lake City. The PDF weighs in at 35 pages, and 39 high resolution figures can be downloaded from the PLoS ONE web page for the paper.

Although there are already three other iguanodonts named from the Cedar Mountain Formation (Eolambia caroljonesa, Planicoxa venenica, and Cedrorestes crichtoni), McDonald lays out substantive morphological and geological evidence for the distinctness of the new taxa. Odds are good that there will be (or are) differing opinions from other paleontologists, so I suspect we're going to be hearing much more about the Cedar Mountain iguanodonts in the near future!

Citation
McDonald AT, Kirkland JI, DeBlieux DD, Madsen SK, Cavin J, Milner ARC, Panzarin L (2010) New basal iguanodonts from the Cedar Mountain Formation of Utah and the evolution of thumb-spiked dinosaurs. PLoS ONE 5(11): e14075. doi:10.1371/journal.pone.0014075

Big Pterosaurs Really Did Fly: Interview with Mark Witton Part II

2010-11-22T04:00:00.000-08:00

A new paper in PLoS ONE, by Mark Witton and Mike Habib, re-evaluates claims that big pterosaurs were too big to fly. To make a long story short, multiple lines of evidence suggest that giants like Quetzalcoatlus really did take wing! One of my previous blog posts summarized the paper and featured the first part of an interview with senior author Mark Witton. That part of the interview focused on many of the scientific aspects of the research. Today, we'll highlight some of the other highlights. I think you'll find it illuminating!

This paper has received a fair bit of press coverage. Is there anything about the research that you wish had received more attention?
Our coverage was really good: as mentioned above, we ended up in the most unlikely of places along with getting pieces in much more familiar territory. In that respect, I can’t complain but, at the same time, the press really focused on the quadrupedal launch idea [illustrated at right, with a Pteranodon launching itself in this fashion; figure from Witton and Habib 2010] which, while still quite novel to most, was actually first proposed (in print) by Mike back in 2008. There was a fair amount of press coverage for the idea back then, too. Prior to that, though, both Mike [Habib] and Jim Cunningham, who developed the same idea independently of Mike, had given the idea considerable airing on the Dinosaur Mailing List. Bottom line: this latest paper really isn’t the first to comment on it in any capacity. We talked about it a lot, but we’re definitely not its origin. Still, the press really ran with it, despite the fact that the main thrust of our paper is that pterosaurs and birds are generally incomparable beyond very basic aspects of their flight mechanics, and that previous assumptions that they were had lead to probably incorrect assumptions about their way of life. Their disparate launch mechanisms are a particularly important part of our considerations, but they are only one part of many. It’s no big deal, really, but I’m a little concerned that some people will now associate quad launching with this paper and I really don’t want to steal the thunder away from Mike and Jim: they did the real work on it. I’m sure People in the Know will realise the score, but I’ve already had e-mails about the presentation of the quad launch in our new paper like we proposed it. Tell the world, folks: quadrupedal launch came from Mike and Jim! They’re the real geniuses here!

With you in the UK and Mike in the US, the paper is a very international collaboration. What sort of challenges, if any, were particular to this sort of cross-border work?
Mike and I met up twice during the work on the project at different conferences, but, that aside, we worked entirely through e-mail. Trite as it sounds, the internet is amazing: a project like this would be so much harder and longwinded without it. Throwing drafts of the MS at each other, bouncing ideas around and working on the figures was no sweat at all. We could have revisions done and sent back to each other as fast as we could turn them around. In that respect it was as efficient as working with someone in the same department, if not slightly more so, as meandering chats and tangential fieldwork anecdotes – always a risk of visiting the office of any academic – were largely kept out of our online conversations (we made up for it at conferences, though). The long duration spent putting the paper together, mentioned above, was mainly thanks to my workload with the pterosaur models, not anything to do with working internationally. The paper spent a long time sitting on my desk as my time for writing disappeared amidst a blur of fake fur, bluefoam and acrylic paints. So no, working internationally presented very few obstacles. I’m sure the story would be very different if we were working 20 years ago or so, but, today, you can work with whoever you want, wherever they are without a hitch. Well, assuming they check their in-box regularly, that is.

Thank you, Mark, for an informative interview!

Citation
Witton, M., & Habib, M. (2010). On the size and flight diversity of giant pterosaurs, the use of birds as pterosaur analogues and comments on pterosaur flightlessness. PLoS ONE, 5 (11) DOI: 10.1371/journal.pone.0013982

[full disclosure: I am an editor at PLoS ONE, the journal in which this paper appeared]

Big Pterosaurs Really Did Fly: Interview with Mark Witton

2010-11-18T21:22:00.000-08:00

Pterosaurs - winged denizens of the Mesozoic skies - get a bum rap. It's bad enough that their name is smeared by the general public, when animals like Pterodactylus are confused with dinosaurs in the news media and in just about every cheap set of plastic dinosaurs. Lately, some scientists have suggested that the largest of these animals just couldn't fly. Is it true that Quetzalcoatlus (pictured here; image from Wikimedia Commons), with its 10 meter wingspan, had wings that were too narrow, a body that was too portly, and bones that were too weak to support flight? Some of the most recent studies have certainly suggested this!

Yet, extraordinary claims require extraordinary evidence, or at least extraordinary scrutiny. Thus, a study by pterosaur experts Mark Witton and Mike Habib takes a close look at the idea of super-lame flightless giant pterosaurs. Using new body mass estimates, revised reconstructions of the wing dimensions, bone strength calculations, and many other lines of evidence, Mark and Mike argue that even the biggest Quetzalcoatlus could fly after all.

This paper, published in PLoS ONE [full disclosure: I am an editor for this journal], has been featured all over the mainstream news media and blogosphere. For a slightly different take on the matter, I decided to go straight to the source. Mark Witton (pictured below; thanks to Mark for the picture, copyright him) was kind enough to answer a few questions about the study - not just on its methods, results, and conclusions, but also on some of the behind-the-scenes doings that led up to this work.

I've split this interview into two parts. For starters, we'll talk about the genesis of the paper, and some of its major findings.

How did this study come about? Did any particular event spur you and Mike [Habib] into working on this issue of flight in giant pterosaurs?
I reckon a paper like ours has been a long time coming, really. There’s been a lot of talk in recent years that pterosaurs may not be what Greg Paul termed ‘ultralight airbeings’, and numerous blogs and internet forums have responded with comments what this may mean for their flight dynamics. It was only a matter of time before the flight of realistically massed pterosaurs was considered in the technical literature (well, beyond saying they couldn’t fly). We were kicked into action, though, when press reports of an abstract presented by Katsufumi Sato et al. were released in April 2009, saying giant pterosaurs couldn’t fly. Keen members of the palaeoblogsphere may remember this ruffled a fair few feathers when it was released, and their paper (Sato et al. 2009) followed shortly to similarly raised-eyebrows. Most folks even vaguely familiar with large pterosaurs were astonished to see them cap flight at such a low size: 41 kg and 5 m wingspans are very middling in the spectrum of pterosaur size (10.5 m spans and 250 kg body masses are considered maximum in our paper). Because plenty of clearly-flight adapted forms got much larger than this, I got to work on a response. Mike and I have fairly regular correspondence and were talking about the project soon after I started, and it wasn’t long before we realised that working together would make the project much stronger.

Plus, I had giant pterosaurs on the brain at that time. I’d just started work on a massive modelling project where I had to build several models of the largest pterosaurs going. The logistics and costs of building a 13 m span pterosaur against a 10 m span animal is quite something, so I figured a little checking of the wingspans of these poorly known animals wasn’t the worst way to spend an afternoon as it would avoid having to find a bigger workshop. The timing of this was spot on for the project with Mike, too, as it meant we could ensure the size estimates for our flight analysis were as accurate as we could make them. These two events combined to form the beginnings of the paper and reminds me that we started it well over a year ago: where did that time go?

What was the most surprising finding to you, and why?
The most surprising? Hard to put my finger on one thing exactly: we covered quite a lot of topics, and each had their own intriguing little revelations. I mean, the 13 m span estimates of Arambourgiania, the giant pterosaur from Jordan, always seemed a little iffy to me because they were based on a single neck vertebra, but not Hatzegopteryx. Being based on forearm material, I figured the 12 m span estimate for this critter was a sound bet but, no, the material just seems distorted to appear bigger than it actually is. The numbers generated in the flight analysis for the speed of flying giant pterosaurs were impressive, too. The thought of a giraffe-sized pterosaur pumping its wings to scream overhead at 75 mph is staggering: this is real ‘if I had a time machine…’ stuff.

That said, for all these little surprises, the biggest ones came from the paper’s release and press coverage: I was really blown away to see just how much interest we had. To be honest, we did want to make a splash because, following the Sato et al. abstract, the internet is awash with articles saying giant pterosaurs couldn’t fly. We wanted to balance it out a little (this is also, incidentally, why we chose PLoS ONE as our venue: we want interested people of all backgrounds to be able to see our rationale for flighted giants: open access is definitely the way forward, folks). However, I was truly taken aback when our work was quoted directly alongside some half-naked chick in the British tabloids newspaper, The Sun. How often do science stories penetrate that far into the press, let alone those dealing with relatively unimportant extinct flying reptiles? I can only assume that pterosaurs are becoming more exciting and cool with every new discovery, or it was a slow news day. Either way, I’ve not stopped telling people about that since.

Next Time. . .the ins and outs of trans-Atlantic collaborations, and what the media should have mentioned.

Citations
Sato, K., Sakamoto, K., Watanuki, Y., Takahashi, A., Katsumata, N., Bost, C., & Weimerskirch, H. 2009. Scaling of soaring seabirds and implications for flight abilities of giant pterosaurs. PLoS ONE, 4 (4), DOI: 10.1371/journal.pone.0005400.
Witton, M., & Habib, M. (2010). On the size and flight diversity of giant pterosaurs, the use of birds as pterosaur analogues and comments on pterosaur flightlessness PLoS ONE, 5 (11) DOI: 10.1371/journal.pone.0013982

Ancient Beavers in PLoS ONE: Interview with Josh Samuels

2010-11-17T07:00:00.000-08:00

An earlier post here detailed a study just published in PLoS ONE, which focused on unraveling the relationship of an extinct Chinese beaver, Sinocastor, to its modern cousins in the genus Castor. Using a combination of morphometrics (shape analysis) and good old fashioned description, a team led by paleontologist Natalia Rybczinski concluded that Sinocastor is indeed quite distinct from today's Castor.

