8% of my love

In this season of grants, in my first big grant-pushing year, I'm facing problems I never conceived of. One is how much of my time to allocate (on paper) to each of these projects. The basic problem is that you can't have funding for more than 100% of your time... the funding agencies are not willing to break the definition of 100% even for sleep-deprived academics. You have to devote 'enough' time to a grant for the agency to feel you will be a competent supervisor of the research and steward of their dollars, and you have to pick a small enough number so that you can potentially obtain additional grants. You can change the allocation of time you have on a project if you need to after you are funded, but I can't comment on how that affects your program officer's opinion of you and your research, or how that affects your chance of non-competitive renewal.

For shorter grants this is less of a problem; if a grant is funded and I over-estimated my time allocation, the grant will expire before it's a problem that prevents me from applying for additional funding.

I know I'm living in a fantasy world to contemplate this ever being a problem for me. I'm not going to get enough grants to be anywhere near a 100% time allocation in the next few years. However, I have to list my projected time allocation for all pending grants when I submit additional applications... and it's starting to add up. This is also on my mind because I am going to be a co-PI on a grant where the only funding that would come to my lab would be summer salary and travel support for me (no money for equipment or trainees). I am contemplating what percent allocation of my time I have to put down for this project in order to ensure one month of summer salary wouldn't be cut from the budget, while preserving enough of my time for grants I'm submitting that can support students.

I also thought of this because of a recent discussion over at Drugmonkey, where it was brought up that percent allocation could be used as a proxy for "lab with too much money" as a rational reason to give lower marks to grants from very comfortable, established labs. I was an ad hoc reviewer on a grant recently that had two PIs -- one junior and not published at all in the proposed experimental system, and one senior who is the queen of the experimental system. But the Queen PI has so many grants she could only allocate 8% of her time to the proposed research. While I think this PI is very good at juggling her responsibilities, it certainly made me wonder whether she'd give the project the attention and expertise it would need. I have seen grants where subcontractors allocate very low (5%) amounts of their time, but this was the first single-digit allocation for one of the major PIs I'd seen. There were other weaknesses in the grant, it wasn't a perfect, incredible proposal with this being its sole potential flaw...

Percent time allocation to different research projects was something I'd never thought about before this year. I have thought about the amount of time I devote to preparing lectures (too much) and the amount of time I spend writing papers up (too little), but I have always just rotated around my research projects as deadlines demand and my interests dictated.

Now we know what NSF employees had been doing in the low-funding-rate years:

looking at porn at work. One particular employee (no longer with the NSF) spent 20% of his time looking at porn and paying $40,000 on his credit cards for chat sites. Nature's blog refers to the NSF's porn-at-work problem as "systemic."

The ranking Republican on the Senate Finance Committee wants a full investigation of the extent of these abuses of government computers and taxpayer-funded salary before the NSF gets their fraction of the stimulus package... which will more likely result in the extra funding for NSF being cut out of the bill than stalling the stimulus package.

*sigh*

The very first problem I ever had in lab management was that an undergraduate I was supervising was using a lab computer to look at porn. I discovered this because it was his first day and he did not yet have his own account on the lab computers, and so he was using my login. I wasn't snooping on his activities, but the following day, when I began typing in a URL into my browser... a site that I hadn't visited, nor one that I thought was particularly work-appropriate popped up. It's apparently gone offline in the last 9 years, otherwise I would have provided the link. I quickly confirmed that it was a porn site, and since my PI was out of town, I decided to solve the problem by sending the undergrad a polite email that said that some sites are better viewed in the dorm than at work. The undergrad never referenced having received this email, and he got his own account, so I have no idea whether he repeated his salacious websearching.

When I asked the PI about it later, he said he would have not said or done anything about it. I don't think I overreacted, but what would others have done, especially in light of the computers having been purchased on federal grants?

