EPIC FAIL

I have to say, I was not looking forward to the point in time when BF stopped providing me with, well, BF. Ugh on going back to soul-searching posts about supplemental data or whatever.

Thankfully (?), not yet!

Today many things became clear:

Jekyll: We'll be diluting the secondary antibody 1:200, meaning 1 part antibody for 200 parts final solution. We've already figured out that we have a total final volume of 4.8 mL. How much antibody do we need?

BF: [writing]

   1      x
 ----- = -----
  200    4.8 mL 

Jekyll: [sigh of relief]

BF: [writing]
4.8 = 200x
So, we'll need to divide 200 by 4.8.

Jekyll: [suddenly gripped by dread]

BF: [writing]

     _______
4.8 | 200

Jekyll: [crying on the inside]
Don't take shortcuts on the math. You need to divide each side by 200 to isolate x, so that should be 4.8 divided by 200.

BF: Oh, right.

     ________
200 | 4.8 

[ominous pause]

Jekyll: [helpfully] Instead of working in milliliters, you could put that in microliters so the math is easier.

BF: Uh, so it'd be...480 microliters?

Jekyll: [suppressed inward sigh] No, let's walk through the conversion.

         1000 uL
4.8 mL x ------- = 4800 microliters
          1 mL

BF: Oh right.

     ________
200 | 4800 

[pause]

Wow, it's been so long since I've done long division.

[excruciating pause]

Uh, 2.4?

Jekyll: [gasping and appalled, yet inwardly joyful that she can later share this precious moment with some anonyfriends] Let's think about the decimal point....


And I'm even sparing you the tedious calculations on getting the 4.8 mL number in the first place.

The good news is, it is now perfectly clear that BF has some sort of math disability, by which I might or might not mean "stupidity." I have no idea how he made it through college (calculus, anybody?) although presumably a calculator was involved. [Or a systematic cheating scheme via his frat.]

The bad news is that he is still in my lab. Tomorrow I will talk with Advisor about the path forward.

I am a broken record

I'm rechristening Tech "Blog Fodder" because that is clearly his role in my life.

Episode 1: So close.

Jekyll: We're going to dilute this antibody 1:1000. That is, one part antibody per one thousand parts total solution. So if we want a final volume of 1 mL, ie 1000 microliters, how much antibody should we add?

BF: Um, one microliter?

Jekyll: [relieved] Yes! That's right. Now we want to make a 1:2000 dilution, again with a final volume of 1 mL. How much antibody do we need?

BF: Uh, 0.2 microliter?


Episode 2: Do as I say, not as you think.

Jekyll: While I'm gone at journal club, add 0.2 mL of this solution to each well of the 24-well plate. There will be leftover solution, but don't throw it out because we'll use it later.

BF: Ok.

[1 hour elapses]

Jekyll: I'm back. Hey, how come there's such a large volume in these wells?

BF: Well, there was a lot of leftover solution, so I just added it all to the wells so as not to waste it.


Episode 3: OH REALLY?

Jekyll: Doing all these molarity and concentration calculations is going to be really important, and I think it would be good if you practiced them. Here are a few websites that have tutorials on how to calculate these things. You should review them and do the practice problems. Later this week I'll try to find a chem textbook so you can go over the material on solutions.

BF: Yeah, I guess you found my weak spot in math!

Jekyll: That's ok, molarity and concentrations just take some practice.

BF: It's been a long time since my last chemistry class.

Jekyll: Oh? What did you major in--psychology?

BF: Neurobiology. I took chem as a freshman and then orgo as a sophomore, but that was over two years ago so I'm rusty.

Jekyll: Hm, what lab classes did you take?

BF: Well, none in bio.

Jekyll: What?

BF: The lab classes were only required for pre-meds, and I wasn't pre-med. I want to go to graduate school.


Let me help you out with that decision, young man. You should not even go near heavy machinery, let alone graduate school.

Gaaah. Advisor has been away for a few days but he will want a report on BF when he returns. I plan on telling the truth. Advisor will undoubtedly ask me if we should fire him. I have to make a decision.

OTOH, if you watch like a hawk, BF can do what he's told. He is indeed improving his hand steadiness by means of forearm support etc. And we really just need a tech for menial tasks that do not involve much thinking. If he can conquer molarity, he should be fine.

