Kickass or kickarse science?

In my last post I referred to "kickass science." My piratical big brother and PiT both asserted it should be "arse" not "ass." So, dear readers, is it kickass...




or, kickarse?




Discuss.

Your science is not enough

There's an awful lot of good advice out there in the blogosphere on how to succeed at many aspects of academia. DrugMonkey and Writedit are great resources for grant-writing, Professor in Training and Prof-like Substance are chronicling the trials and tribulations of being tenure-track assistant profs in the biological sciences, DrDrA is transitioning to the next level, and FemaleScienceProfessor provides a great deal of useful information from the senior level, etc. One thing that I have not seen discussed very much is something I have a problem with...

Assertiveness.

Some grad students and postdocs might be surprised to hear that once you reach the giddy heights of an academic position your kickass science is no longer sufficient. It's what will get you that position, but it's not enough to progress in your field from there. Yes, you can obtain grants and publish based solely on the science, but it's not enough. It's necessary, and importantly, you need some kickass science first and foremost. But kickass science alone probably won't get you invited to speak at a meeting or another institution. It won't set up the collaborations with the heavy hitters and rising stars in your field. Kickass science might make you a familiar name in your field, but not necessarily a presence in the field. It won't necessarily get you the recognition you think you're due.

That's where assertiveness comes in. Want to know how many speakers at meetings (other than the heavy hitters) get those slots? They asked. They pushed themselves forward, told the organizers "I have kickass science, I can give a kickass presentation and I deserve a slot". Ditto for many of those people giving seminars at your institution. Ditto for a collaboration between a heavy hitter and a junior person. Ditto for invitations to submit manuscripts for special issues of journals. Ditto for some publications in GlamourMagz. It goes on all the time. Next time you find yourself thinking "How the hell did they get that invitation/collaboration?", remind yourself they probably asked. Pushed. Lobbied. It's something I'm not terribly good at, but I'm trying to improve (damn it, I'm good enough, I deserve that recognition!).

People are surprisingly often willing to give someone a chance. But just one. You need to deliver. If you promise a kickass presentation of kickass science you had better deliver. Offered a killer collaboration? Deliver it. Pushed for an invitation to submit a stellar manuscript? Make it better than stellar. Otherwise those doors will be slammed shut. Too many doors slammed on you will get you a reputation that's hard to get rid of.

Something to think about and work on.

Just remember though, you have to have the kickass science first.

New Year

2010 already. How did that happen?

No matter. This is going to be a good year for me.

My somewhat recently resurrected research project is making good progress despite the occasional hiccup.



Odyssey's research project has a minor setback.


The bride of the above-mentioned project is showing strong signs of life and is the subject of a proposal about to go out the door.



The bride of Odyssey's research program is alive! Sort of.

And now my project has...

a son!!!!



Doesn't Dad look proud?

Of course he can't walk yet. And he's still on life support. But still, progress looms.


There are papers and proposals to write. Experiments to plan. Talks to give. Meetings to attend. Coffee to consume.


Life is good.

May this be a good year for all of us.

Have a good break!

I'm off for Winter Break and won't be back until the New Year.
I hope you all have a wonderful break and a Happy New Year!
See ya!

An update to "You lost WHAT?!?!?"

An update to a recent post...

Those of you with access to Science might be interested in reading this. I'm afraid it's too long to reproduce here... The whole sorry affair apparently has involved attempted extortion, harassment, a suicide threat and someone failing to make tenure. Science may not be a care bears tea party, but apparently it can be good soap opera material.

You lost WHAT?!?!?!?!?

I was waiting for the lads over at Drugmonkey to tackle this since CPP would no doubt do a better job. But since they haven't as yet, here goes...

In the November 26 issue of Science there's yet another retraction. This time it's from the group of Peter Schultz. For those who aren't in the know, Schultz has made a name for himself developing ways to trick the translational machinery into inserting non-natural residues into protein chains. The retracted paper (Science 303, 371 (2004)) dealt with the insertion of residues with an attached sugar, the idea being this could be used to study glycosylated proteins in a more controlled manner.