Fixing peer review, part 2

I saw this over at DrugMonkey. Cell, a biology GlamourMag, claims that it is redefining its publication standards and policies in response to the digital publishing era:

One issue in particular that we at Cell will be focusing on in 2009 is redefining what constitutes a "publishable unit" in the age of electronic journals and how we can best present the information content of a scientific article online. [...] The scientific article of the future will no longer be tied to the constraints of a printing press and will take advantage of all the opportunities afforded by the web to introduce a hierarchical rather than linear structure, increased graphical representations, and embedded multimedia. Inherent in our thinking about the scientific article of the future is the need to address the current unchecked growth in the amount of supplemental and supporting material and to identify constructive, well-defined guidelines for what is reasonably and appropriately included in a unit of scientific advance.

I agree with everything DrugMonkey said -- what should be in the paper should be in the physical paper. However, I am heartened by one aspect of expanding supplementary online material: I would like to return to an earlier practice of reporting genetic analyses and require that sequence alignments used in publications be publicly available as supplementary material. This would not take up a large amount of space (the nexus file format, which I would propose as the standard, is both compact and informative -- it will preserve annotations of genomic regions if the authors wish to add them).

How would this improve science, and why is this being filed under "fixing peer review?" First and foremost, it allows future groups to build upon previously published work, and know concretely how their analysis differs from the published work. If you start with a published (as supplementary material online) alignment, and you have a serious problem with aspects of the older alignment (e.g., they neglected to take conserved secondary structures into account), this gives you an important point for discussion to explain why you results do not match up with previous results. We would no longer have to speculate -- we could test such an assertion. Secondly, it will speed up research, as fewer groups would have to reinvent the wheel and re-do the same work that has been done by other groups. And, as I argue in the first point, this does not mean that the published work would be used as an unevaluated black box -- it can, and hopefully will, be critiqued and refined. The reason it is on my mind at the moment, however, is the way this will assist peer review. I just spent far too many hours yesterday trying to replicate an alignment in a manuscript I was reviewing to test a theory I had about a phylogenetic tree in it. If my theory were correct, it would undermine all the paper's conclusions, but I could not see if my theory was even plausible without seeing at least a partial alignment. Had the authors been required to upload their alignment with their manuscript, this would have taken me less than five minutes to check. Under our current system... let's not discuss how long it took. I know some will say that I should have just suggested the reanalysis without attempting it, but I have learned the hard way that if you don't provide evidence (a hint of reanalysis, citations) for your comments in peer review, the authors sweet talk the editor and convince them you didn't know what you were talking about.

When sequence analysis was a new field, journals published the entire alignments in the physical paper journals. This quickly became impractical, as computing power and algorithms advanced, and it no longer was required or encouraged to publish your alignments. However, you are always supposed to supply your alignment to any and all people who contact you after your paper is published, and some attempts have been made at alignment repositories (EMBL's closed in 10/2008). After all, bioinformatic analyses based on nucleotide or amino acid sequences are only as accurate as the alignments underlying them. I think requiring alignments as supplementary online material would be a fantastic requirement for the increasingly digital age. Some journals already require this, but none of those I regularly read or review for. Maybe this is not what Cell meant at all... but I'm running with this.

Plus, I am in favor of anything that improves my time-to-completed-review. (I have peer reviews #5 and #6 of 2009 on my computer today. I need to speed things up or I'll never get tenure)

doing it for love

A number of science bloggers have been pretty quiet in 2009... maybe like me they were working on grants. There's good reason to be more excited about grants in the near term: NSF funding rates might not be as dismal as they have been in previous years, and science funding might be included as part of a stimulus package. Despite the current optimism, people are talking about working without funding, or with very very little funding. And even if the funding taps are opened full blast, there will be hard times ahead (boom-bust funding cycles), and some people will be asked to work on a shoestring lab budget, or work for free. As far/near as I can tell, working for the love of science, not financial security, has been asked of generations of scientists (less now than in the past, it seems)... but it's definitely not the sort of thing we advertise to prospective scientists.

Many of us work in labs for credit, or just as volunteers, as undergraduates. Whether this is a time-honored tradition or exploitation has been discussed in the comments here. Regardless, I don't think many undergraduates would think that this early donation of time is a harbinger of future sacrifices they might be asked to make for science.

