Managers ?= cleaners

Our lab is looking to hire a new lab manager, and it turns out that there are differing opinions on what a lab manager's job includes. Some lab members say that it is a lab manager's job to keep the lab clean, including (but not limited to) washing glassware that has been neglected in the sink, wiping down the lunch/conference table daily, tidying the tool bench, and cleaning shared lab benches. Others say that lab members should be responsible for these cleaning duties, and the highest priority in hiring should be administrative excellence.

There's a third way to look at it, which is that if your lab manager is young and inexperienced, cleaning comes with the turf; but if you have an experienced manager, best not to waste his/her valuable time on menial tasks. (Also perhaps an older, wiser lab manager knows how to get trainees to clean up after themselves?)

What say you? There's a poll on the right...

Defending the gates of Journal X

I recently served as a reviewer for a journal. This was the first time I myself had been asked to review, so I was both excited and a bit nervous. Would I have useful things to say? Would it be difficult to assess the paper's suitability for Journal X? After all, it's one thing to aid your advisor with a review, but it's another to be the only person evaluating the work.

The manuscript seemed to me to be a clear reject. And here was the funny thing: I had thought that in the event of a reject, I would feel righteous. Like I was defending the Journal from shoddiness. Like I was a bulwark against the frustrated feeling you have when you read a bad paper in a journal you respect.

Instead, I mostly felt sad for the authors, even though I don't know them. I kept twisting their data around in my head, trying to find a way they could revise the manuscript with just one or two experiments so that it would be publication-worthy. "What if....? Hm, no, that's still not going to cut it. Or perhaps...? No, that would turn it into a totally different manuscript." In place of righteousness, I felt regret that I could not rescue this effort from the reject pile.

I doubt any of this regret came through in my review, though.

-----

ps. Ten bucks says CPP tells me to sack up and quit having emotional responses to fuckwad manuscripts, amirite?

Birth part 2: the bit with the hollering

Into the birth center, where the midwife checks me out. Bad news. Small has a fetal arrhythmia--a hiccup in his heartbeat.

We'd known this was a possibility. He'd had the same hiccup at his last prenatal checkup, and though the midwives were pretty sure it was trivial--the sort of thing that often resolves at birth--we were scheduled for a fetal echocardiogram to make sure. But the echo doctor was out of town and couldn't see us until two days before the due date--and here we were, in labor five days earlier. The midwives had warned us that if the arrhythmia was present during labor, we would have to be in the labor and delivery ward, not the birth center, so I'd willed the hiccup to vanish before then. To no avail.

Ok, we'd known this was a possibility, so down to the L&D. Except, no. L&D had no rooms open. One room was being cleaned up, would be ready in twenty minutes. So, now tethered to the damn external fetal monitor and IV I'd hoped to avoid by being in the birth center, we waited.

Ever waited through a hospital's "twenty minutes"? Two hours passed. The contractions were strong; I was encumbered by the monitor, which slipped if I moved too much, and I felt unable to get up and move around. Sitting across the room, taunting me, was the lovely large hot tub I had been fantasizing about. Full of water, even. Our bathtub at home hadn't been deep enough to submerge my giant belly, and all I wanted in the world was to get into a deep hot tub.

But instead, there I sat with Dr Hyde, the doula, and intermittently the nurse and midwife on duty, waiting. It was like sitting on an airport tarmac. You can't open your laptop because you're not in the air yet. You can't fall asleep because you're anticipating take-off. You are penned into your little seat and aren't supposed to get up. And you wait.

I couldn't settle into labor--my body knew that we would be moving, any time now, and so it sort of went into withdrawal. Not that the contractions stopped! Ha ha, no. But they stopped accomplishing anything. The midwife said my cervix was only 4-5 cm, a crushing bit of news, since it'd been hours since my doula had said the same thing. I dozed a bit more, as did everyone else--I remember waking up for a contraction and being a little affronted that both Dr Hyde's and the doula's heads were lolling back in their chairs. If I am in pain you should be, I don't know, witnessing.

Finally, finally--now about 4 pm--we were moved down to L&D. It was 20 hours into labor, and I was exhausted and cranky. Still only 5 cm. Well if there's one good thing about being in L&D, it's DRUGS. And I wanted some, pronto. If I had to put up with hours of waiting and NO GODDMAN HOT TUB, I was sure as hell taking the one recourse available to me.

Doula D asked, "Do you want an epidural, or do you want a short-acting narcotic?" she asked. "Because if you have the narcotic and you want more, we can always go to the epidural, but once you have the epidural, you can't go back."

So I had a dose of the narcotic Nubain, and then another when the first wore off. It took the edge off the pain and made me quite sleepy--we were back to dozing between contractions. The sleep was good because I was so exhausted (the night before I went into labor I had slept uncharacteristically poorly, and obviously the night of labor hadn't been real restful either). All told, I spent four hours under the influence of Nubain, but alas, the labor made little progress--I was only at 5-6 cm. So that was the end of the Nubain (and you're not really supposed to take it late in labor anyhow due to its effects on the baby).

8:30 pm, 24 hours into this. How to get labor moving again? My midwife had an idea. "We're going to break your water, ok? And everything's going to get more intense--are you ready?"

I peered at her through the haze of pain and fatigue. She couldn't possibly be expecting a hearty assent, could she? I was already miserable, and she wanted me to say, "Yes, please make this worse"?? (Also, was there a choice?) I gave some sort of sullen acknowledgment that she had spoken, the way that as a teenager angry at my parents I knew better than to say "ARE YOU FUCKING KIDDING THAT'S A BAD IDEA" but still had to make clear that I was Not On Board with their plan of going to the farmers' market at 8 am or whatever.

So they broke my water. It felt as though my body was a bathtub and the drain had just been opened. "AAAAAAUUUUURRRRGGGGHHH," I said. In fact, from this point forward you should assume that I was saying something like that nearly nonstop unless otherwise specified.

I couldn't believe the volume of fluid I was disgorging. It felt like I was creating my own personal Slip 'n' Slide, and hurtling down it at Mach 2. Also, pain. The stage of labor from 7 to 10 cm is called "transition," which I now understand as meaning that you will "transition" from a comparatively normal adult in significant amounts of pain to a crazed animal unable to see straight.

The next couple of hours are pretty hazy. I was panting so shallowly that my blood oxygen kept dropping, necessitating yet another damn sensor, this one a finger clamp that monitored blood ox. Periodically someone would tell me that I needed to breathe more deeply to keep my oxygenation up, which never failed to puzzle me because I was breathing LIKE TWENTY TIMES A SECOND LIKE A GODDAMNED MOUSE so how could I be out of oxygen, but I cooperated nonetheless, or at least I think I did.

Time passed. Dr Hyde says that the nurses and midwives changed out the sopping wet bed pads underneath me, but all I remember is the sensation of my toes going squish underneath me whenever I moved. At some point I asked whether it was the pushing phase yet, and someone asked me if I felt like pushing. Instead I felt like dying, which made it difficult to assess much else.

"You're doing great!" the doulas kept telling me. This was so patently false that I was irritated. Pretty CLEARLY, I was hollering at full strength, ergo NOT SO GREAT. But this seemed so obvious that I hesitated to point it out.

10 cm! Only 2-ish hours after they'd broken my water. But a new problem: every time I pushed, the baby's heartrate dropped low. After a few rounds of this, my midwife announced that unless we could get the baby out within 45 minutes, she would have to call in the obstetrician for possible vacuum / forceps / Caesarean.

The doulas helped turn me around so I could hold onto the raised head of the bed for support as I knelt on the (still squishy) lower half, both to accelerate the process and in the hopes that a position shift would fix whatever was causing the rate drop. Still his heartrate decelerated when I pushed. My right leg was pulled up so I was half kneeling, half squatting. Still the heartrate dropped. They decided I should switch to left leg squatting, right leg kneeling. I had had about enough of this, and, in a brief moment of clarity and coherence, much as you might experience during severe drunkenness, said politely, "Actually, I'm ok like this."

They all laughed at me (in my memory, probably not in reality) and said, "It's not for you, it's for the baby!" FUCK THE BABY, I did not say, instead shifting my weight. Still Small's heartrate dropped during contractions.

So now the pressure was on to deliver the baby asap. My hollering had shifted to more of an "OWWWWW" sound. Doula S stood by my head, next to Dr Hyde. "Ouuut," she urged me. "Ouuut."

I could do that. I wasn't hollering OW, I was chanting a fucking mantra! "OWWWWWWWWWWTT," I said, enunciating the final T like I was in goddamn singing class. See? Not a cry of pain. A mantra. A mantra that could be heard two miles away.

I did some pushing. It wasn't apparently doing very much. Doula D uttered the following words of wisdom: "Are you feeling rectal pressure?" (YES OH YES) "Do whatever makes that pressure the strongest and most intense."

