One way of looking at it

I should say up front that my (male) postdoc Advisor has beeen nothing but supportive of both the general notion that the postdoc is a good time to have children, and the specific instantiation, that Dr Hyde and I are planning for IVF. I'm really grateful that he's so awesome.

Still, talking with him is distinctly different than talking with my (female) GradAdvisor.

Scene: Most lab members absent on various trips etc. Advisor pulls up a chair near me.

Advisor: So, Jekyll, how is your health?
Jekyll: It's fine...We're planning on trying a cycle of IVF in November.
Advisor: How does that work, exactly?
Jekyll: Well, I'll have daily shots of hormones to increase egg production. Then they extract the eggs from me, inject one of Dr Hyde's sperm into each egg, wait a couple of days, and put them back in.
Advisor: Wow, I didn't realize it was so involved. Tell me, how do they get the eggs out? Is it with a needle? [gestures at abdomen]
Jekyll: Erm, no, they go in vaginally.
Advisor: [brightening] Oh, so at least it's not invasive.
Jekyll: ....


Confidential to my male readers: Lying back half-naked with your legs in the air, having a guy poke around in your ladyparts, is a truly context-dependent activity.

What's so special about seven?

There are the Four-Figure Wonders (Nature, Science). There are the Go Ahead and Publish Your Last Eight Years of Work in 16 Figures Plus Three Tables (some society journals).

But the majority of mainstream biology papers I've seen contain seven figures. Why?

It isn't as though research just naturally falls into seven figures. Putting together a paper, we often struggle to rearrange the panels for maximum intellectual impact, of course, but we also aim to put it into the magic seven.

The last paper we sent out contained seven figures. One reviewer pointed out that two figures could be plausibly combined; and then suggested that we accumulate enough more data to produce another figure. We did, and we did. Reshuffle, and bingo--still seven figures.

(Speaking of bingo, I'm playing Palinbingo Thursday evening--who's in?)

It's clearly an accepted convention (and yes, there are 6 and 8 and 9 figure papers. But the mode in my field, for sure, is 7.) What are the pluses and minuses?

On the down side, from the author's perspective, it's silly to shoehorn your Great Ideas into a prefab structure. Maybe your paper would unfold best in 5 very dense figures, or 10 thinner ones. But because of the norms, I would hesitate to send out such a manuscript (of course, I'm a junior postdoc; maybe when I'm a big fancy pants person who gets mentioned on YouTube has her own grant I'll have the confidence to buck convention.)

As a reader, though, I rather appreciate it. Especially if I'm skimming a paper, I like to have a sense of how the scientific argument will build, and how many experiments will be synthesized into a picture.

It's kind of like reading a novel: you know that when your hero is trapped in a perilous situation, but you're still gripping three hundred pages in your right hand, that this will not be the final test. Conversely, when the lovers are separated by cruel fate and the pages have dwindled to a precious few, the resolution is not likely to be happy.

Not that any science papers I've read have involved lovers, or peril, but you get the drift.

Here's what I would like to know: how did we converge on seven? The old papers I've read are idiosyncratic--the four figures, or the sixteen, at authorial whim. Do we gravitate towards 7 because of its mystical qualities? (That'd be embarrassing, for us rational scientists.) Have our psyches been colored by the 7 Dwarves, or the 7 Deadly Sins (all depending on your childhood, I guess)?

I don't know the answers to these questions, but since 7 is so powerful, next time I write a manuscript I'm going to try for 7 subheadings, and 7 sentences in the abstract, and maybe 7 supplementary movies. If the voodoo works as expected, then I'm predicting reviews like, "I don't know why, but this paper exerted a strange and wonderful force over me."

Science questions posed to Palin

Katie Couric, whom Sarah Palin must by now privately refer to as She Who Must Not Be Named, recently asked Palin what her thoughts were on global warming. (See, that's how I'm justifying yet another Palin-obsessed rant....it's science questions.)

Couric: Is it manmade in your opinion?

Palin: You know … there are man's activities that can be contributed to … the issues that we're dealing with now with these impacts. I'm not going to solely blame all of man's activities on changes in climate.

Well, that's reassuring, to know that our activities are not due to climate change. Quite a load off, what?