In the old days, students paid universities for the privilege of being a graduate student. In some places, those "old days" weren't so long ago; one of my friends has a 2000 PhD and he had to pay for his tuition and went without a stipend for all semesters he wasn't a teaching assistant (and the stipend was very low when he did receive it, but the accompanying tuition remission was a big benefit). Before anyone tries to guess which university inflicted this on him, let me say his PhD was in biology, in an arguably biomedical field, the school is a large state R01, and he was a stellar graduate student. He just happened to want to work in a lab that while well-respected, was not well-funded. He had a previous career in computer programming in order to save the money to attend graduate school and specialize in the field of his choosing. In general, however, grad students today go to programs and labs where they are supported through four (maybe five or six) years through a combination of RAs and TAs, and don't have to go into the same levels of debt as humanities graduate students while getting a PhD. If their PI runs out of funding early on in their graduate career, the students often change labs rather than work for free and wait for the lab to become better funded. These are perfectly rational decisions, but the same financially-sound decision making doesn't apply when you are an older, getting-ready-to-graduate student whose lab runs out of funding. Especially if you had a guarantee of five years of funding from your advisor when you started, and you need a sixth year... it's not uncommon to have to donate your time for a semester, a year at the end of your graduate work.

Until fairly recently, this unpaid last year of the thesis was codified in the UK. PhDs are supposed to take three years, and students receive three years of support, though funding in the fourth year is now more common for biomedical graduate students. For students outside of these well-funded fields, any funding for the fourth year is ad hoc and is not merit-based.

I spent a semester unfunded at the end of my thesis, but that was more my choice than necessity. I defended and could have gone straight to my postdoc, but I wanted some time to destress and to finish up experiments in my thesis lab. I asked my PI to pay health insurance coverage and the registered student fee (this came to less than $1000), and I spent about half of my time in the lab, but came and went as I pleased. I have known students who had more penurious PIs who wanted the students themselves to pay these continuing student registration fees -- while they had no income -- so I consider myself lucky.

Most postdocs would not entertain the idea of working for free, but I have two friends who have done this. The first I have already blogged about, and she is doing a postdoc in her "spare time" while carrying a full teaching load in order to pay the rent. She is doing so in the city where her spouse has an official, paid postdoc. The other stayed in the town in which he did his doctoral work while his wife finished her degree. Both of these friends were unpaid postdocs for two years, and both had a partner with some kind of income at the time. This also took care of their health insurance needs. In both cases, these free postdocs would not be working for free but for their geographic restrictions.

The working for free does not stop once we get professorships. Many PIs go without summer funding -- calendar year contracts are an endangered species outside of medical schools, and summer salary was a routine casualty in the tight budgets at NSF over the last few years. Even when a PI has summer salary in the budget, there are advisors who, in shoestring budget times, choose to forgo their summer salary to give a graduate student another year's stipend and benefits.

There are concrete downsides to our working for love and not money. Many of us are not independently wealthy, and so we incur credit card debt to help us live through our unfunded patches. [Note: even if you receive a stipend you may be eligible for a Stafford Federal Loan while you are a graduate student... many are interest-free until you graduate and it's a much, much better option than carrying credit card debt for years] It harms our ability to save for retirement, build up a house downpayment, do all those fiscally responsible adult things that we see some of our friends doing. It can stress our relationships when we work all day (and night) and yet are not bringing home any bacon. Similarly, working in science and working a second job in order to pay the bills can create a stressful home environment. Yet, I know very very few people in science who haven't worked at least a few months unpaid while pursuing a science career. I have no idea how common this sacrifice is in other careers (especially those that require much less schooling; I know medical students go greatly into debt and might be laughing at this post). Is working for free one of the ways we distinguish the passionate from the complacent? Is this a continual initiation rite that we ask even professors to go through? Has it become more common while we were living in Bush administration budgets, and will it be more or less common in the next few years?

People I'm taking for granted

I have been busy working on grant applications lately, and I want to publicly, if anonymously, thank all of my non-scientist friends for their support as I work through this.

I am grateful for my supportive academic friends, too! But it's something special to get encouraging and inquisitive Twitters from distant friends who don't particularly care what I study. It's important to them because it's important to me... and maybe because I tend to gesticulate wildly when I tell funny anecdotes about my work.

