Dissertation = Disease

Input:

• International Conference departure in t-15 days
• Committee meeting in t-14 days
• Self-imposed manuscript submission deadline in t-30 days
  
• GrAdvisor breathing down neck re: transgenic mouse, manuscript submission, graduation, post-doc position
• Graduation requirement: transgenic mouse (takes about 8 months) != GrAdvisor's arbitrary defense date: August 2009 (does not compute!)
• Post-doc options inversely proportional to my interest in post-doc position
• Experimental laundry list several pages long
• Critical equipment sign-up sheets booked solid for the next 3 weeks
  

Output:

• Hello, Heliobacter pylori!
• Migraines ^10
• Insomnia
• Nightmares in which I am being chased by specters of my advisor and experiments
• Need for caffeine directly proportional to intensity of shaking in my hands after consumption (why is this suddenly a problem? I used to be able to mainline coffee while conducting microdissections)
  
• Fatigue
• Air-headedness
• General paralysis in face of decisions
  

Is there a drug for this? (Besides the obvious?)

For your amusement.

I love the sombrero.

I *heart* our techinician

Seriously, this woman has some magic hands.

Hated data set has been giving me fits for how long now? We're on the last possible assay for this data set and GrAdvisor wants to give up on it. I couldn't get it to work, so I thought I'd ask Awesome Technician to take a crack at it. I gave her my positive control samples so we wouldn't be wasting the precious and nearly-impossible-to-obtain experimental samples in case it doesn't work the first time.

This morning she gave me the results.

*Cue Handel's "Hallelujah"*

They. Are. So. Fucking. Beautiful!

I nearly cried with joy (so did Post-doc who also can't get this assay to work). I didn't though. Instead, I gave her a hug. She was a little startled by this I think.

Next week she is going to run the real thing. If the experimental samples turn out half as good as the controls, I will have a water-tight story for my committee meeting and my talk at International Conference in April (yes, that's right - just a few weeks from now) and I might be able to get this manuscript out by May. Defending this fall will look one hell of a lot more feasible if I can get that to happen. I am going to buy Technician some flowers. She's also going to get a co-author on this paper whether or not the stupid assay ends up as a figure or not.

I just spent about an hour begging, borrowing, or stealing reagents from other labs so that she can start the Real Experiment on Monday (our replacement order won't be in until too late)...and I don't even care that Other Experiment won't get done today.

I could just kiss her right now...but that would be inappropriate so I will refrain.

Scientist or Fodder for Sexual Fantasy?

Or, "Welcome Sheril! Can you please take off your clothes?"

Some of the commenters on this post are really pissing me off...both on Sheril’s behalf and because it really brings home to me just how hostile things can still be for women in science. At least one commenter (David Kroll - thank you) that followed took the jerks to task. DrugMonkey and PhysioProf were quick to call the asshats out onto the carpet at their own blogs and several other* awesome male bloggers are backing them up in the comments - good on you guys!

I see a lot of men over there issuing the appropriate smackdown - thanks guys! It’s good to know that there are some decent male allies out and about. However I don’t see a lot of women chiming in* (perhaps for fear of being flamed? perhaps not incorrectly, considering that this crap seems to be tolerated by the author of the blog?** or perhaps because of some overly-zealous comment moderation?), so here’s my professional opinion:

As a woman in science I can assure you that the misogynistic tittie-drooling going on over there would most decidedly NOT be received by Yours Truly as a compliment.

Attractive female scientist though I may be, I am incredibly irked when I receive these kinds of comments (!=compliments) because it tells me that the commenter is far more interested in imagining me naked than hearing about my science***. It is disrespectful to me as a person (I am not your sex toy) and it is disrespectful to the work that I do (please pay attention because my science is pretty damn good). This kind of treatment does not make me want to share my science (because that’s really what we’re here for right?) with this sort of audience - what’s the point if the audience would rather add my image to their spank bank than listen to the results of my research?

Do you see now how this creates an environment that is hostile towards women?

* - Whoops! I apparently missed some comments that were/are still in moderation (as is my own) - glad to know I'm not the lone female voice over there.

