Hot pockets of research

In the last couple of years, my subfield of bio has seen the arrival of a new generation of tools for studying stuff. These CoolTools have been developed by a few different labs and address a major lacuna in currently available techniques.

Because the CoolTools are revolutionary, every job talk in my field now ends with these future plans:
--I will continue the stuff I published on during my postdoc.
--And I'll use CoolTools too!

I'm not mocking the job candidates. If I were on the market, I'd sure be talking about CoolTools as well.

I just sort of miss the days when the "future plans" section of a job talk actually stood a chance of surprising me, rather than being about the Cool Bandwagon. Once upon a time, when a job candidate came to speak, what distinguished the Really Exciting from the others is that the future plans portion of the talk would set out the start of a research program that no one else was doing: a new niche, a new approach.

But now everyone's got a new approach--it's CoolTools! End of talk! And I think it's gotten more difficult to evaluate the candidate's creativity and originality as a result.

That said, CoolTools are really physioproffing cool.

Stupid is as stupid does

I would estimate that I spend ~90% of my day feeling stupid.

A colleague asks a question about something I think I should know; but I don't know. A colleague asks a question about my own work; I don't know. I get a strange bit of data and don't know whether it's meaningful or fluky. I spend a whole day perseverating with some solutions that I later realize I should have changed.

So it was heartening to read "The importance of stupidity in scientific research" by Martin Schwartz. GradAdvisor had printed the article for the lab to read. You'll need a subscription to get the pdf, but here's the opener:

I recently saw an old friend for the first time in many years. We had been Ph.D. students at the same time, both studying science, although in different areas. She later dropped out of graduate school, went to Harvard Law School and is now a senior lawyer for a major environmental organization. At some point, the conversation turned to why she had left graduate school. To my utter astonishment, she said it was because it made her feel stupid. After a couple of years of feeling stupid every day, she was ready to do something else.

I had thought of her as one of the brightest people I knew and her subsequent career supports that view. What she said bothered me. I kept thinking about it; sometime the next day, it hit me. Science makes me feel stupid too. It's just that I've gotten used to it. So used to it, in fact, that I actively seek out new opportunities to feel stupid. I wouldn't know what to do without that feeling. I even think it's supposed to be this way.

He goes on to say that science is so infuriatingly difficult for a good reason: we're trying to find answers that don't already exist. That's the basic way in which research is different from even very hard classwork. He further suggests that we should do a better job of educating students about this difference, and of helping them accept that feeling stupid was not a bad thing but instead a good sign that you were pushing on the unknown.

Interesting stuff, take a look if you have a chance.

See also: lizards

Two-inch roach that the cat catches in the bathroom at 4:30 a.m. then plays with until it's flipped over but not dead?

Thank you, Dr Hyde.

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ps) I did some spring cleaning. If you're looking for a particular post and can't find it, email me.

On lizards and marriage

GradAdvisor once made a comment that I'll paraphrase:

"The problem with marriage is that even if you are two like-minded individuals who are not strongly gender-stereotypical, as you live together it will become clear that one of you has a slightly greater preference for certain tasks. Because there are two of you, whichever one is more engaged by something, no matter how slightly, will end up doing it. The problem is that these marginal affinities often do fall along gender lines, and then you end up in the stereotypical gendered-task marriage, even though neither of you is very gender-typical yourself."

A less abstract way of saying this: if I were living alone, and the cat caught a lizard and brought it in to play with, and it was scampering across the floor--I would get a glass and pick up the hapless lizard and chuck it outside. But since Dr Hyde is somewhat less disturbed than I am by the sight of a stumpy-tailed lizard running across our living room floor at 7:30 a.m., the lizard disposal job falls to him. I stand by and wave my hands and make squeaky noises.

(This was not an entirely hypothetical example. Next time, Cat, kill your damn lizard.)

