Dr. Jekyll & Mrs. Hyde

Two points

2009-07-16T22:03:00.000-07:00

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

2009-07-15T21:15:00.000-07:00

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

2009-07-11T20:46:00.000-07:00

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

2009-07-08T21:36:00.000-07:00

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

2009-07-03T18:17:00.000-07:00

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

2009-06-28T07:59:00.000-07:00

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

2009-06-22T10:26:00.000-07:00

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

2009-06-19T21:55:00.000-07:00

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?

2009-06-13T13:38:00.000-07:00

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

2009-06-10T13:30:00.000-07:00

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

2009-06-01T11:04:00.000-07:00

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

2009-05-24T08:46:00.001-07:00

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

2009-04-29T07:10:00.000-07:00

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

2009-04-27T20:14:00.000-07:00

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

2009-04-23T21:38:00.000-07:00

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....

2009-04-20T21:05:00.000-07:00

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

2009-04-15T21:37:00.000-07:00

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.

I am in love (a pregnancy post)

2009-04-12T20:04:00.000-07:00

With Zoe Williams, whoever she may be. All I know about her is that she writes for the Guardian, and that I love her.

I have been spending off hours on PubMed, trying to discover the rational basis for the host of rules pregnant women are adjured to obey:

--Don't eat unpasteurized cheese (Brie, Gorgonzola, feta, chevre...all the good stuff)
--Don't eat deli meats unless they've been heated to steaming
--Don't even think about licking the bowl clean of cookie batter
--Sushi? Do you want the baby to die, or what?
--Lying on your back past the fourth month is going to give the critter brain damage
--A sip of wine? Why not just smoke crack and be done with it?

I'm not talking "old wives' tales your grandmother produces." These things are specifically listed as fetal death-traps in publications ranging from the leaflets I was handed at the ob-gyn to "What to Expect When You're Expecting," probably the single most popular pregnancy book available.

But here's the funny thing. When you look for actual studies about these things on PubMed, you keep thinking that you've entered the wrong search terms, because so little comes up.

For example, many a pregnancy site will tell you that sleeping on your back when preggers will cause pressure on the vena cava, decreasing blood return to the heart and causing all kinds of mayhem to The Little One. What does "pregnancy sleep supine" get you in PubMed? A lot of articles on SIDS, and this saying that blood oxygen drops in pregnant women sleeping on their backs. The same group also says that these lower oxygen levels don't cause any more apnea or less REM sleep, leaving one to wonder exactly what the problem is.

A couple of physicians have gotten so bemused by the onslaught of patients asking them about sleep position that they wrote this piece, opining that back sleeping would only be a problem in a small minority of women, and even for them it was unlikely to cause fetal harm.

Ms. Williams, a tart-tongued Brit (aren't they all?) with a strong sense that the world is deranged, makes the argument that a lot of these rules are based on astonishingly modest evidence, and in fact sometimes directly contradicted by other bits of evidence. She's particularly lit up about listeria, the reason so many foods (unpasteurized cheese, deli meats, and sushi) are verboten, and relays this from a professor of fetal medicine:

Jauniaux cites an interesting difference between Google hit rates and those on PubMed, a collected source of peer-reviewed papers in medical journals. "Listeria and pregnancy - Google, 190,000 hits; PubMed, 107 hits. Cheese and listeria - Google, 194,000 hits; PubMed, 169 hits. Sushi and pregnancy - Google, 628,000 hits; PubMed, 0 hits. Raw fish and listeria: Google, 123,000 hits; PubMed, 49 hits. You can see immediately," Jauniaux concludes, "the disproportion between the epidemiological evidence and the general public hysteria about the disease."

Americans in particular are obsessed with the "right" foods, despite our national inability to figure out what those are, and I think this is one reason that pregnant women here readily accept restrictions on their diet: we've been trained since birth that food is dangerous, and eating the wrong thing will surely give you cancer/make you fat/blemish your skin/diminish your virtue. The idea that pregnant women have to be even more careful follows naturally. Meanwhile, if you told a French lady to avoid Brie, or a Japanese one to shun sushi, you might trigger premature labor due to hysterical laughter.

