Down time

I'm on a couple weeks' vacation. Blogging will be highly sporadic, especially as I am making the acquaintance of my new niece.

Story hour

When I was a lab technician for a couple of years post-college, I spend my weekends volunteering at Habitat for Humanity. (I had oodles of free time then, with a 9-5 and no spouse. What happened? Oh, right.)

Anyhow, I enjoyed swinging a hammer, learning about house construction, and getting to know the other volunteers. After I'd been volunteering for a year, the founder of Habitat, Millard Fuller, came to town for some speechifying, and the local chapter head asked me to give one of the short intro speeches to his talk.

I was terrified. As you may have noticed, I am very anxious about public speaking, even of this 2-3 minute stint in front of a ~150 person group. However, I am also too proud to let fear stop me from getting up there. The big question was, what to talk about?

I had started to craft a rather generic, "Seeing smiles of happiness from new homeowners blah blah blah" speech when my mother called. I told her about this short speech I had to give, and how I was nervous, and she said something both wise and obvious (the way mothers do): "Tell a story. Everyone likes hearing stories."

Now, my mother is a librarian, for pete's sake (as well as an astute observer of human foibles), so this was not a quantum jump on her part. But it really helped me figure out what to talk about. I scrapped the pablum and instead spoke about my first day volunteering and being scared to walk on the "roof," which at that point consisted only of trusses. And the audience, to my total shock, liked it, laughed in the right places, and applauded.

Then Millard Fuller got up, found me in the audience, and said in a wonderful admiring Southern drawl, "Jekyll--you're something else." He then proceeded to give a really good speech whose contents I have forgotten, although I'm sure he told stories.

Complete side tangent:
Later, as I walked Millard to his car, he put his arm around my waist. I was a little surprised when his hand slipped to a location that I might have called grab-ass had he been a boy my own age, but I chalked it up to old men being careless, or forgetting where young ladies' waists ended, or something like that. A year or two later, this story helped me realize that old men do not, in fact, forget where young ladies' waists end.

Back to the point:
It's old news in science that our papers and talks succeed the most when we tell a story. Sometimes it's showmanship, in the best sense of the word--framing the work in logical, climactic fashion rather than in a chronological, meandering mess. Other times it's really about finding the common threads to a story to weave a larger scientific implication out of some disparate bits of data.

I was thinking about all this as I prepare a short conference speech to give to, oh, ~150 people. I'm nervous, of course, but I'm focusing on the story, on capturing my audience with my supercool data held together in clean narrative arc.

Thanks, Mom. And thanks readers for your suggestions about allaying fear by focusing on the data rather than on myself.

After all, I have a whole blog to focus on myself.

And on the age-old paradox that even a guy who dedicates his life to helping those the poor might nonetheless be prone to some grab-ass.

Imagining images

In honor of Iran's Exxxtra FREE Missile!!111!!!1! and discussions over at DrugMonkey's about prettifying your data, I send you all to photoshopdisasters if you haven't been there before. (Variably NSFW, some of the funniest are soft-core porn with misplaced shadows etc.)

And, like, remember not to do the scientific equivalent (cut-and-pasted Western blot bands?) with your own data.

Trends in Book Reading (TiBR)

Looking over a bookshelf in our lab yesterday, I came to a realization: I don't read very many scientific books.

I dip into an occasional college/grad-level textbook if I have a two-minute question. But I don't read the books authored by senior scientists on (as drdrA says) "Poogly-plugs," although there are certainly a host of good ones. I'm worried about shelf life (literally!) of the science therein. Is it really better to read a book than to read five or six reviews in Trends or Current Opinion or whatever? By the time a book has been edited and published and distributed and purchased and read, isn't it scientific light-years out of date?

At the same time, I wonder if I'm missing something. If people are taking the time to synthesize the past, present, and future of their lifelong field into a (dense) volume, shouldn't I take a few days and read it, if I have more than a passing interest in the topic?

Also, these books are too heavy to take along on plane flights, so I can't bring them on vacation and ignore them the way I do with papers.

It's hard to carve out time to make a book a priority. But maybe I should?

Why do we say "Pee-yew"?

Last night, a skunk burrowed past some chickenwire to get into the crawl space underneath the place we are renting (or so we hypothesize). First there was a musky waft from the kitchen, the sort of nose-wrinkling but not unpleasant odor you associate with highways at night.

It was soon followed by a truly lip-curling stench unlike any I have known before. Dr Hyde and I variously identified it as rotting onions, burning plastic, and smoldering insulation before our landlord dropped by and assured us that this was Skunk.

We spent the evening turning on fans, opening doors, etc, and we slept in the guestroom, which was fortunately less pungent than our own bedroom. We don't know if the skunk(s???) is still in the crawl space, or for that matter what will happen if our semi-outdoors cat should encounter him.