Another good example is driving. I enjoy driving, most of the time, and I think I'm pretty good at it. But when Dr Hyde and I are getting in the car, he grabs the car keys, because he wants to drive. I don't particularly care whether I drive or not. Over time, this means that he drives far more frequently than I do. Meanwhile, I coordinate the grocery shopping and the cooking. Not exactly a gender-transgressive setup.

Sometimes this makes me a bit frustrated, especially when Dr Hyde tailgates the car in front of us. Fortunately, though, I'm aware of the dynamic and that helps me calm down. I know that if riding shotgun is irritating me, I can ask for the keys more often.

It's a stretch from here to lab life, but I'll give it a try. Mad Hatter recently posted about collaborating with folks who are outside her normal field:

So I spent most of the meeting just trying to keep up with the discussion. And I did...barely. I now have a decent understanding of the entire process, which is an improvement over my previous state of befuddlement.

But understanding the project is a far cry from being able to come up with good ideas for how to accomplish the project's goals.

To which I say: It's ok to operate outside your comfort zone! Don't leave the thinking to people who seem to know more about the topic than you do.

Grab that lizard!

Judging by appearances

JuniorProf has a great post up about graphical presentation. His point is that appearance and aesthetics do matter, because they help to convey professionalism and high standards. He's certainly right about that.

However, he's also right about something else he mentions in his post: that it takes time and effort to learn the programs that will let you create high-quality schematics (Illustrator et al). With the 1.4 million (approx.) other things that scientists need to spend their time on, should graphics programs be yet another?

One of my friends says that a research institute in our field employs real live graphical designers whose job it is to take your data or your sketched ideas and turn them into clear, attractive graphics. My friend, who is in the middle of putting together figures for his first paper, and attendant cursing, said that our school should do the same thing.

I can see the appeal of this, although I wonder if it turns into just one more job you need to administer that might be a bit faster to do yourself. The simple problem is that YOU are the best person to evaluate what's important in a graphic and what's expendable; what you want to highlight; what the field standards are for a given type of graphic; etc.

The other qualm I would have is that it's often useful to have nice-looking graphs before you have every last data point. I'm probably going to have to redo a couple of graphs for a paper we're on the verge of submitting because I'm going to get one missing data point. But we didn't really feel that that data point was missing until we made nice graphs and wrote the paper...

Much of my training in aesthetic design comes from Edward Tufte, whose marvelous examples of good and bad graphs guide my thinking. Although it takes me time and effort, I can create reasonably good-looking graphs (though JP has a point, schematics are another big leap).

Anyhow, to me it sounds like a hassle to have to explain to graphics designers how to draw your schematics. I'd rather have a savvy undergrad or tech do this for me. But perhaps some of you have experienced your own real live graphical designers and disagree?

Asking for it

GradAdvisor and I (along with a couple of middle authors) are getting close to sending out a manuscript. One of our regular bouts of discussion goes as follows:

Jekyll: There's also this other experiment that we could do before we send it out.
GradAdvisor: Hmm, yes, what are you thinking about that?
J: Well, I don't honestly think it will add much if anything to our conclusions.
GA: So you don't want to do it?
J: Eh. I'd rather let the reviewers ask for it.

In other words, there are a few experiments that I full well expect to be asked to do. They're not particularly hard experiments, and many papers in my subfield include some variation of them, although I don't think they'll add much to the big picture.

But if I expect a reviewer to ask for them, then why not just go ahead and do them now?

Well, it's my (paltry) experience that reviewers like to suggest experiments. It makes them feel like they Did Something in review. Some reviewers only request truly relevant experiments, but lots of scientists will ask for an experiment that doesn't seem germane. I wonder if that's sometimes just to show that they really read your paper. (Or, more cynically, that their postdoc really read your paper.)

Hell, I've helped review papers. I do the same thing. It's a little power trip--"Hey, I can make Fancy Lab run an extra control!" And it feels good to suggest an experiment--it's a little warm glow of, "Fancy Lab might be all fancy and such, but I, Dr. Jekyll, came up with a Good Control for them to do. Hot diggity I must be smart."