Yesterday I caught up with one of the co-authors of the study, Josh Samuels. Josh is an expert on fossil rodents (especially beavers) and morphometrics, working as a paleontologist at John Day Fossil Beds National Monument. He was kind enough to answer a few questions about his part in the project.

You have quite a track record of working with beavers and other rodents. How did you get interested in this group in the first place?
Ever since I was a kid, I have been interested in understanding how extinct species lived. In college I became interested in studying the evolution of mammals, particularly their dietary and locomotor specializations. I learned that rodents are the most species rich group of mammals and have amazingly diverse ecologies, with everything from semi-aquatic carnivores to gliding herbivores and blind burrowers. Despite their diversity, the evolution of rodents has not been as well studied as some other groups. Beavers, in particular, are known for their dramatic impact on ecosystems and have an excellent fossil record. Given their importance today, I find working to understand their evolution to be quite fascinating.

The PLoS ONE paper certainly was a collaborative effort - what role did you play in the research?
Some of my past research used geometric morphometrics to examine how skull shape in rodents relates to their ecology. Natalia approached me about the possibility of using similar techniques to examine how Sinocastor was related to living and extinct beavers. I helped design the methods and ran most of the analyses, and writing the paper was definitely a group effort. Having a group of collaborators with different skills really helped the project come together smoothly.

Was there anything particularly surprising to you about the results?
Given the broad geographic range of Eurasian and North American beavers today, I was surprised to find subtle, yet consistent differences in shape among species. One of the specimens in our analysis was from a peat bog in England, but its skull shape was almost identical to individuals from China and Russia. This really gives me hope that these techniques could be used an effective way to look at the phylogenetic relationships of extinct species.

Thanks, Josh!

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

Full disclosure: I am an editor at PLoS ONE
Image credits: National Park Service website

Re-Evaluating Ancient Beavers

2010-11-16T17:30:00.000-08:00

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

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

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

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

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

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

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

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

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

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

Paleo Project Challenge Check-In

2010-11-12T20:16:00.000-08:00

It's been nearly two months since Dave Hone and I initiated the 2010 Paleo Project Challenge. Turn-out has been fantastic, from all echelons of the paleo world - artists, researchers, preparators, casual fans, combinations of these. . .exactly who we wanted!

What is the Paleo Project Challenge, you may ask? All of us have some project that we started, nearly finished, and then forgot about. It's probably sitting on your hard drive, or a shelf somewhere, or in a sketch pad. The only thing that's stopping us from finishing it is the threat of public humiliation.

So, PPCers - you have committed to finish your project by January 1, 2011. You've signed on the dotted line (or submitted a comment). You're held accountable. If you don't finish it, you shall suffer crushing embarrassment on The Interwebz. In a show of solidarity, I have myself put forth two contributions! These, along with everyone else's, are listed below.

With that, it's time for a status check. In the comments below, tell us a little about what you've been up to! If you have a blog, we certainly encourage you to blog the process - just make sure to tell us about it, so we can link back to you! [Dave Hone has posted his impressive update already!]

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 - finish 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
DeinonychusDinosaur - restoration of Dryptosaurus
Andy Farke - finish paper for ODP; finish paper on ceratopsian anatomy
Nick Gardner - paper piggybacked with one of Casey's
Casey Holliday - either a new croc species description or paper related to frontoparietal fossae
Dave Hone - the necks paper
Jason - finish descriptions for Katian graptolite systematic paper.
David Maas - Illustrating Mallison's Kentrosaurus
Heinrich Mallison - finish Plateosaurus CAE paper; sauropod rearing paper; sauropodomorph rapid locomotion paper
Jay - finish sauropod description
Jordan Mallon - Anchiceratops manuscript
Anthony Maltese - sharks scavenging on mosasaur paper; Niobrara ammonite paper
Paleochick - Cloverly paleobotany paper
Patty Ralrick - 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 - finish 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 - finish biography of Oscar Erdman; finish paper on first helicopter lift of a dinosaur specimen; finish 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

Haven't signed up yet? It's not too late!

Book Review: The Princeton Field Guide to Dinosaurs

2010-11-11T19:22:00.002-08:00

When I was little (9 or 10 years old), my two favorite dinosaur books were Bob Bakker's The Dinosaur Heresies and Greg Paul's Predatory Dinosaurs of the World (PDW). I was lucky enough to get a copy of the former as a birthday present, but never owned a copy of the latter until recently, having to satisfy myself with ordering it via interlibrary loan. Both of these lavishly illustrated books portrayed dinosaurs as active, dynamic animals. Needless to say, my interest and imagination were sparked. I learned that Tyrannosaurus could cruise along at speeds approaching 45 miles per hour, that Velociraptor and Deinonychus were the same genus, that all dinosaurs had mammalian metabolism, Pterodaustro was pink from its diet of shrimp, and that some dinosaurs had feathers.

It was a tragic day when I realized that most of my dinosaur facts were wrong.

But, it was also an important stage in my growth as a scientist. I learned that publication in a book, or scientific job title, or pretty illustrations, weren't sufficient to establish scientific fact. Some really cool and exciting ideas (like the sprinting T. rex) couldn't hold up to scientific scrutiny, or simply weren't testable. And other ideas (like the feathered theropods) just needed the right specimen (which eventually arrived).

Despite their shortcomings, The Dinosaur Heresies and PDW were momentous publications for my generation. They inspired many young paleontologists and spun off numerous artistic clones (you don't have to look far to see the influence of Greg Paul's "running theropod" pose, for instance; see the example at right). Thus, it was with some excitement that I got my copy of Greg Paul's The Princeton Field Guide to Dinosaurs (hereafter just the "Field Guide") in the mail. In many respects, this is the modern heir to PDW.

The book itself is quite pretty, in a durable yet inexpensive hardcover format (I got my copy for under $25). The pages are chock-full of illustrations, ranging from black and white skeletals to full color paintings. The first part of the book includes well-written, succinct text (although certainly with a "Paulian" spin to its claims) that provides a birds-eye view of dinosaur biology. The highlight of the book, however, is the "Group and Species Accounts."

Pretty much every known dinosaur is included, and a great number are illustrated. Images include shaded skull reconstructions, black and white skulls, complete skeletal reconstructions, and color pencil drawings. This is classic Greg Paul (see his website for some samples), with the poses and attention to skeletal detail that we all expect. Many of these have never been widely available in any form - a boon for dinosaur enthusiasts! A number of his paintings are also included; most have been published before, but some are updated based on new information. I am not sure if I like the color pencil drawings as much of the rest of the artwork; many of them lack the "pop" of the skeletals or paintings. Some of this could be a consequence of the scale at which they are reproduced; I get the sense that many of the illustrations would look better if printed at a smaller size.

The species accounts are generally pretty good, although of course there is not sufficient space to go into the supporting evidence (or not) for some statements. For instance, the talk about "enemies" of some taxa is perhaps a little colloquial but at least vaguely supportable - one would think that similarly-sized herbivores and carnivores in a formation were indeed "enemies". Other facts - like stating that ceratopsids defended themselves by "rearing like a bear and tilting [the] frill up to intimidate [the] attacker, followed by a short fast charge with horns and/or beaks" (p. 257) are pure (if plausible) speculation. To his credit, Paul (p. 62) notes that the "reliability of these conclusions varies greatly." Unfortunately, I'm afraid this caution will be lost on the average reader.

My only real major beef, which has been echoed by many others (see this thread on the Dinosaur Mailing List, for instance), is with the taxonomic games played in the book. I do not think that the work is a Major Disaster in taxonomy; as Paul readily admits, the Field Guide is a popular book that is not intended as a valid nomenclatural statement. Publishing scientists are generally going to ignore any taxonomic assessments. One major reason is that many of the generic lumpings form polyphyletic or paraphyletic groups. For instance, Paul's Chasmosaurus (including Chasmosaurus, Mojoceratops, Agujaceratops, and Pentaceratops) is hopelessly paraphyletic by all recent phylogenies (see the Sampson et al. one, for instance, or even Lull's 1933 phylogram, if you're not a fan of cladistics). Similar problems plague the hadrosaur naming scheme in this book - it's not just a matter of having one's "genericometer" set to "broad". On the last point, though, one wonders why the rather morphologically conservative and firmly monophyletic "leptoceratopsids" all got to retain their separate genera! Prenoceratops and Leptoceratops are far more alike than Styracosaurus and Pachyrhinosaurus (all lumped in Centrosaurus by Paul!).

Rather than a scientific issue, the primary problem is that this stuff is going to be soaked up uncritically by the lay public (as we saw with Dinosaur Heresies and PDW). I don't think it's a catastrophe on the scale of Jurassic Fight Club (most of the basic content in the Field Guide is accurate), but it will still be a nuisance in the long term. I'll have to deal with kids who want to know why I'm following an outdated ceratopsian classification, but that's probably about the worst that's going to happen. A dino fanboy (speaking with a voice a la Professor Frink) will tell me that prosauropods slashed their enemies with razor-sharp claws, because he read it in a book by a paleontologist. The world is not ending. My hope is that discussions about what we know and don't know will inspire the next generation of researchers!

Flaws aside, every dinosaur enthusiast should get a copy of The Princeton Field Guide to Dinosaurs. The skeletals alone are worth the price of admission. This book is visually appealing, fun, and a great reminder of why we all loved dinosaurs in the first place.

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The Princeton Field Guide to Dinosaurs, by Gregory S. Paul, 320 pages, published by Princeton University Press. ISBN13: 978-0-691-13720-9. $35 list price.

A Flood of Paleo Articles in PLoS ONE

2010-11-06T09:40:00.018-07:00

It has been pretty incredible to see the rise of PLoS ONE as a major outlet for articles on paleontology, and it has been equally incredible to ride along as an editor for that journal. The past few months have seen many scientifically important and interesting papers wend their way into publication. I haven't had a lot of time for blogging lately, but wanted to take this opportunity to highlight the latest paleo-themed research in PLoS ONE. The following list is in reverse chronological order (newest to oldest), covering work published in the last three months.

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Slater GJ, Figueirido B, Louis L, Yang P, Van Valkenburgh B (2010) Biomechanical Consequences of Rapid Evolution in the Polar Bear Lineage. PLoS ONE 5(11): e13870. doi:10.1371/journal.pone.0013870
Summary: The authors present and interpret finite element modeling results for polar bears and brown bears, showing that the skulls of polar bears are generally weaker than those of their close cousins. Furthermore, these differences probably accumulated rather rapidly.

