Canadian Flag from Flickr user 001fj

Mrs. PA has accepted a post-doc at UBC in Vancouver.  Sometime in the next few months she’ll move out there and get started.

In the meantime, I have my committee meeting in 3 weeks, at which point my situation will hopefully be sorted, and I can start focusing on looking for jobs/finishing my thesis.

Anyone have contacts in the Chem/Biochem departements there?

First, some background. I was lucky enough to be enrolled in the Honors program at my school. In retrospect this is one of the best things that ever happened to me solely because of Honors General Chemistry II lab.  Instead of a “normal” lab where you go in a few times a week and do some experiments out of a manual or something like this, the Hon Gen Chem II lab put us (as second semester Freshmen) into a Real Science Lab to work as assistants.  I don’t even remember exactly how I ended up working in the lab that I did, although I do remember the professor expressing some reluctance at having a couple of freshmen in the lab.  Regardless, he let myself and another student come and assigned us to work alongside a tech that was in the lab at the time.  I really fell in love with the whole atmosphere.  The lab dynamic was great, it was exciting to be doing Real Science, and I just felt like this was what life should be like.

At the end of the semester, Dr. L came to me and said he’d be glad to have me back just as an independent research assistant, and I jumped at the offer.  From then on, if I was at the University I was working in the lab (I took at least one summer off to go home and work).  It might also be worth noting that I was a real sucker - most of the time I was working for free.

It was during my time in Dr. L’s lab that I switched my major from Biology to Chemistry, gained my interest in structural biophysics, and decided that I really wanted to go into academia.  Some of these things had been floating around in my mind, but here I could see people living out the life, and it looked great.

Now a few words about Dr. L himself.  For some reason I have a hard time explaining his personality.  I just recently realized what he’s “got” that most people don’t - the ability to constructively criticize.  For instance, when I wrote him the other day I had mentioned what I was thinking about doing for research for the rest of my life (a topic I’ve given some thought to).  In 3 or 4 short sentences in his reply he completely dismantled the idea in a way that not only made a huge amount of sense, but after a moment’s reflection revealed itself as 100% correct.  On top of that, I wasn’t upset that my dreams had been dashed, but rather excited and fired up about his alternate recommendations.

Another anecdote that still sticks with me:  I was taking one of the classes he taught (I forget the name, structural biophysics maybe… anyway, it’s not important).  It was mostly graduate students with a few undergrads sprinkled in.  He handed around a take-home exam to the class, with the admonishment that we were to work on it alone.  I was sitting next to my friend, another undergrad who worked in the lab, and we both sort of gave one another a “yeah right” look.  Then Dr. L gave the class a short speech.  The root message was something like:

You are all here because you plan on being scientists.  As a scientist, everything you do is based on your personal ethics.  If you cheat on this test, you are cheating on yourselves, and there is no way you will make for a decent scientist

I remember feeling like the biggest chump for ever even thinking about doing otherwise, and determined to take extra measures to avoid even looking like I wasn’t working on the test alone.  Not only that, but this short speech has stuck with me since then and applies to everything I do as a researcher.

I can’t think of a single other person I’ve worked for or with that can so efficiently mentor, inspire, and motivate.  He does it without any obvious effort.  I can’t lie, I think I have a bit of a case of hero worship.  He’s really my role model; I feel like if I ever make it through graduate school and onto an academic position of my own, if I could be 50% of the advisor he is I’d improve on most others that I’ve seen.

The interesting and telling thing is that he is not a “hotshot” scientist as measured by a lot of the metrics considered important (like funding).  I remember one tough period when I was in the lab where we were washing and reusing pipette tips, “borrowing” chemicals and supplies, etc.  Since then I get the impression that things have changed for the better and that the lab is doing fine for itself.  This is so odd to me - I’ve seen dysfunctional, less productive labs that are funded through the ears.  Just another comment on the system, I suppose.

Do you have any figures like this in your scientific or personal life?

From my undergraduate advisor (and still my favorite faculty member):

Keep an eye on what is exciting because that is what will drag you into the lab everyday

After putting it off for far too long, I finally had “the talk” with my graduate advisor.  We went over Mrs. PA’s job offer, our lease situation, the status of my project, and the data I’ve obtained so far, and came up with a pretty concrete plan for getting me out of here

with my Ph.D.