This was the clue I needed. What's more, it helped me focus on the sensation of pressure, as distinct from the pain. Delivering a baby I didn't know how to do, but pooping seemed (barely) within my competency. And that was exactly what it felt like--taking a 7 lb poop, with 8 or 10 people cheering me on (Small's arrhythmia and heartrate had brought an entire NICU team into the room on standby).

Within half an hour, Small had emerged, his hollering picking up where mine left off. The cord was wound around his neck and stomach, but not in such a way as to cause harm. And as soon as the doctors could listen to his heart--not a single arrhythmia to be found. He was as healthy as they come.

Oh but there's one last step! The delivery of the placenta. Pushing something else through my vag seemed like the worst idea anyone had ever had, and the midwife's cheery "Don't worry, the placenta has no bones!" was not in fact reassuring. If someone had offered me an epidural right then, with Small over on the warming table, I would have taken it. In fact I was contemplating requesting a Caesarean. But out it somehow went.

And then they brought over Small and he headed right for my breast as though he'd been doing it for years.

Query

Manuscripts sent out for review may state explicitly that the referee should destroy the manuscript after review. Presumably in this day and age, that would mean "delete the PDF." Does anybody actually do this?

Labor lasted 27 hours so you're damn right it's a two-part post

One tends to hear a lot about pregnancy--the morning sickness, the swollen feet, the constant bathroom trips--but much less about labor and birth. In part this is because birth is a private act, while pregnancy is performed publicly, but in part it is because falling birth rates and delayed childbearing reduce the exposure we have to women giving birth.

In academia, with its further fertility delays, these effects are exacerbated. I was in my late twenties before any of my close friends or relatives gave birth. At the time we got pregnant, I had perhaps heard more about the problems of fistula in impoverished African women (thanks, Nick Kristof!) than about the process of giving birth in upper middle class America.

After I gave birth, I discovered that many of my friends really wanted to know details, but they were sometimes reluctant to ask. Commonly, a group of labmates would hover until someone managed to ask the question--"Did you have an epidural?"--and then all heads would swivel, waiting for the answer. I think both the curiosity and the reluctance to ask are symptoms of how little many of us hear about this basic physiological process. Mainstream depictions tend to focus on the pain, often (e.g. Kirstie Alley movies) for comedic effect.

During pregnancy I found women's stories as reported in a few birthing books (Birthing From Within; Ina May's Guide to Childbirth) to be more helpful than the more clinical presentation of, say, What to Expect When You're Expecting, or the (truly awful) Your Week by Week Pregnancy. As Birthing From Within author Pam England puts it: Millions of women have given birth; how can there be only one right way to do it?

So here's my version, for Arlenna, for other pregnant readers, and frankly for anyone who would like a little demystification of this secret act. Consider it the happy finale to the IVF series.

The first surprise was that it was early. Conditioned by friends and relatives that first babies are generally late, I was expecting an early September arrival for our late August due date. (One nice benefit of IVF--you don't waste time speculating about the accuracy of the dating!) One week prior to the due date, I was happily planning an upcoming week of analysis. As I left work, my advisor called out, "It could be any day now!" and I laughed at him as I walked away.

So that night, while eating the zucchini, tomato, and pancetta pasta that Dr Hyde had prepared, I was nonplussed to feel some cramps. Unlike Braxton-Hicks, the painless if sometimes intense contractions that had been constant companions in the third trimester, these cramps were mildly painful, like minor menstrual cramps, and reached all the way around both belly and back. "Just early contractions," I thought, "probably irregular and will go away." Regular contractions spaced five minutes apart is considered the threshold for visiting the hospital, but most women start out with irregular contractions 10-15 minutes apart.

But after dinner, just to see, I started timing them. Six minutes from the start of one to the start of the next. Then six minutes for the next. Six minutes. And, hmm, six minutes. I called my doulas.

A doula is a woman who accompanies you throughout the process of labor and childbirth. Unlike a nurse, midwife, or doctor, she will not leave when the shift changes; nor will she (necessarily) participate in any medical evaluation or treatment. Her role is to support and encourage the laboring woman and her partner. A doula's presence significantly reduces the rate of Caesarean birth, epidural anaesthetic, prolonged infant hospitalization, rate of forceps/vacuum usage, length of labor, etc. etc. [1, 2, 3]. (Also, more breastfeeding [4].) In other words, doulas are good for women and babies.

Our hospital offers volunteer doulas, pending availability.However, I wanted to meet a doula ahead of time and make sure I liked her. How to find one?

There are websites where you can search for local doulas, but I found mine in an unorthodox manner. The woman sitting next to me on the bus one day had a bag with the name of a doulas' organization on it. I asked her about it and it turned out that she was not a doula, but had a friend who was. She put us in contact, and Dr Hyde and I went to interview her.

Doula S and her partner Doula D were so awesome that I decided not to interview anyone else. They were both midwives as well, so if I wanted to labor at home for a while before going to the hospital (which I did), they were qualified to evaluate my progress. Most important, they were clearly committed to helping me have the experience I wanted, and not imposing on me their vision of how labor "ought" to be.

During several prenatal visits they spent an hour or more answering our questions and asking us some too, to establish our preferences. Were we seeing a midwife or an obstetrician? How did I feel about epidurals and other forms of pain relief? What painful experiences had I had, and how had I handled them?

Eventually the plan we settled on was this: I switched from obstetric to midwifery care, once it was clear that the pregnancy was going normally. At our chosen hospital, this meant that I could labor in the midwife-run birth center, which has big tubs and is generally cozier than the standard OB-run labor & delivery ward. If at any point I decided to have an epidural, or if something was not going well with the labor, I would be transferred a couple of floors to the regular L&D. Also, with our doula/midwife help, I would labor at home for as long as I felt comfortable doing so. The idea was to delay an epidural as long as possible, and perhaps even avoid one.

Why this route? Epidurals typically provide pretty good pain relief, but they're not without drawbacks. Epidural anesthesia requires an additional IV line for fluids; in addition to the numbness produced by anesthesia, this keeps the woman tethered and less able to stand or change positions. Epidurals slow down labor and increase the chance of vacuum, forceps, and Caesarean deliveries. The greater risk of infection and fever increases the usage of antibiotics, and therefore the likelihood of thrush. A urinary catheter is also normally required, again with associated risk of infection, antibiotics, and thrush. (Why this emphasis on thrush? A woman in my breastfeeding group had it and said she'd rather go through labor a second time than have thrush, the pain was so bad.)

At the same time, I certainly wasn't ruling out the magic epi. The prospect of being in a lot of pain for 24 hours was daunting, to say the least. My philosophy was that I'd never given birth, nor even seen someone else do it, and that it would be presumptuous for me to declare ahead of time how things would go. The last thing I wanted was to set up an expectation of unmedicated childbirth that would make me feel like a failure if I chose an epidural after all.

So the official position was--default no epidural, try to use the hot tubs to get through it; but easy access to Plan B if and when I changed my mind.

After I let my doulas know that contractions had started, around 9 pm, we sprang into action. That is, Dr Hyde did the dishes and went to bed; I had a beer and went to bed in the guest room. The beer took the edge off and helped me relax, so I was able to doze between and even through the continuing contractions. Around 2 am I got up and took a lovely hot shower, which helped ease the pain a bit. An hour or two later, I decided that misery would like some company, and woke up Dr Hyde.

The next eight hours or so were not terribly unpleasant. I moved around the house, rocking during contractions and groaning or humming as the mood took me. The nice thing about much of labor is that the time between contractions is calm and painless. If you've ever hiked a steep mountainside, contractions are like the switchbacks, while the intervals are like the straightaways where you regain your breath and appreciate the scenery again.

Around 5 am Doula D came over, freeing Dr Hyde to go out for food. Midwives and doulas will usually encourage you to eat and drink in labor, on the theory that you need to keep your energy up over the long haul. Labor & delivery wards, by contrast, often have no-food policies. The concern is that a woman may require emergency Caesarean and that under general anesthesia she is at risk of aspirating her own vomit. Truly emergency Caesareans--the sort where you don't have time to put in an epidural/spinal catheter if there isn't already one in place, necessitating general anesthesia--are fairly rare (Wiki cites as 5% of all C-sections, so perhaps 1.5% of all deliveries in the US?) While it's understandable that the L&D ward wants to err on the safe side, in practice this means that the other 98.5% of laboring women are denied food.

I'm a good eater, and I get cranky fast if I don't eat for ~6 hours. So I knew I would want to eat during labor (another reason to labor at home or in the birth center, which permits this). Accordingly, Dr Hyde picked up some food, including, on my request, raisin bread. I don't know why I was intent on raisin bread. Normally I eat it perhaps twice a year. But raisin bread I demanded! Must have!

