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]

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!