Geeka over at When Do You Think You’ll Be Done? has successfully defended her thesis!  Hooray!!  Go congratulate her!

Go read acmegirl’s post on semi-adults.  It was like she was talking about one of the people in my lab.  I’m so glad I’m not alone in dealing with this shit.

Taken straight from the “Medication Guide:  Antidepressant Medicines, Depression, and other Serious Mental Illnesses, and Suicidal Thoughts or Actions” which comes with my antidepressant prescription:

Depression and other serious mental illnesses are the most important causes of suicidal thoughts and actions.  Some people may have a particularly high risk of having suicidal thoughts or actions.  These include people who have (or have a family history of) bipolar illness (also called manic-depressive illness) or suicidal thoughts or actions.  (emphasis added)

So, apparently, the people most at risk for having suicidal thoughts or actions are people who have suicidal thoughts or actions.  Very helpful.  Thanks.

Yesterday, I had my committee meeting. Advisor seemed to think that it was very useful. I didn’t really get the same impression. Basically, I went in there, showed them my data, told them what I had left to do for my paper, we talked, I came out of there with the same list of things to do with a couple of exceptions, so there really wasn’t much of a change in my priorities.

Except that they think I don’t need to do the 3-color labeling experiment to which I can only say, “Hallelujah.”

One of my committee members, let’s call him Crazy Yeast Geneticist, came up with several ideas for “easy” experiments that took 15 minutes to explain. I looked at him liked he was whacked. Advisor looked at him like he was whacked. The other two committee members sat silent. Additionally, CYG gave me some advice on how to make my images look better in powerpoint (actually useful) and questioned why some of the experiments for this paper are being done by another grad sudent. His extremely helpful input culminated in a hissy fit about the way I presented a western blot* on a particular slide. I had created this slide for a talk at student seminar and the samples I wanted to show were far apart on the blot, so, for ease of presentation, I had chopped up the blot in photoshop to eliminate the middle lanes. It was obvious I had done this because the two samples were separated by white space. He was not pleased. I tried explaining this was a seminar slide that I wouldn’t be presenting it like this in the paper, that, in fact, I was redoing this experiment because I didn’t trust the detection system I used (which was the point I was trying to make about this data anyway) and when I did that I would be putting the samples side by side in the gel so that it wouldn’t look like this, etc., etc.** We moved on.

After the meeting, Advisor informed me that CYG got on his case about this (the committee tosses you out of the room at the end so that they can talk about you) and Advisor promised him he would look at the original raw data. I thought this would be like so many other things that my committee has said (”We want to see [X] from you by your next meeting,” where [X] is something ridiculous and I never do it and nothing ever happens), but at the end of our conversation Advisor reiterated that he promised CYG he’d look at the data and if he didn’t do it CYG promised to cause me trouble. Clearly, CYG had been much more emphatic with Advisor about the blot thing than he had been with me.**

Which is interesting because it seemed that I was the one that CYG was coming close to saying had manipulated her data in an unethical manner.

So, because I keep a kickass notebook, within 10 minutes of being back in the lab, I located these blots from a year ago and brought them in to Advisor’s office who asked me to scan them and email them to him. And then he said the following:

“If I were you, I’d be very offended by all of this, but if John Kerry’s presidential campaign has taught us anything it’s that when you are accused of something you should respond.”

So, I scanned them in, sent them to Advisor, who sent them to CYG.

So, to recap:

1. Yesterday, I had a committee meeting.
2. I got some useful advice about powerpoint.
3. I heard several suggestions about ridiculous experiments.
4. One of my committee members accused me of scientific misconduct.
5. Advisor compared my experience to smear tactics used by a presidential campaign.

Yes, I can totally see why my department thought it was critical for me to have a committee meeting.

UPDATE (5/5/08):  Just got back from talking to my departmental administrator.  Apparently CYG has been in a mood lately and this isn’t the first very strange and disturbing incident she has heard about regarding him in recent weeks (though she wouldn’t say what the other incidents were about).

*Everytime I try to type “blot” my fingers type “blog.” Possibly I’m spending too much time on the internet.

**Also, I’m pretty sure I did the exact same thing when presenting my data at my last committee meeting with nary a word about the evils of photoshop and blogs blots. Something must’ve happened in between then and now (having nothing to do with me) to piss him off. Nice.

I have to have a thesis committee meeting on Thursday.  I am being forced to do so by my department because I haven’t had one in over a year and we’re supposed to have one a year.  I had been putting off having the damn thing because in about a month I’m going to have almost all of the data I need for my thesis and at that point I’m going to have to have another damn meeting so they can give me permission to schedule my defense.  To have one right now is particularly frustrating because I have to take time away from my experiments to prepare the damn thing.  There’s the committee report, there’s the powerpoint presentation I have to put together (lest you think I’m going overboard, it’s required that we put together a presentation), there’s the damn cookies and coffee I have to get for them (technically not required, but expected).