So throughout the labor, I snacked on eggs, fruit (cold grapes were a magical godsend--something about the high water content, mild sweetness, and ease of consumption--I ate them nonstop), peanut butter, and of course, raisin bread. This strategy worked well for me. Some women vomit during labor as a physiological reaction, whether to pain or some other aspect, but I noshed like the high-metabolism lady I am and it all stayed down.

Much of the morning (around 8 am - noon, 12-16 hours into labor) was spent in the bathtub. You enjoy a hot compress for muscle cramps? Labor is just like that, times 10. I grew bored in the bath, so Dr Hyde sat in the bathroom and read Harry Potter 7 to me. We were both rereading it at the time because we'd just seen the movie of HP6, and now I will forever associate Harry's peregrinations in search of the Elder Wand with labor. Occasionally I dozed between contractions, then made Dr Hyde reread whatever section I'd slept through.

At some point, my doula checked my cervix and said I was around 5 cm. I was pretty chuffed. "Halfway there," I thought, "and this is totally manageable. I am fantastic! I am champion!" Those of you who have been through labor, feel free to start laughing.

Around noon, I started feeling like I wanted to get to the hospital. Contractions were still livable, but I was starting to feel a shade of panic, an urge to be In The Place. We called the hospital to verify they had an open room in the birth center, packed up, and headed over.

to be continued

Blogger scheduling is a SUCK!

Seriously, for some reason I am no longer reliably able to set a blog's post date. If I start a post, then save it as a draft, return to it and publish using the options at the bottom to have it publish now, it still shows up dated the day I started writing the post. And Blogger's help on this topic is, "We're looking into it." LOSE.

So if you see on the feeds that I repost something, chances are it's because I am trying, in vain, to get the publication date fixed. Sorry. I guess I'm stuck copy-pasting into new posts to resolve this.

Meanwhile, here's a link to Breastatistics, stuck down in last week.

A look back

One year ago today, we were giggling about follicles.

One of those follicles became Small.

InaDWriMo 3

Hmm. After the initial burst of activity, the word counter hasn't budged this week.

However, my advisor and I were talking about this manuscript on Wednesday and I mentioned that I'd already written a Results draft. He seemed (pleasantly) surprised and asked to see it. So I've been revising it a bit to a shape where I'm not ashamed to hand it over to him. I'll do a bit more of that today and then email it off. The progress is less tangible, but arguably just as important. Hey, at least that's what I'm telling myself.

Personal statements are not for personal statements

Grad school applications invariably contain a request for a personal statement (or statement of purpose) about your reasons for wanting to pursue a Ph.D. in -ology. From one year as a student representative on an admissions committee, my advice to the applicant: write an IMpersonal statement.

What do I mean by this? Countless personal statements contain the dreaded "grandmother" paragraph. "I want to study -ology because my grandmother suffered from Disease X and the potential of a cure is fascinating to me." [The stilted writing is a separate problem.]

The problem with this statement is not that the applicant is using an ailing grandmother who may or may not have been as beloved as she is described. The problem is that graduate school is very hard, and the skills required have little to do with the intensity of your love for your grandmother. You can really, really, really care about curing Alzheimers and still be a screw-up in the lab.

Instead, applicants should describe the independent research they have carried out, and what their preferred research focus is. Go into detail on the research, both technical and intellectual aspects; it will demonstrate that you knew what you were doing as a tech/undergrad. You can write about how the joys and satisfactions of research thrilled you personally, but really that's about the extent to which your "personal" statement should be about your feelings.

Of course, if your recommendations/grades/GREs are so stellar, or perhaps so bad, that no one will bother reading your personal statement, you can disregard this advice. Personal statements only matter for borderline candidates. But do you feel that lucky?

Where Oh Where Could My PI Be?

In grad school we used to joke about putting a Lo-Jack on our advisor, and sometimes we weren't really joking. A PI has many obligations outside the lab--classes, committees, conferences, faculty meetings, etc.--that aren't also on his trainees' schedules. Some PIs keep their labs, or at least their lab managers, apprised of their plans; others vanish without notice.

Sometimes the information distribution is scattershot. One day when my advisor didn't appear on schedule, I asked a colleague if she was out with the flu. "I guess so," he responded. "She looked really sick on Friday."

Another colleague broke in. "Advisor's at a conference. She'll be gone all week."

I can understand that PIs lead busy lives, and that they might not want to feel obligated to send an all-lab email each time they are headed to another stop on the seminar circuit or whatever. However, I think they'd expect an email from me if I were gone more than a half-day, so it'd be nice to get the same from then.

Alternatively, if I could just give them this little bracelet to wear....

----
"...A conference took her away from me/ She's gone to Europe so I've got to work fast/ So I can see my PI when I...have graphs."

InaDWrMo 2

Progress this week, but thr pace has slowed. I didn't work as regularly on the manuscript, but also I've finished most of the easier part (Results). It takes muuuuch longer to write 150 words of Abstract than of Results. Still! 40% of the way to my goal isn't bad.

And the MS. progress helps counter the sinking sensation from starting to analyze my data from the last two weeks...sigh. Trying to add more N to an already successful graph is always a bad idea.

Breastatistics

Introduction
FSP posted last year about how her love for data had driven her, during gestational diabetes, to collect extra blood glucose data from herself and graph it. Inspired by her example, today I present Dr Jekyll's Milk Pumping Data for November.

Methods
I was away from Small for ~9.5 hrs, 5 days a week. During that time, Small was exclusively fed expressed breastmilk. I initially pumped three times a day, around 9 am, noon, and 3 pm, reducing to twice a day towards the end of the month. Pumping duration of each epoch was typically 30-40 minutes, corresponding with (a) the time required to drain most available milk; (b) the time required to obtain enough milk to make the hassle worthwhile; and (c) the maximum time I was willing to spend, or rather longer. The pump used was a secondhand Medela Freestyle.

On weekends, Small was fed ad libitum direct from the source. Due to the effects of indoor lighting and winter in the northern hemisphere, he was kept on a 14:10 light:dark cycle.

Results
Asymmetry of production
Despite no obvious size disparity, Righty consistently delivered more product than Lefty. Across all observations (n = 50), Righty matched or outpaced Lefty (Fig. 1).

Fig. 1: Righty delivers the goods better than Lefty. R-squared of
best-fit line, 0.59. Dashed line represents unity.

Effect of time on output
We had hypothesized that production would peak early in the week, due to the extra stimulation on the weekend. Surprisingly, there was no significant within-week effect (Fig. 2), although the relatively low N at this point may have limited statistical power.

Fig. 2: We'll see what effect restarting Monday lab meetings
will have. Error bars represent SEM.

It is well-established that milk production decreases in the afternoon relative to the morning. Our data were consistent with this finding (Fig. 3), although the fucking ANOVA is only 0.07.

Fig. 3: I went ahead and ran the T-tests anyhow. Morning > afternoon,
p = 0.045. But the midday versus afternoon is only p = 0.09.
Disregarding the ANOVA made me feel naughty.

Pumping is less effective than slurping
As has been seen previously, a pump is not as efficient at milk extraction as a baby. However, thanks to diligent monitoring, the deficit held steady at an average of 1 oz/day (Fig. 4). The total deficit over the period under study was -16.6 oz, which was compensated for by previously frozen supplies. It is worth noting that an additional 12.2 oz was pumped outside of work (data not shown), reducing the month's net deficit to -4.4 oz.

Fig. 4: Small is an eating machine.

Discussion

Pumping wouldn't suck so much if it were consistently possible to work during sessions. Frequently, though, working reduces output. So we'll see how long I keep this up.

Also, carting one's own bodily fluids around in lab is really weird. But the prospect of writing this post was oddly motivational.

Happy Thanksgiving, Americans.

The cost of a paper

I'm engaged in writing up a story that has resulted from my postdoc. As it happens, I will leave this postdoc as soon as the paper is out, and it is the only paper that will result from this postdoc. Thus, we can reasonably attribute 100% of my costs over the last two years to the production of one paper. How much is this paper worth?

1) My salary of ~($40K + benefits) x 2 years = $100,000.
2) My PI's salary, relevant fraction. Let's estimate he earns $100K, and I use 5% of his time, $5,000 x 2 years = $10,000
3) Mice. Each litter I use has a list price of $50. Let's say I've used 50 litters. $50 x 50 = $2,500.
4) Equipment, amortized. My set-up probably cost around $150K, but most of that equipment will be usable for a decade or three. This is the hardest to estimate, but I'll say 10% of the equipment cost = $15,000.
5) Chemicals. Most of the chemicals I use are cheap, but some aren't. $5,000.
6) Miscellany. Sending me to conferences, my share of our tech's and lab manager's salaries, my share of some infrequently used equipment, etc. Hard to say but I'll guess $15,000. Probably an underestimate since there are likely things I'm not thinking of.

Total: $147,500*

It better be one hell of a paper.


* Plus indirect costs!

To whom it may concern

For the first time, I've been asked to write a letter of recommendation for someone applying to graduate school. This person teched in my grad lab, where I supervised him on several projects and co-authored a paper with him.

