Telephone

The classic children's game of Telephone, in which one person whispers a sentence into the ear of another, who then whispers it to one more person...and so on until the last person in the chain repeats an incredibly garbled or unrecognizable version of the original sentence, is meant to teach children the danger of repeating rumors.

(I don't think that lesson ever "took" with me, but that's not the point here.)

Here's the grown-up version:

Person 1: "Hey, did you go to that seminar this afternoon?"
Person 2: "Yeah, it was pretty good, I guess."
P1: "I was stuck doing experiments. What'd they talk about?"
P2: "Well, the gist was that they think that walnuts are more bitter than pecans because of their shape."
P1: "Huh, really?"
P2: "Yeah, and they did a couple of experiments to show it. First they ground up walnuts and reformed them into the shape of pecans, and the taste-testers found them less bitter than regular walnuts; and then vice versa."
P1: "Whoa, really? That's a surprise, but what if you're changing the chemical composition by the grinding?"
P2: "Yeah, they had some kind of control for that, but I can't remember what it was."
Person 3 [wandering by]: "Are you guys talking about that seminar? I was confused by the talk because I'm not sure they ever actually proved that walnuts really are more bitter than pecans, and it's not just an artifact of the aroma."
P2: "No no, they addressed that in the experiment in the second half with the plugged noses."
P3: "No, I thought during that experiment the eyes were blindfolded but the noses weren't plugged."
P2: "What?? No, they definitely plugged the noses. I think."
P3: "I was pretty sure they blindfolded people instead."
P2: "Really? I could have sworn they plugged the noses."
P3: "I guess I could have missed it, but I don't think so."
P2: "Was that on the slide with all the blue on it?"
P3: "The second slide with a lot of blue, not the first slide."
P2: "I only remember one slide with a lot of blue."
P1 [bewildered]: "So did you guys believe the data, or not?"
(Simultaneously) P2: "Yes." P3: "No."

What's funny is that these scenarios occur even when both seminar attendees are smart, interested in the talk [read: awake throughout], and well versed in the literature.

It's hard to believe that eyewitness testimony is ever considered reliable.

Great expectations

An eye-opener from this paper rejection: while I am disappointed and frustrated, the "grown-ups" (PIs) without exception are quite happy.

GradAdvisor: "Once we strengthen the paper with the functional experiment and a few other things, it's really going to become a great paper. It got rejected because the reviewers thought that if we wanted to overturn the textbooks, we had to provide exceptionally good evidence. And we will!"

PostdocAdvisor: "I don't understand why you are sad. They left the door open, right [for de novo submission]? Anytime that happens, I am just ecstatic, because I am expecting the door to be slammed in my face."

CollaboratorPI in another country: "I think this is quite good news."

Although I am a bit chagrined not to receive the commiseration I expected to get from a paper rejection (and bonus nutty reviewer), it sure is educational.

The PIs seem to have one thing in common: they are all taking the long view. It's a small setback, they say, but the interest the reviewers express in the main finding is terrific, and though it may take some time and trouble to strengthen the paper as needed, the end result will be just that: a stronger paper with greater credibility.

It's harder for me to feel any enthusiasm for these reviews, presumably because I'm a trainee and take a shorter-term view of the results ("I'm going to have to sink a helluva lot more time into this project.") But I respect these PIs, and their opinions are starting to help me look ahead, rather than at my plodding feet.

So that's my droplet of education for this week.

I has a frustrated

We got reviews back on the paper we submitted last month, and it was a "soft" reject--a rejection with an invitation to submit anew if we radically expand the paper and do about 7 more experiments.

Two of the reviewers were perfectly reasonable. They want to see some functional relevance of our finding, plus one or two other quite small additions. The third reviewer, on the other hand...took the liberty of listing several major experiments we needed to do, and announcing that not only would we need to do all of them for publication in the current journal--but we would need to do all but one for publication in a different journal!