I’m really happy now. I’ve got a lot of work to do of course, so my excitement is muted by the sheer stack of things to do, but it’s still one of the better results I could have hoped for.

A lot of our discussion centered around the two things about my work that has troubled me.  First of all, that it’s not a “coherent narrative”.  I’ve worked on several different things which are only weakly related to one another.  I had/have this idea that a Ph.D. project is one grand overarching story, and that’s not what I’ve got under my belt at all.  My advisor seems to feel more that it’s about what you learn and how you solve problems, and therefore I’m ok in this area.  The second thing that worries me is somewhat related to the first: none of my projects have a “punchline”.  I’ve gotten a fair amount of preliminary data in all of them, but there isn’t that final kicker to seal it off nicely.  We came up with a project plan that will almost definitely give me data that fits this bill within the next couple of months at most.  In the meantime I can continue with my work on solving a protein structure, which I’d like to get done but has no guaranteed chance to succeed.

All in all, I’m not sure that it could have gone better.  My advisor really seemed to be supportive and interested in helping me out as much as possible.  Now I’ve just got to buckle down and get the job done.  It is a bit easier when I can circle a date on the calendar and know that graduate school will be done after that.

A few years back, I needed to sell my trusty Honda.  It was a fine car for someone who doesn’t mind the occasional repair.  I decided to sell it myself, by the standard method of listing it in public fora and showing it to interested parties.

The process really was hell.  While preparing to list the car for sale, I found a few marks on it’s history; things that the previous owner didn’t tell us about and which we probably should have found out long before.  I wasn’t too upset because this didn’t change the fundamental fact that the car was solid and in great shape.  I knocked a bit off of my asking price and proceeded.  The listing attracted a fair bit of interest, and I showed the car to quite a few people.  Every single showing went the same way: They’d check out the car, ask a few questions, and eventually I would get around to the things I had found in the history.  At this point the entire deal fell apart, even though I would always say “I didn’t know about this the entire time I’ve had the car and it runs great, and I’ve also taken some off of my asking price because of it”.  I ended up getting totally stressed out and fed up with the entire charade and ended up unloading the vehicle at the dealer for pennies; a decision I still regret.

I was just thinking the other day about how much the experience of applying for jobs has reminded me of this unpleasant time.  It’s sort of worse, because in this case I am the car.  It’s hard to put yourself out there, vulnerable to judgement, and be rebuffed.  I think it’s especially tough because at the moment I’m not applying for just “any job”, but positions that I really think I would love.  When the reciprocal interest from the company lies somewhere on the continuum between lukewarm and nonexistent, it’s hard not to take it personally.

Mrs. PA has managed to “seal the deal”, and has gotten an offer for a post-doc position.  Of course this puts more pressure and limitations on my own course of action, but that’s life I suppose.  She’s got at least one more interview to go on before we have to decide where we’ll be spending the next couple of years.  We knew going in that finding jobs near one another was going to be tough, but I think it would be a lie to say I wasn’t a bit chagrined at how nearly insurmountable the problem can seem at times.

The plethora of job listings over at BioMedCentral is almost enough to make me want to cross the pond. They have positions available in production, web work, editorial roles, and sales.

If you are in the U.K. and interested in OA jobs, make sure to give them a look. They also seem to be one of the better companies at keeping their job offer pages up to date, so even if there is nothing that strikes your fancy now it might be worthwhile to check back later.

Full disclosure: I had some extremely preliminary contact with some people over at BMC in regards to jobs, but this was before they realized that I was a yankee. I had of course been looking at their website for some time before this in the hope of finding a telecommuting-type position. They didn’t seem to be against remote employment, but I’m not entirely sure how the logistics work out for such a long separation.

Yesterday was the closing date for applications on a job prospect that I’m hoping for. I don’t think I’ve mentioned in this space which job this is (I think I’m starting to get superstitious about these things), but it’s an editorial position at an OA journal. The job offer is relatively close to one of Mrs. PA’s post-doc prospects, and therefore it’s just sort of a conglomeration of good things(tm). Of course this makes me even more nervous about the whole thing.