Xu X, Wang K, Zhao X, Sullivan C, Chen S (2010) A New Leptoceratopsid (Ornithischia: Ceratopsia) from the Upper Cretaceous of Shandong, China and Its Implications for Neoceratopsian Evolution. PLoS ONE 5(11): e13835. doi:10.1371/journal.pone.0013835
Summary: Zhuchengceratops inexpectus is introduced; this small horned dinosaur is actually among the largest of its kind, the "leptoceratopsids." Interestingly, it showed up in a big bonebed in eastern China, along with truly giant horned dinosaurs and duck-billed dinosaurs.

Longrich NR, Horner JR, Erickson GM, Currie PJ (2010) Cannibalism in Tyrannosaurus rex. PLoS ONE 5(10): e13419. doi:10.1371/journal.pone.0013419
Summary: Bones of Tyrannosaurus with T. rex tooth marks are described; the implications are pretty self-evident (see the title of the paper, if you're still trying to figure this out). This paper received considerable media attention; Brian Switek has one nice write-up at Dinosaur Tracking.

Cisneros JC, Gomes Cabral U, de Beer F, Damiani R, Costa Fortier D (2010) Spondarthritis in the Triassic. PLoS ONE 5(10): e13425. doi:10.1371/journal.pone.0013425
Summary: Suffering from what is described as the earliest known example of arthritis, an early archosaur had a pretty rough time with some fused vertebrae. Diagnoses of disease in fossil organisms can be pretty controversial; I shall be interested to see how this particular case study plays out.

Smith ND (2010) Phylogenetic Analysis of Pelecaniformes (Aves) Based on Osteological Data: Implications for Waterbird Phylogeny and Fossil Calibration Studies. PLoS ONE 5(10): e13354. doi:10.1371/journal.pone.0013354
Summary: Here, the relationships of pelecaniform birds (including pelicans, cormorants, boobies, and more) is addressed in great detail. The group is not found to be monophyletic, and the unstable nature of the position of several key taxa means that ornithologists will be talking about this question for some time.

Han J, Kubota S, Uchida H-o, Stanley GD Jr, Yao X, et al. (2010) Tiny Sea Anemone from the Lower Cambrian of China. PLoS ONE 5(10): e13276. doi:10.1371/journal.pone.0013276
Summary: What the title says. The authors suggest that their new animal, called Eolympia pediculata, is a stem member of the group including corals and sea anemones. The image at right shows the authors' reconstruction of Eolympia.

Peterson JE, Lenczewski ME, Scherer RP (2010) Influence of Microbial Biofilms on the Preservation of Primary Soft Tissue in Fossil and Extant Archosaurs. PLoS ONE 5(10): e13334. doi:10.1371/journal.pone.0013334
Summary: This article presents experimental support for the idea that microbial biofilms form a protective layer that allows preservation of deeper soft tissue structures in dinosaur bones and other fossils-to-be. Read more about the research here. Interestingly, the article by Peterson et al. disagrees with an earlier paper published in PLoS ONE (written by Kaye et al.), stating that any alleged soft tissue preserved in fossils is a microbial film alone. Thus, the bacterial biofilms exist - but they're not the only biogenic structure in these bones!

Holliday CM, Ridgely RC, Sedlmayr JC, Witmer LM (2010) Cartilaginous Epiphyses in Extant Archosaurs and Their Implications for Reconstructing Limb Function in Dinosaurs. PLoS ONE 5(9): e13120. doi:10.1371/journal.pone.0013120
Summary: Things aren't as they appear; the big dinosaur bones that we see in museums today were probably much longer in life, supplemented by giant cartilaginous caps. Lead author Casey Holliday presents more information here, and Mike Taylor at SV-POW also has stuff to say about the topic.

Oxnard C, Obendorf PJ, Kefford BJ (2010) Post-Cranial Skeletons of Hypothyroid Cretins Show a Similar Anatomical Mosaic as Homo floresiensis. PLoS ONE 5(9): e13018. doi:10.1371/journal.pone.0013018
Summary: Yet another round in the discussion about the "hobbits" of Flores, Indonesia. I get the sense that Oxnard et al. are very much in the minority opinion, but I also get the sense that this debate is going to drag on for awhile more.

Rando JC, Alcover JA, Illera JC (2010) Disentangling Ancient Interactions: A New Extinct Passerine Provides Insights on Character Displacement among Extinct and Extant Island Finches. PLoS ONE 5(9): e12956. doi:10.1371/journal.pone.0012956
Summary: A recently extinct finch, Carduelis aurelioi, is named and compared with its fellow prehistoric finches (some of which are still alive today). Evidence is presented to suggest that the effects of ancient competition between the species still reverberate today. The image at left shows a life restoration of the new species, as imagined by A. Bonner.

O'Rourke CT, Hall MI, Pitlik T, Fernández-Juricic E (2010) Hawk Eyes I: Diurnal Raptors Differ in Visual Fields and Degree of Eye Movement. PLoS ONE 5(9): e12802. doi:10.1371/journal.pone.0012802
Summary: It's not strictly paleontology, but the methods here present actual experimental validation of the true visual fields for extant birds of prey. It would be interesting to compare the visual fields as calculated from the osteology alone with the experimental results - and then see what this means for similar calculations performed for extinct dinosaurs.

Sampson SD, Loewen MA, Farke AA, Roberts EM, Forster CA, et al. (2010) New Horned Dinosaurs from Utah Provide Evidence for Intracontinental Dinosaur Endemism. PLoS ONE 5(9): e12292. doi:10.1371/journal.pone.0012292
Summary: Utahceratops gettyi and Kosmoceratops richardsoni, two new horned dinosaurs, are named, and their implications for Late Cretaceous biogeography in North America are discussed. This paper, on which I was a co-author, received a substantial amount of media attention. See my blog post on the subject as a starting point for more information.

Kraatz BP, Meng J, Weksler M, Li C (2010) Evolutionary Patterns in the Dentition of Duplicidentata (Mammalia) and a Novel Trend in the Molarization of Premolars. PLoS ONE 5(9): e12838. doi:10.1371/journal.pone.0012838
Summary: Here, the authors propose new ways to interpret the anatomy and evolution of rabbit teeth, based on some previously undescribed fossils.

Noto CR, Grossman A (2010) Broad-Scale Patterns of Late Jurassic Dinosaur Paleoecology. PLoS ONE 5(9): e12553. doi:10.1371/journal.pone.0012553
Summary: The Jurassic was an age of giants. The structure of some old, old ecosystems is reconstructed by classifying and comparing the ecomorphotypes of a number of dinosaurs from this time.

Degrange FJ, Tambussi CP, Moreno K, Witmer LM, Wroe S (2010) Mechanical Analysis of Feeding Behavior in the Extinct “Terror Bird” Andalgalornis steulleti (Gruiformes: Phorusrhacidae). PLoS ONE 5(8): e11856. doi:10.1371/journal.pone.0011856
Summary: Terror birds are pretty much what the name says - imagine something the size of "Big Bird" from Sesame Street, preying on Mr. Snuffleupagus. This article, which also received broad media coverage (see the Witmer Lab blog as a starting point), finds that the skulls of these big birds were quite strong in the up-and-down direction, but not so strong from side-to-side.

Lindgren J, Caldwell MW, Konishi T, Chiappe LM (2010) Convergent Evolution in Aquatic Tetrapods: Insights from an Exceptional Fossil Mosasaur. PLoS ONE 5(8): e11998. doi:10.1371/journal.pone.0011998
Summary: A spectacularly-preserved ancient sea reptile shows skin impressions, bronchial tubes, possible skin coloration, and even potential traces of some internal organs. Feathered dinosaurs may get all of the attention, but the specimen described here rivals them in "wow" factor!

Image from Lindgren et al. 2010

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Some parting thoughts:

In my (biased) opinion, most of these papers are presenting some pretty solid science (or at the very least, stimulating science). Now that PLoS ONE has an impact factor (and thus presumably more people interested in submitting to the journal), I hope that the quality of the submitted work is maintained.
There is a pretty major skew towards papers on vertebrates - 15 out of 16 (94 percent) of those mentioned above primarily concern things with backbones . Six out of the 16 papers mentioned above (38 percent) are about non-avian dinosaurs. Let's get some more variety, folks!
Some interesting work on functional morphology and other aspects of evolutionary biology (only a handful of which are sampled above) has been appearing lately. I strongly recommend subscribing to content alerts (start the process here) or regularly browsing the journal's website, in order to keep up on the latest and greatest work that might be relevant to you.
I look forward to more stimulating papers appearing in the near future. And if you haven't submitted something to PLoS ONE yet, please consider doing so!

Full disclosure: I am a section editor at PLoS ONE.

Have You Accepted the Paleo Project Challenge?

2010-10-19T22:28:00.006-07:00

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

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

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

The 2010 Paleo Project Challenge

2010-09-29T03:00:00.004-07:00

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

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

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

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

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

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

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

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

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

Horned Dinosaurs: When It Rains, It Pours

2010-09-22T08:00:00.004-07:00

2010 will surely go down as the annus mirabilis of horned dinosaur research. Between the publications of the horned dinosaur symposium volume (with its myriad new taxa and other exciting pieces of research), a "bagaceratopsid" in Europe, a true ceratopsid in Asia, the hypothesis that Torosaurus and Triceratops are growth stages of the same taxon, and more, it's really tough for a "ceratophile" (to borrow Peter Dodson's term) to keep up!

Today continues the embarrassment of ceratopsian riches. With my co-authors Scott Sampson, Mark Loewen, Cathy Forster, Eric Roberts, Alan Titus, and Josh Smith, I'm pleased to introduce you to Utahceratops gettyi and Kosmoceratops richardsoni (at top and bottom, respectively, in the image at right), freshly published in PLoS ONE. Although it's been a long time coming, our hope is that these new critters will really knock your socks off!

So what's so special about these two animals? Well, for one they're new dinosaurs. And new horned dinosaurs at that. On a broader note, our new critters (along with careful radiometric dating of the Kaiparowits Formation, the rock unit in southern Utah from which they originated) provide important evidence for dinosaur provincialism during the Late Cretaceous. In other words, these big, elephant-sized dinosaurs weren't traveling far. They're the same age as dinosaurs known from much further to the north, yet represent a very different part of the horned dinosaur family tree. This is strange, especially when you consider that today there is only one (or maybe two, depending on whom you ask) elephant species in all of Africa! 75 million years ago, there were three or four closely related species of horned dinosaur living simultaneously on that little strip of beachfront property that comprised western North America. And that's not counting a few more less closely-related horned dinosaurs (centrosaurines) that lived at the same time! Truly weird.

