The ever-elusive carrot

My graduate advisor is a classic carrot-dangler. Unfortunately, it takes forever to get her carrots and when you do, you are so irritated and annoyed that you don't even care about the stupid carrot, instead you want to jump up and down on the carrot or shove the carrot into a dark orifice not located on your own body.

In this case, the carrot is a publication. I believe my graduate advisor means well, but two things typically go wrong on her part and one thing goes wrong on my part. For her, the two problems, usually, are (1) a complete inability to manage her time, ultimately leading to missed deadlines (we're talking months here not days) and (2) an unwillingness to learn from past mistakes and avoid them. My problem boils down to one thing; I continually fall for her claims that things will go differently, resulting in unnecessary frustration and sometimes, homicidal rage.

Let's take the current paper-writing efforts grad advisor and I are making. We started this paper in May or June and she was adamant, adamant I tell you, that we submit it within months. Deep down I knew this was never, ever, EVER going to happen. Why? Because the last two papers I wrote with this person took over 1.5 years to complete. Not 1.5 years until publication, 1.5 years until submission. Not surprisingly, I received her corrections in September. "Fuck this shit," I thought to myself. I put the paper aside, but for good reason.

At the time, I was knee-deep in expressing proteins and getting very close to finishing up a few major experiments for a paper in post-doc lab. I know how paper-writing goes in post-doc lab and suffice it to say, that I could finish data for this paper, write the paper, submit the paper and get the paper published (with time for revisions) before my paper with grad advisor was even remotely close to getting finished.

October rolls around and I get an impatient email from grad advisor, asking for my revisions. She claimed she had all this free time for writing and really wanted to get the paper submitted before the end of the year. She really thinks this can happen if I just send my revisions. So, I send her my revisions the following Monday and guess what, I haven't heard jack shit. It's DECEMBER! Um, that's pretty much the end of the year according to my calendar.

I don't really care anymore that writing with this woman occurs at a glacial pace, but it infuriates me to get rushed along with the promise of reward when nothing happens. Hurry up and wait, hurry up and wait. What's worse is that I fucking fall for it. Mark my words, this paper won't see the journal submission page before this time next year. In the mean time, I'll write, submit, revise and publish a paper from post-doc lab (barring any horrible issues arising).

Damn it! I'm all in a huff about this.

So you're funny now?

I think we’ve all experienced instances where our PI’s say something that makes us want to laugh in their face, particularly when it comes to experiments. For example, “Microbiologist XX, I know you just told me you were going map the 5’ end of your favorite transcript using primer extension, but do you think that will be finished by tomorrow?” Microbiologist XX suppresses laughter and replies “Well, our protocol requires at least two days to complete assuming that you already extracted your RNA, which I haven’t.”

The more time a PI spends away from the bench, the more they forget how long a particular protocol takes to complete. It’s amusing if things are going well, but if you’re already working your ass off and things aren't going as planned, it’s more likely to make you wish you could impale your PI with rusty spatula dipped in nitric acid.

Apparently, my post doc mentor is quite the comedian as well, but not intentionally. My goal is to submit grants by the end of this year/beginning of next year and obviously, more publications are better than less. Magnum, PI asked if I was working on a second manuscript with my graduate school PI and I informed him that I was indeed working on the second paper. Then, Magnum, PI asked me something terribly funny. He wanted to know if the paper would get submitted before my grant? It was all I could do not to laugh. He, of course, does not know that writing a paper with grad. school PI takes at least a year, if not more. He doesn’t know that we will go through 50 revisions. He doesn’t know that the last 25 revisions will center around rearranging 5 to 10 sentences and he also doesn’t know that the 40^th version of the manuscript is almost identical to the 27^th version. I do know these things, and the only way I can keep from losing my mind during the process is to find the humor.

Then it was my turn to accidentally make a joke. I asked Magnum, PI if he thought the paper we were working on would get submitted before my grant. He looked surprised at my question and I am pretty sure he wanted to laugh, but all he said was, “Of course it will. Why wouldn’t it be?” I almost fell out of my chair. Write and submit a manuscript in less than four months? Seriously?

I really hope that this is true. One of my biggest disappointments about grad school lab was how fucking long it took to get papers written and submitted and the fact that I graduated with 3 papers needing to get pushed out the door. I understand going through several revisions, but nitpicking individual sentences where the outcome is basically the same sentence is extremely frustrating.

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.