For those without access to Science, here's the retraction in full:

Retraction

We wish to retract our Report (1) in which we report that β–N-acetylglucosamine-serine can be biosynthetically incorporated at a defined site in myoglobin in Escherichia coli. Regrettably, through no fault of the authors, the lab notebooks are no longer available to replicate the original experimental conditions, and we are unable to introduce this amino acid into myoglobin with the information and reagents currently in hand. We note that reagents and conditions for the incorporation of more than 50 amino acids described in other published work from the Schultz lab are available upon request.
Zhiwen Zhang,1 Jeff Gildersleeve,2 Yu-Ying Yang,3 Ran Xu,4 Joseph A. Loo,5 Sean Uryu,6 Chi-Huey Wong,7 Peter G. Schultz7,*


* To whom correspondence should be addressed. E-mail: schultz@scripps.edu
1 The University of Texas at Austin, Division of Medicinal Chemistry, College of Pharmacy, Austin, TX 78712, USA.
2 Chemical Biology Section, National Cancer Institute, Frederick, MD 21702, USA.
3 Rockefeller University, New York, NY 10065, USA.
4 6330 Buffalo Speedway, Houston, TX 77005, USA.
5 Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095–1569, USA.
6 University of California, San Diego, CA 92121, USA.
7 The Scripps Research Institute, La Jolla, CA 92037, USA.

Reference
1. Z. Zhang et al., Science 303, 371 (2004).

Let's break this down...

Regrettably, through no fault of the authors, the lab notebooks are no longer available to replicate the original experimental conditions...

Say what?!?!? You LOST the lab notebooks???? And it's not the fault of any of the authors???? Okay, I can imagine a number of circumstances where this could happen. A fire for example. But if it's something like that why not give the details???? I'm all for the assumption of innocence and all that, but come on, this smells worse than a bucket of shrimp in the sun.

...and we are unable to introduce this amino acid into myoglobin with the information and reagents currently in hand.

They can't reproduce their own experiments. Now call me old school, but I always go by that tried and true rule that the Materials and Methods section of a paper should contain enough detail that the experiments can be reproduced by someone else. Someone not in the lab that did the work. And the retracted article does have two pages of supplementary material, most of which is the Materials and Methods... But the lab (and presumably the authors) that originally did the work still can't reproduce it even with the combination of the lab's collective knowledge and memory plus the published Materials and Methods. Smell that bucket of shrimp yet?

We note that reagents and conditions for the incorporation of more than 50 amino acids described in other published work from the Schultz lab are available upon request.

We lose our lab notebooks and can't reproduce our own experiments, but everyone should still trust us...


I need to open a window or two.

What's your h-index?

Actually I don't really want to know. Listing h-indices here would be akin to having a pissing contest. Puerile, messy and smelly...

In recent years I've noticed an increase in the number of people who list the number of times their publications have been cited in their c.v.'s and/or biosketches.* Many have started listing their h-indices as well. At first I viewed this as a form of bragging. But now I've seen it enough that I'm beginning to pay attention. We could argue ad infinitum as to whether number of citations and/or h-indices are useful measures of a person's productivity and standing in their field.** That's akin to the interminable Mac vs. PC arguments*** and I'm really not interested in that kind of semi-religious "discussion". What I am interested in is people's opinions as to whether or not this is a reasonable practice. Do any of my readers list citation statistics in their c.v.'s or biosketches? What are your thoughts on this? Do your respective departments take such things into account come annual review time (which is now for many of us)?

I don't list citation statistics in my c.v./biosketch (but might do so in the future if it seems advantageous). And my department doesn't formally consider such things, although I suspect some of the senior faculty spend some time on ISI's Web of Knowledge prior to annual reviews figuring out the stats on the more junior faculty.

