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.