I am in love (a pregnancy post)

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

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

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

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

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

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

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

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.

Science would be so great, if it weren't for other people

We just got word through the grapevine that our recently rejected paper has some competition. A similar finding is under review at another journal.

So now it's a frenzy to try to get some data nuggets of sufficient interest to warrant resubmitting our manuscript, an option the editor left open. We have a couple of these nuggets already, but the key one that should vault this paper to (some) security is missing, and we don't know if we can get it or not.

Meanwhile, it's unclear whether Competitor MS is going to be accepted at this other journal or not. We don't have a lot of details from our mole. Thus I am going to be ear-deep in GradLab research for the next week or so, digging to find out if we can get the clincher experiment and revising the manuscript as I go.

Of course, my co-authors are going full-tilt to help out, and my current Advisor has offered good advice about approaching the editor, so I guess it's nice to have some other people in science.

Just not the pathetic losers who are unaccountably doing MY experiments.

Quasi-scientific pleasures: Graph Jam

Satisfaction

I've been trying to do an experiment with particularly difficult technical issues for, oh, three months. There have been some other experiments interspersed, but this has been the Sisyphean task. I've made little bits of progress here and there, optimizing parameters to advance the technique, rolling the boulders a little further uphill, but never gotten the key N = 1.

Until today.

I had a hunch this would be the week it happened, but then again I had that hunch last week too, only to be crushed by unexpected problems in a successful, yet unsuccessful, experiment. So best not to read too much into my hunches.

I needed it, too. Yesterday was rough for reasons I'll perhaps talk about another time, and also I was starting to get the feeling that my Advisor was wondering if I would ever pull this thing off. I was wondering the same thing, so I can't blame him, but his confidence in me has been supremely reassuring over the last few months, and I didn't want to lose it.

So, yay! And, phew.

And now to get Ns 2 through 5.

Asking questions: Part 2

In an earlier post, I listed suggestions for grad students too intimidated to ask questions in department seminars. Of course, I missed a target audience, the people who are overconfident questioners. To you, therefore, the strangely self-assured grad students out there, I devote this blog post.

1) Take a question-frequency cue from the size of the audience. 150-person conference? Asking a question after each and every talk is going to make you stand out, but maybe not in the way you hoped.

2) You cannot get away with asking questions the same way that National Academies faculty do. When Dr Professor Mega-Famous Who Wrote the Textbooks asks a question, he may preface it with, "I'm fairly ignorant about this field, but...." Dr PM-FWWT can say this with impunity for two reasons: (1) He actually knows everything under the sun, so the modesty is endearing; (2) He wrote the goddamn textbooks, and even if he's off base with one question, everyone will still respect him.

You do not have the same privileges. When you preface a question with, "This might be stupid, but...", everyone will immediately assume that the question will be stupid. People know from your age/status that you are not a giant in the field; if you apologize for it, you are wasting time reminding people of your ignorance. This is pointless, whether it is genuine or (please no) false modesty.

Dr PM-FWWT is also allowed to head off into abstruse, possibly irrelevant asides during her questions. Again, you, not so much. Avoid at all costs the following real-life examples:

--"And if you don't mind, I have a third follow-up question..."

--"The picture I got in my head from your talk was blurghy-de-blargh. Did I paint that picture myself, or did you paint it for me?"

--"I have a question about methods [that doesn't actually bear on any of the scientific issues, nor is it of interest to more than one other person in the room]."

--"Your work reminds me of elements of recursion just like in Godel, Escher, Bach."

In fact, most any references to Your Work As It Relates to Non-Scientific Literature will make you come across as an ostentatious twit. You are not in college bullshit sessions any longer.

3) If you fell asleep during any portion of the talk, you should not pipe up with a question. Again, you may well have watched Nobel prize winners snore through a talk, wake up and ask a surprisingly on-topic question. It is unwise to assume that you have their skills.

4) Leave the wiiiide open questions for Dr PM-FWWT. For example, after a talk introducing a new exciting technology, you should probably not ask, "What is this really going to be useful for?" You might try a narrower question, such as, "I can see the utility of this technology in This Field Aspect. Are there other applications as well?" That is, try to avoid questions that are so open-ended that they suggest you haven't thought about the talk at all.

5) If someone presents a seminar focused on a series of experiments showing that Phenomenon X is not due to Explanation Y, but instead Explanation Z, and your eager question is, "In your opinion, what is the best evidence that Phenomenon X is not due to Explanation Y?" you will really sound like a moron. I don't have a generalizable rule from this one, just a memory of one particular nitwit audience member.

Sadly, of course, no one who needs this advice is likely to be reading this blog.

Still, I feel much better for having gotten that all off my chest. I mean, Godel, Escher, Bach, really.

Does sexism get worse as you get older?

One of my female mentors once said to me, "Some of the men out there are good guys when you're a grad student or a postdoc. But when you're a colleague--especially a successful colleague--that's when the tone changes. They're fine when they get to mentor a younger woman, because the balance of power still rests with them. But when they have to treat you as equals, they can't always handle it.