I told him I'd be happy to write a letter, but pointed out that of course he'd be better off with a more senior person than me, if possible. He's got two PIs writing him letters, and he thinks I'm the best third letter. So here we go.

I've read some grad school letters of rec before, when I was a student member of the grad school admissions committee. As best as I can tell, here are the major components to the letter:

0. Who you are (presumably optional if you're a fancy big name scientist).
1. How well you know the person, and what your interaction has been.
2. Their scientific intellectual capacity.
3. The quality of their lab work.
4. Personality.

Any one of these topics can sometimes go awol, which suggests to the reader that the writer didn't have great things to say on the subject. I don't recall ever reading a letter that said anything less than stellar about the applicant, although there were more-emphatically-stellar and less-emphatically-stellar phrasings.

Am I missing anything? Do you tackle letters of rec in any particular way?

Tormenting your kids with science

One of the stranger ways my parents (both historians) exposed me to science was the weird and wonderful Singing Science records. These albums from the '50s and '60s cover many facets of science--nature, physics, outer space, weather, etc.--and are pitched at perhaps 4- to 9-year olds.

Even if you're not in that age bracket, you might enjoy listening to the MP3s that are online, these records being long out of production. They're best appreciated if you have the goofy sense of humor that responds to rhyme schemes like:

There is no disputin',
There is no refutin',
We're all indebted
To Sir Isaac Newton.

or if you can match their enthusiasm for science and jaunty tunes:

What does the glass of a greenhouse do?
It doesn't let the long heat rays pass through
Trapped by the glass, they bounce back and forth,
Re-radiated and re-absorbed.

Why Does the Sun Shine? was covered, many decades later, by They Might Be Giants:

The sun is a mass of incandescent gas.
A gigantic nuclear furnace,
Where hydrogen is built into helium
At a temperature of millions of degrees.

I remember taking a science test in perhaps 7th grade and humming this tune to myself to sort out whether hydrogen turned to helium or vice versa.

Similarly, the word friction was firmly in my vocabulary--it's "the rub-a-dub-dub rub-a-dub/ Of objects that are moving/ And the rub-a-dub of contact is friction at work"--from a tender age.

The Jekyll grandparents owned these records, and as a result, during Jekyll family get-togethers, the entire clan sometimes bursts into "A shooting star is not a star, is not a star at all/ A shooting star's a meteor that's headed for a fall." Really, it's an odd family.

Of course, the philosophers of science among you won't be pleased to hear, "A scientific fact/ It has to be correct/ It has to be exact," but your children are unlikely to mind.

Anyhow, the Space songs are the best, in part because of the excited speculation about whether we'll ever go to the moon. Go give them a listen.

InaDWriMo

Nat reminded me that if it's November, Dr Brazen Hussy is hosting the InaDWriMo writing challenge. This is literally the only good thing that happens in Novembers.

I had not been planning to get going on this manuscript until December when experiments will be "done," but InaDWriMo is motivating me to get cracking earlier. With some diligent laptop efforts on my daily bus commute, I've already cranked out a lot of the results section. Yeah!

It may not be pretty, but getting a draft on paper is always the first step...

How does your lab grow?

What's your lab's composition? In the recent issue of Neuron, Nobel laureate David Hubel argues that the shape of a lab has changed radically, and for the worse. In today's labs, he writes,

Leading each group is a senior scientist, a full professor, or an assistant professor who can expect to be promoted to tenure in a few years. Under the leader come post-doctoral fellows, graduate students, and a few research assistants. This form of organization is in sharp contrast with what prevailed a generation ago, when a group consisted usually of one person, or two or three, and there was less distinction, if there was any, between group members.

He goes on to say that as a result of today's division of labor, the PI's time is taken up with grants, committee work, teaching, refereeing, and lab management--rarely experiments. In contrast, when Hubel started working at Harvard,

Everyone in the group worked alone or with one other postdoc, on projects they thought up themselves and carried through independently.

Thus everyone was responsible for his own experiments, analysis, and writing, and would use other group members as critical sounding boards.

Hubel argues that the old way was preferable because:
a) Postdocs learned much more independence, as they had to think through projects and data themselves rather than being directed.

b) One thinks best about science when one does one's own experiments, as opposed to dividing the bench and grant chores between two people.

c) Scientists, who are selected for their skills at benchwork, get to continue doing benchwork.

He doesn't point out the corollary to (c), that because good scientists may be bad managers, this system avoids placing such people in positions of power over scads of postdocs. But to me this is a critical point. Numerous blog posts from multiple bloggers detail their frustrations with poor management, whether it comes in the form of the PI overseeing antibody supplies or being unhelpful with projects and manuscripts.

This is partly a rehash of an old argument: should PIs keep doing experiments? The axis of opinion ranges from PhysioProf's point that PIs are good at thinking big picture, so it's best for them not to waste time on experiments, to Ms. PhD's argument that those who can't do, shouldn't teach (= run a lab). (I do think that PIs who continue with experiments generally have a good grip on their labs, while those who don't have more heterogeneous track records.)

Still, the crux of Hubel's argument, and one that I find interesting, is that scientists should be given greater responsibility for their own research earlier on, as postdocs rather than as assstant professors. Too many postdocs must follow their PI's project "suggestions" and don't have an opportunity to design a project from scratch. This produces a lot of disgruntled postdocs and Mini-Me PIs.

Some institutions, like the Max Planck, do offer junior scientists independent research positions leading only one or two other people. My advisor held this type of position and says it was scientifically the best thing he ever did. But very few such jobs are available today.

Of course the current arrangement is probably higher throughput, because savvy PIs can lead squads of unimaginative postdocs through an exciting research program. And there are doubtless many people who prefer the current design, not least because it facilitates interdisciplinary work. But I agree with Hubel that more independent small research programs populated by relative youngsters (in their 30s!) who would otherwise be postdocs would be a welcome alternative.

I wish that more institutions offered Max Planck-style fellowships. For many, perhaps most, people, these jobs would serve as springboards to more traditional faculty positions, while fostering independence and creativity, and eliminating the "pedigree" aspect of the current postdoc system.

And perhaps a few scientists would discover along the way that they preferred it.

Halloscene

Dr. Jekyll: Oh, you guys are Jedi knights, that's cool.

Jedi knights: Look at our light sabers!

Dr. Jekyll: Have some candy.

Younger Jedi knight (fumbling with light saber, loot bag, and candy, then tripping on his robe): This is really hard.

Dr. Jekyll (sympathetically): Yeah, being a Jedi is hard work.

Younger Jedi knight (pointedly): How would you know?

My Hallowe'ens were better/worse than yours

Why they were better

Some people say that children growing up in big cities miss out on important aspects of childhood. I say, those people have never thought about Hallowe'en. Hallowe'en is vastly improved by urban high-density living.

I grew up in an apartment complex of two buildings, each over 20 stories. In the week leading up to Hallowe'en, a sheet of paper would be posted in each elevator so that residents participating in Hallowe'en could list their apartment number. On the fateful night, we would copy down the list of active apartments. Then it was simply a matter of taking the elevator to the top floor, starting with 21B, C, and F, or whatever it might be, and taking the stairs down to 20.

This is the most highly efficient form of candy-gathering known to child. You worked the building like a typewriter, across one floor and then down a row to the next. You didn't need to waste time on decoding Hallowe'en-participation symbols like carved pumpkins, because you had the list in front of you. (Added benefit for residents, those not wishing to serve treats didn't have to hide in the back rooms with the lights off.)

And best of all, because you never went outside, your parents stopped feeling the need to supervise you after you turned, say, 8. Not to mention you avoided the perils of subjecting your costume to the weather. It was independent candy-gathering paradise.


Why they were worse

My parents, bless their thrifty, wholesome, Puritan souls, didn't believe in giving out Kit Kats like the rest of the world. They were the hated household that handed out boxes of raisins for Pete's sake (Dr Hyde, incredulous: "And nobody ever egged your apartment?"). On a few occasions, my mother made giant batches of chocolate chip or oatmeal raisin cookies instead, and we tied them up in little plastic baggies for dispensation, so those were the good years.

Even worse, they liked to give out noisemakers. Ah, but not plastic dime-store noisemakers. My parents had determined that a great fun toy for young children was...wait for it...bubble wrap. They would save up the bubble wrap that came in packages throughout the year, and then actually cut it into somewhat smaller squares so as not to run out on Halloween. "You can pop the bubbles, like this! POP!" my mother explained brightly to each dubious child.

The parents who accompanied younger kids quickly masked their astonishment with praise for the "creativity" of this idea. (And in my parents' defense, the 4-7 year old set usually did get a kick out of the stuff, either popping the bubbles one by one, or, for the adventurous souls, laying the sheet down on the ground and jumping on it for maximum effect.)