OTOH, why does anybody with two university-level chem classes and a B.S. in neurobiology still need to conquer molarity?

Quick tips

Vocab time!

Rostral = noseward.
Caudal = tailward.

Dorsal = topward/backward.
Ventral = tummyward.

If you ever wish to tech in a bio lab, these would be good words to learn.

Let me further suggest that if you learn them, you get them correct, and not reversed.

And as a final suggestion, if you do somehow find yourself getting them wrong in front of your mentor, do not turn the incident into a joke by saying, "Oh, yeah. Just checking if you were paying attention!"

That is all.

I'm not sure that's as reassuring as you think it is.

Thanks all for your helpful tips on hand steadiness. I showed Tech the dissection today and later this week will watch him do one, with the benefit of the various ideas you gave me.

However, Tech just keeps on losing points in my book. Here's today's episode:

Jekyll: The dissection we'll be doing can seem a little gruesome, but I want to assure you that the mice are deeply anesthetized.

Tech: Oh, well, whatever. They're just rodents.

Jekyll: Well, it's still extremely important that we make sure that the animals are not experiencing any pain.

Tech: Sure, because the animal rights people would complain.

Jekyll: [pause] Well, of course we comply with IACUC regulations, but these animals are in our care and only exist because we breed them, and so there's a strong moral ground for treating them as well as possible.

Tech: Don't worry, I'm not going to go all Jeffrey Dahmer on them.


?????????

This is only a loose transcript, duh, and Tech's apparent disinterest in animal welfare is hard to get across. His tone of disregard when he said "just rodents" was a shock.

Before now, I've exclusively trained labbies who were if anything terrified of causing discomfort to mice. That was a great starting position, because it let them work backwards to a position of comfort as they learned proper handling techniques etc.

I have never had to train someone with this sort of attitude. I am at a loss.

I asked some friends for help on this (thanks, friends!) and they gave two primary suggestions:
(1) Ask my Advisor to sit down with Tech and reinforce that animal treatment is of paramount importance, and that disrespect for animals will not be tolerated.
(2) Make Tech read the whole damn IACUC protocol to get a sense of exactly how much thought and care goes into animal treatment, and make it plain that he has to get on board.

Dr Hyde also thought that I should emphasize that if I ever see him mistreating an animal, his ass will be fired pronto.

I think these are all good suggestions. My issue now is implementation.

I've been lucky up til now that basically all of the people whom I helped to train were already awesome. The downside is that I have little to no experience telling people to shape the fuck up. To be honest I am a bit afraid of it. I do not think I have natural managerial talent. My bad tendency is to fume privately (or bloggily!) that a trainee is screwing up, rather than have the nerve to address it head-on.

I am irked that Tech has arrived with such minimal baseline skills. I am dubious about his shaky hands. However, these are presumably tractable problems. I don't know whether respect for animal life is a tractable problem.

But as Dr Hyde points out, no one is going to teach him but me. If I shy away from teaching him, or if I just ask Advisor to fire him (which has certainly crossed my mind....), then perhaps his next mentor won't lick him into shape either.

Apparently I shouldn't have been asking you-all for suggestions about shaky hands, I should have been asking what to do if he doesn't care about the tail-pinch response. Sigh.

How do I pull together the demeanor for the appropriate mix of teaching him, educating him, and scaring the poop out of him?

Mememememe

DrDrA tagged me for the six-things meme, and I perhaps overthought it. Anyhoos, here are the rules:

1. Link to the person who tagged you.

2. Post the rules on your blog.

3. Write six random things about yourself.

4. Tag six people at the end of your post and link to them.

5. Let each person know they’ve been tagged and leave a comment on their blog.

6. Let the tagger know when your entry is up.

1) I am an infant about spiders. A few nights ago before dinner, we spotted a spider on the floor but then couldn't find it. Not three minutes into the meal, I looked down and--you guessed it--spider was crawling on my shirt. I shrieked, stood up so fast I knocked over my chair, and started peeling off all my clothing. After Dr Hyde stopped laughing, he did what he always does and caught the spider for release outdoors. For this I married him.

2) I do not keep a clean house. My parents always did. I admire clean houses. But mine is regularly a disaster. I regret this, but not enough to do anything about it, except when guests visit.

