Quite by accident, while searching for the answer to another question I had about R (a powerful open source statistical language), I ran across a nice set of PDFs from a short course called, "Data Analysis in Paleontology for R." Gene Hunt, curator of Ostracoda at the Smithsonian, ran this nearly two years ago. The PDFs contain slides on topics ranging from the basics of loading data to running a PCA or correcting for phylogeny. As an added bonus, each includes some short exercises to practice your new-found skills. Click this text to follow the link, and then look under "Resources." The slides are posted as five separate PDFs.
I have now switched to R for nearly all of my statistical analysis needs, and have been immensely satisfied so far. Expect a post on this sometime in the next few weeks (hopefully).
Tuesday, March 4, 2008
Saturday, March 1, 2008
Choosing a Graduate School III
Geology or Biology?
Paleontologists straddle two worlds. The fossils we study come from the ground, and this geological context is important for better understanding the prehistoric environment. Yet, we also need to understand the biology of the now-dead organisms - all of those protuberances used to define species are muscle scars, or neurovascular foramina, or *something* that once had soft tissue. Unfortunately, it's also difficult to be a "jack of all trades." Paleontology graduate programs typically are housed in geology, anatomy, or biology departments, and your choice in this matter will have huge ramifications.
Why Does the Department Matter?
In the simplest sense, the type of department will dictate the types of classes you take in graduate school. Don't count on getting the opportunity to take strat-sed in a biology program. In a broader sense, it will dictate the types of resources and faculty at your disposal. A geology department is far more likely to have access to good thin-section equipment, the toys needed for rare earth element analysis, and experts in taphonomy or sedimentology. By contrast, a biology or anatomy department will probably have more to offer for dissecting facilities, soft tissue histology equipment, and experts in anatomy or functional morphology. So, department focus will generally (but not always) offer opportunities and constraints unique to the discipline. As noted below, your training will also define the types of positions for which you can apply later on.
Help! I Don't Have a Background in [Biology / Geology]!
This depends completely on the school and the individual. I originally wrote off my current anatomy department, because I was coming from a geology undergrad program. I didn't think they would ever want or consider a student who didn't have many biology courses - yet, it has mattered very little in the long-run. There's really no adequate preparation for human gross anatomy (other than to just take the course)! For me, and many others, it's been no problem to make the jump from geology to biology. I know fewer who have gone the other way, but that's probably just a sampling bias. In any event, don't write off a program if you are truly interested! Many departments are willing and able to help you fill any gaps in your knowledge, and it's best to talk to someone in the program itself to find out their expectations.
Recommendations
The most important thing to consider in this regard is where you see yourself in 20 years. Both geology or biology backgrounds probably offer equal opportunity for entry into the museum world, but if you're chasing after university-level jobs, give this topic careful consideration. Do you want to be in a geology department? An anatomy department? An evolutionary biology department?
I have a strong personal bias towards anatomical paleontology (just to be upfront). When choosing a graduate school, I saw much better job prospects with a background in anatomy. I could find a home in a biology, anatomy, or even possibly geology department (if they were more interested in a paleontologist than a stratigrapher). Anatomy offers the option of landing a job at a medical school (teaching gross anatomy), or teaching anat-phys at a liberal arts school, or finding a museum job. The options seemed narrower, and the job market smaller, for geology. Additionally, my research interests (understanding dinosaurian anatomy and paleobiology) were much more appropriate for a biology or anatomy department - I didn't feel that I would necessarily get the resources that I needed in the (quite excellent otherwise) geology departments to which I applied. Finally, I felt like I wasn't constrained when it came down to the final job search. I was able to apply for anatomy, geology, and museum jobs (with some success). So, there are no regrets in my mind about the course of action I followed.
Ultimately, the decision is up to you. Readers: feel free to chime in with your own thoughts!
Up next: Miscellanea Part I - Location, Size, Timing, and Job Prospects
Paleontologists straddle two worlds. The fossils we study come from the ground, and this geological context is important for better understanding the prehistoric environment. Yet, we also need to understand the biology of the now-dead organisms - all of those protuberances used to define species are muscle scars, or neurovascular foramina, or *something* that once had soft tissue. Unfortunately, it's also difficult to be a "jack of all trades." Paleontology graduate programs typically are housed in geology, anatomy, or biology departments, and your choice in this matter will have huge ramifications.