In other words, "Don't think that you can just publish this one level lower, because I'll be on your ass about these experiments anyhow." Gee, way to use the anonymity of peer review to threaten that similarly bad reviews will follow us wherever we go.

In addition, this reviewer made some fairly outrageous requests--the most mind-boggling being that we should replicate our main finding in a different, "higher" species. You know, because who the heck studies our stupid organism? (DrdrA, didn't you get a similar weird critique once?)

I'm frustrated for many reasons. First, that this nutjob reviewer may have made the difference between "revise and resubmit" and "reject." This is the first time I've had an outright obstreperous reviewer, and boy does it burn.

Second, that the functional experiment everyone wants to see is going to be technically rather difficult. I understand its importance, but I'm less sanguine than GradAdvisor that we can do it.

Third, that I had thought the worst outcome for this paper would be rejection, after which we'd do a couple little experiments, and resubmit it at the next tier down. It's probably the last first-author paper of my grad lab, and I want desperately for it to be off my plate. But since GradAdvisor wants us to try the revise-and-expand route, it will be on my plate for many, many more months--and I'll be spending some serious time on difficult experiments. All the while I'm trying to get my postdoc experiments done.

I sort of wish that GradAdvisor would call the editor for a chat, just to get more information (did the normal reviewers vote for revise/resubmit? were there other comments we should be aware of? does the editor realize how insane a few of Crazy Reviewer's comments were?) but that doesn't seem to be the plan. I don't really understand how PIs decide whether to bug editors about decisions or not.

I am tired and feel trapped into doing a bunch more experiments that I'm not sure will be workable...but because all the reviewers wanted to see functional results, I don't think we can just submit the paper one tier down and get it published as is. And two tiers down would seem a bit silly for what we think is a major, textbook-changing finding. But I think if I refuse to do all these experiments, GradAdvisor will find someone else to do them, and I will probably lose first authorship, which is not acceptable to me at this point.

So, back to the bench it is.

Is asking about budgets as rude as asking about salaries?

Although Dr Hyde and I have both had fairly forthcoming advisors on topics large and small, the one topic that we find we know nothing about is:

How much money do our advisors receive each year in the form of grants or other funds, and how is it budgeted?

It's not as though we never discuss grants. I know how many grants my current advisor has and I also know what outside funding sources are paying a few trainees' salaries.

But I have literally no idea how much money these grants add up to per year, nor do I have even a hazy grasp on what fraction of the budget goes to salaries, equipment, or mousekeeping. The same is true for Dr Hyde, and again he has a quite outspoken PI who shares plenty of other pieces of information.

Obviously, we both need to get better informed if we are ever to put together our own proposal packages. I would also like to know more just to have a sense of what the impact is for the lab if I want to spend, say, $5000 on a piece of useful but not totally necessary equipment. I know we happen to be flush right now, but how flush?

So this is an etiquette question. Is it ok to approach my advisor and say, "I'd like to learn a lot more about lab budgeting and management so that I'm better prepared for an academic future--can you give me the approximate annual budget for this lab and tell me what percent of it is spent on various costs?" Is this rude, like asking about his salary? Is it just awkward, like asking about his dental work? Obviously I would try to time the question well, but I just don't know if it's something I should ask at all.

And it's still just odd to me, that with all the perspective and advice I've gotten from my mentors on how I would eventually want to run my own lab, none of them has ever told me how much money I would need to do it.

Why forgetful Advisors are a good thing

Many people I know complain that they will propose an exciting experiment to their advisor, only to have it shot down summarily. Then a few days later, the advisor comes by and says, "Hey, I had this great idea for an experiment...." and proceeds to detail their own proposal.

I've never had this happen. In fact, both of my advisors have been generous with intellectual credit almost to a fault. And yesterday my Advisor managed to provide almost the reverse scenario as what others complain about:

One month ago
Advisor: Yes, these will be tricky experiments. Let's see, here are a few possible ways you might get around the problem....X, Y, Z, Q, R, S.