3) I am better at the Times crossword than virtually anyone else I know. Also, Scrabble. The corollary is that if I don't win a game of Scrabble, I am upset and sulky.

4) I once slept with a guy I met on a plane.

5) Although I am generally a good cook, I regularly make the mistake of thinking that if 1 tsp of [ingredient] would be good, then 2 tsp would be even better! It turns out, this is only true of cinnamon, cardamom, and ground coriander. Pretty much everything else, no. Knowledge doesn't stop me, though.

6) When I was younger, I had insomnia. I would lie awake for an hour or two just thinking--replaying conversations, imagining futures, etc. Eventually I found that the best way to shut my brain up was to memorize poetry. A sonnet is about the right length, although once during extreme insomnia/boredom I learned "To His Coy Mistress." After I've spent 45 min or so memorizing a piece, I can focus on repeating it and thereby fall asleep. Something about the rhyming and scansion helps. To this day, if I really can't sleep I will get up and find a book of poetry, or repeat poems I already know. I know a number of poems by heart, plus some unusual song lyrics ("Antimony arsenic aluminum selenium").


I tag Juniorprof, juniorprof, JrProf, JP, Joon-yah, and JUNIORPROF. And Anonymoustache, if he feels like it.

Handyman

When I was just a First Year Graduate Student Jekyll, I saw another student's grad school application in which she mentioned that she had already done fine dissection work, so she knew she had good "hands."

At the time, I scoffed at the relative importance of this metric. So you can dissect--who cares? Science is about Ideas.

A postdoc I was working with put the kibosh on me. "I knew a woman in grad school who had to drop out of her lab because she simply couldn't do the dissection," she said. I listened, but remained skeptical.

This week, teaching Tech the niceties of pipetting, I couldn't help but notice that he has the worst hands I've ever seen. He shook so much that the pipette clattered uncontrollably against the Falcon tube.

When we'd finished for the day, I asked him about the shakes. "Lot of coffee this morning?"

"Well," he replied, "I had coffee, and I didn't eat breakfast, so that contributes. But also shaky hands run in my family. Some kind of inbreeding a while back, I think."

"Ah," said I. "Ok, I'd recommend you cut back on the coffee and eat more breakfast." Two days later, he was perhaps less shaky, but still had significant difficulty picking up a slide with forceps.

Now, I have several friends with noticeable tremors who are nonetheless outstanding experimentalists. I think they use the standard tricks--brace one hand against the other, or against a bench--and perhaps some others I don't know.

So I know that this is not the end of the world. Still, when someone is employed as a new, straight-from-college tech, their primary job is...to have good enough hands to do the work. (Also, molarity calculations.) Not to create Ideas (although that would be great too!) Oh, young Jekyll, why so foolish?

Up til now, I've been showing Tech some histology protocols that are only moderately hands-intensive. But on Monday or Tuesday, I have to teach Tech a dissection. It's not a terribly fine dissection, but it has to be done correctly to be useful. It will be a big waste of precious transgenic animals if he biffs it over and over.

I plan on sitting down with him beforehand to review steady-hands strategies. I don't have those rock-steady hands with superb control that some people do, but I've never had trouble learning dissections, so I don't have a lot to offer him. Do any of you have recommendations beyond what I listed above--bracing your hands or arms on something?

H o p e

When is the last time you saw so many teary faces at a Presidential rally?

I'm not just asking rhetorically here. The first election I was politically conscious for was 1992, and while Clinton had his own throaty choke-ups, I don't recall the same from his supporters. (I remember 1988 too, but wasn't quite reading the newspaper yet...)

Older More advanced blog readers? Did people get all weepy for Reagan? I can't imagine there was this sort of emotion for, say, Carter or Nixon (!)

I alternate between giddy optimism and a deep, deep fear for Obama. The more invincible his lead becomes, the more some crazy winger will want to, well, vince him. Here's a toast to his Secret Service for keeping him well.

In which Dr J is rendered briefly speechless

Dr J: Ok, this P1000 pipette seemed to be having problems yesterday, perhaps due to some fluid inside. Let me show you how we check if it's all right or not.

Tech: Ok.

Dr J: I'm pulling up 1 mL of water here and we'll weigh it on the scale.

Tech: Oh?