Of course, it's one thing to say that a lot of these prescriptives are junk, and another thing to be comfortable flouting them. I made my decision to ignore these rules after an internal conversation along the lines of:

Self: "If you miscarry or the critter has some serious problems, are you going to spend days berating yourself for the salmon sashimi?"
Self: "Uh, no."
Self: "Okay then, carry on."

Obviously if your pregnant self responds differently, then it seems reasonable to stick with the guidelines.

But my sushi-eating, feta-nomming, back-sleeping, wine-sipping ass is pretty happy here at the half-way mark.

ps) Don't tell Dr Hyde that the toxoplasmosis bit is farfetched too, as I have no intention of terminating this vacation from cat litter duties. There's skepticism, and then there's stupidity.

At least I haven't set up an Auto-Reply function yet

2009-04-11T14:07:00.000-07:00

It is sad to learn what managers the world over know, that you will spend far more time managing the incompetent than managing the competent--the competent, of course, not needing you very frequently.

(Unrelated:
The rain it raineth on the just
And also on the unjust fella,
But chiefly on the just, because
The unjust steals the just's umbrella.
--Ogden Nash, or Lord Bowen, depending on your Internet)

I was thinking about this because I am hemi-demi-semi- in charge of an upcoming event, meaning that my email is on a relevant web page. This event's webpage has almost every conceivable type of information on it. It is thoughtfully and professionally organized. It is fairly easy to find information about the event.

And yet I have gotten thirteen emails from one would-be attendee, and at most two from anyone else. Virtually all of Incompetent Correspondent's emails have asked me questions that are answered on the website.

I typically respond to these emails with a link to the relevant portion of the website, only to get a response back that says, "I found Information A there but now I want to know about Question B. Where can I find that information." Gee, whaddaya know, there is a link on that website that provides the answer to question B! It's bafflingly successful, this Internet linky thing.

If my correspondent were particularly old, I would have more sympathy, but in fact IC is a graduate student. The point-and-click business should be straightforward by now.

So I spend 80% of my event-related effort answering emails from this nitwit, and 20% responding to other nice, competent people.

I begin to understand the mindset of PIs who simply stop responding to their trainees' emails, although that is of course a very very bad way to deal with the burdens of management however much I might like to do it.

Working without a net

2009-04-05T10:09:00.000-07:00

Prompted by a few comments on the last post--

Of the many difficult things you learn in graduate school, one of the scariest is that you, and you alone, are truly responsible for what you publish. The logic, accuracy, and weight of what you write are yours to furnish--or not.

I do not mean to say that your PI is not also responsible for your work. His/her name is on the paper too, and if it tanks, the blame will if anything fall more strongly on your advisor, as the senior author.

But as first author you are the one with direct interaction with the actual data. You collect it. You make little tweaks to your protocols to improve your data collection. Are any of those important? And did you do what you thought you did--or did you write one thing in your lab book and pipette another into your eppendorf?

You borrow a colleague's reagent, or code. Does it work as promised? And what makes you sure?

As you're collecting data, you make some snap judgments about experimental success or lack thereof. Is the problem that you put in the wrong concentration of a reagent? Or is the data real, but anomalous, unexpected? Should you trust it?

You analyze the data, and you are the first one to make decisions about what data can and should be excluded; your PI will likely weigh in, but you are on the front line. Are you excluding that data point for legitimate reasons, or because it doesn't fit your hypothesis?

You put the data into graphs. Do those graphs show your data as honestly as possible, or are they covering up something that makes you uncomfortable? When you show your data at lab meeting and someone questions your results, who is right? Is their objection valid, or do you have a better counter-argument?

Some of these questions will be resolved by talking it over with your PI, your lab colleagues, your thesis committee, or even by your reviewers. But in your development as a scientist, at some point you cannot rely on others to catch your mistakes. You will get conflicting advice from the people you talk with. You have to weigh up this advice and eventually reach your own conclusions about the best answer.

