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.

Lazy CRISP question

Let's say that I am looking for a second postdoc. Let us stipulate that as a smart, DrugMonkey-trained bioscientist, I am making sure to check the status of a possible future PI's grants on CRISP.

Let us further suggest that this PI has one R01 that will last a while (but isn't on the stuff that really grabs me), and another R01 (on the stuff I love) that is due to expire in March of 2009.

How do I find out if this R01 is getting renewed? Would it already list an expiry date of 2014 if it had gotten renewed? Presumably by now the PI has heard back on the renewal, but would it be in CRISP already? I have every reason to think that this PI is deserving and has published enough to survive a competitive renewal. If it weren't that our banks are on fire, I would feel confident...but as it is...

(I should mention that I feel sure the PI would have applied to renew this R01. It's not a defunct part of the lab's activity.)

Protocol protocol

Everyone who works with animals is supposed to regularly fill out and update Animal Care and Use Protocol forms that detail precisely what is happening to experimental organisms in the lab.

These protocol forms require description of the experiment, a thorough explanation of how the animal will be treated or sacrificed, any analgesic/anesthetic usage, and an estimate of how many animals per year will be treated in this fashion. There is also a section asking you why you can't do your experiments in "lower" animals or with computer modeling.

Filling out these protocols can be a bit tedious, but the second step, in which the animal committee asks you to clarify or fix what you wrote the first time, often takes even longer. Missing dosages, inappropriate anesthesia, etc are the frequent points of concern.

Now, I'm about as animal-rightsy as anyone working on rodents can be. I take seriously even psychological stress to these critters. So I'm happy that the animal committees demand thorough accounting from investigators.

In theory, these protocols must be filed and accepted before any experiments start. However, because PIs have many uses for their time, and because no one is monitoring the lab on a daily basis, and because researchers often want to start different lines of experiments without waiting for approval, in reality every PI I know fills out an animal protocol form only after the technique has already been in use for some time in the lab.

I would go so far as to say that I have never known a PI to fill out an animal protocol form ahead of experiments, except if the animal department requires the protocol before allowing researchers access to a certain room. Or perhaps when a researcher arrives at a new location and simply doesn't have animals to work with until the protocols are approved (though even then I have seen people sneak around this by getting animals from other labs).

Is there a better way for this to work? Pragmatically speaking, I just don't see any way that full protocol approval prior to experimental modifications is feasible. Labs just won't operate on administrative timescales. What if there were a way to file a sort of Notice of Intent, the way that eateries have to post their applications for liquor licenses before they're actually approved? The Notice of Intent form could be quite short--brief methods description with a comment like "We're piloting this method to see if it will be useful."

The animal committee could take the Notice as an invitation to visit the lab and make sure the investigators knew what the hell they were doing. Then there would be a time window--say two weeks--from the Notice after which investigators were required to file a real protocol amendment or to cease these experiments.

Advantages:
1) Less unregulated work. We all know it happens; we like to imagine that people are respectful of animals even in absence of real protocols; but it's never a safe assumption.

2) Not filing a Notice of Intent could become a serious offense, whereas I've never heard of anyone getting busted for starting their experiments without a protocol in place--because inspections are so rare. But since there would be no excuse for not doing it (ie no time delay between filing and starting experiments), it would be hard to defend if you were caught working without one.

3) Prompt visits from vets/other relevant people following a Notice of Intent filing could help investigators refine their protocols from the beginning, rather than following a back-and-forth with the IACUC several months after the lab has already decided how to do its experiments.

I don't think it could ever happen. It's convenient for everyone to live under the fiction that experimenters only function with approved protocols--neither the PI nor the animal committee need rush to get protocols in place, and meanwhile science goes on its merry way.

But it's sort of sad to me that everyone does operate under this fiction, because I think it engenders routine disrespect for the "meddling busybodies" over at animal care who make you change around your protocol to meet the established standards. Because of this disrespect, some trainees learn implicitly that their goal is to shield the lab from careful scrutiny, and to evade the animal care folks when they visit.

I can't think of any better solutions though.

----

Headed on a week's vacation to home town and environs--happy Presidents' Day to you all.

Trainees training trainees

Today a tech asked me to look at one of her experiments and give my opinion. It became clear that there was a significant artifact contaminating and obscuring whatever real results might have been present. I explained to the tech how she could recognize that this was an artifact, not an acceptable result.

(For those who are wondering, this is not BlogFodder Tech. He is shambling along in mediocrity and exhibiting zero interest in the intellectual life of the lab.)

I then tried to figure out how this artifact could have occurred. It was quickly apparent that the tech was preparing the samples incorrectly, and that this error likely produced the artifact. However, I only noticed that she was making an error in this step of sample preparation because she was mid-task; due to the nature of the mistake, if I had only looked at the final product, I would not have thought to ask her about the possibility of this error.

The error that she was making was quite egregious and when I was trained in this same technique, I was explicitly warned against committing it. There are two possibilities:

1) The person who trained her warned her about this error, but she forgot or thought it wasn't important.
2) The person who trained her didn't warn her.

If scenario 1 is true, this tech is careless, but her carelessness would not be apparent until a lot of time and effort was spent troubleshooting her problem (there are several other steps that could have caused this particular artifact, and they would be considered more likely sources of error). Eventually, if this sort of thing happened enough, I would conclude that the tech should leave the lab. This would be regrettable, but it happens.

What if it's scenario 2? Though most people who could have trained this tech would have warned her not to make this mistake, it's possible that she was trained by the lab's undergrad, who might not have mentioned it.

This is the sort of thing that worries me about lab management. As a PI, you obviously want to trust your lab members to train each other on basic tasks. At the same time, you need to keep up the quality control, which can be difficult if you see the end result and not the process.

In the best situation, I think, the PI trusts other lab members to train new lab members, but still invests significant time, especially at the beginning, in working one-on-one with new trainees. In fact, this is more or less how my current Advisor operates: he was constantly checking in (up?) on me in my first six months in the lab, but has left me more to my own devices of late, now that he is confident I am performing well. (At least, I hope that's the reason.)

But in my experience, PIs are far less likely to invest this time in techs, for understandable reasons (tech duration in lab is often only 2-3 years; techs may be less scientifically engaged; and of course, the main reason one gets a tech is to deal with stuff that you don't want to have to spend time on!) This is where the quality control issue can really fester.

Perhaps the simplest solution is to have a trusted lab member act as direct supervisor to the tech, but this only works in cases where the tech is primarily helping one person, rather than serving as technical support on a few techniques for many people in the lab. I don't know how to keep high standards in that situation, because relying on eagle-eyed lab members to spot problems in someone else's benchwork seems like a recipe for trouble.

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.