** - Phil did in fact respond with a denouncement of this sort of fuckwittitude after I submitted my comment. The part which implies that he condones this behavior is thusly retracted. The rest stands.

*** - Thankfully, I don't get a lot of this on my blog (perhaps because - and certainly the reason that - I don't post pictures of myself)...but I have gotten slightly less in-your-face sorts of comments in the flesh. It makes me so angry when it happens because there is nothing I can do about the fact that my uterus (or maybe it's my breasts?) completely undermines my scientific credibility for some people. I work really hard at what I do and I don't think that it's unreasonable to expect a little respect for that, ovaries notwithstanding.

On learning when to walk away...

I have been toiling away for the better part of 4.5 years now trying to find an answer to my favorite research question. I have a lot of tools at my disposal. Some are better than others. Some are easy to use, and give consistent results relatively quickly. Some involve variable time and energy investments on my part and produce results accordingly. Some are time-consuming and not very easy to use, but give beautiful results.

I've been pinning a lot of my hopes on one of the latter. It is a total bitch to use, but is giving me by far the most promising results of all of my tools. Trouble is, in order to publish the beautiful promising results from this tool I need to put to rest one tiny technical detail...and that detail is proving to be even more of a bitch than the rest of the tool has managed to be over the entire 4.5 years I've been working with it. It should be trivial but it hasn't been. I've sweated through several permutations of 2 of 3 possible assays to address this and they haven't worked. I've just completed the third of 3 possible assays and it looks like that one won't give us anything useful either. Without this technical detail the results from beautiful bitchy tool are unpublishable and these results are at the crux of my paper that I wanted to get out um...last year.

GrAdvisor thinks it's time to throw in the towel on this tool. He may be right. He gave me a little "pep talk" on learning when to let go. I'm scared to - that will mean completely reworking the paper because no one else has another tool capable of addressing this question.

I've invested a whole lot of time and energy into this tool and it's hard to walk away, because it means redefining question, my paper, and my quest. It feels somewhat reminiscent of walking away from a bad relationship. I've known for a while that it just wasn't good for me but I've put so much in at this point that walking away is admitting defeat, admitting I was wrong, and that I was stupid for holding out for so long.

These are good lessons to learn. But still, science can be a real heartbreaker.

Oh! Heck! It's up to my neck!

Apologies for my blogging silence lately...as the title of this post suggests, I am up to my neck in experiments. Yesterday was the first time I left the lab before dark since we switched to Daylight Savings. I'm trying to get a few things hammered out before my committee meeting and international conference next month. If I can manage, my Potentially Interesting Science will become some Pretty Damn Convincing Science - wish me luck!

In the meantime, if you are looking for some more substantive reading, I suggest that you head over to Toaster's blog and check out this post on how scientists can make better investments in public science education. It is an excellent bit of writing and in my never humble opinion, right on the money. An excerpt:

Certainly, we can spend our time debating the global warming deniers and proponents of creationism or the vaccine-autism link. A vigorous debate is necessary to discredit the dishonest irrationality of the opponents of scientific knowledge and progress. However, I posit that directing the bulk of our attentions and energy to this task is stupid. Stupid because it is ineffective, like waiting in the wings with a tourniquet and bone saw as we watch clumsy children try to juggle chainsaws. When we spend so much time interfacing with and disproving the few loud idiot voices in the crowd, we are doing a disservice to that crowd by ignoring it. In effect, we are fighting the flawed output instead of striving to better the input*. Doing so would stem the tide of ignorance and intellectual laziness.

Enjoy!

*emphasis mine

Advocacy - Am I doing it right?

I received a pleasant surprise visit from a junior grad student in my program today.

She has been in a rather protracted situation of harassment in her lab of late. We've been talking a lot over the last couple of months about what she can do about it, and her concerns about doing anything at all. I'm really glad that she came to tell me today that she finally decided to talk to her PI about what's been going on. I'm really proud of her for doing so. I'm also very pleased that her PI was receptive to her concerns, supportive of her position, and has encouraged her to continue to talk to him about what was and is going on. I'm a little disappointed that the PI has not taken some definitive action regarding the perpetrator already.