This is just plain scary. The fear does not arise out of nowhere. You do actually have to take responsibility for results that you may have gotten wrong. It would be strange if that fear did not haunt you from time to time. (I think impostor syndrome, at least in part, arises when the fear becomes continual and uncontrolled.)

When I was an early-stage graduate student, fretting over these concerns, I asked a visiting speaker during a student lunch, "How do you gain confidence in your own data?" Her advice was along the lines of, "Repetition; experience; and talking to all the smart people you can." She was right, but the best part of the interchange was hearing a highly respected scientist acknowledge that she, too, had faced that struggle--and in some ways still did, as she grappled with understanding and shaping her trainees' experiments.

Sending out my first manuscript was transformative in this respect. When we got page proofs from the publisher, it was suddenly clear to me that the assertions and arguments that I had written (and then had heavily re-written by my PI) might be read by someone, some day. Perhaps other people realize this rather obvious fact earlier in the game, but it took the formatted page proofs to stun me into it. My advisor gave lots of feedback and shaped the paper in diverse ways, and the reviewers nudged it as well, but it was now clear to me that in essence, I was working without a net.

I don't think I've been the same since.

It turns out I'm ok with being 2nd

2009-04-01T07:51:00.001-07:00

The other day my GradAdvisor said to me, regarding the exciting functional experiments I'd gotten working, "You are now the world expert on [this stuff.]"

When you start graduate school, you think it will be a thrilling moment when you realize that you are the world's expert on X.

But in fact it is a tiny bit depressing. If I am the world expert at X, and to be perfectly honest the amount I know about X could fit into a sake cup, world expertise is not what it's been cracked up to be. Not to mention, if a dolt like me is the world expert, this is a sad commentary on scientific affairs.

Of course, I imagine that as I progress in my career, the scope of X (where X is the things I know more about than anyone else) will broaden. I just hope that as X broadens, I grow more pleased, rather than more horrified, with the idea that I am the Expert.

New and used

2009-03-25T21:02:00.000-07:00

I'm in charge of purchasing a piece of lab equipment that will cost ~$10,000. I'm the only one in lab who has extensive experience with this piece of equipment, but it will primarily be used by techs to do some of the more tedious work of the lab.

We are demoing models from two companies. Both models are quite nice and seem to do the job just fine. There is hardly any price difference between them.

However, Company A also sells a nicer model with some bells and whistles. We are demoing that as well. I didn't think we would want it because it is an extra $1500, and because I am by nature suspicious that "extra bells and whistles" eventually means "extra reasons to call for repair." The bells certainly improve the instrument function, but not by an extra $1500 plus likely increased repair costs if needed.

The rep from Company A just emailed me to say that she could give me a quote on the actual demo model of the Fancy Version. It clocked in at $9000, a solid $1000 cheaper than either of the regular models and nearly $2500 cheaper than this model would normally cost.

To recap, the options are thus:
Company A, normal machine: $10K
Company B, normal machine: $10K
Company A, Fancy Used machine: $9K

Apparently the service contract is only 6 months with the used vs 1 year with the new machine, but these things never break in the first year anyhow.

So, dear readers: how do I evaluate the worth of a piece of used/demo equipment? The offer is tempting to me, but I am going to kick myself in the head if the Used Fancy machine ends up breaking a lot due to wear and tear. The machine looks pretty nice, nothing is obviously amiss with it, and it is not a very complicated machine to begin with--but how should I decide if this is a good deal?

Also, the lab has plenty of $$ so I am probably overthinking this in my pennypinching way, but I'd welcome general thoughts on whether it's worth buying demo equipment or not.

Car advice

2009-03-21T09:31:00.000-07:00

Not a science topic this time....

Dr Hyde and I are proud owners of terrific, 27 mpg-overall Accord. We love the car and she has been very reliable.

There are two problems. 1) She has only two doors. 2) She is 19 years old.

If this whole child thing works out, it will be time to change vehicles. The question is, what to buy?

Here are the parameters:
--We are urban people and our instinct is to get the smallest car that will do the job.

--We do not live in a location where "no car" is an option, nor are we likely to move to one in the near future.

