Wednesday, August 26, 2009

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 40th version of the manuscript is almost identical to the 27th 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.


chall said...

Not to be all that but your old PI seems a little too concerned aobut the paper. YOu need to say enough is enough, reviewers are going to want to change things anyway and... well... you want the paper out. AS you said, the 40t edition isn't much better than the 27th.. it is more about a feeling of not feeling finished I think, imho.

Good uck with that. I am trying to write a paper now that is supposed to be sent in in less than 2 months ;) my boss is fast with writing, I'll do the M&M and results and figures and see where the intro goes... I would need more time but he can do it in a week or so when he has the figures and the results are in. Practice I would guess?

Thomas Joseph said...

How are you doing your 5' primer extension? You using a fluorescent probe method, or the old fahsioned way?

microbiologist xx said...

chall - My old PI is extremely anal retentive when it comes to just about everything and the paper has to be just right. I've tried to put a stop to it, but unfortunately, it makes no difference. Thankfully I only have to experience this two more times. It's so frustrating.

Good luck with your paper too! It sounds like you should be getting something out soon.

TJ - These days I would map the 5' end using 5' R.A.C.E. It's quicker and doesn't require running a gigantic sequencing gel, but back when that conversation took place we were using the old fashioned way. Radiolabelled probe all the way!

Thomas Joseph said...


You can do 5' promoter mapping using a FITC labeled primer on a capillary sequencer. If you want, I can point you in the direction of some papers which describe the method.

microbiologist xx said...

I'm not familiar with this technique. I would certainly like to take a look at those papers. Thanks!

tideliar said...

rusty spatula dipped in nitric acid

genius. Pure genius.

microbiologist xx said...

thanks ;) I think it hammered the sentiment home nicely.

Thomas Joseph said...

Oh, one last thing ...

MXX: I understand going through several revisions, but nitpicking individual sentences where the outcome is basically the same sentence is extremely frustrating.

You know, I used to get frustrated at this as well, but then I took a course (and read a few articles) by George D. Gopen, Professor of Rhetoric at Duke University. His style of writing is that each sentence looks back at the previous, and leans forward to the next. When you consider writing from that direction, it forces you to crystalize your thoughts and literally work over each sentence multiple times. It's a pain at first, but once you get the hang of it, it makes your documents so much clearer.

For me, it has meant that when I submit my papers for review, the criticisms directed at it are against what I meant to say, not what the reader/reviewer thought I might be saying. Every paper I've submitted after taking this course have come with the comments: This manuscript is extremely well written and easy to comprehend. I have not gotten a "I can't follow this line of thinking." sort of comment either.

So, haggling over individual sentences can be very important. While the meaning behind the revision may be the same, one may be much more clearer to a reviewer and may make or break your entire argument.

Mad Hatter said...

Ugh...I hate endless manuscript revisions. One trick that helped me with my PhD advisor was to only give him a hard copy of the manuscript. This way, he could only write the really important comments in the margins instead of tinkering with every single word.

But I'm guessing you and your former PI aren't in the same place. Perhaps send him a read-only file? :-)

microbiologist xx said...

TJ - I completely agree with you. Unfortunately, that is not the case here. My old PI just can't stop tinkering.
B.T.W. thanks for the info. I am looking forward to checking out that technique. I'm intrigued in a way only a nerd can be.

MH - I could not get away with either of those options with my old PI. She would not have any part of it. However, I will keep those suggestions in mind for the future. ;)