Zotero and Citation Managing

Like many paper-writing academic types, I typically employ a haphazard and ill-planned technique for reference-handling when writing papers. I have EndNote and BibTeX, and I have used them both at times, but I really have never been entirely satisfied. I have liked EndNote at times, but the truth is the version I have is old and clunky, and I am not all that thrilled about plunging another $100 some-odd dollars into an updated version. BibTeX was great while I was using LaTeX, but most earth science journals do not accept LaTeX file submissions, and none of my collaborators are ever comfortable with LaTeX, which means I have to constantly import and export from Microsoft Word to LaTeX and back. A pain. Plus, BibTeX is great for most things, but putting out a .rtf formatted bibliography is not one of them. So to summarize, I want something cheap (read: free) that works well with Microsoft Word (the standard for my collaborators).

Enter Loose Baggy Monster, my better half. One of her favorite things in the world is playing with new word processing related software. Seriously, I'm not joking. She is especially excited about reference management utilities and other things that let her release her humanities dorkosity.

She pointed me toward Zotero, a free reference and bibliography management utility that works through FireFox, and integrates beautifully with Word 2004. I've now become a convert, and decided it is time to spread the word. Now, there are many features in Zotero I don't yet use or understand, and I am sure in the future I'll do a better job showing off it's power, but here are some screen shots describing why I like Zotero. Oh, and if you want, click on the pictures to see higher resolution versions.

First off, Zotero makes importing references into your database very easy. I do all of my reference searching on web-based applications, such as my current GeoRef interface (shown below).

You will notice that in the browser address bar, there is a little orange folder. That means that this page has enbedded bibliographic information that Zotero can read, and import directly into your database. This is a GeoRef search for the term "jimboite."


If you click the orange folder, a window appears with all of references that appear on the page. You select which ones you want in your database, and once you click OK that are imported. You can see that there is another window on the bottom right showing the references that are currently being imported.You will also notice that on the bottom of my browser window, there is the little "Zotero" icon. If you click this, you are taken to your personal database. You can see that one of the articles I had searched for and selected in my "jimboite" search is now in my database. I should mention here that this database is held on your hard drive, so even though it runs through a web browser, you don't have to be online to access your downloaded or otherwise entered database. Nor must you be on the interwebs to use the "cite while you write" functionality in Word 2004.


So now lets go to Word and start writing that landmark paper. You can see that because I installed the free Zotero plugin for Word, I have a little Zotero menu bar up on the top of the screen shot. So I've written my first stunning introductory sentence, and now want to insert a reference. I click one of the menu bar buttons.


And this window comes up. I can select what citation style I want to use. Truth is there aren't as of yet that many earth science citation styles available, but someone did make the AGU general style, which I tend to like. On the Zotero web site you can download and install the AGU style (it does not come standard), and there is also a style-maker that I have yet to figure out.


After I click AGU, I am then shown a window where I select the reference that I want to include. You can chose one or multiple, either way it is pretty simple.
Click "OK" and voila! the paranthetical citation is entered into the word file.

So now I'll add some more text and reference, and then click the menu bar button that says "Zotero Insert Bibliography" and Ka-Bam! Instant formatted bibliography.


Now GeoRef isn't the only web search engine that lets you download references straight away. Most of the individual publisher or journal web pages do as well. There are plenty of other features I like, for example you can take snapshots of web pages if you wish to record and later reference those; you can link references in your database directly to the .pdf's on your hard drive, and so on.

There are some things I want Zotero to improve on. First I'd like more citation styles. Zotero also does not have any decent way to sort out duplicate references, which is a headache. But, Zotero is one of those programs it seems is improving quickly. And hell, it's free!

So as of now I am a convert.

Anyone have a spare Andy Goldsworthy?

I've been a definite blogging rut lately, more than a rut really, more like a chasm, thalweg, canyon, trench, graben........the list goes on. The trouble is that I have some ideas, but I am still unsure of the direction of Apparent Dip. As I've mentioned before, the department I currently work in does an amazing job of bringing in outside speakers. This means that every week I see a new talk, some excellent, most OK, and a few that were truly terrible. I mean embarrassingly bad. Same went for AGU, I saw dozens of talks and posters, had a lot of interaction and feedback, and plenty of blog ideas, but no posts.

My problem is that although I like the idea of blogging about peer reviewed research, I am not sure if my blog is currently a great place for that. I am pseudo-anonymous, meaning I am amazed how many people tell me they like my blog, even though I don't associate my name with it anywhere. I tend to dislike anonymous reviews, so it seems like if I wanted to comment on other people's work, I'd have to remove anonymity completely before posting. But, I am not sure I necessarily like that yet. I will be on the job market again in the not-too-distant future, and I am not sure if random critiques of invited talks is the best thing for the resume.