--There are several grocery stores and parks within easy walking distance of the house; we typically use the car to go to lab on weekends (when transit doesn't run), to go to more exotic grocery stores, to go out to dinner, and to visit Dr Hyde's sister and family. I imagine that all of these except visiting Dr Hyde's sister will fall by the wayside for a while after infant arrival, although there will be pediatrician appts etc.

--We might be moving to a snowier climate next year, so the Mini convertible is out. Boo.

--Based on what we see and the Consumer Reports car issue, we're most excited about the following cars, all in a hatchback or "5-door" format: Honda Fit, Subaru Impreza, Mazda 3, Nissan Versa. However, some people suggest that these cars are too small for 8 lb babies, who apparently arrive with 80 lbs of accessories.

--We are ok with buying a smaller car now under the assumption that if we have a second child or move to a more car-dependent location, that we will need to embiggen or buy a second car.

--We're ok with used cars up to about 4 years old. We could afford to pay $20K for a car, but we'd prefer $12-$15K, since so much money is lost to depreciation, and anyhow the baby's just going to puke on the seats.

Anyone own one of the cars listed above and have thoughts on its suitability for our situation? Anyone own a baby and have thoughts on car selection?

Part (b), amazingly grouchy

2009-03-18T22:19:00.000-07:00

Mostly I enjoy the way that labs are not standard workplaces and therefore we can wear sweatpants to work, turn on music from time to time, play stupid bouncy-ball tricks in the hallway, etc. But when friction arises due to non-standard activities, it becomes much harder to resolve because there's no equivalent of a company manual for our free-wheeling activities.

This may be because we express our freedom in personal fashion. E.g., we may be free to play music in lab, but musical tastes are highly personal, and therefore lab disputes over music can be difficult or impossible to resolve.

Lately in my lab we have run into precisely this sort of problem, where I find someone else's expression of freedom to be disruptive. Let's pretend that the disruption is a cell phone, although it is only a useful analogy.

Although many people bring their cell phones into lab, most everyone puts them on vibrate or quiet rings. One person, however, has a piercingly loud cell phone set to the most annoying ring you can name and receives five or six calls a day.

Requests to turn down the ringer, or perhaps not even bring the cell phone to lab, have been largely ignored. The person occasionally quiets the cell phone for stretches, but then somehow it eventually ends up back on Loud. After enough complaints, the ringer is only on its second-loudest level, but by now I have been conditioned to hate the ringtone, so this is cold comfort.

When I have a low tolerance for irritation, and am trying to concentrate on technically difficult experiments, the cell phone rings again and again. I go berserk, the person who owns the cell phone gets defensive, and things go downhill. Obviously the situation had escaped control and it was necessary to bring in Advisor to reconcile the problem.

It's been interesting to see how what first appeared as a benefit of labs (freedom! no company manual!) has now wasted everyone's time as we worked to resolve a problem that would not have been tolerated in any standard workplace. I'm no corporate shill, but I do occasionally wonder what we might learn from their basic management practices.

However, then I recall Office Space and decide that a few cell-phone arguments might be a small price to pay for not having to wear a minimum number of pieces of flair.

And in any case, I have the sneaking suspicion that people's interactions never will run smoothly, no matter how thick the company manual. Although if I were to write one, there would certainly be a rule about cell phone ringers.

In which I am (a) amazing

2009-03-18T21:54:00.000-07:00

Under the threat of scoopage, I worked all day Saturday through Tuesday in GradLab, and YES! I got the key functional data that we thought might be impossible. N = 4, will probably try to get one or two more but since the experiment is a proof of principle and doesn't need much quantitation, this is sufficient to revise our mostly-rejected manuscript.

I also managed to get some extra N for other reviewer-requested experiments that were already underway. I am feeling pretty damn smug.

However, zero weekend + streaming cold + pregnancy means no Nyquil + waking up coughing every 30 min + stress about revisions + angst regarding assorted lab issues = razor thin tolerance for irritation when I returned to PostdocLab today. Naturally, the karma bank took the opportunity to get some money back.

Expect the next post to cover (b), amazingly grouchy.