Yeah, yeah, yeah, she misspoke, and two sentences in a row that appear to be attributing man's activities to climate change is obvs just a flustered gaffe. So let's ask about evolution now, shall we?

The portions of the Couric interview that have shown up in video clips display Palin agreeing that evolution is a serious scientific theory and should be taught that way, awesome. But then you read the transcript for the parts that are still on the cutting room floor:

Couric: Should creationism be allowed to be taught anywhere in public schools?

Palin: Don't have a problem at all with kids debating all sides of theories, all sides of ideas that they ever - kids do it today whether … it's on paper, in a curriculum or not. Curriculums also are best left to the local school districts.

Nice how she puts it off onto "the kids" to debate. But what we're hearing here, plain and simple, is "The nasty atheist Feds should get their mitts off our school curriculum, so's we can teach The Word of Our Lord alongside the librul science hoohah!" HMMMM.

Finally, I think that most scientists accept that homosexuality is an inborn genetic trait, like brown eyes or curly hair or, um, heterosexuality. Catch this from Palin:

Palin: But as for homosexuality, I am not going to judge Americans and the decisions that they make in their adult personal relationships. I have, one of my absolute best friends for the last 30 years who happens to be gay. And I love her dearly. And she is not my "gay friend." She is one of my best friends who happens to have made a choice that isn't a choice that I have made. But I am not gonna judge people. And I love America where we are more tolerant than other countries are. And are more accepting of some of these choices that sometimes people want to believe reflects solely on an individual's values or not. Homosexuality, I am not gonna judge people.

Yep, that's right. Them homos and their screwed-up "choices." God love 'em!

Not that we expected otherwise, but I thought you might like to have your scientist talking points together for your next cocktail party or swing state recruiting trip.

Link to the transcript.

Terminal terminology

All fields of specialized endeavor use jargon. It's not inherently a bad thing; we need to have short-hand ways to refer to ideas or principles that have developed over years of research.

There are obvious problems with jargon, like how it raises barriers to entry--you can't read the papers of the field until you get the jargon, but you can't get the jargon until you've read enough papers, etc.

But a specific problem we've had recently (writing this paper which had better go out tomorrow or I will shriek) is with a stock phrase which is standard in our field, but slightly inappropriate for our purposes. However, because it is such a standard phrase, we fear that trying to replace it would anger or confuse our reader(s).

The reason we were unhappy with this stock phrase is that it reflects the field's history, during which a lot of research was focused on certain easily studied preparations. We work on a different preparation, which operates under different functional principles than these "canonical" preparations. However, the language of the field has been shaped by the historical research, and is therefore vaguely misleading when applied to our own findings.

In fact, one of the arguments we're making in this paper is that not only is the language of the field biased, the thinking is as well. Many people have been so focused on the "canonical" preparations that they've neglected to recognize that greater biological diversity exists (or perhaps recognized but not embraced).

Anyhow, we took a few passes at coming up with a new jargony phrase, but the effort felt akin to inventing new wheel shapes, so we gave up. Not only would most scientists prefer to use the field-approved jargon, we doubted that we could even think up a truly accurate replacement phrase. (Although perhaps we could have found one that was less inaccurate.)

In the end, while we failed to revolutionize field jargon, the discussion helped me realize that some of the jargon we use conveys not only a concept, but also a whole contextual framework in which that concept is embedded; and that our ongoing use of jargon sometimes traps us in an outdated intellectual framework.

I bet this is the sort of thing the humanities people figured out in, like, college.

ps) physiologist bonus points for guessing the phrase. two words, one hyphenated.

The vision thing

Quarreling with Advisor over figures. The primary reason: Advisor needs reading glasses, but refuses to get them. Axis legends are usually in 8-point font. Hilarity ensues, or what would pass for hilarity if we weren't on a very very tight deadline:

Advisor: I just don't think that's going to photocopy well. [Meaning: I can't read it.]

Take the poll!

Advice requested: manuscript changes

So here's the deal. Reviewers asked us to do some experiments. Done. Now we're revising the manuscript.

The new findings do not change any significant conclusions of the paper, although they have helped to constrain possible explanations for our phenomenon and thereby prompted us to be more specific with one of our hypotheses (which is only presented in depth in the Discussion).

Therefore, in my initial revision, I added appropriate parts to the Results and revised/added to the Discussion, but I didn't touch the Intro.

