Friday, December 5, 2008

It could be worse...

Typically, I can't stand it when someone dismisses my foul mood with the statement "It could be worse." But, no matter how much I dislike this weird version of a silver lining, I can't deny that it is true. (Of course, I suppose you can say "It could be worse" about any bad situation except terminal illness and death.) Just over a year and a half ago life handed me a fantastic example of how things could indeed, be worse.

The prelude to this lesson was the realization that my dissertation project was completely fucked. The person I inherited the project from messed up everything. EVERYTHING! I am NOT exaggerating, and just to prove it, I am going to provide a few examples of just how messed up it was.
  1. We were working with an unsequenced organism and the locus we were studying was sequenced by my predecessor. The sequence was wrong. An examination of the records from our sequencing facility revealed that he only amplified and sequenced the locus one time.
  2. He engineered his own plasmids, but placed the origin of replication into the multiple cloning site (MCS), resulting in bizarre and unreproducible expression of genes placed within MCS.
  3. Strains labelled as single mutants were actually double mutants due to sloppy design of knock-out construct. (No wonder I couldn't complement them.)
  4. Claimed expression levels of genes of interest were extremely low only to find out he didn't induce them.
Finally I realized that the only thing I could do to with the strains, plasmids, etc., was throw them in the trash, which I did. I went through every shade of mad possible and probably would have been arrested for assault if my predecessor hadn't moved to Singapore to wreak havoc in some other lab. I tried to move on and let it go, but I couldn't. This wasted over a year of my time and I was freaking pissed off. The fact that no one was here to pay for such sloppy work only added to my frustration. I started everything anew and things began to work, but that empty space I had on my shoulder was replaced with a little chip, that got bigger with any obstacle I ran into that I could trace back to the jack-ass before me.

A couple of months later I got an attitude adjustment by way of a friend who went from writing his dissertation to flying back to his home country without so much as a masters. This is what happened to him:
My friend, who I will call Carl, was working for a problematic PI. He had a hypothesis that he wanted Carl to prove, but all of Carl's data disproved the hypothesis. Carl's PI pushed him to repeat a certain experiments over and over, convinced that Carl was the problem, even though all the controls indicated otherwise. Eventually, Carl's PI tried to kick him out of school, citing that he was a poor student and was not dedicated to research. Fortunately, his committee disagreed and ultimately Carl was moved to a different project. (Yeah. Big red flag. You never set out to prove a hypothesis. You can only set out to test it.)
Carl's new project went smoothly and within a couple of years he produced enough data to write his dissertation. He also published a couple of first author papers and had another paper submitted (I think). Carl even interviewed for a great post-doc position at a somewhat prestigious lab and got it. Then all hell broke loose.
Before he could defend, his PI came under investigation by the NIH when he tried to publish a paper using a figure that was already published in another paper from his lab. This paper was not related to Carl's work and Carl was not on the paper. Everything from the lab was confiscated, including all computers and lab notebooks.
An examination of these things cleared Carl. All of his data was accounted for in his lab notebook and in logs from using equipment and core facilities at the institution. At this point, things seem like they are going to be OK for Carl. His data was deemed safe, he still had his kick-ass post-doc and he could continue writing his dissertation.
Unfortunately, the school decided not to let Carl defend his dissertation. The university would not even let him get a MS on the work that had been published previous to the debacle. Again, none of his work was related to the bad figure or paper. In the end, Carl spent six years in graduate school, got enough data to write a dissertation, but ended up with nothing to show for it.
As I watched all this unfold my project problems seemed seemed lame. At least I could salvage everything and none of the bad data from my predecessor ever made it into a manuscript. I was still going to get my PhD and I only wasted a year, not six. I flicked that chip off my shoulder and moved on. That doesn't mean I am not still pissed at the person who screwed up my project, but I don't dwell on it anymore, because it could obviously be a shit-load worse.

8 comments:

quietandsmalladventures said...

oh. my. god. the carl situation would be my worst nightmare! hopefully, things worked out for him after returning to his country?

as for your predecessor's work, i too would be furious and seeking revenge.but you're right, thankfully you only wasted a year and not more. :)

PhizzleDizzle said...

wow....talk about suckage for your friend Carl...that blows huuuge chunks. i hope he's doing all right now...

i know how you mean, when someone says "it could be worse" it's supposed to make you feel better but mostly it just sounds dismissive and invalidating. at the same time, we probably should remember that it could be worse and that whatever is happening to us isn't really the end of the world. so i think you've got it right - still be pissed as hell at Stupid Predecessor but able to be grateful things did and are working out for you in the end. go you!

chall said...

geezz.... I don't even know where to start on the "Carl sitaution". That sounds horrible.