Finally, I wouldn't recommend grad students and junior postdocs listing such stats unless they have a really highly cited paper or two. I have seen senior postdocs applying for TT positions list their stats. In some cases it helps. In others, not so much. It's a good idea to poke around and see how you stack up versus your peers before making the decision.







* Yes, in biosketches in grant proposals. At least in NSF and private foundation proposals.
** Personally I find number of publications, average number of citations per publication, plus h-index the most informative combination, but recognize even that has flaws.
*** Mac.

The month that was

I survived my month with two grant review panels, and a grant submission. Did I mention I also went to a small meeting in that timeframe? And had a root canal the day before one of the review panels?

I don't think I want to repeat that month...



And for Prof-like Substance:



The atrium of the NSF building in Alexandria after the review panels have met. My money is on the PD in the red and white tights.

NSF and too much funding

Prof-like Substance has posted a nice summary of the NSF's funding stats for 2008. In it he writes:

"One thing that I found very surprising was the number of grants per PI. In the fiscal years 2006-08, 83% of PIs had one grant! That left 13% with two grants, 3% with three and 1% with four or more. As someone who has three very different projects that they are trying to get funded and has been talking with a colleague about a fourth, I'm not sure what to make of those numbers. If nothing else, it concerns me that reviewers might balk at a proposal just based on the number of grants held by a PI. Now, I'm not thinking that everything I am submitting will eventually get funded in the next year, but if these projects weren't fundable in my opinion, I wouldn't be wasting my time. Perhaps people who have served on a couple of panels (*cough* Odyssey? *cough*) might shed some light on the perception of when someone has "too much" funding."

I was going to reply in the comments but quickly realized this warranted a post all of it's own. Note that this is all based on my own observations and a few pieces of anecdotal evidence. As far as I know the NSF does not have any written policies regarding this stuff.

There are two issues here: holding more than one NSF grant concurrently, and what amounts to "too much" funding.

Firstly, let me address the comment "...reviewers might balk at a proposal just based on the number of grants held by a PI." Based on my experience on a couple of panels, that's rarely the case. A panel member might point out that someone is well-funded, but it doesn't seem to effect the review or panel scores. I believe it's the Program Directors who take current funding levels into account when making decisions as to who to fund.

As far as holding two NSF grants concurrently goes, the NSF stats reflect what I have observed over time. I have rarely come across someone who is PI on more than one NSF research grant. In fact I can only think of two instances. I do know of people who are PI on an NSF research grant and on a second, or even third, other type of NSF grant (e.g. REU site, equipment grant etc.). I would be one of those. So it happens, but it's rare. What's a PI to do? Call your Program Director and talk to them. Feel them out about the possibility of getting two NSF grants funded. One thing I do know however, submitting two proposals at the same time to the same panel is not received terribly well by the panelists. Or Program Director. Spread out your submissions.

So what has led to 83% of NSF-funded PI's holding just the one NSF grant? I have come to believe it's a function of the NSF's working philosophy. The Program Directors appear to view each grant funded as an investment. They want to "buy low", maintain the investment over the long term, and reap large returns. A well-established, well-funded investigator might be a "safe" investment, but often does not (appear to) give the same return per dollar over the long term as a riskier, young investigator.* What does that mean in practice? A senior person with one or more NIH R01's and no track record of recent NSF funding is unlikely to land an NSF grant. A young investigator with little or no other funding is in the running. Someone who landed an NSF grant early on, and subsequently pulled in other major funding while maintaining the NSF grant, remains in the running (the Program Directors want to hold their investments long term - as long as they continue to perform well on average).

I don't know whether this is fair or not. I have certainly benefited from this system. Keep in mind that the NSF's budget is a small fraction of the NIH's, and that they fund all non-biomedical science, plus math and engineering. Giving out multiple NSF grants to one investigator, or one to someone who is otherwise well-funded, means someone deserving misses out.** On the other hand, a single NSF grant is rarely enough to run a truly productive group...

Once again, the above are conjecture based on my own observations, nothing more.