It is like deciding whether or not to give anonymous reviews for papers. I am always proud of the reviews I've written, but end up chikening out and checking the "anonymous" box. Might it hurt me, might it help me, who knows.

So I was thinking about this dilemma and realized how analogous my blog chasm was to my collection of copper ConFlat gaskets. Let me explain. In order to connect equipment in ultra-high vacuum lines, you can either weld things (huge pain), or use special fittings that use metal gaskets to create amazingly tight connections. One of the most common systems is called ConFlat (when you have a leak in a ConFlat fitting it is called ConFlatulence.) Anyways, these fittings use special copper gaskets, and these gaskets are single use only. For some reason when I started working in a noble gas lab I started collecting the used gaskets. At first I had no idea why, but as time when on I decided that I'd collect all of the gaskets used for my PhD and make some sort of installation art out of the whole thing. This was also inspired by my affinity for the art of Andy Goldsworthy. Andy Goldsworthy is one of the most amazing artists I have ever come across. As an earth scientist who love the outdoors and the beauty of the natural world, Goldsworthy strikes a particularly strong chord. I was actually introduced to his work by a professor in my graduate department. He uses materials that he finds locally, and spends hours and days and weeks constructing the work. Many of his pieces are left to erode naturally, that is actually one of the tools he uses, showing the response of the art to time and the elements.

Anyways, if there was a local material in a noble gas lab that one would try to make some sort of art with, I'd have to guess it would be copper gaskets. Every lab I've worked in has a pile of these things, waiting for someone to figure out a good way to recycle them, or for the price of copper to skyrocket. I want to make something out of them, but I'd like suggestions.

So like my blog, I have all these ideas, but for various reasons have yet to pull the trigger. Below are some images of the gaskets, if you have any inspiration by all means pass it along. And if you have suggestions on how to deal with the problems of blogging about peer research pre-tenure, by all means I'd love to hear it.




For scale the viewport (steel ring with the window) is ~3 inches in diameter.

Academic Job in Geology article at the Chronicle of Higher Education

Just wanted to bring attention to an article I read today in the Chronicle of Higher Education written by a post-doc in the geosciences. S/he (it is anonymous) has had a very successful run as a post-doc both from a funding and publication perspective, and is writing about the academic job hunt and the importance placed on teaching at research universities.

So now I'm wondering: Are department heads interested in research because they place such value on the selfless pursuit of knowledge? Or does all that grant money just help them make the case for a new building? Is the learning environment better once a university has that new student center with a Starbucks and Macintosh G4 workstations for checking e-mail? Maybe. Does it facilitate student learning to have those state-of-the art classrooms that wirelessly beam PowerPoint slides to students' laptops? Probably. But wouldn't it be even better if the faculty could put some of that 80-percent effort back into teaching, so those PowerPoint slides beaming across the classroom make sense?

Just as an aside, the Chronicle of Higher Education actually has a fairly steady stream of good articles on all aspects of being in academia. Unfortunately I can't seem to add them to google reader.....

The Tenure Itch

I've had two really interesting discussions in the past week with friends from grad school; first, it was a visit from ..Or Something and his girlfriend Dr. Friday Glasses, and then last night on the phone with a friend we will call Professor rgh. (Neither of the two nicknames have been agreed to by the parties involved, they are simply my suggestions). These were also augmented with lengthy discussion with Mrs. Apparent-Dip-But-With-A-Different-Last-Name, usually during a time when we should have been packing for our upcoming move. ..Or Something, Prof. rgh, and I are all at various stages of the whole academic job process, either in the process of finishing the Ph.D., as a post doc, or as a full blown Assistant Professor. We have also all observed different aspects of many job searches in different departments, and even a very sketchy case of tenure denial.

The aspect of these conversations that has stuck in hy head the most revolves around the value given to junior faculty, or potential junior faculty. Many institutions, at least those I have been associated with, are very keen to focus their hiring on senior faculty, in short, buying faculty who have earned tenure at another institution. Although some faculty searches are restricted to junior faculty (only hiring at the assistant professor, or pre-tenure level), my view now is that these are more the exception than the rule. I fully understand why some departments would want to attract and hire big wigs every once in a while, but as the regular way to replace retiring faculty or fill new positions I think it is a bad idea.