Anyhow. Maybe that's just me. Point is, there are a couple of experiments I know we'll probably be asked to do but that I'm intentionally not doing yet--so that the reviewers can get their glows by asking for an easy experiment.

Because if we do all the easy ones now, they'll ask for a hard one.

I can't believe I'm quoting Reagan

I recently heard the traumatic tale of a local new-ish (read: untenured) lab. They'd written some code for acquisition and analysis of their data, and one of the grad students, poking through it one day in confusion over his analysis, realized that all of the analysis this lab has done for the last THREE YEARS has been wrong.

They had to scurry to retract a submission at a high-profile journal (fortunately not yet sent out for review). And now they have to reanalyze Everything.

This is awfully scary, but there are a few silver linings:
1) It was just the analysis code, not the acquisition code. You can reanalyze data, but you really don't want to have to re-collect it.
2) It turns out that many of their conclusions are not seriously affected by this reanalysis. Phew.
3) The grad students in the lab are all learning a Very Useful Lesson about homewritten code: Trust, but verify.

We had a similar, though not as earthshaking, incident in GradLab. I had to reanalyze half a year's worth of data, though happily the inaccurate parameter was not very important for my research. I was furious about it--had a giant argument with my GradAdvisor about the situation, was grumpy for a full week, etc etc--but I sure did learn Lesson #3 above.

It's not just code, either. Another postdoc's solutions? A friend's summary of a paper? A colleague's bench protocol? Heck, even a significant result in a published article? Trust, but verify.

Fear of flailing

I'm slowly putting together the conference talk I'm giving this summer. As I do, something curious is happening. I'm arranging my figures, trying to decide on the best way to show my data (definitely NOT the exact same graphs we have in the almost-out-the-door manuscript....everything needs to be clear enough to digest in 10 minutes).

And as I do, I'm saying to myself, "Hmm, this graph looks good but it'd be really nice if we had one more data point to extend the range a little further and help tie it in better to the next slide." Or, "Gosh, someone might ask me whether we've ever tried this experiment under Other Conditions, and so maybe I should pop into lab and check that out."

What's funny about it is that the experiments I'm thinking of are the same ones Grad Advisor has been asking me to do for a loooong time. I've been putting her off, because the experiments in question didn't seem particularly critical to me.

But now that I'm the one who will be standing up in front of an audience of Very Important Scientists, I'm suddenly inspired to scoot back to lab and get these data.

Wacky, huh?

Label it another reason why it's good for grad students and postdocs to make platform presentations at conferences, rather than just posters. There's nothing like the fear of hand-waving your way around inadequate graphs to get you to run a few extra experiments....

Things I learned in grad school, part 3: Reading

Papers make me feel slothful. I print them, I try to read them, and then something else catches my attention (email! labmate with new data! teatime! bug on ceiling!) and I cast the critter aside.

Ok, so that's a bad trait. However, since I know about it, I came up with a clever way to force myself to read more during grad school: invite some friends.

From second year through sixth, two like-minded friends and I got together every week or two to discuss a selection of papers. Beforehand, we would pick a topic for the week and email around a few suggestions of what we could read. Usually this meant that one or more of us Pubmedded the topic and chose a few papers based on titles/abstracts. The other two would comment on the list, and we'd whittle it down, typically to 2-3 original papers plus one review.

Inspiration for topics sprang from various sources, but the common ones were:
--New Hot Paper on something piques our interest in the history and background of that topic
--Seminar speaker says something intriguing that we don't understand
--A term or concept frequently gets batted around in our labs or journal clubs, and we always look wise and nod without knowing what the hell it really means
--One of us needs to learn something new for our own research purposes and somehow persuades the other two to help

Then we'd get together for coffee, intellectual discourse, and general raillery. We usually went through each paper figure by figure, talking through the logic and helping each other over the rough spots.

