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.

One way of looking at it

I should say up front that my (male) postdoc Advisor has beeen nothing but supportive of both the general notion that the postdoc is a good time to have children, and the specific instantiation, that Dr Hyde and I are planning for IVF. I'm really grateful that he's so awesome.

Still, talking with him is distinctly different than talking with my (female) GradAdvisor.

Scene: Most lab members absent on various trips etc. Advisor pulls up a chair near me.

Advisor: So, Jekyll, how is your health?
Jekyll: It's fine...We're planning on trying a cycle of IVF in November.
Advisor: How does that work, exactly?
Jekyll: Well, I'll have daily shots of hormones to increase egg production. Then they extract the eggs from me, inject one of Dr Hyde's sperm into each egg, wait a couple of days, and put them back in.
Advisor: Wow, I didn't realize it was so involved. Tell me, how do they get the eggs out? Is it with a needle? [gestures at abdomen]
Jekyll: Erm, no, they go in vaginally.
Advisor: [brightening] Oh, so at least it's not invasive.
Jekyll: ....


Confidential to my male readers: Lying back half-naked with your legs in the air, having a guy poke around in your ladyparts, is a truly context-dependent activity.

What's so special about seven?

There are the Four-Figure Wonders (Nature, Science). There are the Go Ahead and Publish Your Last Eight Years of Work in 16 Figures Plus Three Tables (some society journals).

But the majority of mainstream biology papers I've seen contain seven figures. Why?

It isn't as though research just naturally falls into seven figures. Putting together a paper, we often struggle to rearrange the panels for maximum intellectual impact, of course, but we also aim to put it into the magic seven.

The last paper we sent out contained seven figures. One reviewer pointed out that two figures could be plausibly combined; and then suggested that we accumulate enough more data to produce another figure. We did, and we did. Reshuffle, and bingo--still seven figures.

(Speaking of bingo, I'm playing Palinbingo Thursday evening--who's in?)

It's clearly an accepted convention (and yes, there are 6 and 8 and 9 figure papers. But the mode in my field, for sure, is 7.) What are the pluses and minuses?

On the down side, from the author's perspective, it's silly to shoehorn your Great Ideas into a prefab structure. Maybe your paper would unfold best in 5 very dense figures, or 10 thinner ones. But because of the norms, I would hesitate to send out such a manuscript (of course, I'm a junior postdoc; maybe when I'm a big fancy pants person who gets mentioned on YouTube has her own grant I'll have the confidence to buck convention.)

As a reader, though, I rather appreciate it. Especially if I'm skimming a paper, I like to have a sense of how the scientific argument will build, and how many experiments will be synthesized into a picture.

It's kind of like reading a novel: you know that when your hero is trapped in a perilous situation, but you're still gripping three hundred pages in your right hand, that this will not be the final test. Conversely, when the lovers are separated by cruel fate and the pages have dwindled to a precious few, the resolution is not likely to be happy.

Not that any science papers I've read have involved lovers, or peril, but you get the drift.

Here's what I would like to know: how did we converge on seven? The old papers I've read are idiosyncratic--the four figures, or the sixteen, at authorial whim. Do we gravitate towards 7 because of its mystical qualities? (That'd be embarrassing, for us rational scientists.) Have our psyches been colored by the 7 Dwarves, or the 7 Deadly Sins (all depending on your childhood, I guess)?

I don't know the answers to these questions, but since 7 is so powerful, next time I write a manuscript I'm going to try for 7 subheadings, and 7 sentences in the abstract, and maybe 7 supplementary movies. If the voodoo works as expected, then I'm predicting reviews like, "I don't know why, but this paper exerted a strange and wonderful force over me."

Science questions posed to Palin

Katie Couric, whom Sarah Palin must by now privately refer to as She Who Must Not Be Named, recently asked Palin what her thoughts were on global warming. (See, that's how I'm justifying yet another Palin-obsessed rant....it's science questions.)

Couric: Is it manmade in your opinion?

Palin: You know … there are man's activities that can be contributed to … the issues that we're dealing with now with these impacts. I'm not going to solely blame all of man's activities on changes in climate.

