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.

Got a Question? Ask a Biologist!

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

Royalties for Scholarly Publishing?

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

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

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

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

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

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

Welcome, Seitaad!

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

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

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

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

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

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

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

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

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

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

Mark Loewen with the skeleton of Seitaad ruessi

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

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

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

Image Credits: Mark Loewen and Utah Museum of Natural History

Interview: Brian Beatty, on PalArch (Part 2)

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

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

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

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

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

Thank you, Brian, for sharing your thoughts!

Interview: Brian Beatty, on PalArch (Part 1)

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

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

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

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

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

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

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

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

Open Notebook Science for Paleontology?

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?