* I would dearly love to see a study done on productivity/dollar. Many people, including myself, complain that investigators holding four or more R01's are not as productive per dollar as those with just one or two, but it's all based on anecdotal evidence on non-rigorous analysis of one or two mega-funded investigators.

** A Program Director recently told me the BIO Directorate at the NSF currently has a funding rate of ~15%. Better than NIH at the moment, but still lousy. A lot of really good grants are going unfunded.

Megacool faculty position

A colleague brought my attention to a job listing at Purdue University in Indiana. They're looking for someone in Molecular Pharmacology.

My colleague describes the Department thusly:

"As monocultural as my department looks on paper, everyone here is really cool people, we have a great atmosphere and a very friendly, down-to-earth departmental community. People here TRULY COLLABORATE without fearing for their independence. I have been welcomed without hesitation into the group and feel very at home here, and our department head is really fantastic. In general people here are just straight-up folks. We have a formalized junior faculty mentorship program as well as an informal weekly lunch together that I have found totally invaluable to getting on my feet. Our tenure requirements are very rigorous, but everyone seems to be doing their best to help each other make it through (rather than trying to turf each other out). All in all, I think this is an excellent place to start a career and I couldn't be happier with my choice to join this department."

And just in case you think you're not quite a molecular pharmacologist, check out a recent post by Comrade Physioprof. Now go sell yourself.

Mistake?

I'm beginning to wonder if agreeing to be on two grant review panels in the same month I have a grant due was one...

Real lives and white lies

The title of this post is stolen borrowed from a new opinion piece by Peter A. Lawrence in PLoS Biology titled "Real Lives and White Lies in the Funding of Scientific Research."* Go read it (open access - it's free!). Lawrence is mostly referring to the current system in Britain, but there are clearly parallels with the system here in the U.S.

Lawrence is concerned with the fate of young innovative scientists. However, many of the opinions cited in Lawrence's piece come from well-established scientists, so it's not clear how some of the suggested "fixes" (shorter grant applications, a tiered system of fixed five-year funding blocks followed by review, etc.) would work for young scientists. One of the quoted scientists complains about a 2.5 year funding gap after 30 years in research, which is easy to interpret as the whining of one of those old farts CPP loves to hate. Maybe he is, maybe he's not. Still, it's an interesting read.


Some highlights:

On the system-

“What a strange business this is: We stay in school forever. We have to battle the system with only a one in eight or one in ten chance of getting funded. We give up making a living until our forties. And we do it because we want to help the world. What kind of crazy person would go for that?”—Nancy Andrews, Vice Chancellor for Academic Affairs and Dean of the Duke University School of Medicine

On the advantages of large groups-

"The peculiar demands of our granting system have favoured an upper class of skilled scientists who know how to raise money for a big group [3]. They have mastered a glass bead game that rewards not only quality and honesty, but also salesmanship and networking. A large group is the secret because applications are currently judged in a way that makes it almost immaterial how many of that group fail, so long as two or three do well. Data from these successful underlings can be cleverly packaged to produce a flow of papers—essential to generate an overlapping portfolio of grants to avoid gaps in funding.

Thus, large groups can appear effective even when they are neither efficient nor innovative. Also, large groups breed a surplus of PhD students and postdocs that flood the market; many boost the careers of their supervisors while their own plans to continue in research are doomed from the outset. The system also helps larger groups outcompete smaller groups, like those headed by younger scientists such as K. It is no wonder that the average age of grant recipients continues to rise [4]. Even worse, sustained success is most likely when risky and original topics are avoided and projects tailored to fit prevailing fashions—a fact that sticks a knife into the back of true research [5]. As Sydney Brenner has said, 'Innovation comes only from an assault on the unknown” [6].'

And perhaps my favorite paragraph-

"Universities have whole departments devoted to filling in the financial sections of these forms. Liaison between the scientists and these departments and between the scientists and employees of the granting agencies has become more and more Kafkaesque."

Kafkaesque indeed...