The perp is another member of their lab who engages in repeated unprofessional behavior including contaminating communal stocks, "borrowing" and then breaking other people's personal equipment without permission, damaging departmental equipment and then blaming someone else or claiming ignorance, and more importantly, making derogatory and offensively sexual comments to and around the female members of his lab. In my opinion he should have been fired long ago from a purely productivity-grounded perspective. The harassment issues only came to my attention more recently and are definitely grounds for dismissal.

As I said, I'm really pleased that the grad student finally worked up the nerve to talk to her PI about it. It seems that this person has been creating a hostile work environment for just about everybody for some time, but she is by far the most out-spoken of them and thus the most likely to say something. Even still, this has been a long process - she's been talking to me about it for a couple of months, and it had been going on for some time prior to that. I've been encouraging her to speak to her PI for a while now and on some level I understand her hesitation. It's not easy to accuse another of your colleagues of impropriety. She was afraid that her PI wouldn't take her claims seriously. She was afraid that the other women in her lab, though they also complained of this guy's behavior amongst themselves, would be too reserved to back her up when she went to her PI. One of those women advised her to just get used to it -- that they weren't going to change this guy so the best they could do was adapt. Ugh. Fortunately, her fears were unfounded. Her PI has asked her to continue to bring up her concerns, and it sounds like the other lab members are more willing to do so now that they've seen his positive and supportive response.

I'm glad that things are moving forward, though I'm disappointed that there is not yet an action plan in place for dealing with this - her PI has encouraged her to continue to bring her concerns to him...I just don't know that he's made any commitment as to what he's going to do about it. I've since suggested that she document any further incidents by sending these concerns via email to her PI as they come up. Hopefully, that will be the required impetus for some action, whether it be a "come to Jesus" talk with the jerk, or just getting rid of him.

I'm also a little frustrated that it has taken so long to come to this point. I know she's been really unhappy and uncomfortable in her lab for some time and I understand why it took her so long to work up the nerve to bring it up. It shouldn't have to be that way, but it is. I can't help but feel like I should have somehow done more...but I don't know what it is. I could have approached her PI on her behalf I suppose, but I have not personally witnessed any of the incidents that are at issue. I also think these concerns mean a lot more coming from her. I didn't want to undermine any of the trust between her and her PI. It's further complicated by the fact that she and I are both grad students and therefore subject to the same professional vulnerabilities. Were I another faculty member perhaps I could carry a bit more clout and it would not have been weird for me to step in and say something. I also didn't want to jeopardize her trust in me. I know that she has come to me for advice on this because a) I have validated that her concerns about these things are real and important, and b) let her know that she doesn't just have to live with it. I was a "safe" person to talk to while she made up her own mind about what she wanted to do about it. While I encouraged her to approach her PI from that beginning, I didn't try to force her to take any action she wasn't ready for...but still, I think it went on for too long.

I just don't know - was there something else that I could have or should have done in this case?

How to do Science - An Instruction Manual

Just saw this at Toaster's. If you're not already frequenting his blog, get on it!

The Relatively Straightforward Common Biotech Method:

• Step 1: Break it and compare that to that that ain't broke, then supplement the broken stuff to the level of that which ain't broke and compare again. If breaking it resulted in nothing, or less, happening, then what you broke might be causing that effect to happen in the first place and you may develop sweaty palms.

• Step 2: If supplementing what's broken to non-broken levels restores the effect, then what you broke is probably causing that effect and you may start fidgeting uncontrollably.

• Step 3: But, if you've also broken other related stuff and not seen the same pattern, then you can say that what you broke is causing it to happen (to the best of our current knowledge!) and you may then do a happy marshmallow dance of victory.

See, science is eeeeeeeasy.

Plague Outbreak

I thought it was just allergies, and I thought that I had finally exorcised the science demons after toiling through my Week of Epic Fuck-Ups (you've filled your quota for the year bitches, so go mess with somebody else). This week has gotten off to a better start for sure, but I was wrong about at least one of those things.