But Jekyll, you say, how is this any different than the journal club I go to every week? Well, if your journal clubs are anything like mine, one person has read the paper for discussion plus a few others and gives the whole presentation; the rest of the attendees have possibly not even printed the paper up for discussion, and can zone out if they're sleepy. It's also a fairly passive way to learn science--having it presented to you.

Since there were just three of us, no one could opt out or be lazy. We always read a group of related papers so that each paper provided context for the other two, which helped us understand the issues at hand.

Most importantly, at the start of each paper session we would gossip about our friends, PIs, labwork, and anything else. That made us happy, it kept the meetings friendly and entertaining, and it gave us all a chance to help each other with lab issues (we were all in different labs). So although we were being nerdy, we were also having fun and becoming good friends.

I've recommended doing something like this to some of my younger grad friends, but none of them have created their own sciencecoffeeklatsch, to my knowledge. Maybe it's not for everyone, but it sure helped me learn a lot about my subfield. I've forgotten a lot of what we talked about over the years (hint hint, PhysioProf: you were going to blog about retaining what you read?) but the context and general knowledge about the field (Prof So-and-so works on X, Prof Such-and-such is a careful scientist, etc) have been invaluable. And it kept me intellectually limber to read work outside my lab's turf. So I'd recommend it if, like me, you're feeling asea in the ocean of papers out there.

How do we make any money? Volume.

Despite working all day Saturday, as well as today, I have no more data than I did at the close of Friday. Data-less days are depressing, but one of my grad friends had a coping mechanism (besides alcohol): she referred to them as deposits into the karma bank.

The karma bank, you see, operates on sort of a mash-up of the principles of Samuel Goldwyn--"The harder I work, the luckier I get"--and the Beatles--"The love you take is equal to the love you make." So, working all day on the weekend for absolutely zero return: that's a deposit into the karma bank, which will then repay you with golden figure-ready data on some hapless Wednesday when you only have two hours to do experiments and you're half checking your email anyhow.

I am not sure who runs the karma bank, but I sure wish they'd post their interest rates.


p.s. For some reason, the idea reminds me of the famous SNL "change bank" skit.

+1, PI

I finally told my Advisor.

We went out to dinner with a visiting prof and a few other scientists, and during appetizers Advisor asked me and the other graduate student there whether we wanted kids or not.

[Ignore that his question could be considered invasive or even actionable. It was clearly intended kindly.]

I had had a drink or two, I was PMSing, and we had recently learned what the whole bizarre-o IVF protocol would entail. It took every ounce of self-control to reply calmly, "Sure, at some point," to which Advisor said, "I have to say, I think the best time to have children is during the post-doc." Must. Not. Cry. Must. Not. No.

A couple of days later, I decided to let Advisor know that Dr Hyde and I do indeed want children very badly, and that our options have narrowed to IVF or adoption, and that we were planning on trying IVF in the fall, and furthermore that I was sorry if I'd seemed less than totally engaged at work, but that I was struggling to stay focused despite the gnawing stress.

It all came out in a run-on sentence like that, too.

Advisor was very kind, said that he was happy with me and with my work, and furthermore that he had several friends who had "beautiful babies" from IVF. And that he totally supported us and if there was anything he could do to help with health care or whatever, he would do it. For whatever reason, kindness derails me even worse than rudeness or indifference does, and I watered up but didn't quite let loose the tears, mumbled some thanks, and rushed outta there to cry in the bathroom.

I hate being female, at these times. Crying feels so goddamn weak-assed, but I am often unable to prevent it. It must be hormonal, since I've heard transgender people comment that they always cried when they were female but never when they were male. And it's killer embarrassing in any professional situation, especially a male-dominated one--but knowing it's embarrassing and unprofessional just makes it that much worse.

Despite the near-waterworks, I'm glad I told Advisor what was going on. He would have to know sooner or later because of the incessant doctor's appointments we're planning in the fall, but I elected to tell him earlier because I have felt that at work I'm not as focused or as steady as I should be, primarily because each experimental setback feels like the end of the world and I'll never have kids!! rather than just, Oh hell, another experiment went up in smoke. Fortunately, either Advisor hasn't minded my spaciness or I've covered better than I thought.