To go back to your inistial irritation, your predessor... I always think it shows a bit of strange interaction with the PI/lab when things like that happen. I personally think this might happen when you don't have lab meetings where people show original data but rather are encouraged to show "nice graphs" etc.

Then again I might be a bit cynical? I would've gone mental if I found out that someone had completely messed up the plasmid. Such a ehh... rookie mistake? not even that since it can't be too hard to sequence the plasmid - oh, you said that he seq it once?!

If nothing else you have learned, the hard way, that one should always double check other people's work. sad but true. When I started my post doc I tried to transfect bacteria with a construct I got from the tech. After failing for along time, trouble shooting and all, I realised that there was no DNA in the tube she'd given me... strange that the transfection didn't work huh?!?! ;)

microbiologist xx said...

First of all, Kudos to everyone to making it through that long-ass post.
Carl is doing good. He is working in his country. He worked as a research assistant for a while and now he teaches.
QASA - I was soo furious. That is the perfect word. I am glad too that I only wasted a year.
P. Dizzle - I guess I also have to admit that I learned a thing ot two while trouble shooting, so it wasn't a complete waste, but still...grrrr. :) I got a little pissy while writing the post, so I guess it I am not totally over it.

chall- OMG!! No DNA in the tube. Ug. Yes, I forgot to mention the other valuable lesson I lerned: Assume nothing!
I agree with you about the PI thing too. Mine got a stern talking to from me. She was very sorry, but did take some responsibility for letting him run wild. You see, they actually published a paper before I entered the lab that turned out to be wrong all because of not sequencing. They said protein X was non-functional. Unfortunately, protein X was functional, just not with mutations. Hopefully ALL of us have learned something.

Ambivalent Academic said...

Wow - That's so fucked up for Carl. For a minute there I thought I knew Carl too...but "my" Carl left w/o a degree under similar circumstances not because his program wouldn't let him defend. He was just so fed up with the run-around and the constant suspiscion that every one held against HIS work that he finally gave them all the bird and took off. Not worth an extra year of bullshit while they decided to treat him like a decent human being was what he decided. Not sure I'd make the same decision in his case, but I admired his self-respect. Don't know what became of him when he returned home.

microbiologist xx said...

AA - We might be talking about the same "Carl." Carl told me that his university wanted him to stay around for a year while things got "sorted out," but he didn't see what would be different in a year since his work was already cleared of suspicion. From what Carl has told me, there was no promise that he would get to defend a MS or PhD in a year either. Plus, I think he was just going to be hanging around, unable to work, due to visa issues.
The bottom line (to me) is that the University totally fucked him. If he already had permission to write and defend his work and the NIH believed all his data, that should have been enough for them. Not to mention, my Carl lodged a few complaints against his PI, that should have made it more than clear that he was not in the loop. And the whole committee watching his PI trying to force him to come up with certain data, which he didn't. This situation was very distressing for Carl and we talked about it a lot since it went on for @ a year or so. I just don't know what else they needed to find out.
I don't know if I would have left either, but there is certainly a limit to the amount of bullshit I am willing to put up with. I could totally see myself getting pissed, leaving and then regretting. That kind of self destruction is (unfortunately) right up my alley when I get really pissed.

Cath@VWXYNot? said...

Holy crap - poor Carl. Not to belittle your own situation, which also sounds extremely maddening.

My predecessor was an idiot, but luckily all his plasmids were checked by a tech. It was his bizarre results that caused problems - I just couldn't replicate them. Eventually my PI decided that MY results were probably the correct ones, and we moved on...

microbiologist xx said...

Cath - I am glad your PI believed your data. It is so frustrating when you can't replicate results obtained by someone else before you. In some ways that situation can be even more irritating b/c you never know what (if anything) caused the differences in results. You just have to assume the other person made some kind of mistake or was just plain sloppy.
One of the very few pluses to the whole debacle was being able to point my finger directly at something and say "THAT is the reason this is not reproducible." Of course that didn't make me feel any less homicidal. :)