Paper Jam

Here I am, post Ph.D., knee-deep in papers that need to go out the door. This situation occurs frequently in my graduate school lab. Usually a student from my current lab leaves with one first author paper and publishes the remaining two papers during their post-doc time. I know this is common in other places as well. However, I was sure I would avoid a similar fate for two reasons.

1. Unlike advisor, I can think in a paper-based manner. Actually, think is not the right word. Advisor can think in a paper-based manner, she just gets off track quickly and easily.
2. I inherited a project with compelling preliminary data and the person I inherited it from had already made several mutants and constructs. I thought I would hit the ground running.

Question: What the hell happened? Why am I, at the tail-end of my graduate career, pushing three papers out the door at the exact same time?

Answer: Because I completely started my project over in March 2007. Yes, completely. I destroyed every single construct and mutant that I started with because they were totally useless. I'll post about the spiral into hell that led up to this mass destruction of plasmids and mutants another time, but suffice it to say, I did not have a choice.

Before surrendering strains and plasmids to the autoclave, I spent two years trouble-shooting and I learned a lot. I also uncovered a couple of pieces of data that I felt confident would become papers 2 and 3.

During this time of trouble-shooting my plan was: Uncover the mystery of this project and why the results were not always reproducible, fix said problems, get data, and write up the paper. Then, I would start investigating the interesting finds for papers 2 and 3. I did figure out the problem, and that is why everything went into the trash and I began again.

I decided that when I started the project over, that I would need to work on the other two portions of the project at the same time, or I would never graduate. Just under two years later, I had enough data for a dissertation and almost three papers. I still hoped that paper 1 would get out early, but it was rejected. So now, I am adding two experiments to that manuscript and resubmitting (to the same journal since the editor says they really liked the work) while putting the finishing touches on papers 2 and 3, so that I can submit them as well.

What's the big deal if I still get three first author papers from my Ph.D.? The big deal is interviewing for post-docs with no publications. I think this might pose a small problem for some.

Fortunately for me, it did not, but my situation is far from typical. Since I decided not to move to another city, I was able to rely on my reputation as an excellent graduate student to get my foot in the door. Post-doc PI is very familiar with graduate PI's work. Furthermore, I chose the most well-respected members of graduate school department to serve on my committee and glowing recommendations from them, made the lack of publications a non-issue. Thankfully, I wanted to work in this lab and had been coveting it from afar for a long time, but what if I hadn't wanted to stay in town where people believed my boss when she told them not to worry, I would have publications? I don't know if someone in another city, at the same caliber as post-doc PI would have given me the time of day.

So, here I am, in exactly the situation I was sure I would avoid, considering myself lucky that I really haven't suffered for it. I am glad that my academic career did not stop before it started and that I did not have to spend the next few years in career limbo repairing damage done from graduate school. Now, if I can just regain a little energy and motivation, I just might pull it off.

Brimstone and Fire

It is official. I am completely burned out.
I have lost all motivation to finish my project, write my papers or thesis, write in my lab notebook, make freezer stocks or use one more kit of any kind or sort. I do not want to extract, digest, ligate, transform, inoculate or incubate anything.
This downward spiral into the anti-motivation pit all started when I landed a post-doc. position. Just the thought of a new project, in a new lab at a different institution was all it took.
It started innocently enough. I put off those irritating tasks that must be done, but require very little brain activity to accomplish, like colony PCR or DNA extraction. Then I started doing half experiments. For example, I completed a growth curve (in triplicate) and froze away cells from various time points for later analysis and then I just left them in the -80. The samples are fine, but my point is that they are still in the freezer after three weeks.
The situation was only made worse by the fact that my boss marked off three weeks of vacation and out of town trips for the month of August (formerly known as the month I defend my thesis). So now, September is the month. No big deal. I am not upset or anything, but now the fire under my ass that I so desperately needed won't be lit for another couple of weeks.

The last couple of days have gone like this:
I wake up, I feel relatively motivated to go to work. While brushing my teeth I think to myself: I WILL do items X, Y and Z! Then I get to work and sit down at my desk and I revise the plan I formulated while brushing my teeth. Before I generate more information, I should really fill in my lab notebook so I don't get too far behind. BUT, before I can accomplish that, I decide that what I really, really need to do is analyze the data I currently have on hand. After all, it is data.

Rinse, repeat.

I know that I will return to my productive self and I hope it happens sooner rather than later. Maybe just admitting that I am a lazy bastard will help. We’ll see how tomorrow goes.