There's been a lot said more eloquently elsewhere about these animals, so I'm just going to close with an answer to the question that should be at the top of many people's minds. Given the possibility that Torosaurus and Triceratops might be growth stages of a single species, how do we know that Utahceratops and Kosmoceratops aren't just growth stages of one species? After all, they lived at the same time in the same place, and end up somewhat close together on the phylogenetic analysis. Well, we certainly haven't done much in the way of histology yet, which would lay the issue completely to rest. However, as readers of the paper will note, we have obvious juveniles (based on sutural fusion and cranial element size) of both species. Although these remain to be published, in my opinion they pretty firmly demonstrate that both species of dinosaur were very different very early on in their development.

So, go read the paper!

Full disclosure: I am a section editor at PLoS ONE, the journal at which this new paper was published. However, I had absolutely no involvement in the handling of the manuscript (assigning the academic editor, selecting reviewers, making a publication decision, etc.).

Image credit: Lukas Panzarin

Citation
Sampson, S., Loewen, M., Farke, A., Roberts, E., Forster, C., Smith, J., & Titus, A. (2010). New horned dinosaurs from Utah provide evidence for intracontinental dinosaur endemism PLoS ONE, 5 (9) DOI: 10.1371/journal.pone.0012292

Crossing the Finish Line for the Dissertation

2010-09-14T21:30:00.006-07:00

Well, it's done.

All of the chapters of my dissertation have been published as papers in peer-reviewed journals.

It's been two years and four months since I submitted the final draft of my dissertation to my university, and wow, is it ever nice to finally lay the thing to rest. As a bit of a celebration, I wanted to ~~pontificate~~ share some musings on the whole process, and offer some hope for those who might be working on their dissertation right now. So, how did this all come to fruition? What did I do right (in my opinion), and what might I have done differently?

Start Early
Basically, I knew from the get-go that I didn't want to write one of those perpetually unpublished dissertations. You all know the ones I'm talking about. That really ground-breaking, highly citable, novel piece of research that's been sitting around completely unpublished since the person got his or her Ph.D. back in 1976. I can't really blame them - maybe they dropped out of the field. Maybe they decided research wasn't their thing. Maybe bigger and better projects happened along. These are all legitimate reasons (life happens!), but it doesn't make an unpublished dissertation any less annoying. As anyone in the field knows, journals (and reviewers) sometimes look askance at a reference listed as "unpublished thesis" or "unpublished dissertation."

So, I made a mental commitment early on to strive to get my dissertation published as quickly as possible. This was key in achieving the eventual goal.

Get Your Committee On Board
My dissertation committee wanted to see my stuff published, too. In fact, they specifically requested that I frame each of my dissertation chapters as discrete, publishable units. This was good advice. The days of creating a book-length narrative, which is retroactively turned into publishable manuscripts, are over. If you have the dissertation chapters framed as discrete, submission-ready papers, you can save a lot of time! This is a much more common practice than it used to be, which is a good thing (in my opinion).

So, before I had even finished writing the dissertation chapters, I had decided what journals I was going to submit to. Then, I formatted all of the figures, text, and references appropriately. This saved a ton of time in the end!

Git 'er Done
Once the dissertation is written, the congratulations received, and the diploma framed, the real work begins. Get those chapters submitted for publication. Take a week to rest on your laurels, and then get back to work. Every day you procrastinate is another opportunity to completely forget about submitting the papers for peer review. In fact, maybe even consider submitting some chapters before you graduate, if you can.

In the end, though, the only way I managed to get this done as quickly as I did (not that two years is that quick!) was to guilt-trip myself into doing it. Maybe that's what will work for you, too. And as I tell many people - don't let the perfect be the enemy of the good. Your work will never be perfect. There are always more data. There's always another specimen to measure. But at some point, you just have to call it "good enough."

Submit that paper. Because chances are, there's someone else out there who wants--perhaps even needs--to cite you. And I'm sure they would much rather cite a peer-reviewed paper than an unpublished (if excellent) dissertation or thesis. And for every day delayed, there's just another little way in which you have to revise the manuscript before submission. Science marches on, with or without us.

Regrets?
Not many, on my part. All in all, I'm happy with how my dissertation chapters have turned out. I might have had a few more figures in the ceratopsian one. Maybe a slightly longer discussion in the goat head FEM one. Perhaps I might have pushed to get the ZJLS paper published a little sooner. Oh well. They're done, they're published, and I can clear my plate for new projects.

Speaking of clearing plates, isn't it about time to relaunch the Paleo Paper Challenge?

Return to the Blogosphere

2010-09-08T20:18:00.004-07:00

I'm back! Let's just say that a global circumnavigation, two months away from home, and a move in the middle, don't leave a lot of time for blogging. It was a fun and productive summer, but now it's time to settle back in for the fall.

For this re-inaugural post, I wanted to touch on a few highlights from the past few months, particularly in the world of open access and paleo research. I'll cover a variety of topics in more detail in future posts, hopefully.

Big Happenings at PLoS ONE

The online, freely accessible journal PLoS ONE hit a variety of important milestones this summer, including:

For the first time, the journal received an official impact factor from Thompson-Reuters. The result: a respectable 4.351. Although this value certainly exceeds that for your typical paleontology journal (e.g., Paleobiology has an IF of 2.985, and JVP has an IF of 2.536), it is more properly compared to other general interest journals. For instance, Naturwissenschaften has an IF of 2.126 and Proceedings B an IF of 4.857. Thus, PLoS ONE is doing pretty well in the whole impact factor "game." Although impact factor has come under a lot of fire lately, we still face the reality that many scientists need to publish in journals that have an IF. Thus, the assignment of an official IF is a big step forward for the journal.
PLoS ONE launched a new (and hopefully more user friendly) manuscript submission system. Read all about it here.
PLoS launched a new blog network.
Full disclosure: I am a section editor at PLoS ONE.

Happenings Around the Blogosphere

The venerable ScienceBlogs had a major sea change, with a number of respected bloggers jumping ship. I'm still working on updating my personal blog feeds. But, don't forget that notables such as Tetrapod Zoology remain!
WitmerLab launched a great new blog, chock full of goodies from all of the folks there.
The spam filters at Blogger are horrible. I'm seriously considering transferring over to WordPress.

Research Happenings

The long-awaited proceedings volume of the Tyrrell ceratopsian symposium is finally out. The first review, by Hans-Dieter Sues, is available here. Seriously, if you are a dinosaur enthusiast or researcher, you need to get a copy of this book (and no, I don't get royalties).
The final unpublished chapter of my dissertation (on ceratopsian sinuses) is now officially in press - look for it to come out in JVP within the next few weeks!
Another major paper should be out in two weeks. Stay tuned for details.
I had my first publishing experience with PalArch's Journal of Vertebrate Paleontology, with a paper on dinosaur skin from Utah. Brian Switek had a nice write-up of this over at Dinosaur Tracking. Hopefully I'll have a chance to blog more about this later - for now, I'll just say that you should consider the journal as a publishing venue! In the meantime, you can learn more about the journal in this two-part interview with editor Brian Beatty.
And much more. . .too much to mention here, in fact!

That is all for now.

Interview: Ricardo Araújo on Journal of Paleontological Techniques

2010-06-03T06:00:00.000-07:00

Fossil preparators are the unsung heroes of paleontology. For every paper on a spectacular Archaeopteryx skeleton, or an exquisite new ceratopsian skull, there is at least one talented preparator who freed the fossil from its rocky tomb. Despite the importance of preparators for paleontology, there are surprisingly few formal publications devoted to the trade (beyond the occasional symposium volume). Even rarer are open access publications on fossil preparation. Thus, it is a real pleasure to share this interview with Ricardo Araújo, the executive editor for Journal of Paleontological Techniques.

Tell us a little about Journal of Paleontological Techniques. How did the journal get started?
The Journal of Paleontological Techniques got started due to the difficulties that we felt in the Museu da Lourinha (in Portugal) to get access information relative to preparation. Unfortunately it is extremely hard for a peripheral country to have access to the know-how developed in the great centers of knowledge, namely central Europe and the US. So, we had to find an economical way without detriment of scientific rigor; publishing and editing articles using an open access philosophy seemed the right solution. Furthermore, the lack of a systematic compilation of paleontological techniques is evident in the literature.

What makes Journal of Paleontological Techniques unique?
There are a few things that make our journal unique:

There is no other journal focused on the practical side of paleontology. Some typical paleontological journals publish sporadically on paleontological techniques, and there are a handful of printed publications. However, there is an immense quantity of knowledge acquired by generations of preparators that is hard to access if you cannot go to the main conferences or workshops.
Also, preparation is practical in its essence. Thus, our papers can include videos and as many photos as necessary to make a technique easily perceptible. Most of the time it is difficult to express these techniques in words.
Our publications are edited in volumes. Each article is published by itself as a volume, which decreases the total amount of time for publication. This flexibility allows us, for example, to publish annals of congresses or symposia.
Our journal is totally open access and double-blind peer-reviewed. This doesn’t make our journal unique but certainly a “rare specimen.”

What advice would you give to authors who are interested in submitting their manuscripts to JPT?
Write! The preparation community is not used to writing about their findings, some of which are extremely important and can save thousands of euros for paleontological institutions. To spread paleontological techniques is to advance paleontology as a whole. Preparation is a science as well, in its most Popperian essence. To test and refute paleontological techniques is possible, and in fact, is done by all preparators everyday when we use different products, methods and tools, striving for the best way to do something efficiently.

What kind of difficulties, if any, have you encountered in editing JPT? How have these been solved?
When we embraced this project we quickly realized that the challenge was not to create the space to publish practical-paleontological ideas, but almost to change the status quo that preparators face nowadays. Institutions hire preparators to prepare fossils, not to write scientific articles. However, to my eyes, that is a rather limited view about the role of preparation. Preparation is the technical side of paleontology, and like any other science paleontology has its own methods—methods that are publishable. Actually, methods that are required to be published. Moreover, thinking strictly in an economic perspective, by spreading this sort of knowledge, preparator’s employers will quickly realize that they can save money by KNOWING and SHARING their knowledge.

In order to circumvent this problem, we are trying to present at as many events related to preparation as possible, not only to publicize the journal itself but also to spread the ideas behind it. We are part of mailing lists, groups of geosciences journals, and a gazillion things like that. For every preparation-related paleontological event that we know, we try to contact the organizers in order to publish the abstracts or edit a volume with selected papers. We are currently trying to organize an opinion paper that will be submitted in a mainstream paleontological journal, about the underestimation of the importance of preparation/paleontological techniques as a legitimate science. We recently got a wave of papers submitted, and hopefully it will be sustainable.