Jekyll: Yeah, I'll see what I can do.

Yesterday
Jekyll: Hey, Advisor, you know I've been having trouble with X, Y, Z, and Q, so today I figured I would try R, and you know what? I think it might work for us.

Advisor: Wait, so you mean you could use R to get around this experimental problem? Why that's completely brilliant! That is a wonderful idea indeed!

[pause]

Jekyll: Uh, Advisor, I think you actually suggested it a while ago.

Advisor: Really? I had totally forgotten.


I suppose I could have kept my mouth shut and improved the next rec letter Advisor writes for me, but it hardly seemed worth it. Advisor was clearly happy, if embarrassed to have forgotten his own suggestion, and pleased that it might work.

Besides, I think his rec letter is pretty damn nice anyhow.

Clearing the decks

I've been busy this week preparing for the presentation I told you about and getting a significant piece of writing out the door. Both are finished now, and I am left with the strangest sensation:

There is nothing I need to write right now.

For the last ~2 yrs I've spent most Saturdays (and not a few Sundays and evenings) attached to my laptop, writing and rewriting one thing or another. The past month was one piece of writing; the 3 months before that were a paper that we sent out in December; the 9 months before that were the paper we published last fall; the 3 months before that were my dissertation--etc.

Of course, some Saturdays were taken up with experiments to sort out details of these papers and so forth, but the gist of it is--this is the first weekend in a very long time that I have woken up and thought, "Hey, I don't have any writing goals this weekend."

It was disorienting. We went into lab and I puttered around doing basic lab catch-up things that I've had to cram into the work-week (or haven't done at all--e.g. certain types of equipment maintenance....). When I'd accomplished what I wanted, we went home and I didn't even turn on my computer, let alone try to rework an abstract or find an appropriate reference or tweak a figure or check some statistics or.....It's not even that I dislike writing (the sensation of pushing a final product out the door is deeply satisfying, and I learn so much in the process) but there's just always something to do.

We should be getting reviews back on the most recent paper within the next couple of weeks, and no matter the result there will be work to do. And when that's over, there are some lingering things in GradLab I should still deal with, and so on. This is just a brief respite, the eye of the hurricane.

But oh my, it feels rather nice.

Today's pet peeve--special bird edition

Some headlines from the Times:

"Plane was hit by birds"

"Bird hazard is persistent for planes"

"Geese pose big risk at airports in the region"

Yes, it is surely cruel and unfair that the plane was peacefully gliding along at 10 mi/hr before it was horrifically bombed and shredded by the dangerous 150 mi/hr birds.

Did not a single editor wonder if these headlines could have been rearranged? That one might reasonably consider that the birds were hit by the plane, rather than the other way around?

Or there's this article tidbit:

The proximity of the plane to Rikers Island, home to a large colony of noisy, prolific and seemingly indefatigable Canada geese, suggests that the birds could have been involved.

This is undeniable truth. Geese are noisy, prolific, and seemingly indefatigable. Thank God we have quiet, mousy, easily-tired airplanes at LaGuardia and JFK.

I just wish it weren't right before a major deadline

I have the opportunity to give an unusual type of talk to my fellow postdocs and graduate students. The invitation is explicitly to discuss both our recently published scientific findings and the process by which we developed them. How did we decide to pursue this line of inquiry? What problems did I encounter, and how did I solve them? What was the biggest challenge of this project, and how did I get around it?

I think it's great that my postdoc association is encouraging talks in this format. Discussion of career issues, as I think you'd all agree, is critically important for scientists at all stages, and this talk provides a forum for "what best serves to advance your science" sorts of questions. So I was happy to agree to give the talk.

But because the talk is non-standard format (and because a reasonable portion of the audience is expected not to be in my particular subfield), I can't just recycle the powerpoint from previous talks.