Dr J: See? It should weigh 1 g, but it's only weighing 0.7 g, so there's something dreadfully wrong with it.

Tech: Oh, right.

[pause]

Tech: How did you do that? From milliliters to grams? I'm not so good at conversion factors.

There are two stops...

My postdoc Advisor recently hired on a part-time tech. This guy is straight out of a prestigious college, looking to tech for a couple of years before going to grad school. (Why can't he find a full-time job? Don't know.)

Tech did a little techwork in college, although he doesn't speak of it with much enthusiasm. I was moderately against hiring Tech, but Advisor didn't ask me and went ahead with him.

Yesterday, I was training Tech in some histology he'll be doing for us. Yap, yap, PBS, yap, yap, Triton, yap, yap, pipette, yap, yap, wait what? You say you don't know how to....pipette?

Sweet Jeebus.

(Non-biomedical readers may find this post quite dull. Feel free to stick around, I'm just giving fair warning.)

This led me to try to remember the first time I wielded a Gilson. I can't. I teched in college, and did reams of PCR, so for sure I knew how then (although given my utter failure to produce substantive results with said PCR project, in retrospect I wonder....)

Did I learn in a lab class in college? Huh, maybe. I also teched between high school and college, and perhaps I even learned then.

Dr Hyde remembers his first pipette experience. He says that for a long time he didn't realize there was a second stop. He also says that for several months he pipetted with his forefinger. "That doesn't give you carpal tunnel....if you don't do very much of it," he muses.

The memory of this made us both clutch our sides laughing. Pipetting with your forefinger! What green little lambs we once were.

I now have one of those green little lambs under my wing, so to speak.

Apparently I have forgotten to teach Tech that you have to make a controlled release movement. Two of our pipettes had fluid up in their special no-no holes by the end of the day.

I blame myself. I am becoming that most hated of things, the person who teaches badly because she's forgotten what it's like not to know.

But seriously? How do you reach age 22 and express interest in a biomedical future and not know how to fucking pipette?

Colder....colder....warmer...

You may have thought I didn't have another post about freezers in me, but you were wrong.

The -20 stopped working after we defrosted it. No obvious cause. We get the Sears repair guy out (yes, the freezer was a Kenmore....we're not keeping anything explosive in it). For $70, he tells us instantly that it's probably leaked the coolant (or something like this) and it will cost more to repair than to buy anew. (Sometimes? I really dislike America.)

He also says, "This freezer is designed to be opened and closed about four times a week. How often do you open and close it?"

"Uh, about 10 times a day."

"Yes, that's your problem."

This freezer was about 4 years old when it bought the farm. The question facing us was: do we buy another cheapo Sears freezer (~$600) and assume we'll just have to replace it every four years? Or do we buy the VWR equivalent ($1600) in the hopes that it is designed for lab usage and will last longer, and keep our stuff colder? (One of the reasons we defrosted the original freezer is that we noticed some things in it were disconcertingly unfrozen.)

The second question was, frost-free or manual defrost? I've always heard that frost-free is bad for science stuff, but we don't keep any enzymes or antibodies in this freezer, just drug aliquots etc that can probably stand a few degrees' fluctuation. Interestingly, a Sears freezer costs nearly the same whether it's manual defrost or frost-free. A VWR frost-free freezer costs about 30% more than its manual defrost counterpart. What the heck is going on inside these things, anyhow?

I don't particularly care what the lab does, but I do want to know what the general best answer in this situation is, so that when I have my own lab to run I know if it's worth the money to buy a VWR freezer.

In the end, our lab manager talked with a sales rep. Naturally, on Tuesday we are expecting a delivery of a new, bigger, frost-free, $3100 freezer.

I am none the wiser about how I will run the Jekyll lab.

Oh lordy

Comrade PhysioProf wants to have a drunken confessional session, without the drunken and the face-to-face. Who am I to argue?

Can You Remember The Day That You Officially Became An Atheist?

Yes. First, some history. I was brought up religious by Lutheran parents, attending Sunday school and then church every week. I went to Episcopalian school--nuns and lay teachers (non-nuns?)--for umpteen years. I can still recite the books of the Old Testament, a couple of Psalms, and any number of hymns.