Today I am a walking mucus factory. The allergies, as expected, have weakened my immune system such that I am now susceptible to the Lab Plague. It goes around here every year. I always starts with the parents. I can't really blame them; it's not their fault. It's just that kids are little disease vectors, especially if they spend most of their day in what should be categorized as a BSL-4 facility (a.k.a., DayCare). Don't get me wrong, I like kids. I just don't like getting their sickness. Half the parents in my lab have been sick for over a week. One of them just had to cancel her talk because she's lost her voice. I wish that they would a) stay at home when they're sick so as not to give it to the rest of us, b) keep the kids at home when they're sick so as not to perpetuate the germies. But I also know why they're here. The desperation of losing experimental time to something as mundane as the flu keeps them coming in. I shouldn't judge though. I'm here too for the very same reasons.

If I had any sense I'd go home. I'm not doing the experiment that I had planned for today because I know that there is no way in hell that I can get through it without sneezing tons of RNase into all my solutions and ruining the whole damn thing. That would be a total waste of 4 very labor-intensive days, not to mention the time it would take to make up all new solutions. Instead I'm catching up on my backlog, which also needs doing, but not as much as that damn in situ. I wish I was at home asleep and I can't help but wonder if that would render me more productive over the long run than trying to work through this and prolonging the symptoms.

How far along are you?

Grad students get really fucking sick and tired of being asking the dreaded question:

"So, are you close to graduating yet?"

Or any permutation thereof, really:

"When are you defending?" "Aren't you a post-doc now?" "You're still here?"

What follows is a (sort of) funny story about what happened to me a few months ago.

----------

I was in an elevator with my backpack on, leaning on the the wall trying to stretch my back and catch my breath from an intense bike-ride to work, hence a little poking-out belly (now, I could stand to lose a few pounds, but only a few really). Some maintenance guy gets on the elevator and decides to initiate some friendly conversation. He asks me, "So, how far along are you?"

I think to myself, "Shit! Now even the maintenance guys are asking when I'm damn well going to finish this fucking thesis!!!! I have been here for WAAAAY too long!"

Then I realized he had no fucking way of knowing that I was a grad student (as opposed to post-doc, not that I would expect the maintenance guys to know the difference)...then it dawned on me what he really meant. My response:

"I'm NOT! Fuck you very much for asking!"

He tried to back-peddle "Oh! But I thought you were--. I mean, I'm sorry, I just...."

Yeah, I gathered.

Jerk! I know he was trying to be nice, and if I were actually pregnant and so much so that I was very obviously showing I probably wouldn't have minded. But dude, unless it is so obvious that there could be no other possible explanation (i.e., the pregnant waddle plus stretchy waist-band maternity clothes, or if you want to be really sure active labor/contractions with water already broken) - don't go there! And how many pregnant ladies show up to work all hot and sweaty wearing a backpack and bike helmet anyway*?

I spent the rest of the day being pissed that I was not further along (on the thesis, that is) and being generally cranky about the fact that I don't have enough time in my day to exercise as much as I should. Grad school can be the pits sometimes.

*If any of you ladies actually do/did, you are a better woman than I!

Stem cell ban lifted

I don't have time to post much about this at the moment, but for now I will just say this:

About damn time.

I Lied.

I am in the lab today. But I swear it won't be for long. I had to set up matings for an experiment planned for a few weeks from now and minipreps won't do themselves. The worst thing that has happened so far is that I've dropped a full box of P200 tips on the floor. If I can keep the damage down to that it will be a relatively good day.

[UPDATE]: Disaster averted (excluding P200 tips, and when I nearly tried to resuspend my hard-earned plasmid in lysis buffer *read the labels dumbass!*). Am going home to plant some zucchini in my garden and then off to see "Watchmen" with BH. Peace out.

Dear AA,

You suck.

