Choosing a Graduate School

It's that time of year, when graduate school acceptance letters are starting to go out. In an ideal world, you've received multiple acceptances - which school do you choose? I missed the boat on pontificating about writing a graduate school application, so this go-around I'm going to focus on a more timely topic (although some of these factors can certainly apply to writing the application or choosing schools in which you might be interested for further investigation). Based on my own experience and the experience of friends, this series of posts presents a few things to look for as you search for the "perfect" paleontology program. Note that it's based on the assumption that you are 1) in the North American university system; and 2) going to be a full-time student. Your own situation may be different and might require special consideration.

Do You Want to Do Graduate School?
Grad school doesn't pay well. You aren't guaranteed a job in paleontology at the end, and you will be over-qualified for many entry-level positions. You will have to be independent and self-motivated (particularly for Ph.D. students) in a way that you've never been before. You will have to make hard choices (although many do find a good balance) between research, classwork, and personal obligations (many relationships have been sorely tested for many people!). Don't do graduate school, particularly a Ph.D. program, just because everyone else you know is doing it, or because it's what your parents did, or because you don't know what else to do. If so, there are good odds that you will not have a pleasant experience. If you know beyond a doubt that you love research, that you can kick your own butt into gear (because your advisor won't do it for you), and that you love the challenge of a infrequently-trod path, graduate school might be for you!

Money
It's important, but money should never be the deal-maker or -breaker. First, you should never have to pay to go to graduate school (although some M.Sc. programs may be an exception). If the school isn't giving you a tuition scholarship at the very least, run away. If they aren't going to offer a fellowship, or teaching or research assistantship (no matter how poorly paying), think twice about how you're going to pay the rent. Find out how long you are guaranteed funding, and what the possibilities of getting additional funding are. But, also realize that you aren't going to be rich in graduate school. Talk to students in the programs to which you are applying - are the stipends enough to make ends meet? Is the health insurance sufficient? And in the end, realize this: Nearly every graduate student complains about how low the stipends are - but, we often forget that *we're getting paid to go to school* (even if not always a lot). Very, very few people are lucky enough to have this problem!

Stay tuned: Advisors and the like will be discussed in the next posting.

GIMP

No, this is not an unfortunate slur - it's actually an acronym for "GNU Image Manipulation Program."* And what a program it is! GIMP is one of the most mature and functional open source programs out there, and should be the first choice for anyone looking to do any sort of image editing.

GIMP is available for Windows, the Mac OS, and Linux. The closest commercial equivalent to GIMP is Adobe Photoshop - just like Photoshop, GIMP excels at editing raster images. It is under very active development, and new versions and bug fixes are constantly on their way.

As a tool for editing photographs destined for publications or presentations, you really can't beat GIMP. It has a whole host of very functional tools for selection, touch-up, and flat-out manipulation of images. Want to rotate a portion of the image? Easy enough. Need to remove a black background and replace it with white? No problem. There's not much more I can say - GIMP is fantastic! To be perfectly honest, I haven't missed Photoshop at all since making the switch (although I am sure Photoshop "power users" might disagree).

So are there any downsides to GIMP? Some users may report slow speeds, but this seems to be largely fixed in the more recent versions. For folks who may want to do extremely hard-core editing of color images for later printing, GIMP only supports RGB color formatting (although you can choose colors on the palette using CMYK standards). This may pose a problem if you want to send your files to a professional printer, but it should not affect the average user (or the paleontologist who is usually working in grayscale images). Finally, the GIMP toolbar and image editing pane open as two separate and discrete windows, rather than as subwindows within a main window (as in versions of Photoshop that I've used). This sometimes creates a cluttered editing experience, but it's more an annoyance than anything. Integration with a tablet can be a little bit of a hassle, but it works pretty flawlessly once you get it running (and I've never tried the same task in Photoshop, so I don't know how it compares in that regard).

*GNU = a type of open source software license; it has nothing to do with the African savannah.

Zotero 1.0.3 now available

Some readers may remember my endorsement of the Firefox plug-in Zotero as one of the best open source options for reference management. You will be pleased to know that a nice little upgrade - from 1.0.3 from 1.0.2 - is now available. It includes some added functional support for downloading references from some major sites, such as PubMed, updated output styles, and some handy fixes for a few bugs in word processor integration. Zotero 1.0.3 is a must-have release for anyone who uses this program (and is worth a look for those who don't use it yet!).

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.

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:
EvolDir
SICB Job Listings
American Association of Physical Anthropologists
HigherEdJobs.com
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!

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.

ImageJ
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
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.

ParaView
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.

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 OpenOffice.org 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.