* Peter A. Lawrence (2009) Real Lives and White Lies in the Funding of Scientific Research. PLoS Biol 7(9): e1000197

Monday

By 8am this morning I had reinstalled a toilet*, showered, shaved, breakfasted, read the newspaper, drove one of my daughters to school, and built towers out of wooden blocks with my son. I'm not sure I can maintain this pace...









* I tiled the floor yesterday.

PSA: How to schedule a dissertation meeting

In the last three or four weeks I've had five grad students email me trying to set up meetings of their dissertation committees. Let's call these students A, B, C, D and E. Student A's email read:

Dear members of my committee,
I want to have a meeting of my dissertation committee on SpecificDay at SpecificTime.
A

Students B thru E all sent emails along the line of:

Dear members of my committee,
I want to have a meeting of my dissertation committee. When are you available?
B/D/C/E

No, no, no, no, no. Neither of these approaches will do. In fact, these are exactly how NOT to go about the process.

Let's start with student A. The odds of all of your committee members being available at the specific time and date you chose are quite small. In fact, I'm not available then. So now what? You choose another specific time and date? What if I or another committee member aren't available then? How many rounds of this will we have to go through?

Students B thru E. What timeframe are we talking about here? Sometime in the next week? Two weeks? Month? Year? Decade? Millennium?

Okay, so we can probably rule out millennium. And decade. At least for students B, C and D. You guys should have graduated and be long gone by then. E on the the hand...

Even if you pin it down to specific period, say sometime in the next two weeks, do you really want me to send you a list of when I might be available? My calendar currently looks like something Jackson Pollock created on the floor, as do, I suspect, the calendars of all your other committee members.



Pollock's No. 5 1948 is a reasonable representation of Odyssey's calendar.

Why, oh why are you creating so much work for your committee and for yourself?

As a public service here's how you should approach the process:

Send a preliminary email asking if everyone is in town during the period you're hoping to have a meeting in.

Based on the results of the preliminary email, provide a list of five or six times and dates and ask your committee members to indicate which they are available for.*

Based on the replies, choose a time and date that works for everyone. Let everyone know as quickly as possible so they don't inadvertently fill that slot with something else. If there isn't one, try again.


Simple isn't it?





* If your committee is composed of computer savvy faculty you could go high-tech and use something like www.doodle.com.

Factor this

Wolfgang G. Stock of the Department of Information Science at the Heinrich-Heine-University in Düsseldorf has an interesting essay titled "The inflation of impact factors of scientific journals" coming out in ChemPhysChem (subscription required). In it he makes the point that impact factors (IF), h-indices and even eigenfactor scores for journals are flawed and really not very informative. For starters, he points out-

"For example, the British library holds more than 40000 scientific serials and adds about 800 new journals each year, whereas the two most comprehensive multidisciplinary databases, namely Elsevier's Scopus and Thomson Reuter's Web of Science (WoS) cover only 16000 (Scopus) and 10000 (WoS) periodicals."

Note that because of the differences in periodicals surveyed by Scopus and WoS, the IF's obtained from these two sources often disagree on the IF for a given journal.

Stock notes-

"All indicators that work with relative frequency measures (ie, all Group 2 indicators) suffer from serious statistical problems. It is a precondition for calculating average values (in our case: average cites per publication) that there is a Gaussian distribution... In journal informetrics this is not the case."

Seems like a serious flaw to me...

He asserts-

"In no case is it possible to use a journal impact factor on the article level to evaluate the influence of an article, an author or an institution."

Of course we all knew that.

Wish the bean-counters did...

PSIfi careers

Recently there was quite a bit of discussion in the blogosphere regarding a former SLAC National Accelerator Laboratory technician destroying $500,000 worth of proteins crystals. This incident occurred at the Joint Center for Structural Genomics, a part of the NIH-funded Protein Structure Initiative (PSI). You can read about this incident over at DrugMonkey's place.