What has been the best part of editing a journal like JPT?
What I enjoy most about this project is actually the spirit of the journal and the challenge it represents. I believe the actual scenario is difficult, but not impossible to surpass. Ideally we would like to get help and cooperation from various areas of the preparation community, starting from the preparators themselves, up to the heads of departments, and paleontologists.

Image credit: courtesy Ricardo Araújo, originally published at Palaeontologia Electronica.

Interview: P. David Polly on Palaeontologia Electronica

2010-05-20T21:45:00.006-07:00

This blog has been hosting a sporadic series interviewing the editors from various open access journals for paleontologists. This time around, I am very pleased to highlight Palaeontologia Electronica (PE for short). PE has a special place in my heart for two reasons. First, it was the earliest open access paleo journal around (that I know of). It began publication in 1998, before "open access" was even a part of the scientific vocabulary! Second, one of my first peer reviewed publications graced the pages of the journal, back in 2004.

PE's executive editor, P. David Polly, was kind enough to answer a few questions. As is only fair, he has asked me to remind readers that any opinions stated here are his alone, and do not necessarily represent official views of the journal.

How did you get involved with PE?
I got involved with PE in 1996, just after its inception and before the first issue was published. As I recall, the idea of an electronic journal of paleontology had been the idea of Norman MacLeod, Tim Patterson, and William Riedel in 1995, who then enthused the group of people who made up the first editorial board. Mark Purnell, my co-executive editor, Peter Roopnarine, the special issue editor, and Jennifer Rumford, our production editor, were all part of that group. So there are four of us who have been with PE for more than 14 years.

Given your long history with PE, have there been any particular surprises for you in how the journal has developed?
The main surprise was how hard it was to get people to publish with PE in the early days. Younger scientists were the ones most attracted by the idea, but they were also the ones to whom "impact factors" were the most important. The journal wasn't indexed by Thomson-Reuters until a few years ago and has only had an official "impact factor" since 2007. Before then we often struggled to get enough submissions to fill an issue, but since then the number of papers that come in is similar (or greater) than many other paleo journals.

Within the growing ecosystem of open access journals, what makes PE unique?
PE is unique in that it is completely sponsored by professional societies so that neither readers nor authors have to pay. Many so-called "open access" journals allow readers to have free access, but charge authors a steep fee. In my opinion, that funding model is even worse than high subscription fees for readers because funds for publication are not equally distributed among fields (paleo as a field has far few funds available for publication costs than does, say, medicine), nor are they equally distributed among researchers, institutions, or countries within a field. Publication is a fundamental part of science, or any academic discipline for that matter-- it's imperative that reserachers be able to publish their work and that others be able to read it.

In my mind, it is an obligation for anyone involved in a professional academic field to donate their time to reviewing papers, serving on editorial boards, paying dues to professional societies, and working for those societies to help facilitate and subsidize scientific publication. Sadly it is becoming increasingly difficult to get people to review papers, serve as editors, or otherwise commit time to these activities, which increasingly leaves academic publishing in the hands of corporate publishers, much to the detriment of fields like paleontology. No service that is offered by corporate publishing houses couldn't be offered by the academic community. The goal of PE is to publish quality science at the least possible cost, without taking a profit, and to reach the greatest possible audience.

What advice would you give to authors interested in submitting their research to the journal?
Format their papers correctly and, regardless of whether you submit to PE or another journal, to be willing to review at least five papers for every one you publish.

Are there any myths about PE that you'd like to see busted?
The main myth about PE that should be busted is that publication is instant. Once papers are accepted to PE, they come out in the next issue, which is faster than most journals, but the process of review and revision happens at the same speed as for any other paper. The thing that slows papers down the most is finding reviewers. I probably have two or three people decline to review for every one who says yes.... it can sometimes take a couple of months to find two suitable reviews for a paper. But once reviews have been found, revisions have been made, and proper formatting done, the papers come out quickly in PE.

Thank you, David!

Tony Martin Interview, Part 2

2010-05-06T06:21:00.007-07:00

Yesterday, I ran the first part of this two-part interview with Anthony (Tony) Martin, senior author on a new paper in PLoS ONE. The research details a rare trace fossil (figured below) left behind by a bottom-feeding fish over 50 million years ago. Yesterday's questions focused on the science - in the final installment, we'll learn more about the publishing process. (Full disclosure: I am an editor for PLoS ONE, and was the editor who handled this manuscript.)

Why did you choose PLoS ONE as a venue for the manuscript?
All three of us really liked the fact that by publishing in PLoS ONE we could better share our research with both our colleagues and the general public. All too often I’ve published papers that were read by maybe two or three dozen of my colleagues (if I’m lucky), rather than a broader audience that might also find the work really interesting. I’ve also published in journals with “pay walls” erected to prevent non-subscribers from seeing articles. I know this really frustrates some science bloggers who want to write about the original research instead of just relying on press releases or news articles. So I am becoming more enamored with making sure all science enthusiasts have free access to original research results. PLoS ONE also has published some top-notch paleontological articles in the past few years, so it’s become a high-profile place to publish, while also permitting laypeople to learn from our science.

We also thought this research made for an interesting “fish story” combined with a “detective story,” sort of Sherlock Holmes-meets-fishing-meets-paleontology-meets-spatial analysis. The study also has some visually interesting elements, which through publishing in an electronic journal we could better share through our new (and very cool) application of the Deep Zoom™ software (link here). Now anyone with an Internet connection can check out the same trace fossil analyzed in the study through the pan-and-zoom function of the software.

Was there anything about the PLoS ONE process (good or bad) that surprised you?
Not really. One of my coauthors, Gonzalo [Vazquez-Prokopec] had previously published in one of the PLoS journals and said it was a straightforward process, with timely peer review and good, thorough feedback from the reviewers and editors. I’m pleased to say that our experience was the same, and it encourages me to consider PLoS ONE for future contributions.

Which of the Green River fish would have tasted best?
I would have loved to try Priscacara liops, either pan-fried or steamed with ginger, garlic, scallions, and soy. I’m not so sure that Notogoneus osculus [the focus of the current paper] would have been nearly as tasty, especially considering that we’re even more certain now it was a bottom feeder.

A big thank you to Tony, for taking the time for this interview. Don't forget to check out the paper, if you haven't already!

Reference

Martin, A., Vazquez-Prokopec, G., & Page, M. (2010). First known feeding trace of the Eocene bottom-dwelling fish Notogoneus osculus and its paleontological significance PLoS ONE, 5 (5) DOI: 10.1371/journal.pone.0010420

Image credits: Image of the ichnofossil modified from the original paper at PLoS ONE.

Something Fishy in PLoS ONE (and it's pretty neat!)

2010-05-05T16:50:00.000-07:00

The open access journal PLoS ONE has published a lot of neat paleontology articles over the last few years (see here for a reasonably comprehensive listing). Charismatic, terrestrial vertebrates (whether dinosaurs, Ice Age mammals, or prehistoric humans) seem to dominate. But what about the poor, neglected fish?

Today, PLoS ONE published a nifty article by Anthony (Tony) Martin [pictured at left] and colleagues, discussing a 50 million year old fish feeding and swimming trace fossil from Wyoming. In the build-up to the release of their paper, Tony (a paleontologist with a specialization in trace fossils, over at Emory University) was kind enough to answer a few questions about the paper. Part 1 (focusing on the science behind the paper) is posted today, and Part 2 (focusing on the open access angle) will arrive tomorrow. [Full disclosure: I was the academic editor at PLoS ONE who handled this submission]

Briefly, what is the importance of the finding described in your new paper?

Several parts of it are important, and they’re all related.

One is that this is the first fish trace fossil described in detail from a formation that’s world-famous for its fish body fossils, the Green River Formation near Kemmerer, Wyoming. The Green River Formation was made by a series of lakes about 50 million years ago, and it preserved many gorgeous fossil fish, which have been collected and studied since the 1850s. However, fish trace fossils, such as trails made by their fins while swimming along the lake bottom, have been mostly neglected. Trace fossils can be extremely valuable for directly reflecting ancient behavior, and because the trace fossil we studied was extraordinarily detailed, it gave us some new insights we might not have gleaned from the fish body fossils.

Secondly, we are very sure about the species of fish made the trace fossil, namely, Notogoneus osculus [figured at right]. This fish had always been interpreted as a bottom feeder, and this is the first trace fossil to confirm this behavior. Our identification of the tracemaker is unusual, because oftentimes it’s tough to tell just what animal made a particular trace fossil. This one, though, gave us some great clues about “who done it.” The trace fossil [see figure below] has beautiful sine-like waves and other marks that show it made by a fish with a downward-pointing mouth, two pelvic pins, an anal fin, and a caudal fin. What really cinched it, though, was that this same species is also found as a body fossil in the same layer as the trace fossil. So our conclusion about the tracemaker is a pretty tight fit in every respect.

Thirdly, we figured out the size of the fish by applying some mathematical and spatial-analysis techniques that had never been used previously on a fish trace fossil. From these methods, we were calculated that the fish was 45 cm, or about 18 inches, which is exactly the average size of Notogoneus osculus. So not only do we know which fish did it, we know how big it was! This makes for a great fish story, because we can say that it was “the one that got away,” we can tell people what it was, and hold out our hands to say, “and it was THIS big (45 cm).” The kicker, of course, is that we’re talking about a fish from 50 million years ago, and in a lake that dried up nearly that long ago.

Lastly, this trace fossil shows a fish behaving normally, swimming and feeding along the lake bottom. Yet it was made in the deepest part of Fossil Lake, which supposedly excluded live fish because of low-oxygen conditions. So this fish trace fossil, along with a few others we mention in the paper, should give future researchers a good reason to reconsider the paleoecology of Fossil Lake. We now know that fish feeding on the bottom of the deepest part of Fossil Lake was a part of its benthic ecology, giving us a new insight about this long-studied deposit.

If you could share one thing about the research that didn't make it into the paper, what would that be? Is there an interesting back story to the project?

Actually, two things should be mentioned, the back story and a philosophical perspective.