Anyhow, to sum up: Advisor was awesome; I'm relieved; now it's easier to focus at work; I hate that I cry so easily.

Critical and criticaller

I've been musing lately about critical thinking in science. (Duh, it's totally important.) What interests me is the friction between open-mindedness and realistic thinking.

If a trainee shows up in your office brandishing a humorously unlikely hypothesis, what should you do? Do you exert your critical thinking skills and explain calmly how patently implausible this idea is? Guide the trainee down that same path? Or do you entertain it seriously for a while, long enough to see if maybe your reflexive "no way" was too hidebound, too rigid, too establishment?

I've actually been thinking about this because of the reverse situation: GradAdvisor proposed, to another grad student, an experiment that I found laughably naive and uninformative. The idea was dropped. Six months later, I find myself suggesting the exact same experiment. Better framework, new interpretation, but still--the same experiment.

I can't decide if I was wrong to shrug off GradAdvisor's original suggestion. I think I was wrong to dismiss it so quickly. Still, at the time the rationale for the experiment was piss-poor, and consisted largely of "Whaddya think would happen if we looked at this other pathway?" My rationale for renewing the idea was much better defined ("This experiment would tap into the bigger question of whether these two pathways are really different"). But I doubt I would have come up with this experiment if GradAdvisor hadn't suggested it in the first place. So: if I had taken this idea more seriously six months ago, maybe we'd have hashed out the rationale then and there'd already be data.

It's difficult to keep an open mind about experiments when you're simultaneously trying to prioritize among several plausible lines of research--who wants to think about the implausible routes? Put another way, how do you filter out the useless off-the-wall approaches without also filtering out the useful off-the-wall approaches?

Probably another reason why it's good to be sharing your data with smart folks on a regular basis--it's sometimes easier to think creatively about a project you're not emotionally invested in....

Blogoviation

What do I know about politics? I'm a goddamn biologist. But it's my blog.

Forthwith: Dr Jekyll's uninformed and unrealistic Obama veep handicapping! Alphabetically!

% is the likelihood I give it of happening. Mind you, I am (a) whimsical and (b) soused.

Name	Pro	Con	Note	%
Joe Biden	Thinks Obama is clean and articulate.	Says so.	Mega-gaffer = mega-fail, no matter what foreign relations committees he's on.	1
Wesley Clark	Wins both anti-war libs and military types	No governing experience	No election know-how = fail points	5
Hillary Clinton	Wounds--we heals them!	Inspiring get-out-the-vote....for the 'Pubs.	Michelle says no, and I sure as shit wouldn't cross her.	2
Chris Dodd	Foreign policy wonk; reassuringly white	Carries the critical swing state of C "the middle C is silent!" T.	Have you no sense of fun?	2
Chuck Hagel	Crazy bipartisan pick overshadows even McCain- Lieberman!	Crazy bipartisan pick descends into its own special level of infighting hell!	Double super bonus points: opening up a Senate seat in the Republican incumbent column	3
Claire McCaskill	White female senator of swing state	First-term senator of said state	“If I were asked, I would ask some mental health professionals to visit Barack Obama. I just think Sen. Obama is way too smart to pick me."	1
Bill Richardson	Popular Latino governor of swing state knows his ambassadors	Also knows his ladies (h/t BikeMonkey)	We're sooo postracial now. Wait, not that postracial.	15
Kathleen Sebelius	Lady guv'nor of crimson Kansas holds bipartisan appeal	Kansan foreign policy: Visit Oklahoma!	She's nearing the end of her second term....Magic-8 says O-yeah!	30
Ted Strickland	O, hi, Ohio!	"Vice-Presidential" and "sing-along" aren't usually in the same sentence	Patent ploy for swing votes is very 2004	1
Jim Webb	Neutralizes McCain's veteran advantage and pulls in the working class. Foshizzle!	Might turn off the wimminfolk; might bite a reporter	Veep debates against any pansy-ass Pube would be Most Fun EVAH!	25
Out on his own	?? ??	?? ??	Obama's good at flouting the conventional wiz. Look for a surprise* none-of-the-above.	15

