Open Notebook Science for Paleontology?

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

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

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.