Why Does the Department Matter?
In the simplest sense, the type of department will dictate the types of classes you take in graduate school. Don't count on getting the opportunity to take strat-sed in a biology program. In a broader sense, it will dictate the types of resources and faculty at your disposal. A geology department is far more likely to have access to good thin-section equipment, the toys needed for rare earth element analysis, and experts in taphonomy or sedimentology. By contrast, a biology or anatomy department will probably have more to offer for dissecting facilities, soft tissue histology equipment, and experts in anatomy or functional morphology. So, department focus will generally (but not always) offer opportunities and constraints unique to the discipline. As noted below, your training will also define the types of positions for which you can apply later on.
Help! I Don't Have a Background in [Biology / Geology]!
This depends completely on the school and the individual. I originally wrote off my current anatomy department, because I was coming from a geology undergrad program. I didn't think they would ever want or consider a student who didn't have many biology courses - yet, it has mattered very little in the long-run. There's really no adequate preparation for human gross anatomy (other than to just take the course)! For me, and many others, it's been no problem to make the jump from geology to biology. I know fewer who have gone the other way, but that's probably just a sampling bias. In any event, don't write off a program if you are truly interested! Many departments are willing and able to help you fill any gaps in your knowledge, and it's best to talk to someone in the program itself to find out their expectations.
Recommendations
The most important thing to consider in this regard is where you see yourself in 20 years. Both geology or biology backgrounds probably offer equal opportunity for entry into the museum world, but if you're chasing after university-level jobs, give this topic careful consideration. Do you want to be in a geology department? An anatomy department? An evolutionary biology department?
I have a strong personal bias towards anatomical paleontology (just to be upfront). When choosing a graduate school, I saw much better job prospects with a background in anatomy. I could find a home in a biology, anatomy, or even possibly geology department (if they were more interested in a paleontologist than a stratigrapher). Anatomy offers the option of landing a job at a medical school (teaching gross anatomy), or teaching anat-phys at a liberal arts school, or finding a museum job. The options seemed narrower, and the job market smaller, for geology. Additionally, my research interests (understanding dinosaurian anatomy and paleobiology) were much more appropriate for a biology or anatomy department - I didn't feel that I would necessarily get the resources that I needed in the (quite excellent otherwise) geology departments to which I applied. Finally, I felt like I wasn't constrained when it came down to the final job search. I was able to apply for anatomy, geology, and museum jobs (with some success). So, there are no regrets in my mind about the course of action I followed.
Ultimately, the decision is up to you. Readers: feel free to chime in with your own thoughts!
Up next: Miscellanea Part I - Location, Size, Timing, and Job Prospects
Friday, February 29, 2008
Choosing a Graduate School II
Even though you are ultimately responsible for your graduate education, having a good advisor certainly doesn't hurt! The qualities of a good advisor depend just as much on the student as on the professor - one student might flourish with a professor, while another might founder. So, choose carefully, and think about what you want to get out of the advisor-student relationship (and what your major professor will expect!).
"Big Names"
Many folks will choose an advisor based on his or her reputation - and this is certainly something to consider. A "famous" advisor may be able to open doors that wouldn't be available otherwise, in terms of contacts and opportunities. But, be careful - a famous scientist is not necessarily a good advisor. Be especially thoughtful about the other factors outlined below. . .
Advising Style
What sort of advisor do you want? Hands-on? Hands-off? Both kinds of advisors are out there, and both can be excellent - if your personality is matched to theirs. If you are a little less sure what you want to do, and if you feel like you'll need a little more guidance through your graduate career, a more hands-on advising style is probably appropriate. The "hands-on" style covers a whole range of styles - from weekly meetings and heavy guidance in choosing a project, to occasional reminders to provide manuscript drafts and dissertation outlines. A hands-off advisor won't beat down your door for constant progress reports, or nag you about dissertation progress. This is nice in that it might let you do your own thing - but it can be a double-edged sword if you need a little motivation now and then. And, will the hands-off advisor be there if you need him or her to read papers, write letters of recommendation, or offer career advice? Here, it's best to talk to other students of the advisor.