(Besides, my scientist friends are still on the hook to read my drafts... they'll get their thanks later ;-))

The force of PSAs is on our side...

The TV just informed me that January is national mentoring month. January 22nd is "Thank your mentor" day.

It's not good when the things you've been blogging about are part of a problem big enough and hopeless enough for public service announcements...

Professorial Advisory: explicit content

There's a lively discussion over at YFS about various aspects of mentoring and sexism (street smarts, how men pass on information to male students, etc). There is a recurring theme of unstated expectations, of mentors, mentees and of people who are evaluating the junior scientists.

Ideally our supervisors would be true mentors, and want to help us figure out what it is we want to do, and to help us achieve our goals. In reality, professors often only want students who are very sure they want to go research track, in academia or industry. This is largely because professors, especially those earlier in their careers, need trainees who will be motivated to publish many papers, as an ambitious trainee would want to do.

After the mentorship is over, though, what are the benefits to the advisor of the trainee becoming a prominent member of the scientific community? What do advisors need/get from former advisees?

1. Reflected glory and success. Their work is partially attributable to you... when you go up for full professor it will look good that you trained a couple of bright, active R01 assistant profs. Maybe some schools quantify it -- you get to add 10% of the papers published by former trainees to your publication count...
Pedigree can be a very big deal in certain fields, but it primarily benefits the trainee. Sometimes people will say they want a "BigName" person to fill this symposium slot, or faculty position, etc.

2. Someone who owes you a few who is a colleague in your field. Need something onerous reviewed? Want to know the latest review on XYZ without doing a search? Want someone whose vote you can maybe influence on that committee? (That last one is speculation -- the other two I happily do for mentors on a somewhat regular basis)

3. Advance knowledge of the cool results coming out of the mentee's lab. We all want to know new things first!

4. A network of people whom you can rely on to train your future students. If your mentee was a tissue culture savant, send your new student who is struggling to the mentee's lab for a month or two.

But your mentees can't review your grants, probably shouldn't review your papers... there's a potentially lifelong conflict of interest. I suppose the mentee's trainees -- the academic grandchildren -- will not have such conflicts and could be favorably disposed towards the original mentor. Collaborations with former mentees can also be problematic for the mentees. We're supposed to be illustrating our independence in our pre-tenure years, and we have to obtain funding and publish without our PhD and postdoctoral advisors. So there are some things mentors cannot expect from former mentees.

While enumerating the concrete benefits to having successful trainees, I realized, with the exception of reflected glory, they all rely on the mentor-mentee having cordial relationships. Cordial relationships, however, can't just be assumed. Many people have discussed toxic mentor-mentee relationships on blogs, and some (many?) of these trainees survive and stay in science. For instance, one of my colleagues is the most successful trainee to date of his famous postdoctoral advisor, but they left things so badly, they haven't spoken since a very abrupt end to the fellowship. There probably is a positive correlation between getting along with your advisors and succeeding in ambitious academic/industry careers, but it's no guarantee, and no requirement.

Maybe I'm missing something important from my list (please tell me in comments!), but if the major impact that trainees have on their mentors' career success is from papers published while working together... then as long as the mentee pursues a 'sufficiently' ambitious track while with working with BigName, PI... it doesn't matter so much what they do afterwards. Even if they drop out of science to home school ten children... or opt for one of the many career tracks that require a PhD that are not academic research. Yes, someone whose career ambitions won't be advanced by publishing may have trouble feigning enthusiasm for publishing. And if the PI is under the false impression that the student wants to be/should be publishing, the PI will become disappointed, frustrated and perhaps resentful of the student. However, if students are honest about their less-than-R01 goals, many PIs repay their candor by investing less in the student... so what can be done to create realistic expectations on both sides?

I feel it's the advisor's job to train people in the ways and means of science, and it's the trainee's job to figure out how to use that knowledge in their life. We will overinvest in some trainees, and underinvest (a failure of debatable magnitude on our part) in others, but it's our job to invest somewhat in our trainees. Ideally, our trainees also recognize they have a vested interest in their advisor's career success.

