Friday, December 18, 2009

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!

Thursday, December 17, 2009

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.

Tuesday, December 01, 2009

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:


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:
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.

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.

Friday, October 30, 2009

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.

Friday, October 23, 2009

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:

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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.

Tuesday, October 13, 2009

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.

Monday, October 12, 2009

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.

Thursday, September 24, 2009


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...

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Tuesday, September 15, 2009

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, September 14, 2009


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.

Wednesday, September 09, 2009

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.

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?

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.

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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
  • Tuesday, August 18, 2009

    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...

    Friday, August 14, 2009

    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.

    Thursday, August 13, 2009

    Thursday, August 06, 2009

    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...


    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.


    Tuesday, July 14, 2009

    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.

    Image Hosted by

    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?

    Monday, July 13, 2009

    Odyssey's 3 Rules for Smartphone Use

    Female Science Professor recently had a post on why she hates iPhones. Based on some of the comments that resulted from that post I've come to realize that a great many people don't know the correct protocols for smartphone* usage. So here I present:

    Odyssey's 3 Rules for Smartphone Use

    Rule 1: Thou shalt not just use it, but flaunt it.

    We've all seen people engrossed in cellphone conversations at restaurants, ignoring their dining companions. Such behavior is totally unacceptable. Crass. Rude. Except in those cases where an iPhone is in use! In such cases it is acceptable behavior, but only if the user makes it very, very clear to all and sundry that he/she is using an iPhone. The following examples demonstrate incorrect and correct usage:

    Incorrect Usages-
    (Ranging from bad to absolute worst)

    a) Ring, ring!
    iPhone owner quickly and unobtrusively retrieves iPhone from pocket, apologizes to dinner companion(s), answers thusly:
    "Oh hi. I'm at dinner right now. Can I call you back later? Thanks."
    Hangs up, apologizes again while silencing phone and putting it away.

    b) Ring, ring!
    iPhone owner quickly and unobtrusively retrieves phone from pocket, pushes a button to send the caller into voicemail, silences phone, and quickly pockets the device. Apologizes to dinner companion(s).

    c) iPhone owner silences iPhone before entering restaurant.

    Correct Usage-
    Ring, ring!
    Cellphone user smiles knowingly and slowly retrieves iPhone from pocket.
    Ring, ring!
    Holding iPhone at eye-level owner carefully checks to see who is calling.
    Ring, ring!
    Keeping iPhone at eye-level, owner glances to make sure people at nearby tables are watching and, maintaining that knowing smile perfected by iPhone owners, carefully taps "Slide to Answer".
    With a flourish owner then moves to iPhone to his ear and answers in a loud clear voice:
    "Hi Bob, you've reached me on my iPhone. What's up?"

    During the loud conversation that follows, the iPhone owner makes sure to mention that he is talking on his iPhone at least twice more, and then ends the call with:
    "Well Bob, must run now. I'll talk to you soon on my iPhone. I'm hanging up my iPhone now. God, it's great to have an iPhone! Bye."

    Rule 2: Thou shalt use thy Apps. And use them. And use them. And use them.

    Why else would you have them? Suggested uses:

    a) Use Maps to show everyone exactly where you are. This is good at least once for every location.
    b) Use Maps to get directions to your next location, even if it's to the restaurant you're standing outside of.
    c) Use the in-built camera to make a visual record of every event, no matter how trivial. And immediately send the photos to everyone on your contact list.
    d) Make a Voice Memo of every important thought you have. Remember, they're all important!
    e) Check the time in Timbuktu using Clock. While you're there, what time is it in Zurich?
    f) Show off the last four Youtube videos you watched. Doesn't matter how good they were.
    g) Check your Stocks. Don't own any? Check the ones you wished you did own.
    h) What's new at the iTunes store? Or the Apps Store? Gotta keep up to date!
    i) Look it up on the internet. Doesn't matter what it is. Look it up! "You're ordering the linguini? Look, here are 2,018 pictures of linguini on my iPhone!" "Did you say 'boorish'? Let me look that up on my iPhone!"

    Be sure to hold your iPhone at at least eye-level and talk about it in a loud, clear voice while using your Apps. Make sure you say "iPhone" multiple times with plenty of with extra emphasis. And remember, there's no limit to how many times you do this an hour. The more the better!

    Rule 3: Email be thy master.

    Email is perhaps the most abused aspect of smartphones. Really, the way people use it is pathetic. One should never, ever write "I'm sending this from my iPhone" in an email. Pitiful!

    That's what the signature is for! And frankly, the standard "Sent from my iPhone" signature just isn't good enough. It's way too small. Bump it up!

    Sent from my iPhone!

    See how much better that is? Gain some eco-friendly bonus points by going big and green!

    Sent from my iPhone!

    Extra bonus points for going all caps.

    And don't forget, with your iPhone you're available to answer emails at all times (make sure you have a piercingly loud incoming email notification!). You're available 24/7! Just send it! There's nothing like a "SENT FROM MY iPHONE!!!!!" at 3:30am!