Research Topics
Many students (myself included) gave the research interests of their advisor some heavy consideration. It's certainly important - after all, you want to find someone who can give you the best guidance and feedback on your graduate research. But, this isn't necessarily hyper-critical. Many excellent paleontologists have trained under advisors who worked on completely different taxonomic groups or research techniques. And, you probably want to avoid becoming a clone of your advisor - this might make for a very smooth grad school experience (or not!), but it is critical to start developing skills as an independent researcher as soon as possible.
Other Options
Perhaps the most important piece of advice I can offer - don't just choose an advisor. Choose a department. By this, I mean look for a place where there are several people who might be potential advisors (even in the most informal sense). In a worst-case situation, it means that you have a back-up plan if your advisor leaves for another position or if you have personality conflicts (this does happen!). In the best case, it means you have that many more people with whom you can interact. Some of the best feedback I've gotten on my dissertation has been from the physical anthropologists in my department - and they've never touched a dinosaur in their lives! Yet, the fundamental questions are the same - and good science is always good science, no matter what the topic.
Up next: Geology or biology?
"Big Names"
Many folks will choose an advisor based on his or her reputation - and this is certainly something to consider. A "famous" advisor may be able to open doors that wouldn't be available otherwise, in terms of contacts and opportunities. But, be careful - a famous scientist is not necessarily a good advisor. Be especially thoughtful about the other factors outlined below. . .
Advising Style
What sort of advisor do you want? Hands-on? Hands-off? Both kinds of advisors are out there, and both can be excellent - if your personality is matched to theirs. If you are a little less sure what you want to do, and if you feel like you'll need a little more guidance through your graduate career, a more hands-on advising style is probably appropriate. The "hands-on" style covers a whole range of styles - from weekly meetings and heavy guidance in choosing a project, to occasional reminders to provide manuscript drafts and dissertation outlines. A hands-off advisor won't beat down your door for constant progress reports, or nag you about dissertation progress. This is nice in that it might let you do your own thing - but it can be a double-edged sword if you need a little motivation now and then. And, will the hands-off advisor be there if you need him or her to read papers, write letters of recommendation, or offer career advice? Here, it's best to talk to other students of the advisor.
Research Topics
Many students (myself included) gave the research interests of their advisor some heavy consideration. It's certainly important - after all, you want to find someone who can give you the best guidance and feedback on your graduate research. But, this isn't necessarily hyper-critical. Many excellent paleontologists have trained under advisors who worked on completely different taxonomic groups or research techniques. And, you probably want to avoid becoming a clone of your advisor - this might make for a very smooth grad school experience (or not!), but it is critical to start developing skills as an independent researcher as soon as possible.
Other Options
Perhaps the most important piece of advice I can offer - don't just choose an advisor. Choose a department. By this, I mean look for a place where there are several people who might be potential advisors (even in the most informal sense). In a worst-case situation, it means that you have a back-up plan if your advisor leaves for another position or if you have personality conflicts (this does happen!). In the best case, it means you have that many more people with whom you can interact. Some of the best feedback I've gotten on my dissertation has been from the physical anthropologists in my department - and they've never touched a dinosaur in their lives! Yet, the fundamental questions are the same - and good science is always good science, no matter what the topic.
Up next: Geology or biology?
Sunday, February 17, 2008
Building an Open Source Poster
Poster presentations are invariably a lot of work, but they can be an effective way to communicate your research to a lot of people at a scientific meeting. The commercial standards for building posters include Adobe Illustrator and Microsoft PowerPoint. I've used both previously, and wanted to weigh the open source alternatives against these. My last two posters (for the Ceratopsian Symposium and the 2008 SVP meeting) were constructed using the following software (running in Ubuntu 7.04 and 7.10, respectively).
Inkscape
This program (now in version 0.45.1) is a wonderful vector illustrator (and I'll be reviewing these features in a future post), but it's not at all intended to handle large amounts of text. You can forget about having any control over paragraph spacing, bullets, indents, or any of the other 2,000 things you need in order to make an attractive and readable poster. In the end, I used this program to put together some of the figures for the posters, and that's about it.