Everybody keeps telling me it’ll be good to get my committee’s input right now.  This assumes that my committee actually gives me input which they don’t.  I have yet to have a committee meeting where someone suggested an experiment or a new way of looking at things.  Pretty much, I go in there, I show them my data, I tell them what I’m going to do, they nod and ask questions and that’s about it.  Yes, I can see how that’s going to be terribly useful to me right now. *rolls eyes*

I think the idea of having thesis committee meetings is great.  But, in practice, they just haven’t been useful to me at all.  The thing is, the faculty on your committee are pretty much going to bow to whatever it is that your advisor wants you to do.  So, for instance, when I went into my committee meeting as a 5th year student and I had exactly one piece of data that I had been working on for years and I told them it was going into a paper that I was third or fourth author on, my committee did not say, “Um, shouldn’t you be keeping that for yourself so that you have something for your own first author paper since you’re a fifth year student and all that?”*  So, I’m not really sure what the difference is between me having regular committee meetings and me just being advised by my advisor.

So, what with one thing and another, I’m pretty pissed off at having to have a committee meeting right now.  Since there’s nothing I can do about it, I should probably just quit whining, suck it up, and stop sleeping so that I can get everything accomplished before Thursday

*Yes, I argued with my advisor about putting that data into that particular paper.  I did not win.   It’s a long story.

I am currently in 3-color hell.  I need an anti-mouse secondary that I can use alongside GFP and RFP.  I’ve tried Alexa350 (blue) and Alexa680 (infrared).  Neither worked for shit.  Anybody out there have a suggestion?

A while back, Geeka had a post in which she says this:

I keep going on these interviews trying to figure out what I want to do with my life. I don’t know. I keep thinking that at some point I am going to go on an interview and be excited.

PhysioProf, in his infinite wisdom, said something that really resonated with me:

Even under the absolutely best of circumstances, by the time a grad student reaches the dissertation phase, it seems like life totally sucks, academic science sucks, and just everything sucks. This is the worst possible condition under which to be making big decisions about the rest of your life.

This is pretty much where I am right now. Some days I feel like if I have to look at another immunofluorescence image, I’m going to poke out both of my eyes with a pipette. Or, if I have to dump another bag of plates because the person we pay to pour plates can’t seem to get it right, I’m going to go on a shooting spree in the autoclave room. I hate everything. I hate my project, I hate yeast, I hate science, I hate my program, my university, and sometimes my advisor.

And, in the midst of this, I’m supposed to figure out what I want to do next. Here is what I want to do next:

1. Sit.

2. Have a baby.

The thought of doing any more bench science makes me want to vomit. Except that, counting the years I was a tech, I’ve spent the last 12 years of my life in a lab. And, I remember a time when I loved the lab. When I loved it so much I thought research was what I wanted to do for the rest of my life. I wish I could remember what that felt like. Now, I get the impression that on the day I defend, all I’m going to think is the same thing I thought when I graduated high school, “Thank God I never have to go back there ever again.”

So, my plan has been to teach science. To whom and in what capacity, I have no idea. But, I have been saying for awhile now that I when I leave my university I’m leaving benchwork far, far behind.

And then, I had this conversation with a labmate the other day in which my labmate (who has the goal of becoming faculty at a big research institution) said how frustrating it must be to be a prof at a place where they only have undergrads because you must not make very much progress on your research (this was during a conversation in which we were discussing our lab’s experience with undergrads). I suggested that maybe at such a place, you aren’t so worried about making huge amounts of progress and publishing in Nature or Cell, that in fact, mostly you have undergrads doing research with you simply to give them a sense of what it’s like to do research and to teach them how to function in a lab (I should point out that I’m not entirely certain this is true, having no experience with such an institution). At which point, it occurred to me that having a small lab at a small liberal arts college is one of the best ways to provide a hands-on science learning experience. And I got really excited by that idea.

Now is the time to point out that never ever doing benchwork again and having a small lab at an undergrad college are completely incompatible goals.

So, I’m pretty much back to not knowing what the hell I want to do except that if I go straight into a post-doc now I’m likely to have a mental breakdown and have to get locked up in some facility. I think, though, that it’s possible I could teach as an adjunct for a year and still be able to get a post-doc at the end of that, if–after a year away from the bench–I decided that’s what I wanted to do. Or, maybe, at the end of the year I’ll decide I love teaching above all else and I truly never want to do benchwork again.

I am officially exhausted.  Last night, I practically fell asleep at my bench and I think I left the lab with the UV bulb on the microscope still burning.  Not good.  Apparently, I can only work so many 12 hour days in a row before my body just says, “Basta!” and I collapse.

But the good news is I’ve gotten TONS done and I’m putting together my paper figures and if I can just hold it together for a few more weeks, I’ll be able to start writing my thesis and get the hell out of here.