What do you think the best set-up for such a talk is? My tentative plan is to spend the first half (~15 min) or so giving more or less my regular scientific talk, albeit with more explanation and less detail to accommodate the non-MyFieldists in the audience. Then I want to give the talk again, but in the order of how it happened, and what actually motivated our steps from one experiment to another, rather than the standard scientific Well Thought Out Post Hoc Justifications that I use in the first half.

That is, in contrast to the first half of the talk which will begin, "This system we study is of vital importance and we wanted to understand the mechanisms underlying one of its most salient characteristics," the second half should start something like, "I had finished up one project and was just messing around with ideas for another project, and really had no idea what I wanted to do...." etc.

For the second half, I'll put the figures in the order they were actually done, and I'll highlight the point at which the project turned the corner from Random Observations in Our Corner of Science to Hey We Have a Cool Paper Here (brilliant feedback from a member of my thesis committee, as it happens.)

What do you think? What would you most want to hear about in a "how it really went down" sort of talk?

A depressingly modest definition of utopia

Many (most?) journals have an explicit reviewer policy which says something like, "If you have a real or perceived conflict with the paper you're signing up to review--for example if your lab is planning to publish a paper on the same topic--then you should decline to review, or at a minimum tell your editor about the conflict so s/he can decide."

It will be a terrific day when all PIs see fit to abide by these principles. Or at a minimum, when those who don't at least refrain from teaching their trainees that of course as a PI you can decide for yourself if you can be "fair" in a given situation, regardless of this "perceived conflict" stuff.

It will also be a terrific day when the schools have all the money they need and the Defense department has to hold a bake sale...oh hell, why do I bother.

Cranky with collaborators

Happy New Year to you all! I thought I'd start this year's blogging off on the right foot, by complaining.

My current lab project is very exciting. We have a significant amount of data obtained via one technique, and the resulting data suggest something that will be of broad interest to the community. When Advisor lays out his vision of the eventual paper, he does so by listing four figures.

However, the findings will be immensely strengthened if we can back them up using a completely different technique. We have a good idea how to do it, too! But--we need a specific experimental material to accomplish this goal. This Material is not something we can whip up on our own.

Another lab has recently produced and published on a few variations of this Material. One of them could be ideal for us. The problem is, in neither the publication nor the supplementary info did this lab provide enough information for us to decide if any of their Materials would work for our particular question.

Advisor emailed his counterpart in this lab, who promptly said that a postdoc would send us the relevant information so that we can decide if we should order any of the (extremely expensive!) Materials.

This postdoc and I have now been emailing for six weeks. Repeated promises to produce and send the information have gone unfulfilled.

I am desperate to see this information. I have sent all the clues that could be useful so that the postdoc can select the appropriate information to send me. However, I can't think of anything I can do to speed the process up. We are the ones importuning another lab for something. I have no leverage, since the postdoc is certainly not going to get publication credit out of sharing this information with us.

If any of the Materials will be useful to us, there is a significant delay--perhaps three months--between our ordering them and the key experiment being feasible.

I am going to a conference in the spring for which these data would be incredibly useful, and I am theoretically having a child in August. Delay is not on my agenda right now. If the Materials will not be useful to us, I likewise need to know right away so that I can start a workaround experiment (which will be much harder and more time-consuming, if it's possible at all).

I understand that I am low on the postdoc's priority list. I'm sure there are many other people emailing this lab for information on the Materials.

Meanwhile, I am impatient and helpless. 2009 is not winning my heart just yet.

Hiring humanities-style

My college roommate recently finished her Ph.D. in Renaissance studies. She and I met up today and, as we often do, ended up comparing and contrasting the academic life in the sciences versus the humanities.

In particular we discussed the new faculty hiring process. As many of you probably know, the annual Modern Language Association convention is a hotspot of hiring committees. Here's how it works.

1) Nearly-finished graduate students and postdocs send applications to programs that have announced interest in hiring junior faculty.

2) The faculty hiring committee selects perhaps 10-20 of these applicants for a first-round interview. "Meet us at the MLA. We'll be in Hotel X Suite Y!" they say.

