There is a date on the calendar I can point to.  As of this writing, on that day:

• We won’t have a place to live (lease runs out on our house)
• Which is sort of good, because our household income will consist of a single grad student stipend

Needless to say, since that date is less than 3 months away, I’m a little nervous these days.

Mrs. PA and I are going into major job hunt mode.  She’s got a few candidates kicking around, but unfortunately I have work to do on getting my grad school situation sorted.  I’ve got a few things out there, but I think it’s (past) time for “the talk” with my adviser, and also a redoubling of my own hunt for a position.

More later.

The time has come to make a decision.  Perhaps it is past time, but here we are.  I’ve been putting this off for some time because it is one of the most important and most difficult decisions I’ve ever had to make: do I try to power through and get my Ph.D., or do I write up what I have and move on with a Masters degree?  The issue is that neither solution is without drawbacks, of course.

I had some tough conversations with several groups of friends this weekend (it just seemed like everyone wanted to talk about it).  These made me realize that I’ve been sort of doggedly remaining on autopilot, when I should have been spending more time thinking about how to resolve my situation.

Since I like to obtain input from as many sources as possible before making big decisions (I research everything to death), I thought I’d lay the situation out and see what you have to say.

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When Mrs. PA successfully defended her thesis, I thought it might finally light a fire under me to push through whatever I needed to in order to finish up here so we could get on with our lives.  Instead, I’ve found myself in a more or less continuous state of ennui.  I have no motivation or interest to work on my thesis project.  Partly it’s because I don’t really believe that it will ever generate results, and therefore I don’t really see the point of even trying.  I know that this sort of defeatism is not unusual among graduate students, but I’m having a hard time yanking myself out of it.  I can’t even manage to use the reasoning “just finish it and you can get out of here” as enough impetus to apply myself.

On some level I feel like my reserve of “well it didn’t work that time, let’s tweak the parameters and try again” has just run out.  The “reward” from a scientific standpoint is more or less the same whether I actually do the experiments or not, because the experiments never work.

I think this is made worse by my particular situation.  Most graduate students at this stage would have enough data to just sort of drag themselves across the finish line.  Since I had to change projects, I’m left sitting in the middle of a pile of half-completed projects and seemingly intractable problems with each of them.

I really wish I could think of a way to snap myself out of this funk.  I know that it’s not helpful in any way.

Those not intimately involved in science sometimes think that a given researcher is fully versed in the entire body of knowledge their field has ever produced.  For instance, since I am a biochemist, I should be able to perform MacGyver-esque transformations of household products into psychedelic drugs at a moment’s notice.  Also, since I’m a biochemist, I am fully familiar with the migratory patterns of african swallows.  Of course those of us who are involved with science know that this is definitely not the way of things.  In truth, science is incredibly specialized, almost to the point of balkanization.  Even when I go to our weekly biochemistry seminar, at times it can be a stretch to wrap my head around anything deeper than a basic understanding of the work being presented.

Of course, the reasoning for this is that the things we study are remarkably complex, and it’s often necessary to immerse yourself deep into the intricacies of a given system in order to make advances in understanding.

The problem that I have with this specialization at the moment is that it makes finding a job pretty tough.  It’s abundantly clear from most postings that the hiring party has a very specific candidate in mind that has a very particular skillset matching the duties they will be expected to perform.  As a job candidate, this makes me feel like I’m locked into doing the exact same types of experiments on the same systems indefinitely.

Professors seem to have some ability to break out, but it’s still tough.  In some ways, they are even more restricted - funding agencies aren’t very likely to give someone money to do something that they’ve never done before.  On the other hand, once the money is in hand, the investigator has more leeway to use whatever tools are necessary (including those that they might not have a history of using before).

My question is to those who are in science - how do you deal with this in finding jobs?  Is this a problem in your field?  If you are in the position of hiring, do you always look for candidates that will be ready to run your experiments on day 1 due to prior experience, or do you just look for the best overall candidate, even if they may need some training?

Last night I was having a discussion with Mrs. PA.  She was worried that a paper she was writing (yes, it’s a two scientist household) was a bit long for publication.  I told her “Hey, I bet you can find an OA journal, such as PLoS One, that will not bind you to arbitrary page limits”.  I then launched into my (new and unpolished) sales pitch on why publishing in an Open Access journal would be better overall for the paper, and showed her some other papers in her field that have been published in PLoS One.  Then I came to the hard part - the increased page charges that she would have to sell her advisor on.  I mentioned that for PLoS One these come to $1250, which probably isn’t that much more than they would end up paying anyway to the closed-access journal they were thinking of publishing in.  Then I noticed a line on the PLoS site which stated that Institutional Members got a discount on top of this.  Not hoping for much, I went to the list of members, and lo and behold, our school was on it!  I’m really excited about this, because I think it will make convincing faculty to publish (in at least this particular OA journal) much easier.

I also learned that the University has put in place a support system for graduate students who lose their adviser.  If you read my 3-part post on misconduct, you’ll realize that this is very important to me.  I’m checking into it for more details, which I’ll probably write about later.  Unfortunately, the current policy on research misconduct investigations (dated 9/07) fails to mention students once, and is still chock full of the secrecy and careful political maneuvering that caused problems in the situation I was involved in.

I’ve been writing my thesis in LaTeX.  It’s really magnificent, because I can focus on the content rather than all of the manual formatting that using a standard word processor (like OpenOffice) would require.  Things are made even easier for me because my school provides a LaTeX template file for theses.