Scribus
This is billed as "open source desktop publishing" software (now in version 1.3.4 or so), so I gave it a spin as the primary program for my posters. As you would expect for a desktop publishing program, you get excellent control over page size and orientation. Things started to fall apart a little once I began working with the poster text. Scribus was incredibly buggy when saving my text formatting. The superscripts in the title header (denoting author affiliations) either reverted to standard text or were applied to the entire section of text once I reopened the file. Sometimes the program crashed while I tried to reformat a section. It was not straight-forward at all to format bullet points, and it required about four layers of dialog boxes to finally get everything set. It wasn't easy to incorporate multiple levels of bullets, and I had to do a lot of manual formatting. And even then, I experienced relatively frequent crashes. After a little while I figured out what set of steps to avoid, but let's just say I wasn't terribly impressed. Resizing images was also a pain - the bounding box initially served as a clipping box, until I found the option to make the image resize with the box. I muddled through, and got two posters that looked quite good, but it was a much more frustrating and time-consuming experience than it should have been.
An Alternative?
Back in my Windows days, I used PowerPoint as my program of choice to generate posters (after resizing the page appropriately). It just worked, and although it didn't have all the options of Illustrator, it produced some nice-looking posters. For my next poster, I'm going to give OpenOffice.org Impress (the PowerPoint equivalent) a whirl. The current version (2.3.1) allows much larger page sizes than the last version, so I think it will do the trick. Text formatting is certainly quite flexible, too. So, I expect that presentation software (like PowerPoint) will remain my choice for some time now. . .
Conclusion
Open source software for building a poster just isn't that mature yet, but you can build a poster without Illustrator. I would advise all but the most patient user from using Scribus for this purpose and suggest Impress as probably the best alternative at present. I am optimistic, however, that our options will get better as open source software continues to mature.
Inkscape
This program (now in version 0.45.1) is a wonderful vector illustrator (and I'll be reviewing these features in a future post), but it's not at all intended to handle large amounts of text. You can forget about having any control over paragraph spacing, bullets, indents, or any of the other 2,000 things you need in order to make an attractive and readable poster. In the end, I used this program to put together some of the figures for the posters, and that's about it.
Scribus
This is billed as "open source desktop publishing" software (now in version 1.3.4 or so), so I gave it a spin as the primary program for my posters. As you would expect for a desktop publishing program, you get excellent control over page size and orientation. Things started to fall apart a little once I began working with the poster text. Scribus was incredibly buggy when saving my text formatting. The superscripts in the title header (denoting author affiliations) either reverted to standard text or were applied to the entire section of text once I reopened the file. Sometimes the program crashed while I tried to reformat a section. It was not straight-forward at all to format bullet points, and it required about four layers of dialog boxes to finally get everything set. It wasn't easy to incorporate multiple levels of bullets, and I had to do a lot of manual formatting. And even then, I experienced relatively frequent crashes. After a little while I figured out what set of steps to avoid, but let's just say I wasn't terribly impressed. Resizing images was also a pain - the bounding box initially served as a clipping box, until I found the option to make the image resize with the box. I muddled through, and got two posters that looked quite good, but it was a much more frustrating and time-consuming experience than it should have been.
An Alternative?
Back in my Windows days, I used PowerPoint as my program of choice to generate posters (after resizing the page appropriately). It just worked, and although it didn't have all the options of Illustrator, it produced some nice-looking posters. For my next poster, I'm going to give OpenOffice.org Impress (the PowerPoint equivalent) a whirl. The current version (2.3.1) allows much larger page sizes than the last version, so I think it will do the trick. Text formatting is certainly quite flexible, too. So, I expect that presentation software (like PowerPoint) will remain my choice for some time now. . .
Conclusion
Open source software for building a poster just isn't that mature yet, but you can build a poster without Illustrator. I would advise all but the most patient user from using Scribus for this purpose and suggest Impress as probably the best alternative at present. I am optimistic, however, that our options will get better as open source software continues to mature.
Wednesday, February 13, 2008
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.
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.
Tuesday, February 5, 2008
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.
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.
Saturday, February 2, 2008
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!).
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