I believed the whole thing. In fact, I was quite the religious child. Loved the Narnia books when I was too young to get the religious metaphor; loved them even more after I did get it. My parents are socially liberal and so I never imbibed the whole hate-thy-neighbor branch of Christianity that seems to drive certain politicians. I thought Jews and Muslims and Christians all prayed to the same God, and we would sort out the tricky details when we were dead/in heaven.

I didn't have a problem with evolution; I thought it was real, and happened on the time scales science dictates. I just thought that God sort of oversaw the whole thing. I took the Bible as a parable, not a science text.

Arriving in high school, I started hanging out with a generally atheist crowd. They thought I was a curiosity item, but a really fucking smart curiosity, and so we engaged in a lot of high school Big Picture Aren't We Grownups Now debate. (CandidE--some of it in diners. Yes, we were that adult.) I learned that atheists were not immoral, as I had previously assumed; they learned that not all Christians were wingnut morans, as they had assumed. Belief: unshaken.

I started dating one of them.

Within a year or so, I made a terrible discovery. I tried to pray. And couldn't. The belief that had been a significant part of my identity and life for so long, that (seemed to have) weathered the endless debates, was gone. And really, really gone. As certain as I'd been only a week or two earlier that God was in his Heaven and all was right with the world, it was now utterly clear to me that he wasn't, and maybe it wasn't.

I didn't really register how deeply this conversion had shaken me, but I did pick a lot of fights with the boyfriend over trivial issues, and we eventually broke up. Hmm, transference much?

Anyhow. It took me a while to heal from the loss of this part of my life. There are some things I still miss about organized religion. The comfort. The music. The sense of shared community with fellow worshippers, and even with people in different faiths. The confidence that death wasn't really The End.

But plenty of things I've gained, too. Greater perspective on religion. A sense of urgency about getting experiments done, NOW (no afterlife!) A new understanding of morality as generated internally rather than externally. And a good lie-in on Sunday mornings.

Do you remember the day you officially became an agnostic?

Never was.

How about the last time you spoke or prayed to God with actual thought that someone was listening?

I was 18. Doubt I prayed for anything profound. World peace, boyfriend, etc.

Did anger towards God or religion help cause you to be an atheist or agnostic?

Sex, maybe. Anger, nope.

Were you agnostic towards ghosts, even after you became an atheist?

WTF is up with the ghosts? What next, UFOs?

Do you want to be wrong?

You betcha! This shit would be much easier if someone were in charge. Sadly, I see no evidence that an Almighty Bureaucracy is at work.

Tag! Um, who didn't CPP and Doubledoc tag? I'm not sure about the religious leanings or otherwise of many of you, but I'll take a guess and say YoungFemaleScientist? Candid? Only if you feel like it. Or heck, Isis, you can go ahead and invert all the questions if you like. Good luck with making figures for this one though.

Illegal vs Irritating

A good friend of mine recently visited the Office of Sexual Harassment to complain about a faculty member's behavior lo these many years ago, back when we were meek interviewees.

During said interview, the faculty member was generally abrasive, with a lot of aggressive questions about my friend's undergrad research and whether or not it was believable. But he won this particular OSH complaint because of the following comment: "Why should we accept you into this grad program since you're female and you might just quit to have babies?"

Six years later, my friend was prompted by a feminist faculty member's talk to lodge this complaint. During the course of filing the complaint (which I'm happy to report was taken seriously), my friend also noted that this guy had been a jerkwad in the rest of the interview too.

The lawyer/OSH person with whom she was speaking said, "Yeah, but we can't do anything about him just being a jerk to everyone."

My friend: "Let me get this straight. If the guy is an asshole to women and says shitty things specifically to women, we can file a complaint; but if he's just an equal-opportunity asshole, there's nothing to be done?"

OSH person: "Um, yeah, that's about right."

Anyhow, obviously in this case the faculty member had made sexist shitty comments, so the OSH was helpful and took the report down and everything.

But as my friend put it afterwards, it's odd that you can easily file a complaint about someone who's a dirtbag to women, but not someone who's a dirtbag to everyone.


(Yes, I'm aware that someone who is a jerk to everyone will perhaps have trouble making tenure anyhow. Still, it's not like there's a formal Office of Jerkwad Behavior to complain to about that.)