Anyhow, the point of this post is that my jeans, which had been hanging in the bathroom to dry after laundering, have taken on the Eau de LePew. I spent today in lab, emanating odor. While this was distressing to me and, one may presume, to my colleagues, I must say that things could be worse.

Reasons to be Glad I Have a Lab Job When I Reek
a list I never thought I'd make

** Labs are well ventilated, with something like 8 full air changes per day. Thus my wafting skunkness is not encouraged to linger.

** While the lab has an open floor plan, we're not sharing office cubicles. The nearest person sits about 12 feet from me and is often not at his desk. So I have some space to fumigate.

** There are many smells in lab that compete with, if not dominate, my own. Mouse cages, bacterial growths, chemicals--heck, even Advisor's dog, in a show of solidarity, peed on a desk today. Malodorousness loves company!

If you're wondering, Dr Hyde gave me a useful idea that markedly improved my experimental setup, and that's why I am so cheerful in the face of our odoriferous misfortune.

Decisions, decisions

So I'm putting together a talk for Big Conference, and I am in rigid paralysis.

It's not the choice of this graph vs that, or which data to keep, or how much intro I need.

It's the elephant in the room: What color should the slide background be?

I'm almost paralyzed typing this.

White: standard (for everyone who blanches at the once-default powerpoint royal blue plate special); bright and contrast-y; but glaring, often too contrast-y, and a disaster if you have any dark immunofluorescence images or similar--the white background blinds your viewers before their eyes can adapt to darker hues. I don't actually have any of those images, but still--the whole Very Bright Screen in Kinda Dim Room thing bugs me.

(I write as I type on my laptop in the dusk.)

Dark: dramatic, but then you're faced with the question of whether to make all your graphs with white axes etc, or to put white boxes on the dark background and plop your graphs on there, which doesn't seriously annoy me but has a certain ad hoc quality to it.

JrProf, I expect you to take some time off your high-minded projects to address this quasi-sartorial dilemma.

Happy Congressional Recess!

A happy Fourth of July to you all. And a happy Independence Day to my fellow USA inmates.

Did you know that John Adams and Thomas Jefferson, two founders who kinda hated each other for a while, both died on July 4th 1826, the 50th anniversary of the Declaration of Independence? (Actually independence was declared on July 2 and the D of I signed in August, but let's not get all nitpicky here.) And both died thinking the other still lived, it being back before the days of Twitter.

David McCullough's John Adams, in which I learned this tidbit, was a bit of a hagiography but terrific reading nonetheless.

Enjoy the day. We, naturellement, are celebrating with Korean barbecue.

Picture this

Making figures of your research can be gratifying in the "Gee, when you put it all together like that it's kinda impressive!" sort of way. It can also be tedious in the "Criminy this is tedious" sort of way.

What aspect of figure-making would I term the tediousest, if I were inspired to abuse my mother-tongue? The candidates:

* Gathering together all the data that despite your best organizational efforts is scattered across three binders, two lab notebooks, and seven computers, one of which has a dead hard drive and another of which you've forgotten your special login/password combo for.

* Finding figure-quality examples. You know the data add up.....so how come no individual example is ever "representative"? A mystery for the ages.

* Scale bars. Even when you have the Photoshop file with pictures of your calibration slide, there is always some sort of problem: you've changed the resolution of your picture, you've montaged several pictures together and they're no longer the same pixelage, your old camera died and the new one takes slightly different photos and no one has updated the Photoshop calibration file....

* Realizing that you analyzed your older data differently from your newer data and you have to go back to re-analyze months of work. Yum.

* Trying to make 5 equal-sized graphs fit into a multi-panel figure. "Hmm, 2x2 +1? Or, um, 3x2 - 1? Fuck it, I'm creating an unnecessary graph just to make it all fit right."

Of these many options, I surely loathe scale bars the most. Because even when you've gotten it all finished, you print out the graph triumphantly and then think...."That's odd, there's no way in nature that that object could be that size. Ohhell."

30 published papers can't be wrong!

Recently I happened to see a reviewer's comments on a manuscript submitted to a good journal (not my manuscript, and I didn't help review it either). The review, heavily paraphrased, went something like this:

"The authors show evidence in favor of a strange result.

"The evidence per se isn't bad; however, many respected labs do the same type of technique as these authors, and the respected labs don't see these results.

"Ergo, Strange Result is likely the result of inexperience or idiocy on the authors' part.

"Vote to reject."

I am of mixed feelings about this. On the one hand, this is the sort of dismissive attitude that makes it difficult for revolutionary research to get published in good journals. It contributes to the do-safe-research-with-expected-results mindset: if your research turns up something too novel, you can't even publish it!

On the other, I think the reviewer might be right.

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.