Advisor is suggesting significant rewrites of the Intro and also some of the Results (even portions that aren't related to the new data): not to add in allusions to the new data, but to improve and clarify sentence structure and word choice.

I'm annoyed by this plan. Two reasons:
--I was proud of the manuscript because although Advisor had driven me to rewrite it many times, a lot of the writing was still mine, however edited. So I'm cranky about the proposed changes from (I'll admit) a partly protective, ego-driven standpoint. I feel like this rewrite supplants my voice with Advisor's. I realize that FSP has touched on this attitude recently, but I don't think I'm just being a prima donna here. Though maybe?
--We're on a deadline, and I think we should focus on rewriting and tuning up the new bits. Time is tight, and I don't want to spend it evaluating the Intro unless it's necessary.

Can I get some outside opinions here? Should I just bow to the presumed greater wisdom of the Advisor and suck it up? Do you rewrite unaffected manuscript portions when you have a "revise and resubmit"? And a tight deadline?

Or should I tell Advisor to go stick these revisions in outer Wasilla that I don't find the revisions effective and would prefer to change only the relevant sections? Is that just silly? I'm maybe being blinded by my protective feelings towards the manuscript, but also I don't think the revisions are significant improvements.

Who moved my chair?

I am confident that if a corporate-style self-help book were to be written for lab scientists, it would be entitled Who Moved My Chair?

Most of you are familiar with the setup. You spend a significant part of your day at the bench, microscope, or culture hood.

At this station there is a Chair. The Chair has five wheels, is covered in vinyl, has at least eleven levers underneath, and was sent from Satan, or facilities management.

One of these levers controls the height of the Chair. When you want the Chair to elevate, you stand slightly and pull this lever, at which point the Chair fails to do anything, until after repeated yanks it shoots upwards and hits you in the butt, causing you to topple forwards.

When you want the Chair to sink, you pull up on this lever while bouncing on the seat like a fun ride, or a small child struggling with sphincter control. If you are very thin or the Chair is particularly recalcitrant, sometimes you have to perform a more complicated maneuver, like putting your knee on the seat as though restraining a struggling crime suspect, and repeating the pull lever-bounce action.

At least this is what you would do, if you could ever find the right lever. Instead, you inevitably pull the wrong lever, which has the effect of tilting the whole seat forwards and depositing you on the floor. When, rubbing your tailbone, you get back up to fix this problem, you will never be able to find this same lever again.

Instead, you will find the BarcaLounger holdover lever, which causes the back of the Chair to give way behind you, causing you once again to slide to the floor.

At this point, you take advantage of your location on the linoleum to gaze at the underside of the Chair, hoping to take a scientific approach to figuring out the levers once and for all. You spot a strangely shaped lever, more pole than paddle, and grab it triumphantly. This must be the up and down lever! you think. You straddle the Chair, since it is now too tilted to actually sit on, and yank confidently on the new lever.

Nothing whatsoever happens.

In your frustration and rage, you stand up and start shaking the Chair by the armrests. In the process, you accidentally press new levers that cause the armrests to detach entirely, leaving you waving them about concernedly as though you just ripped the arms off a baby, while the Chair watches with amusement.

For a while, you utter profanities that, if there were any justice, would melt vinyl.

Eventually, you calm down, sullenly reattach the armrests, and wait until the lab is empty. Then you scoot your Chair over to the bench of someone junior to you and make off with their Chair, which looks positively angelic by comparison. You discover that their Chair is in fact a little too short for you.

You decide to live with it.

Busy busy busy

I'm burning the candle at both ends right now, not much time for substance. (Although if I were inclined to substance, it would run thusly: Do the freshmen actually get stupider each year?)

Instead I leave you with a question.

The Onion writers:

Satirists?

Or psychics?


hat tip, some libtard commenter over at the Kos.

Tumult II: By when??

The Manuscript of Uncertain Fate has now met a Different But Equally Uncertain Fate.

We are invited to revise and resubmit, blah, blah, told we should address reviewers' questions, blah, do any additional experiments to strengthen the paper, blah blah, due back by Sep 29, blah blah WAIT WHAT?

Entering activity level Frightened Scamper.

