Thursday, January 31, 2008

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 I generally try to do this anyhow, if an otherwise unpublished dissertation or thesis brings up some ideas that were later discussed (usually and hopefully independently) by other authors.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.

Friday, January 25, 2008

Finding that Job

Let's face it - how many paleontologists actually are in jobs with a title of "paleontologist"? This can also be a plus, in that there are many different kinds of jobs to which we can apply. In my own search for a job, I have found a number of resources that are quite helpful - here are some of the best. Keep in mind that I'm more of a "biological paleontologist" these days, so obviously my links are perhaps a little biased. But here goes. . .

Society of Vertebrate Paleontology
A must-see jobs board for anyone hoping to find a "strict" paleontology job. Generally quite frequently updated, and many of these jobs aren't posted anywhere else.

VRTPALEO mailing list
This is an email list, not a web page - again, many jobs that are posted here aren't posted anywhere else. Unfortunately, internet archives for this list don't exist (that I know of).

Geological Society of America

I haven't used this one quite as much just given my career path, but it's still something to check out for those looking for jobs in geology departments.

The Chronicle of Higher Education
This website is one of the most useful job-hunting websites out there. The link above takes you to their "job search" form - you can also sign up for email alerts of new job postings, etc. They also have an extensive career advice section, which has been most helpful for me.

AAAS Science Careers
From the same people who bring you the journal Science, another searchable academic jobs site (also with the option of email alerts). I've generally found it to be more useful than the equivalent site from Nature, in that the AAAS site more frequently has jobs I'd actually think about considering.

Anatomy Jobs Sites
As someone from an anatomy background, I've also applied for jobs at various medical schools. The American Association of Anatomists and American Association of Clinical Anatomists both run jobs boards.

Other Sites of Note
Here are a few other sites of note:
SICB Job Listings
American Association of Physical Anthropologists
Higher Education Jobs

Final Recommendations
When it comes to finding the jobs for which you'd want to apply, check early and check often. Some sites have RSS feeds or email alerts - take advantage of these, because they can save you a lot of work in the long run. And if you're really, really wanting those jobs just in vertebrate paleontology, pay close attention to the VRTPALEO list and the SVP web pages. Word-of-mouth doesn't hurt, either!

Wednesday, January 23, 2008

Managing 3D Data

Many folks out there in the paleo community are starting to use three dimensional data in some form or another. So, what free or open source options are out there? This post introduces a few of the major programs. Over the next few months (and probably between other posts), I plan on reviewing each piece of software in more detail. But, here's a quick review of some of the "shining stars" out there in the open source world. These are the programs that I *always* have on my computer.

The classic scientific image manipulation program. This program is free, fast, and flexible, and it will do a variety of tasks (automatic counting, generation of AVI files from stacks of images, DICOM viewing, simple reslicing and 3D rendering, calibrated measurements, to name a few), many of them quite well. A robust and active plugin library, along with cross-platform compatibility (ImageJ runs in Java), make this a "must have" for anyone dealing with images.

3D Slicer

If you ever want to generate three dimensional surface reconstructions from CT scan data, look no further. 3D Slicer is powerful, relatively fast, and in very active development (the beta for version 3.0 was just released). Use it to make 3D renderings, measure volumes, or segment data for analysis in other programs.

MIPAV, another Java-based image manipulation program, picks up where ImageJ left off. MIPAV's big strength is the ease with which it manipulates large stacks of images, and its easy export to pretty much any medical imaging format.


This program is fantastic for manipulating or rendering those surface models that you generate in Slicer. ParaView also is capable of doing renderings of other forms of data, such as FEM results, volume renderings from CT data, etc. This is another very active and useful open source program.

Sunday, January 13, 2008

Do Your Presentations Impress?

Pretty much everyone has to give a presentation at some point, whether in class lectures, conferences, public lectures, or as part of a class assignment. Microsoft PowerPoint has swiftly taken over from the old days of slide projectors, overhead transparencies, and chalkboards. It's a point of debate whether or not this is entirely a good change, but it's the world within which we now live.

When I switched to from Microsoft Office, I was delighted to see a fully functional presentation program within the open source office suite. I've since used this program, Impress, to put together several new presentations, as well as edit some old ones. In this post, I'll briefly review my experiences.

Interface: The switch to Impress from PowerPoint was an easy one, interface-wise. Many features closely parallel those found in PowerPoint, and features that don't are logically arranged and pretty easy to find.

Software Features: I can do pretty much everything in Impress that I could do in PowerPoint. There are enough slide transitions, special effects, drawing tools, text formats, and other goodies to put together a truly hideous presentation, if one desires. One possible downside is that the default installation doesn't include a lot of prepackaged slide templates. This may matter to some folks, but I don't use templates often as it is.

Importing PowerPoint Presentations: I've found that my old PowerPoint files import nearly flawlessly in most cases. I hear that sometimes the really fancy special effects don't always import well, but should you really be using those in a talk that colleagues and potential employers might see?

Export PowerPoint Presentations: This can be a little more finicky. I like to build multiple bullet points on a slide, and have them fade to gray as I move on to subsequent points. This works fine in Impress, but for whatever reason the exported PPT files fade the text to a bluish gray. Annoying. I haven't found a workaround for this (other than creating multiple slides for the fade in and fade out of each point). Fortunately, this has been the main quirk I discovered.

Video Clips: This is the one area where Impress has consistently let me down - its support for embedding video clips within presentations stinks. It won't let you put an AVI file directly on a page, and I haven't even gotten the supposedly supported MPEG or MOV files to embed properly either. So, I've had to develop a work-around. Specifically, I create a hyperlink that links to the video file I want to play. Click on the link during the presentation, and up it appears! Of course, this might lead to trouble if you have to run your presentation on a computer other than the one which housed the video file originally.

Practical Realities: There isn't anything that would make me bail on Impress to return to PowerPoint. The program does what I need it to do, and does it pretty well (for the most part). If I can run off my own laptop, I can - this eliminates the problems of file export. If I have to export as a PowerPoint file and run it from PowerPoint, I make darned sure to test the file out beforehand. I haven't run into any true disasters in export, but there are occasionally those little quirks that annoy the perfectionist in me.

Sunday, January 6, 2008

How Not to End a Presentation (and a plug for SICB)

". . .Thank you to all of these funding agencies, and I'd be happy to take any questions."

I just finished up my time at the SICB (Society of Integrative and Comparative Biology) annual meeting in San Antonio, Texas. SICB is a great meeting for those paleo-types who are interested in understanding extinct life as living organisms. It's a shame that more of the SVP and GSA attendees don't take advantage of the venue, because it's a great chance to interact with neontologists who are asking the exact same research questions. The student funding options are fantastic, too (I only had to pay $75 for four nights in the meeting hotel, in exchange for two hours of turning lights on and off in a conference room).

At any rate, just a recommendation for anyone doing a talk at a professional meeting or giving a department seminar: Never, ever, ever end your talk with "And I'd be happy to take any questions. . ." Not that you shouldn't solicit questions, but it creates an awkward moment of silence. People aren't sure whether to applaud (hopefully they'll want to do so) or to raise their hands (hopefully with fawning praise and some intelligent but answerable questions). Furthermore, it wrests control away from the session moderator, who is really the person to decide if there is time for questions. If I had a nickle for every time I've heard a moderator say, "Actually, you ran 10 minutes into the next time slot, so we don't have any time for questions," I sure as heck wouldn't be pursuing a Ph.D. in paleo.

So, end your talks with a simple "Thank you." The session chair (or host faculty person, for a departmental seminar) is usually quite capable of opening the floor for questions - it's his or her job, after all!