Pack rats and neat freaks

Most scientists enjoy tinkering with little bits and pieces of equipment, kluging together a new thingamajig from the discarded old parts of the broken whozeewhatsit. It's a make-do approach that helps us solve minor (or major!) experimental problems.

Perhaps as a result, labs are havens for pack rats, even to the point of ridiculousness. Broken printer? Well, don't trash it--maybe we'll want to scavenge it for parts one day. (Also, nobody feels like calling around to find out how we dispose of it.)

Two defunct large laserjet printers lurk in the common room of PostdocLab.

Friday, I got fed up with the fact that our primary freezer had such a thick build-up of permafrost that the top shelf had become the Tomb of (8 or 10 bottles of) Unknown Solutions, none of which could be extricated.

So I organized a defrosting. When, after several hours, the ice had melted enough for the bottles to be removed, I announced that I was going to throw them out.

I was met with resistance. "What if someone wants those?"

"Well, someone wrote their initials on here when they made up these drug aliquots, and nobody in the lab has those initials so I doubt anyone was counting on these drugs being here."

"Yeah, but if they're useful we shouldn't throw them away."

"Since the permafrost has been here since I joined the lab nine months ago, it seems safe to assume that these bottles are not in high demand. [Reads off label on a bottle] Do you ever use that?"

"No, but maybe we'll use it in the future."

"Look, do you even know whose initials these are? No? Neither does Advisor. Drugs this old should probably be thrown out anyhow."

"It's only a few bottles, it's not like they take up so much room, I think we should keep them."

"Go to hell."

Ok, it didn't reach quite that stage. (Ok, maybe it did.) My point is, although no one on earth would ever call me a neat freak, I do think that obsolete printers, drug aliquots from 2003, and unlabeled freezer contents are not a good use of our storage space.

So I poured the old drugs over the printers for maximum landfill toxicity, and threw the whole mess out the window.

No, not really. (But I really, really wanted to.)

Rate my PI!

We agree that women in science are systematically shafted by deep-seated biases. On the one hand, there have been giant improvements in our lot over the last several decades (thanks, feminism!)

On the other, the bias that exists today is often subtler than in years past--and that much harder to eradicate. How do we create a social cost for the under-the-radar daily problems: Dr BigShot treats female trainees as helpmeets, and male trainees as colleagues?

One solution I've recently heard proposed is as follows: Create a RateMyPI.com website, akin to RateMyProfessor, but for graduate students and postdocs. Trainees would be encouraged to post judgments of PIs they've interacted with, with special attention to equal treatment issues.

The downside: these anonymous forums can end up dominated by the dissatisfied, with gripes exceeding praise (the same way letters to the editor are more commonly complaints than attaboys). A PI who was unfairly trashed by one or two angry trainees could have trouble recruiting nice people. Also, it could be hard to maintain anonymity, although if people were careful to post about many PIs they interact with (first year rotations, conference meetings, etc), any one grouchy grad student will be hard to identify.

The potential upside: a repository of information about Dr BigShots the world over, with comments ranging from "He always impressed me with his respect for women and minorities" to "He always depressed me with his sexist put-downs." If commenters regularly disparage a given PI, grad students and postdocs might think twice before joining that lab. It'd be sort of like letters of recommendation (the currency by which PIs help or hinder their trainees), in reverse.

What do you think?

Less whining, more bragging!

Hey, some good news: my paper of dubious repute was finally accepted at some journal or another. Huzzah etc!

I acknowledge a strange sensation (aside from the post-debate inebriation, that is): relief. You'd think I'd be excited, happy, and so forth--but instead what I feel is primarily relief. Relief that we don't have to run this manuscript through another set of a reviewers, another journal; relief that my internal plans ("Get this paper into hot journal") matched up to the external reality.

Relief, above all, that I wasn't let down.

It's a little odd, no? You'd think I'd be swilling the postdoc-appropriate Champagne knock-off. Instead, it's as though an expected, but necessary, checkpoint has been met. Phew, publication!

I think I should stop and enjoy this more, but somehow in the face-off between relief and joy, relief wins. That sounds quite ungrateful, even entitled. But I think it's more about what GradAdvisor sometimes talks about: we are often driven more by our fear of failure than by our satisfaction in success.

And now to focus on the next.

ps) Still, pretty happy though.