The back story is that this may be the only paleontological paper in which the coauthors consist of an ichnologist (me), a disease ecologist (Gonzalo Vazquez-Prokopec), and a geographer (Michael Page). I know it sounds like the start of a bad (and really nerdy) joke, as in, “An ichnologist, a disease ecologist, and a geographer walked into a bar one day…”, but it was a great opportunity for the three of us, all in the same Environmental Studies department at Emory University, to work together in a creative and synergistic way. I did the primary detective work, interpreting the trace fossil in the broadest sense, Gonzalo did some spatial analysis and Fourier transform calculations, and Michael put together the Deep Zoom™ application that allows a viewer to look at a detailed digital image of the trace fossil. This shows how science can work in imaginative ways!

The philosophical point I want to make is summarized by a sentence buried in the paper that refers to places where the fish’s fins lifted off the bottom of the lake and left no marks:

“In other words, these breaks in the continuity of the fin trails also constitute parts of the trace fossil, and have behavioral significance.”

A metaphor I will use to describe this is that the moments of silence in a piece of music are also part of the music. Likewise in this trace fossil, wherever the fish did not touch the bottom, these “empty” places are still part of the trace fossil, and filled with meaning.

Stay tuned for Part 2, to be posted tomorrow!

Reference

Image credits: Notogoneus image from Wikimedia Commons; picture of Tony by Ruth Schowalter; image of the ichnofossil modified from the original paper at PLoS ONE.

Got a Question? Ask a Biologist!

2010-04-19T19:27:00.003-07:00

In case you haven't yet heard the news, the UK-based "Ask a Biologist" web site has just undergone a major redesign. A whole host of bio-type scientists from around the world, including many paleontologists, are available to field your every question (within reason, of course - they can't do your homework for you!). Congratulations to all of the folks behind AAB - great work! As for the rest of you - go ask a biologist!

Royalties for Scholarly Publishing?

2010-04-01T00:00:00.009-07:00

I scarcely believed my eyes when I picked up the mail today. . .my first royalty check ever! It wasn't a lot - only $180.84 - but that's $180.84 that I didn't have yesterday. It's also making me reconsider some of my (previously uncharitable) thoughts about for-profit academic publishers.

One of the big criticisms of many commercial publishers is that they get the content written, typeset, and reviewed for free by the scientists, and then turn around and sell the content back to libraries (and individual consumers) at an exorbitant price. Furthermore, many of these publishers continue to show major growths in profits even in the face of an economic downturn. Well, it turns out that they're not as heartless as we thought. In response to pressure from open access publishers (some of whom make their authors pay ridiculous rates), libraries (who are having to cut back on all journal subscriptions), and researchers, the commercial publishers have had a change of heart. They've banded together into a consortium (with the rather euphonious name of BENT, combining portions of the major publishers' names) with the stated purpose of giving back to the academic community.

So how does it work? Well, let's say that an academic journal from a for-profit publisher costs libraries $1,200 per year. By comparison with non-profit journals of equivalent number of pages (and assuming that these non-profits are only breaking even), this means that each subscription nets around $850 profit per year. Assuming a 20 percent profit margin for the company (the investors deserve to be compensated, after all), this leaves around $610 of "spare" cash from each subscribing institution. Of course, we also have to remember that many libraries are only getting the journals as part of a bundle. Assuming that these bundles cut journal subscription costs in third, this still leaves around $200 from each subscribing library per year. If 500 libraries worldwide subscribe to a given paleontology journal in some form, this means a minimum of $100,000 left over!

Here's where the publishers have done something really, really smart. Recognizing that academics put a lot of time and effort into writing and reviewing articles, all of these after-profit proceeds are going back to the researchers. The amount designated per article is based on the length of the article within the years volume. The authors of an article get 75 percent, and the editors and reviewers get 25 percent.

What's that boil down to in real terms? Well, a co-author and I published a 6 page article in a journal that had a total of 1,400 pages last year. Proportionate to the $100,000 left-over money, this means our article gets a $428 cut of the proceeds. $107 goes to the reviewers and editor (split three ways), and the remainder ($321) goes to us authors. I was the junior author, so I got only 1/3 of that amount - $107. But, I also reviewed a 12 page article for the journal ($71 for that!). And better yet, the publishers now compensate us authors for profits from sales of PDFs! Frustratingly, I don't know how many copies of the article were sold, but I do know that I earned $2.84 as a result. Not too shabby - I'll quit complaining about having to pay $35 for a single article, knowing that the authors now reap the benefits.

This move by the publishers is a huge blow against the open access movement, and it means that I'm going to think twice about just giving my hard-earned research away for free (or worse yet, paying a publication fee). Regardless of what happens, I can't wait for another royalty check to arrive this time next year!

Welcome, Seitaad!

2010-03-23T17:05:00.013-07:00

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

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

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

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

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

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

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

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

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

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

Mark Loewen with the skeleton of Seitaad ruessi

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

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

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

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

Image Credits: Mark Loewen and Utah Museum of Natural History

Interview: Brian Beatty, on PalArch (Part 2)

2010-03-03T17:31:00.000-08:00

This two-part series (part 1 is here) focuses on the open access journal, PalArch's Journal of Vertebrate Paleontology. We're talking with its managing editor, Brian Beatty (who also blogs at The Aquatic Amniote).

As a managing editor, what sort of things do you do?
As a small outfit with relatively few submissions, I find I spend most of my time requesting suggestions for reviewers from the editorial board, asking reviewers to review papers directly, and passing manuscripts and revisions back and forth between the authors and reviewers. I consider myself lucky to be able to learn so much from these contributions and from the editing and review process itself, though I must admit that it saddens me to think that there are probably plenty of people that think poorly of me because I've had to request revisions, or even reject their papers. I try to be gentle and constructive, as that's my only intention, but it never seems to be enough. I also try to be fast, even though I am a full-time professor and researcher, as well as a father of two young children, which also rarely seems to satisfy anyone. I don't mean to whine, especially because I understand why authors want things to move quickly (I do and feel the same way for my own papers).

So, ultimately, as managing editor I basically have to deal with running the whole review process, even though I have help from the editorial board. Andre Veldmeijer and Ilja Nieuwland are tremendously helpful and talented with copyediting, formatting, and reviewing, and none of this would be possible without them. That isn't to suggest that is all they do, and their roles in the board of PalArch and as editors themselves is integral to the function of the journals published by the PalArch Foundation. Recently my father passed away, and Andre and Ilja were there to back me up and shoulder some of the burden while I was otherwise occupied, and they are as much a part of of making this journal function as I am. Andre started the whole thing, and if it were not for him, the Foundation and journals would never have been possible.

Are there any "myths" about your journal that you'd like to see "busted"?
I don't know of any myths about the journal, and if you do I'd love to hear them. The only thing that comes to mind is that some people might think we have lower standards because we don't have name recognition and that we welcome topics that are not popular. Any idea about our standards being low are misguided by the perception that other journals have maintained, that by rejecting papers they are proving their importance and high standards. What goes on too often is that popularity (or shock value) often wins over good science in other journals. One can see that in the way that papers are often worded so as to convey that there is a controversy, and that their work proves some alternative viewpoint. That may be a popular way to write things up, sensationalizing science, but I like to think that PalArch's priority is publishing good science, even that which only confirms other people's work, even papers where the statistics indicate that the results are insignificant or that the controversy is not needed.

The fact is, if the science is good, then that's all that is needed. I hate to say this, because it sounds like the same way other journal brag, but we have a fairly high rejection rate. I think that's just because some people think of PalArch as the last resort, but I hope that will change. This rate isn't the result of the same cause for rejection I have witnessed for my own papers, as well as those of others, but because PalArch simply cannot save every paper from being fundamentally flawed in their structure, data, or writing. Many of the papers we have in review take longer because we actively try to help the authors improve them, but some people refuse to edit their papers and take constructive reviews seriously, but EVERY paper is sent out for review, and EVERY review is intended to be constructive and have an aim of helping the author get the paper to a publishable state. I would love it if every submission started out that way, then publication would occur more quickly, but that is rarely the case. I find it worthwhile helping authors get it there, though I fear I may be too idealistic in thinking that everyone's goals are to patiently publish strong science.

Thank you, Brian, for sharing your thoughts!

Interview: Brian Beatty, on PalArch (Part 1)

2010-03-02T17:00:00.007-08:00

Regular readers of this blog probably know that I'm a big proponent of open access publishing. Today, I wanted to highlight another open access journal, PalArch's Journal of Vertebrate Paleontology. So, I contacted its managing editor, Brian Beatty, for more details. In addition to his editorial and academic duties, Brian blogs over at The Aquatic Amniote (and, coincidentally or not, most of his research involves. . .aquatic amniotes!).

How did you get involved with PalArch?
Back in late 2004 I saw a message on the VRTPALEO listserver from Andre Veldmeijer, asking for volunteers for the editorial board of this new journal based in the Netherlands. I was a PhD student at KU at the time, and though I had a lot on my plate, I was eager to learn about editing and peer review, and contacted Andre. I only had a single peer-reviewed publication to my name then, but had lots of projects in progress, had just finished my MS at Howard University with Daryl Domning, and was eager to be done with being a student and wanted to just focus on getting work done. My undergrad advisor at the FLMNH, Dave Webb, always spoke about how peer review was perhaps more beneficial to the reviewer than the author, always keeping one up to date, and so when the opportunity to get involved on an editorial board came up, I jumped at it.

Ironically, when I introduced myself to Andre, I gave him some background, including mention of my recent advisor, Daryl Domning. Andre specializes in the archaeology of ancient Egypt, particularly the leatherwork and rope, and Daryl was one of the few other people that had dabbled in writing scientific papers describing unique knots that ancient Egyptians used. Andre excitedly asked me, "Do you mean, THE Daryl Domning?", and when I finally understood why he found that interesting, we had a laugh at the improbability of it.

Since then, I've tried my best to be a consistent help to the journal, and as time passed and Andre needed more and more help, I volunteered more and more of my time to it. He has always been respectful of my opinions about how journals should be managed, and it has been a great 5+ years of working together.

What kind of papers are you looking for?
PalArch's Journal of Vertebrate Palaeontology is interested in anything and everything related to vertebrate paleontology, including reviews and commentaries, but especially new information, including reports of new specimens of rare taxa that highlight new insights about it, faunal studies or contributions about the distribution of fossil taxa, paleopathology case reports, novel paleobiological methods, and even new taxon descriptions. We've been in contact with the ICZN for years about how to comply to the rules about publishing new species names, and because we deposit printed versions of the journal in clearly identified libraries, all names published in PalArch are legitimate. Though we would love to have more high-profile papers submitted, such as recent studies of hominids from Wallacea (Plas, 2007) and Flores (Heteren, 2008), I am eager to get more submissions in general, and hope to see a more prolific submission rate so we can fully realize the journal's potential.