I had this in mind when reading Candid Engineer's recent post, and follow-up, about not experiencing sexism in the workplace. I've experienced only modest issues with sexism, or what I perceive as sexism: not the full-blown harassment crap, but the way that men sometimes talk over women during conversations; that they can be slow to share credit; that they can compartmentalize women in rapid and demeaning ways that make me antsy (e.g., recently someone in my lab referred to a woman in another lab as a "crazy bitch"--language that he might not have used if he were surrounded by women, rather than by men.)

Most male faculty treat me with respect and courtesy, which is great. But my mentor's words linger in my mind. Right now I treat faculty with some deference (I can hear the people who know me falling off their chairs with laughter right now, so perhaps it would be more accurate to say that I treat them with a mixture of deference, ease, and sarcasm, whose relative values depend on many factors). The point is, even when I'm challenging male faculty, I do so from a position of comparatively less power.

Plenty of them may not care at all that I am female. But some of them may be predisposed to be pleasant to me now because the older male/younger female relationship is a well-established setup. The May-December marriages; the father-daughter relationship; and here, the mentor/mentee.

What I don't know is this: when I reach the faculty level, will the same guys who liked me as a postdoc still treat me respectfully as a colleague, an equal?

And if so--how come the junior faculty I know are still predominantly male? Could it be that the leap from postdoc to faculty slices the ranks of women not only because of child-rearing issues and suchlike, but also because the men who were happy to mentor a 25-year-old woman feel threatened by a 40-year-old?

That is, are some men happy for women to go into science--just not to succeed at it?

Lab handicaps

I have never known a person with a significant physical disability who worked in a lab. By "significant" I'm including things like: deafness; confined to wheelchair; missing a hand or limb; etc. Dr Hyde hasn't either*.

This is of course in part due to the fact that bench science recruits from the part of the population with the lowest incidence of disabilities--young, educated, upper/middle class. Why else might labs typically contain non-disabled people? One possibility is that people with significant disabilities recognize that the lab bench will be a particularly tough place to find accommodations, and thus steer clear. The other, darker, possibility is that anyone hiring scientists will avoid taking on someone who requires accommodations.

Here's the relevant bit of ADA law, as found on the EEOC site:

A qualified employee or applicant with a disability is an individual who, with or without reasonable accommodation, can perform the essential functions of the job in question. Reasonable accommodation may include, but is not limited to:

• Making existing facilities used by employees readily accessible to and usable by persons with disabilities.
• Job restructuring, modifying work schedules, reassignment to a vacant position;
• Acquiring or modifying equipment or devices, adjusting or modifying examinations, training materials, or policies, and providing qualified readers or interpreters.

An employer is required to make a reasonable accommodation to the known disability of a qualified applicant or employee if it would not impose an "undue hardship" on the operation of the employer's business. Undue hardship is defined as an action requiring significant difficulty or expense when considered in light of factors such as an employer's size, financial resources, and the nature and structure of its operation.

Boldface mine.

This is purely hypothetical, because I'm not hiring people, but I'm just plain curious: have any of you ever been approached about a job (or grad student position etc.) by someone who would require the types of accommodations listed above? Ever worked with one?

I'm fully supportive of the idea that people with disabilities deserve an equal crack at science as the rest of us, but I'm struck dumb at what would be involved in adapting many types of bench science to someone with a major disability. Wheelchair? Let's start with lowering all the lab benches by a foot or more. Deaf? An available interpreter as needed. Amputee? I don't know, but it would have to start with those damn Eppendorf caps that sometimes defy even the two-handed among us.

So I'm asking out of sheer ignorance. What accommodations would you consider reasonable to implement? Who among the disabled could find a home in your lab? Has someone? Is bench science considered to have a "nature and structure" such that any major accommodation would be "undue hardship"? Are there ways that certain types of lab work could be made more accessible?


* Actually what he said was, "I've sure known some people in labs with apparent mental handicaps, does that count?"

Introductions aren't for discussions

There are two schools of thought on what should be included in the introduction of a full-length paper (i.e. one with defined sections for intro, methods, etc.) The first is that the introduction should set up the problem that the paper addresses. The second is that the introduction should both set up the problem and summarize the paper's findings.

I see a lot of papers in the second category these days. Many authors seem to prefer the opportunity to state their conclusions early, so the reader can make no mistake about the direction the paper is taking.

But I personally prefer the older-school style in which the introduction functions more like the start of a murder mystery, leaving the reader to consider the problem without having an answer immediately presented. It's a trope, of course, because no one on Earth reads the introduction without having first read the abstract, which has already established that it was Professor Plum in the drawing room with the pipe wrench.

But it's a nice trope, even a civilized one. It's as though the author has said, "If you care enough to read this paper start to finish, then let's lay out the groundwork of intellectual premises together, without knowing the foregone conclusions. I'll tell you how I plan to address the question, but not what I found. You can sit for a moment and think about how you might have chosen to approach the problem, or what you might expect to find, without being told my conclusions at the outset."

Besides, there are already at least two other spots in the paper where the authors have a chance to summarize their findings: in the abstract and in the first paragraph of the discussion. Do you really need another?

I understand, of course, that the goal of a paper is to persuade the readership that you've found what you claim, and that repetition of the findings can aid you in this goal, but still and all--I prefer the classic intro.

Then again, I'm still using Pine in a Unix shell to check my email, so you might just want to file this entry under Cranky Granny Jekyll.