The older children were generally less successful at disguising their contempt. (Dr Hyde: "You didn't at least get toilet papered?" Me: "Hard to mess with someone's place when they're on the 18th floor.") When I was younger, of course I thought that bubble wrap was a pretty decent hand-out, but as I grew up I began to see Hallowe'en as vaguely shameful, particularly when I had to help my parents cut the bubble wrap into pieces. Anyhow, for those of you who know me, it probably helps to understand my psychology, that my parents thought that raisins and bubble wrap were treats on the most candy-filled holiday of the year.

Dr Hyde and I hand out Kit Kats.

Having a child made me pro-choice

Ok, that's an overstatement--I was pro-choice to begin with. But before having a baby, I was pro-choice in a somewhat abstract way. "Women's medical decisions are private! No one should be forced to bear a child!" etc etc.

Now that I have one? I would personally help out, with money or time or support, any woman I knew who needed help procuring an abortion. I would go so far as to say that I am baffled that any woman with kids could feel otherwise.

Everyone assures me that the newborn phase passes and things get better. That is cold comfort when one's child chooses not to sleep for seven hours straight. And demands constant rocking, jiggling, nursing, bouncing, repeat ad nauseam (mine) for the duration. Small is a lovely baby, and fun to play with when he's happy, but staying home alone with him all day is intermittently dreadful. On days when he refuses to sleep, I would be willing to hand him off to a passing stranger. Once a week or so he screams his head off for a few minutes while I sit in another room, unresponsive, because I simply cannot stand to deal with him for another moment.

And lest we forget, I really, really, really wanted this baby.

The point here is not that I am dealing with new motherhood and continuing vicious sleep deprivation, although that is also true. The point is, some days are difficult enough even knowing that this is a dearly desired baby, a baby we went through many medical procedures to achieve, a baby I am (generally) happy to have.

If I had not wanted this baby? The neglect would have started early and often. If I didn't have the vast amount of support that I do in fact have, things would be even worse. Who thinks it's a good idea to encourage this?

And don't tell me that adoption is the solution unless you yourself have adopted a few children.

So there you have it. I've always been pro-choice, but having a child has radicalized me. This is a hard enough path even when it's been chosen. I could never tell a woman to go through it unwillingly, nor could I live with putting a baby in a situation where it wasn't wanted. I really don't understand how any woman with children could feel otherwise.

------

Dr Hyde points out that posts like this will send Small into therapy, when he's old enough. "Your mother said that having you made her support abortion!" To which I say, therapy is healthy.

For the love of God, do not litter up the comments with suggestions on how to get babies to sleep. Your white noise, your swaddling, your slings, whatever, sometimes (as today) nothing works, it is miserable for everyone involved, and don't presume to tell me otherwise. And in any case, that is not what this post is about.

First day back

There is nothing like a six-week hiatus spent entirely catering to the whims of a small but angry dictator to make you appreciate your job.

I know that many women (and some men) discover that they prefer staying home after having a baby, but I can assure you all that I am not one of those people. It was fabulous to go to work, where nobody screamed at me or pooped on me, and I could go to the bathroom whenever I pleased.

Also, I had the chance to think about my hot science and run some meta-analysis of data collected Before Small. Even though the meta-analysis was tedious and ultimately didn't tell me anything of note, it was heaven.

As a bonus, I was excited to see Small in the evening, rather than wanting to dump him in Dr Hyde's arms as I do when he's been at work all day.

It's clear that pumping milk, which was easy to schedule into an analysis day, will become a big hassle on experiment days, but we'll cross that mammary-supplied river when we come to it. Right now I'm just happy to have a semblance of my normal thinking life back.

Vanishing act

Some basic etiquette when a colleague goes on maternity leave: She is not dead.

If, for example, lab renovations are going to cause her lab space to be completely torn up and covered in plastic sheeting for two weeks, she would probably prefer to learn this news via email, rather than discovering it for herself when she manages to leave the baby in someone else's care so that she can go into work for a few hours.

That is all.

It sounds so obvious when you put it that way

It is really, really hard to read grants when someone is sucking on your nipples.

How our conversations have changed

Dr Jekyll: I never thought that a person who weighs 8 pounds could fart as loudly as a person who weighs 140.

Dr Hyde: It's really amazing, isn't it?

Dr Jekyll: I feel kind of intimidated by it.

Dr Hyde: I've dealt with newborns before but I don't ever remember one that could fart this loudly, or this long.

Dr Jekyll: Yeah, usually babies are impressive at burping, but it's hard to get a good burp out of Small.

Dr Hyde: Our baby saves it up for the other end. We should video it and put it on YouTube. "Amazing Farting Baby."

Dr Jekyll: Yeah, it'll go viral.

Dr Hyde: The Asians will make T-shirts with his face on it.

Dr Jekyll: We'll make our first million!

Dr Hyde: And then there's the ringtones.

Creative technology usage

There have been some strange rustling noises underneath the house. Last year when this happened, it was due to a resident stinky skunk. After waiting one evening past midnight for the skunk to exit, Dr Hyde had carefully blocked up all the entrances to the crawl space with loose bricks, so we were surprised that anything could have gotten back in. But sure enough, some of the bricks in one location were displaced.

Dr H wanted to brick up this entrance again, but I pointed out that if there was another skunk under the house, and it was trapped and died, I would be wrathful in the extreme. How to make sure the beast was gone?

Dr Hyde's solution: he took the baby sound/video monitor, which we usually use to make sure the cat has not smothered the baby, and planted the camera portion outside over the crawl space entrance, running the power cord in through a window. Then he stayed up late with a fussy Small, watching the video monitor.

A little after midnight, an animal exited--a sleek possum. Dr H waited to make sure there were no more possums, then re-bricked up the crawl space.

Today, the camera is still outside, and I am relying on ESP to make sure the cat hasn't leapt into the bassinet.

Some observations

1) When you hear about toothless older folks having to gum their food, you may be left with the impression that this is sad because gums are soft and lack chomping power. This is so very not true.

2) In the first couple of weeks, Small just stared at my armpit while breastfeeding. Now that he is a bit more aware of his world, he often looks sideways up at my face. As only one eye is visible in this position, he bears more than a passing resemblance to a large whale underneath one's boat, gazing upwards at the humans crowding the rail.

3) Wow, do I owe my mother.

Well that was an interesting experience

Small Hyde enters the world.

All well and healthy. More later.

How Americans distrust science

This week's Times Week in Review section sports a lead article by an ex-physicist, James Glanz, whose thesis is that the failure of the Large Hadron Collider in Geneva is reminiscent of the giant abandoned pyramids of the Mayans: a symbol of our hubris in trying to understand too much.

Glanz doesn't use the word "hubris," with all the Greek mythological implications it entails, but substitutes the "your business model was bad" term "overreach." Nonetheless, his point is clear: we were trying to probe too far into the limits of the cosmos, and so naturally we were doomed for failure.

Well excuuuuuuse us for trying.

Glanz doesn't seem to have a problem with the experimental question itself: whether the Higgs boson (a) exists, and (b) underlies the concept of mass. (I'm no physicist, but I think finding out whether a particle is responsible for one of the most salient characteristics of our physical world is yeah, pretty important.) Instead his beef is that the electrical and magnetic problems with the LHC are a sign of our unwonted temerity in probing such questions.

I call serious bullshit. As the saying goes: If I knew what I were doing, it wouldn't be called an experiment. Yes, it's a vicious disappointment that there's no data out of the LHC yet, leaving hundreds of physics grad students with theory-only theses.

But if an experiment beset with unexpected problems is a sign that we are overreaching, then I guess I'm pretty much all washed up as a scientist, because most of my experiments are overrun with unexpected problems. I call myself a scientist because these problems don't make me don't throw up my hands and head for the bar (ok, sometimes) but instead cause me to find solutions, to troubleshoot, to analyze whether the problems are inherent to the experimental question or simply to the method in use.

Glanz's article reflects (embarrassingly, for an ex-scientist) the basic fear with which many Americans view science. If it doesn't work out right the first time, it's because we wanted too much! We tried to learn Something We Shouldn't Have. We angered the gods.

Just last night Dr Hyde and I were talking about our collective failure to teach the right lessons about science in school--that science is not so much a collection of facts as a form of rigorous critical thinking. I think Glanz's article is an extension of that problem: he equates a failure to obtain facts on schedule with a failure of science.

If more Americans understood that this idea was perniciously wrong, we might not be in the era of creationism - global warming denalism - disrespect for reality that we are. Thanks for helping, "Dr" Glanz.

Texting while driving

Normally when I am doing experiments, they only occupy about three-fourths of my brain. The remaining brain is answering email, thinking about other experiments, thinking about dinner, humming a little tune, whatever.

So you would think that I could perfectly well carry on a conversation and answer a few questions about what I'm doing while I do experiments. But no. With people watching, I forget which way caps twist to tighten. I forget to press important buttons. I drop things, like my experimental prep.

