Introducing the Dental Microwear Image Library

Dental microwear, seen in the tiny pits and scratches on a tooth, provides lots of detailed data for inferring diet and chewing behavior in animals. Analyses are often conducted by digitizing highly magnified images of the tooth surface and counting up and classifying the various microscopic features. Animals with a certain percentage of pits and scratches may have browsing habits, whereas those with another profile may be grazers. By measuring extant animals with known diet, we can (hopefully) infer the diet of extinct animals.

Dental microwear; modified from figure 3 in Mihlbachler et al., 2012

In this age of increasingly open science, microwear studies can be problematic. A cornerstone of science is reproducibility - yet, inter-observer variation and error can greatly affect measured data. Furthermore, one study alone may generate dozens or hundreds of images. Even if you wanted to re-analyze teeth, it's pretty tough - how could you get access to the necessary images? Ideally, we want a world where anyone can access the raw image data, make their own observations, double-check published analyses, and add new data for comparison.

Thus, a new project - called the Dental Microwear Image Library, or DMIL - may change things. Assembled by Brian Lee Beatty and Matthew Mihlbachler, the website aims to become a clearinghouse for dental microwear images. This will allow greater standardization of analyses and hopefully better interpretations of paleoecology and diet for extinct organisms and modern organisms. The first data (from a recent paper in Paleontologia Electronica) are now posted, along with many other data sets.

Brian Lee Beatty (who blogs at The Aquatic Amniote and tweets as @Vanderhoofius) was kind enough to answer a few questions about the DMIL. Thanks, Brian!

Was there a particular moment or incident that inspired you to build the DMIL? If so, what was it?
As we set out to test and develop the method that Nikos Solounias and Gina Semprebon started, we found ourselves frustrated by not only the lack of information on methods that were given in most microwear papers, but also the inability for people to check their work. Interobserver error is a major cause of problems for microwear, and the only way for anyone to be aware of those differences is if they compare interpretations of microwear surfaces, not just their numbers on a spreadsheet. The DMIL was the only possible solution to the need to share such images.

How has community response been so far? Is there any particular type of skepticism that you're working to overcome?
The DMIL hasn't yet come up against skepticism, but our first paper on this method that uses it has.

What license, if any, are the data housed under? Or is it on a case-by-case basis?
There is no license for the data. We want it to be completely open-access and simply available.

How would you envision the DMIL 10 years from now? What goals might you have for the long-term?
We hope it will be a place that people can use to learn how to use the methods we are continuing to develop. I most sincerely hope that it will not only be home to our own data, but also be a place for others to deposit their data using similar methods so that more work of this sort is available in a similar, comparable format.

Authors of the recent paper in PE, along with a research assistant. Photos courtesy of Brian Lee Beatty.

For more information, check out the DMIL, or read the recent paper (open access) about the work.

Citation:
Mihlbachler, Matthew C., Beatty, Brian L., Caldera-Siu, Angela, Chan, Doris, and Lee, Richard, 2012. Error rates and observer bias in dental microwear analysis using light microscopy. Palaeontologia Electronica Vol. 15, Issue 1;12A,22p.

Life After Death At Yellowstone: An Interview with Josh Miller

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.

Youngina, Undergrad Research, and Nick Gardner

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]

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

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

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

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

Interview: Ricardo Araújo on Journal of Paleontological Techniques

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:

1. 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.
2. 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.
3. 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.
4. 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

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

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!)

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

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

Interview: Brian Beatty, on PalArch (Part 1)

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!