3) First-round interviews give the committee a chance to weed out anyone who is less impressive in person than they were on paper. Perhaps 3 of the candidates survive this cut.

4) Those 3 candidates are then invited to the university on the standard expenses-paid two-day interview with a talk, faculty meetings, and perhaps a demonstration teaching opportunity.

5) Someone is hired (or not).

Compare to my department's setup, where the hiring committee labors long and hard to cut all of the applications down to 5-6 people, each of whom will be invited for a two day on-campus interview.

The advantages to the two-step hiring system are obvious.

a) The department only ends up flying 2-3 serious candidates out, as opposed to the 5-6 for our bio department positions. Costs cut in half.

b) Along with that, fewer schedules need to be coordinated for serious candidates--the usual "is all the hiring committee in town on a date that the candidate can visit?" bit is cut in half. The committee needs to be available for 2-3 days at the MLA, which they might well have attended anyhow, and then just a few on-campus dates.

c) The committee can also afford more risk-taking on the first round. Because people pay their own way to the MLA, there is no added cost (besides an hour or two for the interview) to interviewing a controversial or apparently borderline candidate.

d) In fact, the committee can also invite Europeans or Australians etc with no added cost, in marked contrast to the hiring process in my department. Again, this increases the opportunity to find a gem of a candidate who isn't from a Big Name lab, and whose application just looked a bit "risky."

Of course, I'm just a postdoc and I've only watched hiring committees in action, not served on one. What do you think? The two-step process offers many advantages and I can't think of any disadvantages, as long as your field holds an annual convention with significant attendance (as mine does). The initial costs of interviewing are borne by the candidate who flies to the conference, and the committee has a much better idea what they're getting before they invite people out to campus.

My roommate, incidentally, was one of two people invited to an on-campus interview at her target school, and she proceeded to knock the faculty's collective socks off. They voted unanimously to hire her. They said that even if she declined, they would not hire the other guy at all. (She found this all out after the department chair accidentally cc'ed her on an email to the Dean about the salary range they could offer this new hire. My friend, having seen the max they were willing to offer and the interest they had in hiring her, successfully negotiated the maximum salary. She is awesome.)

Anyhow, I am curious what the advantages are to our more expensive and arguably more conservative, "only Nature paper and BigShot recs need apply" approach.

Coloring outside the lines

The more prestigious the journal, the more likely it is to have draconian word and even reference limits. (Just kidding, PLoS! You're totally prestigious too.) This is especially true of brief-format style articles, like the one GradAdvisor and I are currently writing.

I am by nature a follow-the-rules sort of person, but GradAdvisor had this to say as I proposed hacking our current manuscript down to the bone to meet the journal's requirements: Put in everything you want in the first version. Otherwise, you run the risk of pissing off reviewers by not including enough information for them to evaluate the paper properly. Also, if you cut the reference list to meet some arbitrary standard, and your reviewers' publications are the ones that get cut, you could be in trouble. If the manuscript is accepted, you can always trim later.

I find this advice both hilarious and frightening. Hilarious, because it's absurd to conjure a situation where critical information is included for the reviewers--but not for the final (hopefully larger?) audience. Frightening, because, same reason.

Is this how you also approach tight length limit manuscripts? Obviously try not to be egregiously beyond limits, but otherwise figure that you'll cut it down if necessary? And if so, do you think this is a bad sign of how publishing operates--pleasing the reviewers if not the world? (Not you, PLoS! I know you already thought about how terrible this is.)

Of course, besides better reviewer mojo and sheer laziness, there is another reason not to cut the manuscript to size quite yet: if it gets rejected, the next journal down the pipe has longer word limits.

We're in Detroit, stealing your money

Andrew Sullivan found a good one. Click to get the text at the bottom, which is genius.

I don't know enough about the auto bailout to know if it was a critical stop-gap or a giant money squander, but either way this is hysterical.