Today two people were watching me prep and (try to) carry out experiments, and it was borderline disastrous. (Some of this had to do with bad luck for the day, but then again why is it always on the days that my prep is a total failure that people are watching? They never seem to come by when I am my usual genius whiz self.)

And it got me to thinking, why is it so damn hard to do experiments when people watch? I have four explanations:

1) Observers make you self-conscious, leading to obvious problems with routine tasks of coordination that proceed most effectively without conscious control.

2) The cortical load imposed by answering even very easy questions about your experiments is far higher than one realizes.

3) A more hypothetical possibility: that there is a non-trivial burden placed on your brain simply by being in a social situation--i.e. with observers--so that even if those observers are silent, a surprising portion of your brain is being used to monitor them.

4) Though I routinely can spare a quarter of my brain for email etc., there are brief periods (as short as 5-10 s) during which I use all of it to focus on the experiment at hand, and any social burden is problematic.

Of course these are not mutually exclusive, though I would love to know whether anyone has ever studied the possible existence of effect #3.

The whole situation reminds me of the recent brouhaha over texting while driving (ed: who the hell was surprised that texting is bad for driving?!) and the attendant reminders that the "hands-free" policy espoused by many states is essentially useless, because it turns out that the mental load of carrying your end of the conversation, rather than the physical act of holding the phone, is the problem.

I wish the Senate would pass a law preventing me from having to train up other people on my experiments when I am very pressured for time by the impending bomb in my belly, and also all the rest of the time too because let's face it, that shit's annoying. If I get a petition going, you people will be the first to know.

Well there goes my Friday night

Yes, yes, scientists do amazing and interesting research that pushes the limits of our knowledge for the betterment of humanity.

Also, stuff on zipper-trapped penises and flatufonia. Thanks (I think), anonymous graduate students running NCBI ROFL.

Apparently this is Whine Week

When I am typing a document in Microsoft Word, it turns out that I never want to insert the phrase SPECIAL DELIVERY.

SPECIFIC AIM, however...

Two points

1) If you don't like a book, write as caustic a book review as you choose.

2) I think it's a pity when ScienceBlogs, which has won prominence in the NY Times' Science section, and represents a selection of scientists who have chosen to do a blog-form of outreach to the public, turns into a childish, cryptic den of finger-pointing, particularly on the very topic of....outreach to the public.

If I were the scientifically engaged public (which is how I'd have described myself circa 1993, before I started doing lab work), and clicked over to SciBlogs after reading my usual Tuesday Science Times, I would sure as hell click right back to more pleasant, not to mention more comprehensible, waters. And I say that as someone whose blood pressure is roughly doubled by reading Tierney's sad excuse for a "science" column.

Post about science. Post about the culture of science. Post about your life as a scientist and how it functions, or doesn't. Post about your life to give non-science readers a window into how three-dimensional scientists are.

But for chrissakes, don't post about your backroom spats with other science bloggers (whether or not they're still on SB!) and waste one of the better opportunities we have of engaging laypeople.

Drs. I and Z, I think you're capable of much more interesting work. I fully agree that you should call out misogyny when you see it. But the full-scale SB war, with blog posts being lobbed like hellfire missiles, coated in links and comments-on-comments, is boring and ugly, and worst of all, utterly uninteresting to the public. It's not like we have so very many chances to bring them on board.

Things I learned in grad school 4: Thinking vs doing

One of the most difficult aspects of science for me to deal with when I entered graduate school was empiricism. I came to a love of science from the intellectual, not the practical, end. I liked the questions, ideas, and logic. I was under the impression that, because scientific phenomena underlie our whole existence, any sort of practical problem could be solved by application of reason and logic.

I probably spent the first three years of grad school unlearning this idea.

For a long time, the idea that logic would triumph held me captive to massive frustration. It turns out to be, appropriately enough, right in principle but wrong in application.

I spent years kicking tables out of anger at problems like electrical noise in my setup. Now, there are some straightforward rules governing electricity. You learn a number of them, probably all the relevant ones, in college physics if not earlier. You can apply them all in a logical, orderly manner. You can still have inexplicably bad electrical noise.

You can learn some special rules of thumb for the particular configuration you have. Still, electrical noise.

What drove me up a tree was that invariably I'd get advice from a senior student along the lines of, "Well, just try a bunch of things like this and see if it helps." Why? There is no earthly reason that I should have to try random things. I should be able to solve this problem using a multimeter and my brain.

As I say, I wasted a lot of time on frustration before learning that in fact, some problems are best solved empirically, by trying a bunch of stuff and seeing what works. You can reason your way back to an explanation (maybe!), but some problems are more or less intractable without just trying things out, even things that you think shouldn't matter.

I know plenty of good scientists who entered grad school from the opposite pole, that of being do-ers who love nothing more than to plunge in and try stuff, and think about the results later. Those people usually do really well at carrying out experiments, and their challenge is often to make sure those experiments are thoughtfully designed.

If you are headed for or starting graduate school, I'd encourage you to contemplate which of these--thinking or doing--you consider your strength. I certainly knew heading in to grad school that I loved scientific concepts, but struggled with benchwork. If you know which half you find easier, recognize how much you need practice with the other half, and find someone to help you with it. Perhaps you have a fellow labmate who has the skills you lack, or a friend in a neighbor lab. This person's approach to problems may seem totally foreign to you, but that's exactly why you need them.

I was thinking of this today as a colleague and I were troubleshooting a completely bizarre problem with some fancy equipment we both use in his lab. We spent at least half an hour fighting two seriously disconcerting glitches, one of which seemed hardware-related and perhaps unfixable (and which would cast doubt on several published papers that use this hardware), and the other of which seemed software-related but equally unfixable.

Five years ago, I would have given up, or thrown a fit, or called up the company to yell at them, probably uselessly. Instead I suggested we try changing a software parameter that had nothing to do with anything we were having trouble with. Why? Not because I thought it was relevant, but because I have learned respect for empirical outcomes.

Presto. Both glitches cleared up. (Not with the first irrelevant parameter we changed, mind you! More like the 4th.) The other postdoc and I gaped at each other. We tested some more. Solved.

We tried to come up with any possible reason this parameter might have caused these problems. Nothing. But you know what? I don't really care (though I might still go back with some BNCs and an oscilloscope to see if I can figure it out). It's clear that the software has a bizarre bug that causes this inexplicable behavior. And now we know how to steer clear.

This is not to claim that I never get frustrated with inexplicable problems any longer. Ha ha, no. But that graduate school taught me to take seriously the attitude, "Just try it and see what happens."

More simple requests

Pubmed, you have some good qualities. Also, some not so good ones. To wit:

--Why must the cursor automatically jump to the search field when a page loads? Like all right-thinking, i.e. keyboard-shortcut-using, people, I am a fan of using the space bar to page down. But on each new results page, the space bar just....adds space, unless I click somewhere else on the page first.

--When I type the first few letters of a recently-performed search into the search field, you bring up a helpful drop-down of my recent searches. I key down to the desired one and press Return to put it in the search box.
(a) You immediately re-run that search. Sometimes I wanted to add something else to that search term.
(b) Not only do you immediately re-run that search, for reasons beyond me you sometimes fail to run the full search term, but instead use only the fragment that I had typed in. For example, when I type in "Ph" and then key down to select "Physioprof" from the drop-down, sometimes you produce Physioprof's papers. Sometimes you produce every single goddamn paper with "ph" in it. All 8 million of them. [This is just an example, people. In reality, "physioprof" produces no search results in PubMed. Don't waste your time.]

--Select some unique author ID method and implement it. I don't care which one. But if I have to try searching for a paper by "Xu X" ever again, I will maim you.

I'm lookin' at you, VWR

Welcome to ConglomerateScienceSupplyCo!

Please indicate your country to continue.

But you know my IP address.

Please select from the following menu:

[List of all countries starting with A, because we don't discriminate] or
[List of all countries starting with United States and United Kingdom, because let's face it]

The first version annoys me because I have to scroll all the way to the bottom. The second version annoys me because it reminds me that I am a spoiled American. Also, why the hell do I have to do this at all? You know my damn IP address. You could tell me what university I'm coming from, if you so chose.

Thanks for your selection! Would you like us to remember this selection for future visits?

Go right ahead, although you've never succeeded in remembering it before and I am doubtful that you even know how to place a cookie on my computer, given that you don't seem to have figured out that you know my goddamn IP address.

Referencing dross

Everyone's had this problem: you need to cite a paper in your field. The paper is totally ghastly. You know it's crap, and probably (?) your readers do too.

But you can't not cite it, because it's one of the few precedents relevant to your work--perhaps the only precedent for a certain facet of your work. Perhaps it's well-cited within your field and your failure to cite it would be seen as a glaring omission; perhaps your advisor or a reviewer has told you to cite it. Whatever the cause, you have to reference this bit of rubbish.