Well, that's reassuring, to know that our activities are not due to climate change. Quite a load off, what?

Yeah, yeah, yeah, she misspoke, and two sentences in a row that appear to be attributing man's activities to climate change is obvs just a flustered gaffe. So let's ask about evolution now, shall we?

The portions of the Couric interview that have shown up in video clips display Palin agreeing that evolution is a serious scientific theory and should be taught that way, awesome. But then you read the transcript for the parts that are still on the cutting room floor:

Couric: Should creationism be allowed to be taught anywhere in public schools?

Palin: Don't have a problem at all with kids debating all sides of theories, all sides of ideas that they ever - kids do it today whether … it's on paper, in a curriculum or not. Curriculums also are best left to the local school districts.

Nice how she puts it off onto "the kids" to debate. But what we're hearing here, plain and simple, is "The nasty atheist Feds should get their mitts off our school curriculum, so's we can teach The Word of Our Lord alongside the librul science hoohah!" HMMMM.

Finally, I think that most scientists accept that homosexuality is an inborn genetic trait, like brown eyes or curly hair or, um, heterosexuality. Catch this from Palin:

Palin: But as for homosexuality, I am not going to judge Americans and the decisions that they make in their adult personal relationships. I have, one of my absolute best friends for the last 30 years who happens to be gay. And I love her dearly. And she is not my "gay friend." She is one of my best friends who happens to have made a choice that isn't a choice that I have made. But I am not gonna judge people. And I love America where we are more tolerant than other countries are. And are more accepting of some of these choices that sometimes people want to believe reflects solely on an individual's values or not. Homosexuality, I am not gonna judge people.

Yep, that's right. Them homos and their screwed-up "choices." God love 'em!

Not that we expected otherwise, but I thought you might like to have your scientist talking points together for your next cocktail party or swing state recruiting trip.

Link to the transcript.

Terminal terminology

All fields of specialized endeavor use jargon. It's not inherently a bad thing; we need to have short-hand ways to refer to ideas or principles that have developed over years of research.

There are obvious problems with jargon, like how it raises barriers to entry--you can't read the papers of the field until you get the jargon, but you can't get the jargon until you've read enough papers, etc.

But a specific problem we've had recently (writing this paper which had better go out tomorrow or I will shriek) is with a stock phrase which is standard in our field, but slightly inappropriate for our purposes. However, because it is such a standard phrase, we fear that trying to replace it would anger or confuse our reader(s).

The reason we were unhappy with this stock phrase is that it reflects the field's history, during which a lot of research was focused on certain easily studied preparations. We work on a different preparation, which operates under different functional principles than these "canonical" preparations. However, the language of the field has been shaped by the historical research, and is therefore vaguely misleading when applied to our own findings.

In fact, one of the arguments we're making in this paper is that not only is the language of the field biased, the thinking is as well. Many people have been so focused on the "canonical" preparations that they've neglected to recognize that greater biological diversity exists (or perhaps recognized but not embraced).

Anyhow, we took a few passes at coming up with a new jargony phrase, but the effort felt akin to inventing new wheel shapes, so we gave up. Not only would most scientists prefer to use the field-approved jargon, we doubted that we could even think up a truly accurate replacement phrase. (Although perhaps we could have found one that was less inaccurate.)

In the end, while we failed to revolutionize field jargon, the discussion helped me realize that some of the jargon we use conveys not only a concept, but also a whole contextual framework in which that concept is embedded; and that our ongoing use of jargon sometimes traps us in an outdated intellectual framework.

I bet this is the sort of thing the humanities people figured out in, like, college.

ps) physiologist bonus points for guessing the phrase. two words, one hyphenated.

The vision thing

Quarreling with Advisor over figures. The primary reason: Advisor needs reading glasses, but refuses to get them. Axis legends are usually in 8-point font. Hilarity ensues, or what would pass for hilarity if we weren't on a very very tight deadline:

Advisor: I just don't think that's going to photocopy well. [Meaning: I can't read it.]

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