IVF 3: Aspirin

Among the many medications our IVF doc lists as important is low-dose aspirin. Every day during the IVF-month-of-hell.

What's the evidence for this recommendation? Doubtless, compelling articles like these:

* Low-dose aspirin does not improve ovarian stimulation, endometrial response, or pregnancy rates for in vitro fertilization.

J Exp Clin Assist Reprod. 2005 May 31;2:8.

* Low-dose aspirin use does not improve in vitro fertilization outcomes in poor responders.

Fertil Steril. 2008 May;89(5):1113-7.

Oh, oops, those must be the wrong ones. Maybe the good doctors were thinking of this paper:

* Low-dose aspirin does not improve ovarian responsiveness or pregnancy rate in IVF and ICSI patients: a randomized, placebo-controlled double-blind study.

Hum Reprod. 2005 Aug;20(8):2211-4.

No, crap, I meant to cite:

* Pregnancy-related death associated with heparin and aspirin treatment for infertility, 1996.

MMWR Morb Mortal Wkly Rep. 1998 May 15;47(18):368-71.

Erm. And under the category of "Articles that make you think scientists have too much damn time on their hands":

* Evidence of absence or absence of evidence? A reanalysis of the effects of low-dose aspirin in in vitro fertilization.

Fertil Steril. 2008 Jul;90(1):71-6.

* Low dose aspirin and IVF: 'Is it time for a meta-analysis' continued?
Hum Reprod Update. 2008 Sep-Oct;14(5):537-8.

Offerchreissakes, people. Let me help you out: YES it's time for a meta-analysis, NO you're not going to find any effect of low-dose aspirin.

Either I am psychic, or a marginally successful PubMed user, because lo and behold:

* Pretreatments before the induction of ovulation in assisted reproduction technologies: evidence-based medicine in 2007.

Ann N Y Acad Sci. 2008 Apr;1127:31-40. Review.

JG Bromer and friends publish this timely (pour moi) meta-analysis. Abstract:

Studies were limited to women treated prior to undergoing controlled ovarian hyperstimulation in IVF cycles with low-dose aspirin, metformin, growth hormone, oral contraceptives, or corticosteroid supplementation versus placebo or no supplementation.... We conclude that, currently, no clear evidence indicates that using any of these pretreatment modalities is superior to no treatment in IVF cycles.

So to recap: Some studies have shown that low-dose aspirin increases IVF success, with the hypothesized mechanism being increased blood flow to the uterus. Meanwhile, several more studies have shown that (a) aspirin does not increase blood flow to the uterus, and (b) actually aspirin doesn't improve IVF success at all. AND MIGHT KILL YOU. But whatever!

Meanwhile, of course, my doctors still recommend it. And when I say "recommend," I mean the same way they "recommend" I don't drink while trying to get knocked up.

What's a girl to do?
Go with the doctors? Or go with the evidence?
Do what she's told? Or think for herself?
Cave to the Establishment? Or be free, free like the motherfucking wind?

Yeah, you guessed right, I'm taking the aspirin. As Dr Hyde helpfully points out, "You won't die of stroke that month."

The thing is, aspirin is one of the world's oldest drugs. I know it's safe, which is a lot more than I can say for the cow hormones I'll be injecting into my ass.

And frankly, given the giant headache this is going to be, a little aspirin might be nice.

For you gay musical lovers

And by "gay" I mean "sprightly, lively."

A YouTube of Obama staffers singing to Les Mis.

Somehow the first time I watched it I was kinda "eh" but then I watched again, and again, and now I'm addicted.

Tumult I: The reviewers said what?

We finally found out why the official response on my manuscript was "No Editorial Decision At This Time."

Turns out, although all three reviews were quite positive, only one of the three reviewers recommended that the manuscript be published in this journal.

The other two recommended the dreaded "Appropriate for a more specialized journal."

I was rather shocked by this news. These (now totally loathed) two reviewers had written things like

" I found the results interesting and intriguing. They represent one of the first serious attempts to understand poogly-plugs at the cellular level. Thus, the work is of great importance and interest to the poogly-plug field. In addition, I believe that these findings are also of broad interest to researchers outside the poogly-plug field."

(Props to drdrA for the poogly-plug terminology.)