You can
1) Cite it. "Our data provide one of the first demonstrations of bleg-de-blug (Loser et al.)"
2) Bury it. "Previous research has not focused on the area of bleg-de-blug (Loser et al.)"
3) Trash it. "With the exception of a dubious report (Loser et al.), our data provide the first demonstration of bleg-de-blug."
4) Trash it cryptically. "Bleg-de-blug is without precedent in this field (Loser et al.)"

Sigh.

And thus does everyone's h-index creep up.

---------------

For the other junkies out there, my odds run thusly:

2:1 Looming indictment/impeachment for ethical problems related to Troopergate.
3:1 Levi's inked a book deal.
6:1 Being blackmailed by Levi or someone else, and needs to raise cash.
10:1 Sex tapes.
18:1 Another pregnancy, hers, Willow's, or Todd's mistress's.
100:1 Actually thinks this is her best route to the presidency.

Reporting the story

Presumably most of you have read Gina Kolata's take, in the Times, on why cancer research hasn't cured cancer yet. It's the super-conservative grant review process that rewards only incremental research and variations on well-established themes, it turns out.

Well, yes, that's something that all of us, cancer researchers or not, complain about fairly regularly: the requirement for in-depth preliminary data that signals "The first aim is all but complete" before funding shows up.

But I think she buried the real story. Anyone else catch the graph?


Let's take a couple of years here for illustrative purposes.

In 1996, we spent about $3 bn on NCI total, of which $0.6 bn went to "Other expenditures--non research." That's 20%.

In 2005, we spent about $5 bn on NCI total, of which $1.5 bn went to "Other expenditures--non research." That's 30%. Aka, a 50% increase in proportion of non-research expenditures.

Now, there are plenty of other remarks to be made about the article, including "Biology is really complex and simplistic formulations like 'The War on Cancer' are downright silly;" and "You see how funding flatlined and then actually sank? That might have something to do with reviewers becoming conservative." Neither of which was ever addressed in Kolata's article.

But looking at that graph, all I can ask is: where is this non-research money going? Is this due to an increase in overhead/indirect costs? And if so, why? Did it really get that much more expensive to administer and run science buildings starting around the year 2000?

For 2005 alone, if these non-research costs could have been kept at their original 20%, there would be an extra half-billion dollars freed up for cancer research funding. At, say, $250,000 per project/year, that's an extra 2000 projects that didn't happen. In 2005 alone.

This article felt like one of those talks where the speaker doesn't address some really fundamental issue up front, and I can't even process the rest of the talk because I'm so focused on this problem raised by the graph on the third slide.

Leave the epic similes to Virgil, sir

A PI to a classroom of students and postdocs, regarding a scientific issue of signal propagation:

“Here’s an analogy. It’s like when you’re on the same floor as the secretaries, and there’s only one thermostat, and the secretaries, who are always young women with very little body fat and they’re wearing kind of skimpy clothing, are always turning the thermostat way up, and it affects you even though you’re at the other end of the hall, but your feedback doesn’t change the thermostat.”

Cruel to be kind

Good old Blog Fodder the Tech, who astounded me with his many iniquities before shaping up as a reasonable lab member, has announced his plans to attend graduate school.

BF had previously mentioned grad school as a possible future, but had acknowledged that he was just as interested in business school (poll: which requires a better grasp of basic arithmetic?). Now, however, he is actually studying for the general and biology GREs (and taking a Princeton Review course). Last week he came into lab on Saturday to do a couple of small lab tasks and grind away at a practice exam.

The problem is, of course, that BF lacks the fundamental curiosity, let alone the determination, to make it through grad school. He asks questions....about the tasks he is given. Perhaps once a month, he asks a question about the research presented in lab meeting, but these questions are not typically experimental in nature--they are more likely to run along the lines of, "Does this relate to phenomenon X that I read about in Science/the Times/the Economist?" Sometimes it's an interesting question, but it's pretty much never what I would expect from a first-year grad student--i.e., a question about experimental details, or whether one could follow up with Experiment Z, or even just what the heck the significance of an observation is.

(And no, this is not because he fears me; he doesn't ask these questions of anyone.)

When he told me recently that he was studying up for the GREs in preparation for grad school applications this fall, I asked him more about his research interests. In the past he has mentioned labs that do fairly similar work to our lab, but this time he mentioned some labs that are further afield. It's fine for your subject affinity to shift over time, but I think in this instance he's probably just hoping that the work of Other Labs is more interesting to him than the work of This Lab.

In any case, I tried, gently, to dissuade him from Ph.D. programs. I pointed out that if he's still thinking about going into business in some capacity (the business end of a pharma company, for example), then an M.S. would likely give him the training he needs for much less hassle.

"I just figure that if I'm going to grad school, I might as well go the whole hog," he replied. "Besides, I'd be happy to spend six years in [City With His Dream Grad Program]."

Blink. Blink.

Despite BF's many failings as a scientist, I have developed a certain fondness for him, the way one does with household items. So I should probably try again to steer him in the direction of the M.S., or even an entire life re-evaluation. (Note to readers, BF is loaded, so the cost of doing an M.S. should not be a hurdle.)

On the other hand, it's not as though he's coming to me asking for advice or help, and often it is easy to irritate people by profferring unasked-for advice, or so I am told. Since I've already suggested the M.S. to no effect, I could just wash my hands of the situation.

Still, though, I dread the moment that BF asks Advisor for a recommendation. The problem is that BF likely won't ask until it's actually grad school application time, i.e. November, by which time it will be harder for him to change his plans in response to Advisor's anticipated reaction ("You are applying to what?")

So I feel as though the Right Thing To Do would be to sit BF down and try again to persuade him to think this all through. It might be a waste of my breath, because he has a certain unshakeable confidence, but I think it's worth a try, on the theory that a little effort now might save some misguided university the cost of his tuition and stipend for 2-3 squandered years. Have any readers ever successfully talked someone out of applying to Ph.D. programs? Particularly someone who is a bit stubborn and ignorant, and perhaps also very bad at math?

Why do you write a training grant?

I've been funded off an NIH training grant (T32) at two different points previously, and I'm applying to be put on another training grant in the future.

My participation level in these training grants has been, at maximum, to write a paragraph of application explaining why I should be on one, and another page or so each year I'm on the grant to update NIH on my progress. Ridiculously easy.

But the person administering the training grant seems to do an awful lot of work. They write the grant, pick trainees, and generally deal with the flow of funds. My question is, what's in it for them? It seems like a giant hassle for very little professional benefit--perhaps you can stick one of your own trainees on the grant, but beyond that it just looks like scut work. Yet the two training grants I've been on have been administered by high-ranking PIs (and sniffing around T32s at other institutions on CRISP, this doesn't appear to be uncommon).

Do you just get departmental brownie points for writing/running a T32? Is it the sort of service activity that gets you out of jail for some other service activity, like being on a search committee? Is it just out of the greatness of your heart? (And if so, how to explain the presence of some T32 administrators who are well known not to have hearts at all?)

I'm grateful to have this funding, but can't imagine that "postdoc gratitude" inspires a lot of would-be grant-writers. So I have to assume there is something I don't understand about the apparently selfless action of these folks. Internet, please explain.

Your personal eigenvalue

This just cracked me up:

http://www.pnas.org/content/106/17/6883.full

PNAS publishes a letter on the "Eigenfactor" version of citation ranking, some attempt to come up with yet another version of impact factor. The fawning conclusion? That you can "publish in PNAS with the full knowledge that you are contributing to one of the most influential drivers of scientific progress."

Also, apparently, in JBC, which way outranks Cell.




Who amongst you doesn't want to know what those tantalizing unlabeled dots near Cell and Phys Rev B are? J Nobody Reads This?

A very small snippet that says oh so much

From this week's NY Times Week in Review:

But Justice Ginsburg said her own influence in all sorts of cases at the justices’ conferences was uncertain. “I will say something — and I don’t think I’m a confused speaker — and it isn’t until somebody else says it that everyone will focus on the point,” Justice Ginsburg said.

That is, she is one of the nine highest-ranking judges in the nation, with the power to define and defend constitutional law, and she sometimes kinda feels like people ignore the points she makes...until a guy says the same thing ten minutes later.

Staying awake, staying (scientifically) alive

I can't imagine I'm the only person with this problem: I sit down at a seminar by a visiting scientist, or at a conference talk, and my mind drifts.

Who's that sitting in the third row? What's the name of that grad student I just met? How should I persuade my PI that my proposed Experiment X is higher priority than his proposed Experiment Y? What is Experiment X, anyhow? Also, dinner.

It isn't necessarily because of fatigue, though some days that plays a role; and it isn't only for boring speakers--it's just easier to retreat into Headworld than to stay focused on whatever's going on in Realworld. But I always feel ashamed fifteen minutes later when I turn my attention back to the seminar and find myself hopelessly lost. Back to musing on dinner.

