Nedoceratops - Random Thoughts

The last two posts here have focused on my most recently published paper, fully describing the skull of the horned dinosaur known as Nedoceratops hatcheri and critiquing the hypothesis that it, along with Torosaurus latus, is simply an older individual of what we call Triceratops. Because I've already talked about the science of the paper, and some collegial interactions, I'm going to spend this final post in the series talking about a few odds-and-ends that just didn't fit anywhere else. Most of these are little windows into the process behind the paper - from writing to review to revision. And we'll start with. . .

Open Source Composition

I'm proud to say that every single step of the authoring process for my paper happened in open source software. I wrote the manuscript in OpenOffice.org Writer, formatted most of the references in Zotero, did initial image editing (contrast adjustment and background removal) in GIMP, assembled the figures in Inkscape, and submitted the manuscript through the journal website on the browser Firefox, all of which were running on various releases of Ubuntu. Score one for open source software (and open access publishing)!

On Organizing the Paper

I'm under no illusion that everyone (?anyone?) will agree with my conclusion that Nedoceratops is a valid taxon. In fact, I'm quite accepting of the possibility that I may be wrong. But even if this is the case, I still want my paper to be useful. So, I made my best effort to separate data from interpretation in the description section of the paper. Of course, I couldn't be completely successful on this point - after all, I had to compare Nedoceratops with Triceratops and Torosaurus (the most likely candidates for synonymy) - but I like to think that I mostly achieved my goal. If nothing else, I have pretty pictures. And. . .

Speaking of Pictures

My figures went through some pretty drastic changes during the evolution of this paper. In the first round of reviews, it was pointed out that in the text I kept referring to various structures illustrated in the figures, but only a ceratopsian geek could figure out what I was talking about.

For example, we have this lovely sentence:

The narial strut is inclined rostrally towards the dorsal end of the element, and enough original bone surface is preserved to indicate that a posterior internarial flange did not project from the caudal surface of this structure (Figure 4).

My original Figure 4 looked like this:

The photo is relatively pretty, but only a die-hard ceratopsian nerd could locate the narial strut or know where to look for a posterior internarial flange if such a thing even existed in this animal. So, for my next iteration I added some labeling:

Of course, all of the abbreviations are explained in the caption (not shown here). "ns" refers to the narial strut I was talking about above. Finally, the editor mentioned that I should do a better job of indicating the "cpf" (canal at the edge of the premaxillary fossa). It wasn't just at the tip of the arrow, but over a somewhat broader area. Thus, that brings us to version 3:

This, with the extra arrows showing the position of the canal, was the version that appeared in the paper.

If I learned anything from this experience, it was about the importance of good labeling and interpretive drawings for non-expert readers. Most of the labeled interpretive drawings alongside photographs (with the exception of parts B and D in Figure 1) were added at the direct request of the editor. Looking at the end product, this addition was a major improvement to the paper. Of course, I must also admit that having relatively unlimited space in an online journal allows this luxury!

Editorial Ethics

It's probably not a surprise to many of you that I am a volunteer academic editor at PLoS ONE. And those of you who have been paying attention probably noticed that the Nedoceratops paper was just published in that very same journal. This sounds pretty problematic on the face of it.

Thankfully, PLoS ONE has pretty strict editorial controls when one of their own editors submits a paper (in addition to a competing interests policy that covers this and similar situations). My experience as a submitting author was exactly the same as for any other author. Once the "submit" button was pressed, I had to wait just like everyone else. I couldn't control which editors handled it, who reviewed it, or even have a sneak peek at the reviews on-line. In other words, the system functioned exactly as it should.

My authorial feet were held to the fire by Leon Claessens, the handling editor for my submission. Leon, in my opinion, did a very professional job and didn't let me get away with anything (even sending the manuscript back to me a second time for a few last corrections and improvements). The reviewers - Michael Ryan and Peter Dodson - also did their jobs (in my opinion). And, as mentioned in my last post, comments by John Scannella and Jack Horner offered additional constructive feedback.

One thing I really like about PLoS ONE is that my competing interest - as an editor at the journal - is stated up-front in the paper. Although it's somewhat scary seeing it there, I think such notices are certainly appropriate.

Final Thoughts

It's nice to finally have this paper out there - these ideas have been floating around in my head for awhile, and I've always had a secret desire to be the person to describe Nedoceratops. I'm relatively pleased with the final product (of course, there are always one or two typos that slip through, and why couldn't some of the figures in the PDF have been bigger?), and look forward to the discussion that this paper generates. Thank you to all who helped out (see the acknowledgments for a comprehensive list)!

