Crossing the Finish Line for the Dissertation

Well, it's done.

All of the chapters of my dissertation have been published as papers in peer-reviewed journals.

It's been two years and four months since I submitted the final draft of my dissertation to my university, and wow, is it ever nice to finally lay the thing to rest. As a bit of a celebration, I wanted to pontificate share some musings on the whole process, and offer some hope for those who might be working on their dissertation right now. So, how did this all come to fruition? What did I do right (in my opinion), and what might I have done differently?

Start Early
Basically, I knew from the get-go that I didn't want to write one of those perpetually unpublished dissertations. You all know the ones I'm talking about. That really ground-breaking, highly citable, novel piece of research that's been sitting around completely unpublished since the person got his or her Ph.D. back in 1976. I can't really blame them - maybe they dropped out of the field. Maybe they decided research wasn't their thing. Maybe bigger and better projects happened along. These are all legitimate reasons (life happens!), but it doesn't make an unpublished dissertation any less annoying. As anyone in the field knows, journals (and reviewers) sometimes look askance at a reference listed as "unpublished thesis" or "unpublished dissertation."

So, I made a mental commitment early on to strive to get my dissertation published as quickly as possible. This was key in achieving the eventual goal.

Get Your Committee On Board
My dissertation committee wanted to see my stuff published, too. In fact, they specifically requested that I frame each of my dissertation chapters as discrete, publishable units. This was good advice. The days of creating a book-length narrative, which is retroactively turned into publishable manuscripts, are over. If you have the dissertation chapters framed as discrete, submission-ready papers, you can save a lot of time! This is a much more common practice than it used to be, which is a good thing (in my opinion).

So, before I had even finished writing the dissertation chapters, I had decided what journals I was going to submit to. Then, I formatted all of the figures, text, and references appropriately. This saved a ton of time in the end!

Git 'er Done
Once the dissertation is written, the congratulations received, and the diploma framed, the real work begins. Get those chapters submitted for publication. Take a week to rest on your laurels, and then get back to work. Every day you procrastinate is another opportunity to completely forget about submitting the papers for peer review. In fact, maybe even consider submitting some chapters before you graduate, if you can.

In the end, though, the only way I managed to get this done as quickly as I did (not that two years is that quick!) was to guilt-trip myself into doing it. Maybe that's what will work for you, too. And as I tell many people - don't let the perfect be the enemy of the good. Your work will never be perfect. There are always more data. There's always another specimen to measure. But at some point, you just have to call it "good enough."

Submit that paper. Because chances are, there's someone else out there who wants--perhaps even needs--to cite you. And I'm sure they would much rather cite a peer-reviewed paper than an unpublished (if excellent) dissertation or thesis. And for every day delayed, there's just another little way in which you have to revise the manuscript before submission. Science marches on, with or without us.

Regrets?
Not many, on my part. All in all, I'm happy with how my dissertation chapters have turned out. I might have had a few more figures in the ceratopsian one. Maybe a slightly longer discussion in the goat head FEM one. Perhaps I might have pushed to get the ZJLS paper published a little sooner. Oh well. They're done, they're published, and I can clear my plate for new projects.

Speaking of clearing plates, isn't it about time to relaunch the Paleo Paper Challenge?

My Dissertation - Now Open Access

ProQuest's UMI Dissertation Publishing is pretty much the distributor of dissertations and theses in the US and Canada (beyond an author posting the work on his or her personal website, or an ILL to the relevant academic library). ProQuest/UMI offer the service of permanently archiving and making your work searchable and accessible - and readers pay $36 for a PDF or $43 for an unbound print copy. To be fair, I personally consider this a reasonable price for documents the size of a dissertation (considering that Elsevier and kin charge roughly the same for the PDF of a 2-page paper from a second-rate journal), and the authors do see a (small) royalty check for any sales (and I do know folks who have gotten such royalties - good luck getting Elsevier or other commercial publishers to ever agree to any author royalties, ever!).

On the other hand, I realize that $36 is a deterrant for those casually or even non-casually interested in a piece of research (no matter how relevant it might be). So. . .open access seems to be the best way to go, in terms of ensuring a wide audience. This then leaves us two options: 1) post a PDF on a personal website; or 2) take advantage of open access through ProQuest (or both 1&2).

For long-term accessibility, I decided that #2 would be a good way to go. Sure, I'll post it on my own website (as I work on designing this), but it also made sense to make it available through as many sources as possible. Lots of folks use the ProQuest search engine (at least I do, whenever I want to check up on a dissertation), and this could very well be the main way interested parties find my dissertation document.

So, when submitting all of the paperwork before graduation last spring, I signed on the dotted line and wrote the little check (right now, it is $65 for their standard processing fee, which everyone pays, and an extra $95 for the open access fee*) to make my work open access, through PQDT Open. This meant that my work would be indexed in their database, made searchable through Google, and that nobody (me or ProQuest or UMI) would be earning any more money off of the document (but how many people were going to buy it in the first place, right?).