What are the advantages of publishing with PalArch? What does PalArch offer that other journals might not?
The fundamental reason I got involved with PalArch was because of the journal's primary goal, which was to provide an avenue for publication of good science that might otherwise be too long, not popular or sexy enough, or controversial to make it into the restricted world of printed journals. The idea was simple, and yet at the time when I started I hadn't realized how few journals did that, I only knew I was frustrated by some.

PalArch is completely not-for-profit, volunteer run, and though we are all human and have our inevitable biases, we try to stay focused on the validity and quality of the science, not the popularity of it. There are no pages charges, and no limitations on length or color figures (similar to that of Palaeontologica Electronica). We try to get reviews done quickly, though we've had a longer than desired lag time in publication because we have a tendency to spend time helping authors that are not native english speakers with their editing and writing, which can often take longer than initially hoped for. I have been trying to get reviewers to be more rapid and responsible about reviews, though I think most editors would agree that that is easier said than done. So, one selling point is the time it should take - though reviewers slow things down, we really try to get things formatted and published online as soon as they are accepted, meaning that a publication could occur within less than a month, IF reviews go well and revisions are managed rapidly.

Tune in tomorrow, for Part 2 of the interview. Image credit for picture at top: Photo by Mo Hassan, proprietor of The Disillusioned Taxonomist. Another blog well worth checking out!

Open Notebook Science for Paleontology?

2010-03-01T20:02:00.007-08:00

Open notebook science is kinda like open access for your data. In other words, it recognizes that a scientific contribution is more than just the resulting publication. These publications are often underlain by hours of thought, months of data collection, and weeks of analysis. In an open notebook approach, these "behind the scenes" activities are tossed out there for others to view, critique, utilize, and build upon. Note that this is different from open access, which is usually taken to cover only the final publication.

While at ScienceOnline2010 back in January, I sat in on a stimulating session about open notebook science. Our presenters (Jean-Claude Bradley, Steve Koch, and Cameron Neylon - all with blogs that are well worth checking out) shared their own experience with open notebook science, and the entire group discussed the ups, downs, plusses, minuses, and issues associated with the concept. It got me thinking - could I make at least some of my research open notebook? In this post, I want to explore the issue briefly, and solicit your feedback.

Why we need open notebook science
Good science is about reproducibility. There's no way around this. In a historical science like paleontology, "reproducibility" might involve remeasuring a specimen, retaking a photograph, or rescanning a bone. Some stuff we just can't reproduce. Once a bone is out of the ground, you'll never be able to retake the same precise stratigraphic or taphonomic data. Some data are ridiculously difficult to reproduce - not everyone can afford to fly to every country to remeasure some limb bones, or get the permission to rescan a specimen. Is it really necessary to have to reinvent the wheel?

And let's consider the long term. Whether we like it or not, we're all going to die someday. We can't take our data with us - why should they be locked up in some archive, or tossed out by whoever has to clean out the filing cabinets? Why don't we treat our data with the care that we show our specimens?

Objections (and solutions) to Open Notebook Science
In my own thought on the subject, I've wrestled with a number of issues relevant to open notebook paleontology. Many of these were covered in the ScienceOnline session, and I would refer anyone who is really interested to check out the YouTube videos when they get posted. In brief, objections include:

-Time and money. It takes time to digitize notes and put them into a form usable by others, and long-term data repositories cost money. This is a valid concern - particularly if you have years of undigitized data. When it comes to my museum research, my past three or four years of notes are almost entirely digital, though. And, the issue of a repository is a serious problem. Beyond journals' supplementary information, there is no permanent system for our field.
-Embarrassing errors. When taking notes, our interpretations of specimens change. Sometimes we make a mistake. Do we want to broadcast that to the world? Worse yet, what if someone else uses our mistake? This too can be a genuine concern - but I don't think it's an excuse for locking up raw data. A prominent caveat would probably be sufficient.
-Being scooped. Again, this is a legitimate concern that becomes irrelevant after publication. If you are worried about being scooped, just don't post in-progress data prior to publications. Or, consider the fact that having a time-stamped observation out there on the Internet is pretty unambiguous evidence of priority.
-Being scooped (2). I've heard multiple times (and used to subscribe to this philosophy myself) that one shouldn't release data until every single possible piece of information or side project is leached out of it. Wrong. Simply wrong. If your data are used to create a published summary table, graph, or even other types of figure, they need to be available. This doesn't mean you necessarily should release all of the "extra" data - but at the bare minimum, an interested individual should be able to see the information directly related to your methods, results, and conclusions. And the whole enchilada should get out there at some point.
-Locality data. Another common objection is that we should release precise locality data for sites, to avoid poaching. I agree with this 100 percent. But, there are still tons of data that could be distributed.
-Image rights. Have you ever read the agreement that museums make us sign in order to take pictures? Sadly, most of us don't own the photos that we take of specimens. I would love, love, love to have a Flickr stream of every specimen photo I've ever shot, but it just ain't happening yet. It is understandable that museums don't want someone profiting off of a giant coffee table book of fossil photos - but I'll be the first to admit that 99.9 percent of my photos aren't commercially saleable. Could anyone conceivably profit off of 20 closeup photos of a fragmented ceratopsian jugal bone? And, don't forget that a significant number of specimens in American museums are property of the American people (situations may vary elsewhere). A museum is seriously forgetting one of its reasons for existence if the institution actively hampers scientific progress by not allowing non-commercial distribution of specimen photographs. I don't have a good solution.

Thoughts? Comments? Is this ever the sort of thing that paleontologists will buy into?

Two articles of note

2010-02-24T06:55:00.006-08:00

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

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

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

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

Petrified Forest in PLoS ONE

2010-02-18T19:49:00.008-08:00

Congratulations to Jeff Martz and Bill Parker on their latest publication in PLoS ONE! It's a wonderfully detailed description of the Sonsela Member of the Chinle Formation as exposed in Petrified Forest National Park.

This new paper resolves a number of niggling problems regarding this portion of the Chinle Formation. It has all sorts of implications for how we understand faunal turnover in the Triassic, among other things. And, the work is ridiculously reproducible! Every measured section has detailed GPS coordinates and photographs. . .contacts were walked out to the bitter end. Geology at its finest!

One of the advantages of an online publication like PLoS ONE is that there are no page limits and unlimited color figures. Jeff and Bill took full advantage of this - the PDF of their paper weighs in 26 pages of geological goodness, and that isn't counting the supplement of 29 pages of measured sections and dozens of megabytes of full-color, high resolution photographs. In short, it's a geological monograph.

Part of the Chinle Formation, with random geologist for scale. Modified from Figure 12 in Martz and Parker 2010.

Another neat thing about this paper is that it's one of the first strict geology papers published in PLoS ONE. With the groundswell of paleontology papers as of late, it's nice to see some geology making it into this major open access journal also. The authors deserve major kudos for their willingness to be guinea pigs.

For more about the paper, check out Bill's post at Chinleana. Or, you can read the whole article here. Do you have a comment or a question, or want to rate the paper? You can do all of that at the PLoS ONE website!

Citation
Martz, J.W., and W.G. Parker. 2010. Revised lithostratigraphy of the Sonsela Member (Chinle Formation, Upper Triassic) in the southern part of Petrified Forest National Park, Arizona. PLoS ONE 5(2):e9329. doi:10.1371/journal.pone.0009329

[Full disclosure: I was the academic editor for this paper, and am a section editor for the journal]

Book Review: Am I Making Myself Clear? A Scientist's Guide to Talking to the Public

2010-02-15T07:51:00.004-08:00

It's no secret that paleontology fascinates the public. New prehistoric-themed television air practically weekly, and even comparatively minor discoveries make the science section of the local newspaper. But, it's also fair to say that we paleontologists have a love-hate relationship with the news media. On the one hand, the exposure educates the public and shows the importance of an "esoteric" field like paleontology to skeptical funding committees. Yet, nearly everyone has some horror story about how they were taken for a ride by the press. Stories are misreported or overhyped, and television programs are sometimes painfully inaccurate. How is one to navigate this potential minefield?

Enter Am I Making Myself Clear? A Scientist's Guide to Talking to the Public, a trim, timely book by science writer and former NY Times editor Cornelia Dean. The title indicates great ambitions, and Dean generally delivers on these, speaking with the authority and candor of someone in the trenches.

Fifteen chapters cover practically the entire spectrum of scientific communication, from print and electronic media to public policy and the legal witness stand. Dean's writing is concise and readable, with an appropriate number of relevant anecdotes sprinkled throughout. Her perspective as a journalist adds quite a bit to the narrative, particularly in the sections on working with reporters. Although I like to think that I know at least a little about the media, I found numerous tidbits to incorporate into my own efforts. Don't be disappointed if an hour-long interview doesn't produce any attributed quotes in a news article; your information is still crucial for reporters who may not know the field. Thank reporters who do a particularly good job. Use press releases judiciously. It's ok - in fact, even a good thing - to cite opposing points of view during an interview. Sound bites are your friend, if you prepare them carefully.

The short format of the book (indeed, it's just slightly larger than pocket-sized) means that many topics are covered in only the briefest fashion. For instance, the scant 17 pages devoted to book writing and publication is surely only the beginning for someone who is truly serious about such an effort. I personally would have liked to see a little more on preparing a public lecture. Thankfully, a carefully chosen bibliography offers some excellent suggestions for deeper reading.

One message echoes throughout the entire book: We scientists can't just sit back and let the journalists do the talking for us. As citizens, we have a responsibility - an obligation, even - to get involved. Sure, there might be bumps on the road, but in the shifting social, political, and economic sands of the early 21st century, communication is more important than ever before. If you are at all serious about communicating science to the public, you must read this book.

Citation
Dean, Cornelia. 2009. Am I Making Myself Clear? A Scientist's Guide to Talking to the Public. Cambridge, Massachusetts: Harvard University Press. 274 pp. $19.95 (hardcover) - available for $13.57 on amazon.com.

Four-Winged, Psychedelic Dinosaurs

2010-02-13T07:20:00.015-08:00

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

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

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

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

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

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

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

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

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

Citation

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

New OpenOffice.org Release

2010-02-12T06:42:00.005-08:00

The latest release of OpenOffice.org (version 3.2) just came out. I've been using release candidate 4 for the last week or so, and love it. For those of you who aren't familiar with the package, it's an open source office suite, with full-fledged word processing, spreadsheet, presentation, and database software (my experience is primarily with the first three). Plus, it's free! For the last four years, OpenOffice.org has been my primary office suite - my dissertation was written on it, all of my slides (and many poster presentations) are composed in it, and the great bulk of my data collection happens with this software. In that time, I've seen the software evolve from a decent package to a great package!