Aetosaurs and the Open Access Dissertation

It's done. The Society of Vertebrate Paleontology has weighed in on allegations of plagiarism and claim-jumping centered on those spiny aetosaurs. The end verdict is "not guilty" on one charge and "inconclusive" on the other (but please read it for yourself), and I won't comment here where others have already (summarized here). I do wish to discuss, however, one point from the official SVP document that has not been addressed elsewhere.

"Sixth, the expectation that theses and dissertations that have not been republished in widely read periodicals will be read by most workers or manuscript reviewers is unlikely to be realized. If students publish material in theses or dissertations that they intend to republish in other venues, they should be wary about circulating their work until publication is well under way, if they are concerned that their work is topical enough that other workers might want to draw immediately from their findings." [p. 3 of SVP executive committee statement; italics are my own]

My main concern here is with the statement that it's unlikely that dissertations and theses will be read by other workers. This may have been true 20 years ago - today, this is changing very rapidly. You can find dissertations on Google Scholar, Dissertation Express, Theses Canada Portal, and DATRIX, just to name a few (although it's admittedly easier on some of these options than others). UMI now offers the option to distribute your dissertation under an open access scheme (with options for an embargo, for those concerned about such things). I have chosen to release my dissertation on open access (and will update here when my dissertation is readily available). Searching for dissertations and theses on a research topic should be part of any basic literature search (although whether or not this would have avoided the problems leading to the ethics investigation is certainly debatable).

The responsibility runs both ways. Students have an obligation to ensure that their thesis or dissertation is available and accessible via the information superhighway. This means making it available through relevant databases (and UMI's dissertations and theses have been crawled by search engines since 2006, apparently, with more complete access since 2007), and in most cases could [?should?] probably entail open access (with or without embargo). All paleontologists have a responsibility, too - to keep on top of the literature and other researchers' work. Even without a search engine, it wouldn't take a genius to figure out that a student who has had one or more conference presentations on thesis-y sounding research may have a thesis in his or her name on that topic. And with a search engine, there really is less of an excuse now. Sure, there will still be dissertations that slip through the cracks - but is this any different from not finding a peer-reviewed article just because it was in a journal outside your normal reading list? So--make those dissertations and theses available, and spend a few minutes on Google!

[This discussion is not intended to comment on the correctness or incorrectness of the SVP's general ruling about the charges. As Kevin Padian said, "There’s something for everyone to like – and dislike – about the statement. . ." I'm just calling attention to an area that fits in nicely with the mission of this blog.]

Ethics and the Open Access Dissertation

Doctoral dissertations and master's theses have always been considered real, citable pieces of work (even if they aren't sufficient for the purposes of establishing new names). I've certainly cited some theses and dissertations in my own work, particularly if they represent the only printed evidence of a certain line of research. Yet, these academic products aren't necessarily considered as high impact or "important" as the final, independently peer-reviewed products that usually (hopefully) come out of the required document. For this reason, the lowly dissertation may get ignored - or worse.

The Internet (or at least, the paleo-nerd component of it) is abuzz about an article in the latest Nature (the discussion there includes links to additional information as well as statements from folks connected to the affair in various ways), alleging academic misconduct, at least some of which allegedly involved the. . .appropriation. . .of ideas from a master's thesis (among other alleged. . .incidents). The matter is reportedly under investigation by a relevant professional society. No bones about it - this is a serious situation Regardless of how things turn out in the end, or what actually happened, this is an issue about which every researcher must think carefully.

As a grad student, I want to put my money where my open access mouth is, to quote Dr. Vector. In (hopefully) a few short months, I'll be signing the line that makes my dissertation open access. Do I worry about being scooped? Maybe a little. . .but that's a risk I take by publishing an abstract or presenting at a conference, or even just talking to a colleague. Without these actions, science would certainly grind to a halt. And, getting my dissertation out there hopefully means I can mark my territory. But, the whole situation does make me think twice now.

So what can we do? One key step is to be extra, extra aware of what is happening in the grad student community. Although it is probably little solace to the grad student concerned, aetosaur workers might consider citing a certain M.Sc. thesis over articles published by other researchers (or at the very least, calling attention to the priority of ideas, if it's necessary to cite both). I generally try to do this anyhow, if an otherwise unpublished dissertation or thesis brings up some ideas that were later discussed (usually and hopefully independently) by other authors. UMI has a freely searchable database of dissertation titles and authors (the full abstract database requires a subscription, unfortunately) - it doesn't hurt to take a quick look to see if there is anyone that should be cited!

Increased communication brings with it increased productivity, as well as increased risk of skullduggery. VP is a small community, and it doesn't take long to acquire a good or bad reputation. Here's hoping for an ethical and uncontroversial future.