Add onto that the tough spot we’re in. Mrs. PA defended her thesis a few months ago, unfortunately without having a job lined up in advance. Since then it’s been a ticking clock until her contract runs out, which is very soon now. Because of that hard deadline, there is some urgency to resolve the situation as soon as possible. We’d prefer not to commit to living apart for a terribly long time, and the two jobs we’re hoping for here are the first that we’ve found close enough to one another so that we can live together.

The situation has made it tougher for me to get off the fence with my graduate school trajectory as well. I feel like if we had a concrete lead on where we were going next, it would ease my decision on how best to finish up my work here. The nebulous situation that we’re in, without any sort of specific location or date of a move, makes it tougher to set hard deadlines in my own work.

What makes the situation even a little more bothersome is that we might be doing something similar in a few years, when Mrs. PA finishes her post-doc. Once again, this is a selling point of the location that our current prospects are in; it’s a major area, and hopefully she’d be able to find gainful employment there without us having to move again.

There have been one or two other times that I felt we were close to sorting all of this out, and those have all fallen through so far. It makes me a bit pessimistic, but at the same time one can always hope.

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.

(more…)

Using web-based tools to manage labs is a key interest of mine.  I believe that these tools are more or less already available, and would greatly aid investigators who are already spread thin due to competing demands on their time.  This is why I’ve made calls for open source LIMS packages as well as taken some initial steps towards building one myself.

My efforts to create a system have not had a high sense of urgency about them.  There are several reasons for this; it will be some time before I have to worry about this myself (if ever), I have other work to do which is actually related to my Ph.D., and because I tend to get discouraged when I run into programming challenges that I can’t handle quickly.

The whole thing has become more important to me, however, since one of my good friends (who posts in the comments occasionally as The Argonaut) is preparing to begin his career as a tenure-track professor.  He needs a solution, and rather soonish.  I’m not sure if I’ll be able to create something functional in the time period he’s got before he starts his job, so I thought I would try to cobble together a list of already-available technologies that I think are really useful, and can be installed today.

First of all, set up a Google Calendar.  Use it.  Post everything there, and share it with your lab.  I’ll repeat this - use it.  It’s easy to think of taking the time to list what you are doing on a calendar as an inconvenience and waste of time, but it’s invaluable (both for your own scheduling as well as your students).

Install some sort of version management system.  Trac + Subversion is a good way to go.  This sort of system is used very often in software development, but I think it has applicability to any project, including research projects.  The system is designed to assign and monitor workflow of a project - just think of it as a file folder of your progress, in every project going on in the lab.  Trac has a built-in Wiki, which you can use to store protocols and other lab-wide documents that you’d like to share.  You can use Subversion to get version control of your grants and papers, rather than dealing with endless iterations of new word documents.  It’s becoming more trendy to use a distributed version control system, so you might look at using Git as opposed to Subversion.  Both should integrate with Trac, although Git requires a plugin (makes sure to check out the entire trac-hacks site, as there are many useful plugins there).

If Trac seems too daunting, you can try out MediaWiki, the software that runs Wikipedia as well as OpenWetWare and many other great sites.  The version control isn’t quite as rigorous (you’re left looking at page edit histories), but it’s a bit more user-friendly.

So at this point you have a calendar and project management running.  This is a pretty solid base, and you’re blowing most labs out of the water as far as organization.  I would leverage the wiki functionality of Trac to build in some other things like inventory management as well.

The last thing you probably want is a public-facing website.  You have several options here, although a content management system (CMS) of some type is going to make life a lot easier.  If you just want a simple website, you can use blogging software such as Wordpress, or MovableType.  These are relatively easy to install, theme, and update with new content.  If you’re looking for something more powerful, you may consider the free and open-source Drupal.  It’s more complicated to use, but also has a lot more functionality.

If you can manage to get all of these running and convince your lab to use them, congratulations!  It will probably take some time to become familiar with using each of these systems, but for the most part they are accessible to novices.  The effort it takes will be well worth it.  Of course, it would be best if all of these functions lived under one roof, rather than split across 3 or 4 different software packages.  This is the goal of a LIMS, and I should probably GB2W on my pet project…