What is even worse, I feel, is that on the odd chance that junior faculty are hired, their chance at tenure seems almost comical. I wonder how many of the current faculty would have earned tenure with such requirements. I am not sure what is worse, not offering the positions in the first place, or setting the tenure bar far higher than could be expected, or is even possible.

I've heard many arguments for hiring senior faculty whenever possible, but all of the points completely devalue what junior faculty bring to a department and ignore the role senior faculty play in the development of young scientists. For example:

1. Senior faculty typically are more proven at bringing in large research grants, and are therefore a better economic decision for a department. You cannot compare someone who has been a faculty member writing grants for 20 years with someone fresh out of graduate school. What you have to do is try to predict what the young person will be like in 20 years. Although the senior faculty may bring in more, or publish more, or have more accolades, they will also contribute to the department for 20 fewer years. Departments should be interested in the integrated contributions, not the present rate.
2. Junior faculty are risky to hire. In some ways this is true, you have less information to base your decision on with younger hires, they are risky, but cheap-risky. If the don't work out, there is a built in way to not keep them around, called the tenure process (which I still think is abused, but more on that later). Senior faculty, on the other hand, are typically brought in already tenured. Their start-up packages and salaries are often many times larger than what a junior candidate would expect, and if they don't work out, you are hosed. What can you do? Unless they kill someone they can't be fired, and you spent an absurd amount to bring them over. I have seen senior faculty get hired, be given an absurd amount of start-up money, and then become what I consider dead weight. They have no interest in performing any of the boring and annoying but essential aspects of being a professor (you know, teaching, advising students, collaborating, etc..). This is not true for all, I know plenty who have continued to be productive and valuable members of a department, so let's move on to point #3.
3. Hiring high profile faculty is a good way to make a department more respected and competitive. This may be true, but it is often a false and ephemeral way to improve a department. When I think about what departments are really solid, I always associate the department with certain faculty. These professors made their name at the university, and they are the reasons departments gain a certain stature. If they move to another university later in their career, I don't necessarily transfer their accomplishments to their new campus. I think the best way to improve a department in a long term sense is to let faculty develop and prove themselves. I call this the Michael Jordan rule. When I say Michael Jordan, most people think Chicago Bulls. Who associates him with the Washington Wizards (or even better the Birmingham Barons)? Maybe a scattering of Wizards fans who hoped he'd spark the team, but I think it is safe to say that 99% of folks who know of Jordan associated him with the Bulls. It is where he made his name. Seriously improving a department takes time and investment, end of story.
   

What I think is really tragic about these reasons (all of which I have heard) is that they completely ignore the role senior faculty have in mentoring and developing younger faculty, as well as all of the positives young faculty bring to a school. Many of the assistant professors I have interacted with are exceptionally motivated. They are hungry to prove their worth and make a name for themselves, and they have a serious interest in what the department will be like in 20 or 30 years. These are all great things.

In addition, when faculty searches are restricted (officially or not) to senior faculty, you might as well throw any hope for diversity out the window. Earth science departments (at least in the US) have a tough time attracting students, or making a case for increased university and/or government funding; homogenous departments of old white dudes do not help the matter (although in interest of full disclosure I hope one day to be an old white dude in a department).

And then there is tenure. Even when a department hires an assistant professor, how many actually have a realistic shot at tenure? For some disciplines in some schools, junior faculty positions are little more than 6-year post-docs. I am sure plenty of us have seen exceptional junior faculty denied tenure. Are the bars set unreasonably high? Would present senior faculty have received tenure with those expectations? Is denying tenure to solid and productive faculty a way to try to boost the image of the depatment? I know there are plenty of factors that I, as a student or post-doc, are not privy to, but in my conversations I keep getting the sense that another big factor is an overinflated memory of what their tenure packages looked like 20 or 30 years ago. I've been looking for statistics on the average age of faculty when they receive tenure, but haven't found anything too useful yet.

Just as it is the role of faculty to help guide the development of students, I believe it is the job of senior faculty to guide the development of junior faculty. This creates productive, stable, and competitive departments. It is also a positive feedback loop, departments that help develop faculty create excellent senior faculty who in turn help guide the next generation of scientists.

Again, I am not always against the hiring of senior faculty, and I understand why that is sometimes a good idea. But it can't be the norm. Geology will need geologists in the future, so it is the professional duty of anyone who thinks geology is important to help foster that new generation.

I'd be interested in your thoughts; I'd especially be interested if anyone knows sources for relevant statistics on hiring and the like. Or, if you have been involved in more faculty searches than I, I'd be interested in the perspective.