Also, both of these reviewers had given suggestions for a couple of experiments, and a couple of discussion points, to strengthen the paper. I always thought that if you were recommending "revise and resubmit" you would include these comments, whereas if you were recommending "turf it down a level, losers" you would be more likely to critique the novelty or the general interest of the findings.

A mystery indeed.

---
edited 9.15

Slough

Up until now, I've enjoyed being in a new lab for a post-doc while getting the GradLab papers out the door; my days are spent playing with new experiments, while my evenings and weekends are spent writing, revising, figure-making etc. It's been busy but I always feel productive--if experiments are stalling, at least I can make progress on publishing, and vice versa.

The last couple of weeks, though, I've hit the wall. After GradAdvisor and I got one paper out the door last month, I've been focusing on our third (and penultimate) paper together. This one has an unusual property: I lay out the figures, and they look great. The "storyboard" fits together nicely in my mind.

But when I sit down to write, it's like grasping pudding. The beautiful arc keeps slipping away. Each paragraph is knotty, or else blandly uninformative.

In part these problems arise because this manuscript requires me to pull together diverse literature, much of which is unfamiliar to me.

The main issue, though, is that I'm trying to write on a part-time basis. I'm confident that if I plunked myself down for two weeks straight with a pile of papers and a computer, I would have a spiffy draft at the end. (Okay, I do have a draft--it's the version in my thesis. The story's mutated since then, plus the standards for submission are much higher than for stuffing in a destined-for-microfilm thesis.)

But experiments in the post-doc lab are ramping up in excitement, and productivity, and my mental energy has drifted to the Big Picture--for my post-doc. Not my grad work. On top of that, it's now time to return to working on my previously submitted paper, which needs some more experiments and revision before resubmitting.

So I'm finally reaching the point where I wish I hadn't started this post-doc so quickly after graduating. I'm still very happy in NewLab, just feeling pulled in twelve different directions at once and inadequate for all of them.

I'll think of it as good training for being a PI.

W00TY-WO0T-WOOT!

Close on the heels of doubledoc's awesome day, we just got reviews back on the manuscript we submitted to One-Tier-Down. Because a kind-of-related paper recently came out in C/N/S, I was worried ours would get shot down.

It might be counting my chickens before they publish, because the official response was no decision yet, but all three reviews were quite positive and the editor just seems to want reassurance that we will throw in a couple more experiments to keep our paper exciting.

We fully expected to be asked for these types of experiments anyhow, so we're happy to oblige. Even though the manuscript's not accepted (so I shouldn't be celebrating....), I think this will end well. Huzzah!

Why didn't we become journalists?

Dr Hyde and I were discussing this evening a mystery: why is it that we don't know any journalists?

We both went to the greenery-draped schools. Many of our college friends headed off to be doctors, lawyers, consultants, i-bankers, etc. But we couldn’t think of a single one we knew who even considered being a journalist.

What’s that all about? When did journalism become so disrespected?

It's not like we only hung out with bio-nerds, either. Most of my friends were politically active; off the top of my head I can think of three or four who regularly wrote columns for the student newspaper. They majored in political science, or in English. But none of them ended up being a journalist.

For that matter, anyone with an inquisitive frame of mind (check!), a passion for finding the truth (check!), and a good grasp of language (check!) is well suited for journalism. But Dr Hyde and I both became scientists instead. As did most of you readers.

I was prompted to write about this because DrdrA was pointing out some of the dreadful hypocrisies the O'Reillys of the world have gotten caught in lately. But again--why is it that the Daily Show does a better job ferreting these out than any "real" news organization? Why aren't any of my peers working at NBC or CNN and fighting to get some reality on the air?

Yes, the television is owned by corporate overlords with terrible agendas, but the same can be said of the healthcare industry--but we have plenty of doctor friends fighting the good fight.

When I hit a low ebb of fear (as when I see the Right get all excited about joy-oh-joy Sarah Palin being President one day), I often think that I am failing my country by being a scientist. I should be out fighting for everything I care about--by engaging in the political process for real, not just sending O another $100 and writing snarky blog posts.

The only thing that holds me back is that I'm utterly awful at political arguments--I get too angry to continue. Today Advisor opined that we should be drilling in ANWR and off-shore and everywhere else, and it was just hypocritical of the Dems not to. I kept my cool, but barely...