You ran your gel backwards and lost your DNA. That is a stupid, stupid mistake that you haven't made since you were like a freshman in college. You are trying to do too much at once and this is causing you to do all of those things very, very badly. You are tempted to start again even though this means you will be in the lab until stupidly late tonight. This is a bad idea. Don't do it. You are too tired and too frazzled and in this state you will just do something else badly, something even stupider. You need to slow down. You need a vacation. Or at the very least, a good night's sleep. Go home and try again tomorrow...and try not to fuck it up again, OK?

XOXO
-Your Slightly Saner Self

Dear plasmids,

You suck!

That is all.

XOXOXO
-AA

How many accountants does it take to create an Excel spreadsheet?

I'm coming to the end of my position on the training grant so I'm getting emails from grant accountants/administrators about spending the rest of my research money. Their balance sheets are, um, how shall we say? Unintelligible? Incomprehensible? Completely wrong?

It seems to me like there is a very basic solution to this problem - check your figures before you start sending people their balance sheets.

I have been in a protracted email conversation with the Accounts Manager to try and figure out what is going on here. She has sort of explained done some hand-waving about leftover balances and overdrafts from last year but even if I plug those figures in (in every possible permutation) the sum still doesn't match the (made up?) one on her Excel spreadsheet. Grrr.

It's really very simple - all of the expenditures should add up to the figure that appears in the "total expenditures" box. This sum, subtracted from the total money available for research supplies will equal the remaining balance. Not difficult. I mean, hell, I can manage it! And yet, no dice.

I have deduced that Accounts Manager does not actually use the handy-dandy "input equations" function provided by the Excel software. It's actually very easy to use yet she still seems to resort to scratch paper, or a calculator, or (heaven forbid) mental math to tally the sums. Which as you might imagine introduces a lot of opportunity for human error...like entering an expenditure and failing to tally it as part of the sum total, or somehow adding mysterious extra purchases to the sum total which do not appear on the balance sheet. (And don't even get me started on the fuckwittery with my travel money.)

We have paid accountants to do this stuff for us, and yet I find myself correcting their books on my accounts at the end of each year because they can't figure out how to input a simple correct formula into Excel. Can I get the accountant's salary too? I mean really I am doing her job. I'd settle for just this week's salary, or at least a bonus for providing her with a brief Excel tutorial.

The last email (of many) I got from her yesterday: "I am at home. I won't be back until Monday. I suggest you talk to [grant administrator]." Yes, I think that she would be more helpful, except that she relies on you to keep the books in order and so she also has only your non-sensical Excel spreadsheet from which to attempt some resolution of this matter.

Goddammit! [UPDATE]

This week is clearly one of those weeks when nothing is going to go right. Fuck.

I've got a shit-ton to do and it's all very simple and straightforward but of course none of it is working and for no apparent reason. Double fuck.

To top it all off I seem to have misplaced some very important samples. I distinctly remember processing them and putting them in the freezer box two weeks ago, where they were to patiently wait for me until I had time to finish with them. I scheduled the finishing of them for today. And now I can't find the fuckers. What - did they go sneaking out of the freezer box sometime in the last two weeks for a little -80 pub-crawl and never made it home!?!?!? Triple fuck!

It's times like these that make me feel like a tremendous fuck-up. How could I possibly lose my own samples?!?!? Where else would they be?!?! Did I do something stupendously stupid like mislabel them?!?!

Stupendously stupid isn't outside the realm of possibility right now but mislabeling seems unlikely. Then again, I've been so frazzled over the last couple of weeks that it has become much more likely that I have and will completely fuck up my own shit lately. This week needs to end already. Fuckity-fuck-fuck-fuck!

UPDATE: Heh. I just checked my logs and it turns out my samples aren't missing (yay!). They never existed in the first place (boo!)...while I did collect a set for this experiment, none were of the appropriate genotype, so I got no usable samples from that collection and thus I did not process or freeze any of them. The samples that I so distinctly recall processing and putting in the freezer were a completely different set for a completely different experiment and they haven't gone walkabout. I'm losing it - my mind that is, not my samples.