PQDT Open also offers an "author embargo" option, in which you can delay full dissemination of the dissertation for a specified length of time (six months, one year, or two years, I believe). I chose to delay by a year, in order to allow me a little lead time to get most of the chapters through the review process and into press. I was 2/3 successful for my three big chapters, and the third big chapter is now in review. Would I do it this way again (i.e., delayed access), or allow immediate access? I'm not sure. I see costs and benefits to both ways.

So, this is just a long way of announcing that my 2008 dissertation on cranial pneumaticity and ceratopsid sinuses is now available permanently and free of charge as a PDF through ProQuest, right here.

I should also give a big shout-out to Matt Wedel (aka Dr. Vector), for first getting me thinking about the issue.

The appropriate citation for the dissertation is:

Farke, A. A. 2008. Function and evolution of the cranial sinuses in bovid mammals and ceratopsian dinosaurs. Ph.D. dissertation, Stony Brook University, Stony Brook, New York, 226 pp. (available for download here)

The component chapters (with the exception of the introduction, conclusions, and occasional small sections of the other chapters) are either published or wending their way through the publication process. Relevant citations include:

Farke, A. A. 2008. Frontal sinuses and head-butting in goats: a finite element analysis. Journal of Experimental Biology 211:3085-3094. (PDF and full text now freely available here; see here and here for my blog posts about the article)

Farke, A. A. In press. Evolution and functional morphology of the frontal sinuses in Bovidae (Mammalia: Artiodactyla), and implications for the evolution of cranial pneumaticity. Zoological Journal of the Linnean Society. (Should hopefully be up on EarlyView shortly - I am happy to send a PDF of the final draft to anyone who is so interested)

Farke, A. A. In review. Evolution, homology, and function of the supracranial sinuses in ceratopsian dinosaurs. (Look to this blog for further updates)

(*note - I updated this post to reflect the open access fees current as of fall 2008)

Open Access Dissertations in Physical Anthropology

My colleague Biren Patel (who is doing some awesome research on primate locomotion and functional morphology) passed on this link to open access dissertations in physical anthropology and paleoanthropology, hosted by the Paleoanthropology Society. A number of very nice dissertations from major centers of anthropological research are posted here, some that have been published formally and others that have not. We paleontologists would do well to heed more closely the world of physical anthropology - oftentimes the "hot new techniques" presented at SVP have long been old news in the anthropology world. Furthermore, a number of our anthropological colleagues are asking the exact same questions we are! It pays to keep up on their literature.

The Paleoanthropology Society also hosts an on-line, open access journal called (oddly enough) PaleoAnthropology. Go check it out!

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.]

The Open Source Dissertation

My university has done a wonderful thing, in accepting only PDF files for deposition of a thesis or dissertation with the graduate school. Gone are the days of printing 5 copies of a 300-page document on acid-free paper that costs 20 cents a page (and then finding out that one of the margins is 0.1" too wide, so please correct and resubmit before the deadline in three hours). The transition is a wonderful step forward, and also means that it is much easier to distribute the dissertation.

As a proponent of free and open source software (having made the big switch about a year ago), I wanted to do as much as I could within the realms of that universe. This posting summarizes the software I used, with the hope of inspiring others to follow a similar path (whether in whole or in part).

Data visualization: I processed all of my CT scan data in 3D Slicer. For segmenting structures, generating surfaces, and measuring volumes, look no further! [I still need to do a more complete post on this one.] Additional analysis was done in ImageJ.

Data analysis: Initial data entry in OpenOffice.org's Calc, with analysis primarily in R and an occasional venture to PAST.

Figures: Raster image editing was done in the GIMP, and line drawings or composite figures were assembled in Inkscape.

Word processing: All done in OpenOffice.org's Writer. The PDF output function was very nice for sending drafts to committee members and advisors, and the software's Microsoft Office compatibility is such that I could also send and receive marked-up documents (in .doc format) pretty easily. For the final document, I exported each chapter in PDF format.

Referencing: All of my references were sorted, organized, and rendered as bibliographies with Zotero. Along the way, I created custom styles for Journal of Vertebrate Paleontology and Zoological Journal of the Linnean Society. More on this process in another post.

Document assembly: To assemble all of my dissertation's chapters into a single PDF document, I used Ghostscript. The output was quite pleasing, and easily accomplished through the command line in a matter of seconds.

Presentations: For my oral dissertation defense, I created my presentation using OpenOffice.org's Impress.

Back From Hiatus - With a Ph.D.

After an unannounced hiatus, I'm now ready to resume posting! Many of you probably knew I have been dealing with a dissertation over the last month - submitting a final copy to my committee, preparing for an oral defense, and then working on revisions. Today, at 11:45 a.m., I received final approval of my document from the graduate school. Which means - I'm done! Thursday is the hooding ceremony.

So I've a few posts that have been on the back burner, that will be up here soon, hopefully. I'm first going to finish the "Data and the Open Source Paleontologist" series, and then move on to some of my experiences with crafting a dissertation primarily using open source software.