A couple of the comments following DM's post made the point that these PSI labs are little more than large protein structure factories. 'Tis true. According to the global repository of all that is worth knowing, Wikipedia, PSI labs produced >3400 new structures between the inception of PSI in 2000 and November 2008, with ~1900 being new folds. One can argue whether or not the scientific output is worth the (so-far) >$700 million cost - many people have, including prominent structural biologists such as Greg Petsko. I don't really want to get into that here. What I do want to talk about is one of the human costs of PSI.

PSI employees a great number of scientists. Many of these are employed as postdocs. The problem with this is that many of these "postdocs" aren't really receiving research training.* Sure, they solve many structures, but that in and of itself is not research. The PSI labs are trying to solve as many representative protein structures as possible and each (at least initially) tend(ed) to focus on a single organism (or maybe a couple) as the source of material. A postdoc in a PSI lab could solve a whole bunch of structures, but the only relationship between the proteins would be the organism they were derived from. Many of the proteins were/are of unknown function. And the vast majority of the publications reporting the structures are short letters or notes with many authors... This is not research and it is not research training.

We're not associated with PSI, but do happen to have very good facilities for x-ray crystallography at Big State U. Consequently, in recent faculty searches we have had quite a few applications from PSI-trained crystallographers. Despite long publication lists, none of them have ever made it to the interview pile. Why? Well, an unusually large portion haven't written a coherent research plan (unusually large compared to applications from non-PSI trainees). I suspect they simply don't know how to construct a worthwhile/fundable research project. They haven't received the training. Many of the remainder suggest decent systems to work on (proteins of medical relevance), but propose nothing more than crystallography, which nowadays is not enough to get funding. And they have no preliminary data. None.

You could argue that a postdoc who takes a position in a PSI lab hoping to move on to an academic career is naive. They are. Judging by the applications we've seen, there are a bunch of naive postdocs out there. However, I think the PSI labs share some responsibility here. They should make it very clear to postdoc applicants that the positions they are applying for are unlikely to provide the training necessary for an academic career. Perhaps some of them do. Even better would be to call the positions by a name other than "postdoctoral scholar/fellow/trainee" - something employing "technician" seems more appropriate.

Petsko has stated "As a structural biologist, I want to train people who use structure determination as part of what they do. It is not the end in itself, nor should it be, not any more."

Sounds about right to me.





* Many, not all. I am aware that some PSI postdocs receive excellent research training.

It's party time!!!!!!!!

DrDrA is having a blog party!!!! I'll bring the bourbon.

iPhone apps

I have a question for my iPhone-wielding compadres: what apps do you find truly useful? Other than the ones that come standard.

I've grown partial to the following:

Evernote - particularly useful since it automagically syncs with my laptop via the internet. Good for recording notes, saving web pages etc. A useful catchall and organizer for information.

TripIt - useful as long as you're comfortable with them potentially having access to your travel info. It's also available on LinkedIn if you happen to have an account there. I like the built-in flight status and map features.

UrbanSpoon - for when you're traveling and have a need for good Thai food...

Liberation

We had one humungous mother of a thunderstorm come through a couple of days ago. Knocked out the power in the building I work in.

It fried my office phone.

Woohoo!!11!!!11!!!

Herding cats

I'm in the midst of writing an equipment proposal for a bright shiny new toy that will be really, really useful. To a lot of the faculty here. Although I've never written this kind of proposal before I'm not finding the writing terribly difficult - I know enough about the instrument and what we'll do with it to wax lyrical. No, it's not the writing that's getting to me. It's extracting information from my fellow faculty. It's like herding cats.



Odyssey trying to corral fellow faculty.

All I need from each of them is a biosketch, list of current and pending funding, and a paragraph or two describing the research they would do with the instrument. Is that really so hard?

Apparently it is. To the point that I can now confidently state a new law...

Odyssey's law of equipment proposal writing:

The ability to obtain from a faculty member useful information required for an equipment proposal is inversely proportional to just how useful that piece of equipment would be to that person.




Anyone got a good bullwhip I can borrow?