IVF 17: One bun in Dr Jekyll's oven

Well, we cheated. We've been doing some home pregnancy tests this week. You have to be cautious about interpreting them because the hormone being tested for, human chorionic gonadotropin (hCG) is also part of the IVF regimen as a shot to trigger ovulation. hCG is estimated to clear out of the system with a half-life of about 28 hrs, meaning that if you had a trigger shot of 5000 units (as we did), it will take at least 10 days for the exogenous hCG to drop below testable levels on the home pregnancy tests.

So we waited until 14 days after the trigger shot for our first home pregnancy test, which was Monday. Two lines! One faint, but clear. We had a three-pack, and on Tuesday morning the line was stronger, and on Wednesday morning even stronger. hCG levels rise dramatically during early pregnancy, so this was reassuring. Still, we waited to celebrate until today's blood test, which is quantitative rather than qualitative.

And the good news--we are way past the "dubious" hCG level and are officially 4 weeks and 2 days pregnant! Huzzah!

This means that back when I was posting angsty perorations about IVF, I was technically knocked up. Creepy.

It is a bit bizarre to have so many people know that you are just barely pregnant. The whole family knows, of course, as do a number of our friends and most of my work colleagues, just because this process was too complicated and emotional to hide. As my mother said, "Yeah, at 6 weeks pregnant I was just thinking my period was running a bit behind."

In any case, although it is still many weeks before the nerve-wracking first trimester is over, we are grateful and happy to have come this far.

I don't plan on blogging much about the pregnancy itself, in part because I want to get back to science blogging, and in part because pregnancy is just not that novel a topic. Of course, I'll let you know if there are any crazy developments. Thanks everyone for your encouraging comments.

Author, author!

We are readying another paper from GradLab for publication, and dealing with that age-old problem, authorship.

This paper began when a tech in the lab made an experimental observation. Advisor and I thought this observation was remarkable, and encouraged/drove him to follow up this observation with more experiments. He performed admirably, shoring up the original data and adding some new pieces to it.

What would turn this observation into a paper? Advisor and I debated a few different ways that it could become a paper. I did a set of different experiments myself to help flesh out the manuscript. In all, I contributed about 1/4 of the experimental data of this paper. The tech's data represents about 2/3, and remaining technical help from others in the lab rounds out the story.

At about this point, both Tech and I left GradLab. I wrote up this paper for publication, and GradAdvisor and I have been tweaking it for several months.

When I sent the close-to-finished manuscript out to all authors, I listed me and Tech as co first authors, in that order. I thought this seemed like the best solution given that
1) He had contributed much more than I had experimentally
2) He had made the original interesting observation that launched the whole paper
3) I had provided the writing and intellectual drive, plus ~1/4 of the experiments.

GradAdvisor disagreed. "You conceived of this paper, and you should be sole first author, with Tech second."

I was surprised and not a little concerned by this. Should I be first author on a paper whose experimental data is 3/4 someone else's? (It's not as though I'm a theorist!) Yes, the intellectual drive was primarily mine, but it would never have mattered if Tech hadn't made the first key experimental observation--which forms the "cool" factor of this paper; my experimental contributions are nice but not the main point.

A friend of mine familiar with the situation gave me the same advice--that the intellectual contribution was what mattered most, and therefore I deserved first authorship.

Because both Advisor and my friend agree, even over my objections, that I am selling myself short on authorship, I am changing myself to be sole first author. But I still feel a bit as though I cheated Tech out of a joint-first authorship. Will this fade over time as I come to recognize the primacy of intellectual over experimental contributions? Or will I keep feeling guilty that I got a "free" paper?

In the end, I wrote one of those "author contribution" sections that you see occasionally nowadays, and this left me feeling better. It is now public record who contributed what to this paper (although of course the intangibles remain just that). This decision has helped reconcile me to the authorship order, because I no longer feel as though I'm pretending to have done more than I have.

Now I just have to break the news to Tech...