Improvements in this release include a faster start-up time, better copy-and-paste functionality in Calc (the spreadsheet), and much more. I've also noticed some bug fixes for the track changes and comments feature when working with Microsoft Word documents (something I do quite frequently, particularly for collaborations). All of these are mostly minor steps beyond the previous release, but it's still well worth the download time for the upgrade.

The Decline of Documentation

2010-02-04T22:16:00.008-08:00

I'm a huge fan of Matt Wedel's "Measure Your Damned Dinosaur" philosophy. For those of you who aren't familiar with his post on the topic (and seriously, it's probably one of the best pieces of research blogging from 2009), the title is pretty self-explanatory. Despite scads of new techniques, a bloatload of journal options, and the rise of endless supplementary data files, we paleontologists just ain't doing our job anymore when it comes to publishing measurements of specimens. As Wedel said,

"It blows my damn mind that a century ago people like Charles Whitney Gilmore and John Bell Hatcher could measure a dinosaur to within an inch of its life, and publish all of those measurements in their descriptions, and lots of folks did this and it was just part of being a competent scientist and doing your damn job. And here we are in the 21st century with CT machines, laser surface scanners, ion reflux pronabulators and the like, and using a narf-blappin’ TAPE MEASURE is apparently a lost art."

Just for giggles, I decided to find out if things really were better in the past, or if we're just waxing nostalgic for a golden age of documentation that never existed. Being someone who is number-inclined, I grabbed a bunch of ornithischian data from The Open Dinosaur Project. Using some handy-dandy spreadsheet functions, I extracted data for the year of publication for a series of measurements as well as the number of relevant limb bone measurements for that paper that made it into our database.

Then, it was time to run statistics! I wanted to see if there was a correlation between year of publication for a specimen's measurement and the number of measurements published for each specimen. So, I ran a non-parametric test of correlation (Spearman's rho, or ρ). Care to guess what I found?

Sadly, Wedel is right. There is a negative correlation between year of publication and number of measurements: ρ = -0.44, P less than 0.0001.

So then I thought, there are a lot of papers that have just published a single measurement of an isolated bone, or a whole table of single element specimen measurements (e.g., femur length for 20 different species). Maybe that was biasing the dataset. Thus, I trimmed out all of the entries that had only one measurement. Still, there was a significant negative correlation (ρ = -0.27, P less than 0.0001). The average paper published between 1920 and 1930 had 18.5 measurements; between 2000 and 2009, 14 measurements.

Have our dinosaur skeletons gotten less complete? Or have we given in to the need to squeeze less information in less space, and perhaps a little laziness on the side? What will it take to change this trend? It's all food for thought.

Caveat: This is a highly unscientific, probably very non-random sample. Oh well.

Where is paleontology?

2010-01-28T06:42:00.007-08:00

Last week, many of the leading journals in evolutionary biology - including The American Naturalist, Molecular Ecology, Journal of Evolutionary Biology, Evolution, and a number of others - announced a data archiving policy. In short, this policy states that the data behind the results of a paper should be publicly archived in well-known respositories such as Data Dryad, GenBank, or TreeBASE. Do you notice anything missing in this illustrious list of publications?

Not a single one of those journals explicitly focuses on paleontology. Last time I checked, we paleontologists like to think of ourselves as evolutionary biologists. Time and time again, we lament how we're not allowed a place at "The High Table" of evolutionary thought, and how paleontology is viewed as largely irrelevant by the "people who matter." So why weren't any paleontology publications on this list? Will we see any on the list in the near future?

The article in The American Naturalist gives a good run-down of the arguments for sharing data, so I'll only briefly summarize them here:

It allows reproducibility of analyses.
It allows others to build upon your work more easily.
Papers that release their data may get cited more frequently.
The data will be lost to science otherwise.
It's the right thing to do.

And to counter some potential objections:

This would only request the release of data directly relevant to the study. Not your pages and pages of raw notes. Just that Excel spreadsheet that you already generated on your way to the analysis. Seriously. It's not a lot of extra work, if any.
This is not requesting the digitization and distribution of video, CT scan, or similarly large and unwieldy data (although that would be nice in the future).
No, it does not mandate the release of locality data, or similarly privileged information.
The policy does not require immediate release of the data, if there's a good reason (i.e., another pending publication) to do so. I'm not sure I entirely support this (if you're publishing the analysis, you should publish the data), but I understand it as a necessary compromise to get more individuals on board. I won't let the perfect be the enemy of the good.

Some of the most ground-breaking and high-profile work in paleontology is happening on account of large meta-analyses of data pulled together from the literature - largely thanks to efforts like the Paleobiology Database. This work has real implications for big questions facing our science and our world: Climate change. The pace of evolutionary radiations. The origins of modern biological diversity. These sorts of databases focus primarily on geographic, stratigraphic, and taxonomic data - but think how much more powerful they could be if all of the morphological data ever published were available! Or if the PBDB volunteers didn't always have to transcribe the information from a PDF file. And look at the great strides that molecular biology has made with the ready availability of sequence data on GenBank! This would not have happened with a mentality of data hoarding.

Look. Amateur hour is over. If we want to play in the big leagues, we have to start acting like a real science. Real science is reproducible. Real science is data-driven. Real science involves sharing data. Yes, I know it's hard. It's new. We haven't done things this way before. There are potential problems. Not everyone is adopting it quickly. But if we always wait five years to "see what happens," we paleontologists quite frankly don't deserve a place at the High Table. Let's be leaders, not followers.

References
Piwowar, H. A., R. S. Day, and D. B. Fridsma. (2007). Sharing detailed research data is associated with increased citation rate. PLoS ONE 2(3):e308, DOI: 10.1371/journal.pone.0000308.
Whitlock, M., McPeek, M., Rausher, M., Rieseberg, L., & Moore, A. (2010). Data archiving. The American Naturalist, 175 (2), 145-146 DOI: 10.1086/650340

For previous posts on data sharing in paleontology, see here and here. Want to get involved? Spread the word. Talk to your local journal editor. Let the people who count know what you think.

ScienceOnline2010 Report #scio10

2010-01-17T22:48:00.005-08:00

I am just freshly back from ScienceOnline2010, where I was graciously invited to talk about the Open Dinosaur Project by Bora Zivkovic (who co-organized the "un-conference" with Anton Zuiker). Simply put, this is one of the best conferences I have attended in a long, long time. So what was it that got me so excited about the event?

Meeting new people. Coming into the event, I had met precisely three of the 251 other attendees in person before, and wouldn't say I knew any of them particularly well. Some folks I knew from cyberspace (either through blogs, or PLoS-related functions), but there is something entirely different about in-person interactions. Even better were the unexpected and unplanned meetings - bumping into someone completely new who had wonderfully convergent interests, or a stimulating viewpoint, or was just plain interesting. All in all, it was a tremendously friendly bunch.
The civility and positivity. When I (a major proponent of open access) can sit down over a beer and have a really enjoyable, wide-ranging chat with an employee of Elsevier, that's pretty cool. This friendly tenor was by-and-large a hallmark of the meeting. For instance, I was enormously impressed by Pete Binfield's presentation on article level metrics [full disclosure: I'm a section editor at PLoS ONE - Pete is the guy at the helm of the journal]. It wasn't a rant against impact factors, or how PLoS ONE's article level metrics are going to put all of the commercial publishers out of business. His presentation was a factual overview of the plus's and minuses, some genuine recognition of the good things other companies are doing, and an open invitation for others to join the article level metric club. Why can't some segments of the blogosphere be more like this?
Seeing the cutting edge. For better or worse, paleontology is a conservative discipline in many respects. This is not to say that every other discipline is lightyears ahead (they're not - scientists of all sorts have tremendous cultural and institutional inertia), but simply that the innovations aren't necessarily happening in our field. I was incredibly energized by the discussions of improving public outreach over the internet, open notebook science, open access publishing, and much more. Some of the concepts will fade into oblivion, some will be superseded by unforeseen technology, and some will become the dominant way of doing things within a few short years. It's going to be very fun to look back, 10 years from now, and remember when issue X or technique Y seemed so new and fresh.
The openness of the conference. Nearly every session was YouTubed (videos to go up soon), blogged, livestreamed, and tweeted. The more I see how effective this format is, the more I like it. Yes, yes, I know that it's just not possible for "real" science conferences. . . .But why not?
The librarians. Yes, really. Prior to this, I knew librarians as the people who put books back on the shelves and sometimes process an interlibrary loan. During this meeting, I learned that if we want any hope of saving our data (not just our published papers), the librarians will be key in making it happen. If you're looking for some readable and interesting blogs, I would recommend checking out Confessions of a Science Librarian, Christina's LIS Rant, and The Book of Trogool. I got to hang out with both of their authors, and they're really cool people.
The Shiny Digital Future isn't just for, or being engineered by, white male nerds under the age of 30. Readily identifiable asocial weirdos were pretty darned scarce, and I was impressed by the number of people past the first few years of their career. We were all geeks, but I think many of us (?some of us?) could pass as normal if you ran into us at the supermarket.

In the afterglow of the conference, the wheels in my brain are turning in multiple directions. This is a sign of a great event, and a sure indication that you'll be seeing more blog posts (and projects) inspired by my weekend here.

Paleo Paper Challenge: The Final Round-Up

2010-01-12T21:26:00.003-08:00

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

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

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

Results of the Paleo Paper Challenge

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

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

Lisa Buckley
Papers to be decided
Final status: Unknown

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

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

John Foster:
Morrison critter paper
Final status: Unknown

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

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

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

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

Thomas Holtz:
Tyrannosaur heterochrony/paleoecology
Final status: Unknown

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

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

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

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

Bill Parker:
Revueltosaurus manuscript
Final status: Unknown

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

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

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

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

Mike Taylor:
The Archbishop description
Final status: Major progress

Matt Wedel:
Final dissertation chapter
Final status: Unknown

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

For All You Pterosaur Fans

2010-01-07T20:35:00.006-08:00

Dave Hone has asked me to pass on his announcement of the launch of pterosaur.net. This new web page is a collaborative effort by a number of pterosaur experts to provide a gateway to accurate, scientifically-based information on this fascinating clade. It looks great, both in terms of content and some eye-popping artwork, so I strongly recommend checking it out!