Some mentors don't begin investing in trainees until the trainee has jumped through hoops and concretely proven their intentions to stay in science... but that means 1) all the trainees are getting subpar mentoring in their first few years in that lab, and 2) the PI has absolute power in determining what's an appropriate level of sacrifice or productivity to show such intent. I bet these PIs do not reveal their secret formula to their trainees, and I'm equally sure they change the formula, move the line for trainees based on personal prejudices. Would it help mentors to be more explicitly contractual with their mentees? For instance, inform the student early on: "whatever you want to do, I need you to write the first draft of at least three first-authored papers from a PhD thesis." Or: "I expect that you will fulfill your teaching requirement as part of your degree, but I don't like my students to take so much time away from research and I will not support you if you want to TA additional classes."

PI-trainee contracts would also force PIs to think about their expectations and what they are prepared to offer a student. Some of the unconscious mentoring/gender bias issues being discussed at YFS might be resolved if professors had to articulate what it is they do to provide mentorship. They would necessarily become more aware of how they differently treat each trainee, and it could be a step towards limiting unconscious preferential treatment.

I know some PIs who thrive on keeping their students unsettled, on edge, not knowing the PI's expectations... I can't comment on whether that makes the lab more productive, but I am certain it's not useful for the trainees to spend years marinating in stress hormones. I imagine individual PIs would craft their own contracts, reflective of their lab cultures and mentorship styles. Short of that, it might be worthwhile for departments to ask for specific mentoring plans in annual faculty reviews... and perhaps elicit feedback from the students on the mentoring, under the promise of anonymity. But people gossip, and the anonymity would likely fall apart.

I know that some granting agencies have been asking for mentorship plans on training grants, and that could be one of the first steps towards codification of what trainees should expect of their PIs.

I have trouble knowing how honest, how contractual to be with mentees, especially when such discussions are not expected or typical when joining a lab. I feel that if you tell a first year PhD student what you genuinely expect of them over a ~5 year PhD, they will run screaming from your lab and will work for someone who is less upfront with them, even if eventually that PI expects as much, or more. Even if that PI's unstated expectations will cause problems down the line. By the time that student is a 3rd or 4th year, and has enough background and experience to realize that the upfront PI might have been a much better mentor... they have hitched their wagon to a less palatable, less productive situation. However, I see being open about expectations early on as one of the only ways to make sure that my mentees feel comfortable discussing whatever career plans they are considering with me, and to make sure they know what it is I want/need from them even if they don't want to stay in science.

Like any contract, like any cooperative agreement, either side can choose to unilaterally end the cooperation. A student can choose another mentor, a student can drop out... but a PI can also take a job in a place to which the student is unwilling to move. Or the PI can leave science (this happens even when the scientist is tenured). Or the PI could say the student has repeatedly violated the expectations both the student and PI agreed to, and that the PI would like to end the mentorship. These are unavoidable possibilities, and I don't know how to smooth these situations. I think how well it goes is up to the individual maturity of the PI and trainee, and formal agreements won't necessarily help these potentially tense situations.

My perspective may sound very naive, and it's because I can't speak from the other side... yet. My department has a tradition of some students going into policy positions, so I absolutely will end up mentoring people who will have different career goals from my own. I look forward to having students that will become science journalists, or go to work for the government, including (dare I dream?) at a funding agency. What's bad about having a student who goes to a primarily four year college -- if you two still get along, wouldn't this create synergistic opportunities for creative 'outreach' and 'broader impacts' for future grants? I also hope I don't feel negatively about students who completely eschew science and academia. If you care about your mentees, and they are happy doing what they are doing, and send christmas emails assuring you of this... that has to count for something. I don't know how successful I will be at this, or how frustrated I will be after a few years. I remember being chilled by reading Too Many Bad Apples on the CofHE a while ago, and I don't know how confronting dishonesty in my mentees will affect me. My strongest mentor experienced this (masters student plaguerized large portions of a thesis... from a book the mentor had on his bookshelf!) and it did not change his warmth and his willingness to extend himself to his subsequent students.