Back when I first started in my lab, I started with a continuation of a former grad student’s project.  I hadn’t yet gained the maturity to come up with my own experiments and I was sort of blithely moving along, doing experiments that my advisor suggested.  These experiments were testing a particular model of how we (and by “we” I mean my advisor, really, because I hadn’t put that much thought into it) thought our system functioned.  It was a tough experiment for various reasons and it took a long time before I actually had results (1.5 years), but when I got the results they did not fit the model.  I was crushed.  I thought there might be something wrong with my results.  Then, I desperately tried to make the data fit the model.

My advisor, however, was not too bothered by my results and said we simply needed to revise the model.  I did not want to revise the model.  I liked the model.  The model explained everything I thought to be true but hadn’t proved yet.  And now, I had this bit of data that was fucking it up.

Eventually, I learned to let go of that model and trust my data.  Since that time, we’ve been through two or three revisions of the model and when I’m gone I’m sure the lab will go through many, many more revisions of the model.  My attitude towards models has changed so much that I’m actually excited when I get new data that blows apart the previous model because I know that I’ve made a big leap forward and I’ve really contributed something worthwhile to the field.  It’s also scary, though, because I’m trying to wrap things up and publish and graduate and I can’t do that if I’ve just discovered the way I’ve been approaching your problem is wrong and I’m going to have to do ten more experiments.  Sometimes, when a labmate proposes an experiment to me in lab meeting, and I argue against it, I have to ask myself why I’m so against doing the experiment.  Often, it’s because I’m afraid that the result won’t be what I want it to be and my model will be in big trouble.  And those are the experiments I know that I have to do.

Last week, at lab meeting, I had one of those moments which I later discussed with my advisor.  And he agreed that if a possible result from an experiment scares the crap out of me, then it’s an experiment I should do.  This is maybe the best thing that came out of lab meeting.

At that same lab meeting another student, Problem Child, presented.  She has a model for a different system.  Like any good cell biologist knows, a good way to learn about a system is to try to screw it up.  So, Problem knocked out a gene that she thought should have a significant effect on the system.  It took her a very long time to get this knock-out strain of yeast.  Then, she looked at her cells via immunofluorescence.  If she had significantly screwed up this pathway, it would be obvious by IF.  But, there was nothing obvious there.  She thought maybe, if you squinted, and turned your head so you were looking out of the corner of your eye while jumping up and down on one foot, there was a phenotype.  So, she looked by EM and did some quantitation, but there was nothing there (although she has yet to show us those results in lab meeting, she has told me there is no discernible phenotype).  THEN, she did live cell imaging and took multiple movies of her strain which is what she showed us at lab meeting.

My friends, there was nothing in them worth noticing.

We said as much.  And, at the same meeting, she talked about other ways she could screw up the system.  We thought those were really fine ways and actually much more promising.  But, she wants to continue with this knockout strain.

So, I asked her, “Let’s say, in the best possible scenario, there is a very subtle phenotype in this strain.  What does that tell you?  Aren’t you looking for something much more dramatic?  Wouldn’t it be a better use of your time to pursue these other possibilities?”  Advisor agreed.  Everyone else in lab agreed.  But, she still thought it was worth making more movies and taking more EM images.  “In my spare time,” she said, “while waiting for the other strains to grow up.”  But, she doesn’t spend that many hours in lab and I know that she’s spending a ridiculous amount of time making movies and so on because I have seen her analyzing them.

So, after lab meeting, in a private conversation, I suggested to her that it seemed as though there were two ways she could take her project.  One was a characterization of the protein for the gene she knocked out.  Nobody else has done much work with it.  There are a number of things she could do with it that would be publishable and she could even publish some of the data she has collected.  OR, she could go full force trying to get the phenotype she wants by knocking out her other candidates one by one or in combinations and spend 6 months doing that and if she’s able to get her phenotype, then great.  From what I can tell, this is what Advisor is telling her she should do.

She insists that she really is working toward making those knock-outs but she really believes there is something in this first knock-out strain.  She will not be persuaded–not by her labmates, not by her advisor, and not by her data.  She is in love with her model and she is bound and determined to make her data fit it.  This is dangerous for many reasons.  First, and foremost, I think this sort of blindness to what the data are telling you is how people end up falsifying data.  If I were Advisor, I would demand to always see her raw data and not just her analysis of it (which I believe he does; Advisor loves looking at raw data–it’s what he lives for).  Second, this devotion to a strain with no phenotype is not getting her anywhere.  It’s wasting lab resources and it’s wasting her time.  She is never going to graduate if she doesn’t move forward.

It reminds of talking to a teenager, trying to convince her that the guy she is dating is bad for her.  No matter what you say, she is going to remain with this guy.  Emotion has blinded her to the truth.  Parental guidance holds no sway and she will sneak out in the middle of the night to be with her guy.  Likewise, Problem Child ignores all advice and comes in–literally in the middle of the night–to work on this strain that she insists proves her model.  And there is nothing to do but to sit and watch it happen.

By a very narrow margin, the ja-ja posts won so I have submitted them to the carnival.