Petrified Forest in PLoS ONE

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

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

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

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

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?

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

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.