Sure, it'd be nice if all speakers were so dynamic that they engaged us from the first slide, but the horrid truth is that there are some very smart scientists doing interesting research who speak in monotones, or use tiny fonts, or work outside your immediate area so they're just plain harder to follow. The challenge is, how to maintain attention even if they're not making it easy for you.

My new solution is this: Pretend I am the host (if at seminar series) or session leader (if at a conference). What's that person's job? To be ready to ask a question, any question, at the end of the talk if no one else in the audience has a hand up, to avoid the dreaded awkward no-questions silence.

The criteria aren't very stringent for my ready-to-ask question. I try to stay away from just "Have you tried that experiment under Condition Q?" unless there's a valid scientific reason to think that Condition Q might be relevant for the topic.

Ok questions, even if a bit anodyne, include things like:

"What's the behavioral outcome in that transgenic fly/mouse/worm?"

"Would your new technique be applicable to Issue Z?"

Better questions of course are more analytical, even if still pretty open-ended:

"Could that result be due to some developmental compensation?"

"Are there any other consequences to that manipulation?"

Obviously if I can manage to come up with a really good question, hey presto, I'll just ask it. But the point of this exercise is that if you are the person responsible for starting a discussion in the face of a quiescent audience, you just need to have something coherent ready to go. It needn't be fancy, but the speaker shouldn't have already answered it during the talk, either.

Simply setting this goal is usually enough to keep me focused and engaged with the talk, even in the face of poorly-designed slides or, heaven forbid, Comic Sans.

The downside being, I don't manage to figure out dinner.

What I've learned in the last 24 hours

1) If a reviewer appears batshit crazy on the first round of review, you should not assume that you can reason with or placate him/her. Madmen are only enraged by appeals to logic. Get the reviewer rejected before resubmission or you will regret it, forever.

2) Chocolate chip cookies, standard recipe: after substituting in 1/2 whole wheat flour in response to the Mom-voice in your head, also add 1/4 tsp ground cardamom. NOM.

3) Synecdoche, New York is not, as its title might suggest, a charming pastoral about the vagaries of upstate.

Dr Jekyll's Guide for Reviewers

Thanks for agreeing to review a paper for Glamour Biology! Forthwith, some suggestions you may find helpful for your reviews.

1) There sure are a lot of techniques out there these days, aren't there? We don't want you to be deterred by the prospect of reviewing a paper whose central technique is unfamiliar to you. So we'd like to encourage you to apply the standards of your technique to other techniques in the field, whether or not you have any experience with them.

For example, if you request an experiment from the authors of a manuscript, and they decline to do it on the grounds that it is technically impossible, you have every right to insist. Pushing authors to accomplish the impossible is the only way science progresses!

2) Similarly, different biologists study different organisms. Again, don't let this get you down! If you review a manuscript in which the model organism is different than your model organism, you are encouraged to suggest that the authors expand their study to include your model organism. This is a great way to foster communication among biologists.

3) Our special checkbox review portion asks you whether you think this manuscript would be equally appropriate at a more specialized journal, i.e. Unglamorous Biology. Some reviewers have mentioned concern that they think Unglamorous Biology and Glamour Biology are actually equally respectable. Um, ha ha! If this is your concern, please contact the editorial office straightaway so that we can put you on an internal list. This list isn't for any purpose, just that we like to keep track.

4) Think that the authors didn't read your first review carefully enough? Here's a handy tip: during re-review, write the critical point in ALL CAPS. That way, the authors won't miss it.

5) Sometimes, a manuscript lacks a certain je ne sais quoi. What can you say? Perhaps it's just not feasible to explain your underlying dissatisfaction with a manuscript. Your best bet in these circumstances is to be vague. Don't try to detail experiments that should have been done, or questions that need to be resolved; this will only clutter up your review. Just say that the manuscript is "unsatisfying" or "needs work" or "lacks a certain something." Most authors don't like being told to do additional experiments, so avoiding any detail on this point will help them feel better about your rejection.

6) Do the authors have a Nobel Prize? If so, we will EZPass(tm) their submission so that it goes right out for review, and you as a reviewer are encouraged to overlook any inconsistencies in the interests of expedience.

7) We're regularly asked by prospective reviewers whether the fact that they've been declared non compos mentis disqualifies them from reviewing. Not at all! The pool of possible reviewers is so very small; also, we do not like to exclude people on the basis of intellectual discrimination. That would be wrong.

8) We know that we just rejected a paper from your lab. Still, no hard feelings, right? Could you please review this paper? From a competitor? That looks suspiciously like your rejected paper?

9) Any questions, just hold onto the manuscript you're reviewing until an answer comes to you! We don't want you rushing into any rash decisions.

10) Please don't question our authority to make decisions. All of the editors here have rigorous scientific training, and the fact that none of us was ever able to publish our own scientific work in a journal like Glamour Biology gives us the proper respect for the high standards to which these submissions must be held. We are unbending in our defense of this journal's scientific rigor mortis.


All the best,

The Editors

Life's little mysteries

What genius thought it would be a good idea if two major microscope brands (Olympus and Zeiss) used opposite conventions for which direction you turn the knob for "focus down" vs "focus up"? So that after you are accustomed to one and have to use another, you end up wasting half your time focusing the wrong direction, or if you are very lucky, crashing the expensive 63x objective into the specimen?

Anyone who wants to clear this up for me, go right ahead.

When the PI's away....

What happens in your lab when your PI goes to a conference or vacation for a week or longer? (Or if you're a PI, what do you imagine happens in your absence?)

For the most part, of course, people just keep working. We're not there to please a boss, we're there to get our science done, and the boss's presence or absence makes little difference.

But on the basis of very little evidence, let me offer this hypothesis: in labs with involved, ever-looming PIs, lab members are more likely to skeeve off work when the PI is gone for significant periods; whereas in labs with fly-by PIs, lab members keep up their pace when said PI is gone.

(There could be two explanations for this hypothesis, if true: first, that the trainees with omnipresent PIs work harder when the PI is in town, necessitating a break when s/he's gone; second, that the trainees with absentee PIs sometimes don't even notice that their PI has vanished for a week or two, because it makes so little difference in lab life.)

I hasten to add that I, of course, work virtuously and steadily, unaffected by my PI's absence, much less by absurdly warm and sunny days that occur during said absence.

Blog Fodder update

Some of you may have been wondering how Blog Fodder, our haplessly ignorant tech, has been doing. Last I spoke of him, this Ivy graduate was learning how to use a pipetman, revealing remarkable deficits in conversion factors and even arithmetic of the simplest sort, unwieldy with his hands, and dismissive of animal welfare.

I am happy to report that he has cleaned up his act a great deal. His fine-motor skills are somewhat improved, but more importantly he has figured out how to compensate for his shakiness. I still wring my hands when I watch him do anything delicate, and he's slower than I would like (on some tasks where speed is important), but he doesn't biff everything he touches any longer.

I haven't dared to watch him do conversions again, so I don't know how well he's learned the necessary arithmetic. The jobs I give him either don't entail making calculations, or rely on protocols with the calculations pre-done, and if he's screwing up other people's experiments, I don't know about it.

He appears to have figured out pipetting.

He has become the go-to tech for the animal colony, and it became clear that his initial stupid comments were due more to awkwardness, or mild idiocy, than actual disregard for animal welfare. Recently he wrote an email to the animal facility director pointing out some problems with the animal care in our room, and requesting specific improvements.

He is still slow to understand what I consider straightforward instructions, but those of us who supervise him have taken to making sure he writes down what is said--and then reads it back to us--so that we know we are on the same page.

What has caused his improvement? I would like to think he was afraid of my wrath, but in reality I think there are several causes.

1) He became more at home in the lab. We all know the experience of joining a new lab and feeling ignorant and out of place. Some of us perhaps learn sooner than BF did, but he did eventually adapt.

2) As we got to know him better, we made more use of some of his previously unappreciated skills. He is extremely neat, and he keeps various benches and cabinets about 1000% cleaner and better organized than they had been before. Once we saw this, we started asking him to do more organizational tasks.

3) He has many friends who went to work in the financial industry. I suspect that in the last six months, he has come to value having a steady job more than he did at first.

4) This is his first serious job, as far as I can tell. He may have simply needed to learn what having a job is all about.

He still shows little to no interest in the intellectual life of the lab, but while it is nice to have techs who care about the science, they can be time-consuming in their own way (since they always have questions about what's going on), so this is only moderately disappointing. I wouldn't recommend him to another lab, particularly, but I no longer dread dealing with him. I'm hopeful that he will someday figure out what he is truly excited about, because science is not for him, but at least he's reached a sufficient competence level for us.

What have I learned? That pampered undergrads in their first tussle with the workplace can actually learn to be decent citizens, I suppose. That's useful to know, even if I never again wish to watch this process in action.