UPDATE 2: One of my "not working" experiments is still being a bitch but I think I can get past this step. I'm sub-cloning a fragment into a very stingy vector. I had tiny wee under-developed colonies this morning. So I grew them up for a few more hours and found that of about 200 on the plate, all of them were blue. Fuck! But wait, what's this I see? A single white colony hiding there amongst all the empties? You thought you could escape unnoticed, you sneaky little bastard, didn't you? Ha! Gotcha! More would have been better but I only really need one. Onwards!

An Open Letter

Dear Departmental Copy Machine,

What ever have I done to offend you? I treat you rather nicely I think. I never ask for anything difficult like collation, double-sided copies, or too many pages in the auto-feeder tray. On the rare occasion that I have reason to partake of your services I only want a single page copied onto another single page. Is it really so much to ask?

Perhaps you take evil delight in making me stand on my head and hop on one foot in order to get what I need from you. Perhaps you are a sadistic beast that takes pleasure in making me look like an ass in front of my colleagues.

Take today for example. I marched up the three flights of stairs from my lab to your new place of residence (nice digs by the way - the graphics lab rocks), armed with 3 of the 4 pages I needed copied as well a post-it note with the new copy code that Departmental Administrator kindly provided to all of us (which is incidentally, the same code as the one it was changed from 6 months ago). My inability to remember important things like all of the pages I need copied or a simple 4-digit code is not your fault of course. I am not reassigning blame for my personal failings.

However, I am assigning some blame for your obstinate insistence that I go through far too much hassle to acquire something as simple as a facsimile document from an office appliance that is designed and employed for precisely that purpose. Seriously, do your job!

I dutifully entered the new four digit code and you snarked at me that it was incorrect and sarcastically suggested that I should contact Departmental Administrator for the correct code. Now, you and I both know that DA is very busy putting together grants right now so I'm not going to bother her. And besides, she just gave me this new code last week. It should work. But it clearly does not, so I tried entering the previous code. It also does not log me in.

So I called the lab to see if I was somehow left out of the loop on any newer than new super-secret copy codes. Thankfully, I got Helpful Student on the line, who suggested just what I had already done. I told her that you liked neither code, and she said she was on her way up to help. I didn't really see the point since we both knew only the same two codes, both of which you rejected...with a rather pompous air I might add.

While she was trekking up three flights of stairs, I tried again. And again. And finally, magically, you dear copy machine, logged me in! The seventh time is the charm?

So Helpful Student arrived to find me successfully logged in and making copies...only the copies you gave me initially were blank. I didn't give you blank pages as templates, nor did I load them upside down. So Helpful Student offered to push the "copy" button and lo and behold - copies! As in reproductions of the original documents! Huzzah! Was that really so hard?

Why do you like her so much better than me? Does she give you new toner? Tickle your paper rollers in just the way that you like? I'm pretty sure that DA does that. What gives?

Anyway, thanks for the copies (finally), but you should know this: I think you suck. And I hope you choke on a giant paper jam. And you can tell your friend the automatic stapler that I've got a bone to pick with him too. Watch yourselves office appliances. I'm not joking around here. If this kind of crap continues I'll have to go all Office Space on your asses.

Sincerely,

AA

Whiiiiiiiiiine.

Waaaaaah. I am so tired. And I got 8 hours of sleep last night. What gives? Oh. Yeah. The stuffy head and itchy eyes and sneezing all the damn time? Shit. It's that time of year again. Since moving to Current City I have terrible seasonal allergies. I have no idea what exactly I'm allergic to. It doesn't make any sense. I grew up on a fucking farm for creeps' sake! Farm kids are supposed to have fewer allergy and respiratory problems for the rest of their lives. I have never once had hay fever on the family farm (despite actually growing, baling, and bucking hay several times a year), but there are a few weeks out of every spring here that whateverthefuck is blooming or making spores or pollen just kicks the shit out of me. I wish I knew what it was because I would go out right now and launch a campaign to sterilize it...or at least I would when I'm over the headaches and am able to wade through the sea of crumpled Kleenex on the floor and get out the door in the first place (seriously, I'm completely useless right now - at least this is not yet contributing to a month-long sinus infection like last year - that was fun!).

Stupid plant sex!