One thing that is a bit cumbersome, however, is handling references.  To date, I’ve just been using Hubmed to export BibTex citations for any papers, and pasting them into a running BibTex file.  This does not deal well with duplicates, and is cumbersome to search rapidly.

Today, I saw a link to Referencer (via Lifehacker) and decided to give it a go.  Just a note here before people go scrambling to the comment box: I do know about other packages such as EasyBib and JabRef.  I’ve tried them, and just can’t seem to get into them for some reason.

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I mention in some of the background information on this site that I’m currently in the process of writing my thesis.  However, you won’t find this work-in-progress on any publicly accessible site.  Does that make me a big hypocrite?

Before jumping in, I’ll point out that some people do (rarely) write their thesis and academic publications online and in a raw sort of “as you go” style, although to be fair these are often researchers who are at the bleeding edge of open access.  See Pimm or UsefulChemistry for examples.  I’ve thought about doing this myself, and as someone who cares so deeply about advancing Open Access, why not?

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When we think of a scientist at work, we usually imagine a lone figure (probably caucasian male, unfortunately) in a lab coat standing at a bench loaded with apparatus.  Just check out the Google Image search for scientist…

The fact of the matter is that unless the scientist in question is very rich and/or a misanthropic hermit, they probably aren’t working in a lab all by themselves.  There will be other scientists there as well.

My question today is to those who have worked in labs themselves.  Do you prefer a setup with individual bench space, or one in which all of the areas are “common use”, and you can just plop down and start working wherever you please?

I’m a fan of everyone having their own space.  I think that this makes people more likely to keep “their” area clean, and if someone chooses to have a messy bench it doesn’t impact you.  Also, it means you can sort of keep things that you use often close at hand, and configure the space to suit your work.  There are drawbacks, of course - territorial disputes being the most common.  In labs where all the space is common use, it’s nice to be able to do your work near whatever piece of equipment you may be using at the time.  In my experience, however, people don’t do as good of a job at tidying up the space when their done, and it can get crowded when several people are using space near one another.

So, what is your favorite way to work?  Why do you like it as opposed to the other way?  How is your lab set up now?

If you aren’t a scientist, are there similar environments in your work space?  How do you handle them?

There has been a growing movement in education for probably the past 10 or 15 years.  Call it the “positive reinforcement” model.  Instead of “fail” you have “needs improvement”.  The point of this system seems to be to avoid discouraging students, and instead work with them to improve their learning.  This is an admirable objective, but I often feel like it’s taken too far.

Grade inflation is a serious problem these days, all the way through college in my opinion.  It’s easier for a teacher to barely pass a student who should otherwise fail: they don’t have to deal with as many administrative headaches, the parents won’t come screaming, and hey, they don’t have to teach that poor student again!  The problem is that I feel people have forgotten what it means to “pass” a student - that they sufficiently understand the material to advance to the next level.

Although grad school doesn’t really have “grades” for the most part, I think that this same sort of “positive reinforcement” method has started to negatively impact even the pursuit of a higher degree.  For instance, our department gives a weekly Journal Club, at which a graduate student presents a recent paper from the literature.  In my early years here, it was known that: you should pick a paper that is broadly relevant, not just the latest paper in your specific field; also, you should prepare well and understand the background research.  It was a matter of common knowledge that the faculty would rake you over the coals if you went in without understanding at least the basic supporting information.  While I’ve been here, both of these aspects have changed dramatically.  It’s typical now for a graduate student to choose a paper that is more or less directly tied to their research - you can almost predict the paper if you know the lab the student is from.  Also, the faculty don’t seem to have quite the same fire during the questioning.  Students often get away with a simple “I don’t know” as an answer, without any requests by the faculty for them to at least speculate.  At least this would demonstrate some basic scientific understanding and deductive reasoning.

I think that this has made these Journal Clubs superfluous.  The audience gets nothing out of them, as the papers are so esoteric as to be more or less uninteresting to the majority.  The student gets nothing in the way of education, since they don’t need to do any more than drop the main paper’s figures into a powerpoint and mumble for about 45 minutes.

This is just one small example.  I know that people feel that graduate school is often very tough (and it can be), but the faculty need to hold the students to a higher level of competency if a Ph.D. is going to mean anything 25 years down the road.  With this continual backsliding due to the “positive reinforcement” paradigm of education, it won’t be long before we’ll need to tack another degree on after the doctorate.  Hmm… what percentage of doctorates go on to post-docs again?

The Scientist magazine has released their annual survey of the best places to work as a postdoc.  It’s an interesting list, as usual, with a lot of the typical candidates near the top.  I find it interesting that the best places tend to be smaller, less well-known institutes rather than the large research behemoths that most people have heard of.

Part of me feels like they should name this list “Greener Grass Grows Here” or “Places You Won’t Be Working in 2008″, because while I’m sure these might be fantastic for the people who are already post-docs there, it  doesn’t mean that they are hiring, or that you will be able to land a job there.

The other issue, of course, is that “quality of employment” is not a factor that you hear budding scientists talk too much about.  We have been conditioned to deal with long hours at little pay with no benefits - it’s called graduate school.  Most people when applying for postdocs are following the science, not a particular working environment.

Well, regardless it’s always interesting to see what the more progressive institutions are doing as far as benefits and perks for their post-docs.   Most of the time professors just want to hook their new post-docs up to the data milking machine and work them until they collapse.  A big part of me thinks that the standard term for a post-doc fellowship has held steady near two years simply for medical purposes.