* And by "surprise" I don't mean "Ever Bridesmaid Evan Bayh."P.S., check out the McCaskill link for some more entertaining Senatorial responses to the question “If you were asked, would you accept an offer to be the VP nominee?” I'm personally fond of Ted Kennedy's “I plan to stick with my current job until I get the hang of it." A tip of the beret to Radar.

Sunshine policy

PhysioProf recently posted over at DrugMonkey about his method of encouraging lab communication--everyone emails a weekly update to the lab about their recent progress and upcoming plans.

I like this policy, in part because it reminds me of how, when I was a lab technician, the PI ran lab meetings. He was a more advanced prof, secure in tenure and lab-head duties, and he visited the 8-10 person lab regularly but was not intimately involved in experimental carry-out.

In order to keep communication lines open, he had a wonderful habit of going around the room at the start of lab meeting, saying something like this: "Pete, your project is going great and we agreed you'd have figures for us to talk over by--what'd we say, Friday? Carol, you gave me a draft of your paper yesterday and I will have it back to you by Thursday with comments. Jen, I know you're hitting some complications with experiments; let's sit down together after lab meeting and walk through things." etc, etc.

This was wonderful for three reasons. First, it made everyone--including him--publicly accountable for their progress. He hadn't just said to Carol that he'd have read her manuscript by Thursday--he'd promised it in front of the whole lab. Similarly, it wasn't only Pete who knew he was supposed to be working on figures.

Second, it helped to verify that he and each lab member were on the same page about their projects, eliminating many a crossed wire. ("Oh, you meant this Friday? Ok then.")

Finally, it fostered a sort of sunshine policy on lab management. While the labbies still gossiped about the PI periodically, there was much less opportunity for gripefests. You didn't need to complain to your labmates that you'd given the PI a manuscript but had no idea when he was going to actually read it; you (and everyone else) knew what the PI's stated plan was.

Of course, none of this would have mattered if it weren't that the PI was also outstanding at follow-through. When he said he'd read your paper by Thursday, he generally did so. But I do think his manner of making the whole lab aware of each person's plans was beneficial to lab running. I hope to copy it one day.

Also, don't breathe the air

When I first arrived in my postdoc lab, I had to figure out all the usual newbie things--how do we order stuff, where are the Kimwipes, etc etc. One of my questions was: Where's the drinking water? In GradLab there had been a common kitchen space for several labs that included a filtered water source, and I assumed a similar space existed in NewLab.

To my shock, I was told that most people just drank the deionized lab water. For those who aren't familiar with biomed lab water sources, there are often 3-4 of them: tap water, which is often industrial water and therefore unsafe to drink; deionized water, which has been run over a resin or something to remove mineral content; and double distilled water, which is extra super clean and used in applications where you want complete control of ionic content; and RNase and DNase free water, which is for molecular applications.

Now, I might argue against drinking dI water on basic principles that water ought to have some minerals and other goodies in it. But the lab dI water in particular: we also use that sink--and even that water source--to wash off all manner of lab equipment: dirty or even bloody tools, beakers that once contained various drugs, etc. I don't even want to think about what may have splashed back onto the tubing the dI water runs through. I certainly don't want it in my tea.

It turned out that there was a normal Arrowhead water supply around, it just involved exiting the lab, going downstairs, and turning a few corners. Ok.

But the entire episode left me wondering: why was I so appalled by the idea of drinking lab dI water, while my labmates (including Advisor) were so blase? Are they filthy idiots? Am I Miss Priss? Do people in other labs drink lab water? Or add lab sucrose to their coffee?

I don't know the answers to these questions, but I do enjoy the health benefits from jogging downstairs a few times daily for my water.