    * Although my rules mention iPhones, by "smartphone" I am referring to all such devices (e.g. Blackberries, Palm Pre's etc.)**.

    ** "Smart" refers to the device, not the user.***

    *** I'm a user. I own an iPhone.

    Wednesday, July 01, 2009

    DIY ideas...

    ...available here.

    I didn't say they were good ideas...

    Tuesday, June 30, 2009

    I need a secretary

    How I feel at the moment.

    Saturday, June 20, 2009

    Danger!! Danger, Will Robinson!!!

    Organism Designed for Yelling, Scientific Sabotage and Efficient Yardwork

    Get Your Cyborg Name

    The yardwork part is debatable...

    Cyber-hat tip to Drugmonkey.

    Friday, June 19, 2009

    This and that

    I heard this morning that my late Nanna's house was sold. She passed away earlier this year. I knew the house was on the market but hadn't really thought about it in depth. It's actually quite sad - I have some fond childhood memories of that old place. The fig tree in the backyard, the lanes out the back and on the side, the "old house" smell*... Sigh.

    On a brighter note, I'm off to a smallish six day meeting this Sunday. Lots of good people will be there. My goals (you should always have goals, otherwise why attend?) are to:

    i) get feedback on my new major research project - progress has been slow but steady,
    ii) get feedback on my new major research project's bride, which is showing signs of life,
    iii) catch up with old friends/collaborators,
    iv) make new friends/collaborators,
    v) score at least two seminar invites, and
    vi) not make a fool of myself.

    Goal vi) might be the hardest.

    And finally a quote from my supertech: "Cloning always works. One day."

    * Or was it an "old person" smell?

    Monday, June 15, 2009

    Do Science Scouts have a secret handshake?

    After reading DrDrA's post I couldn't resist going over to the Science Scouts site to see what badges I could award myself...

    The “I somehow convinced someone to part with a lot of money for science” badge (LEVEL II).

    Haven't quite made it to Level III yet...

    The “non-explainer” badge (LEVEL I).

    It's been this way since grad school. Or even before. I'm trying hard not to earn Level II...

    The “has done science whilst under the influence” badge.

    Let's be honest now, who hasn't?

    The “works with acids” badge.

    This one's a bit of a gimme for anyone doing benchwork. Of course I did once dissolve part of a bench using acid...

    The “I’ve set fire to stuff” badge (LEVEL III).

    I did train as a physical chemist.

    The “statistical linear regression” badge.

    A necessary evil.

    The “I’m a scientist who is fundamentally opposed to administrative duties” badge.

    Another gimme.

    The “has frozen stuff just to see what happens” badge (LEVEL III).

    The irresistible lure of liquid nitrogen...

    The “talking science” badge.

    Of course!

    Now I really should go do some science...

    Monday, June 01, 2009

    Silence is the enemy (Do what I say, please) [Updated]

    Please go read CPP's latest post. Then go here and here and here. Click until your fingers bleed.

    [Updated link to Isis' post on Silence is the Enemy]

    Tagged for the covers meme...

    Prof. Anon. was nasty kind enough to tag me in the current covers meme. It's taken me a while to respond because I simply cannot think of a well done cover that someone else hasn't already used... But I do have a stinker of a cover for you.

    Rolf Harris does Led Zepplin's "Stairway to Heaven"!

    Don't know who Rolf is? He's an Australian entertainer who used to have his own variety show. He sings, paints, and plays the didjeridoo and wobble board. No, not the fitness wobble board, this thing. Anyway, he's playing one in the following video so you'll get the idea.

    Rolf butchers "Stairway to heaven"

    This was performed on an Australian comedy show called "The Money or the Gun." They had many performers come on and do "Stairway to Heaven." Eventually these were all released on an album. Yes, an album with 22 performances of "Stairway to Heaven."

    So now on to something completely different. Since I couldn't come up with a cover I really liked, I'm going to attempt starting a new meme...

    How about a song that describes your career as you see it, but without actually mentioning the career explicitly?

    I'm in academia, so I present to you the following:

    Harvey Danger and "Cream and Bastards Rise"

    The version on the "Little by Little" album is much, much better. You can download it for free from the band's web site.

    Wednesday, May 20, 2009

    Ultimate proof that evolution is real

    If this doesn't convince you we're closely related to the apes, I don't know what will.

    Wednesday, May 13, 2009

    Challenge grant haiku

    Twenty thousand grants.
    Overload the reviewers.
    NIH. Turkeys.

    Friday, May 08, 2009

    Blog on, blog off

    I was very disappointed to read about Damn Good Technician being forced to shut down her blog. Apparently her superiors in Big Pharma weren't overly impressed with what she had to say. This event has had others wondering about the prudence of continuing to blog or to outline their personal rules of blogging.

    It's got me thinking too. My first post to this blog was on September 22, 2005. In four and a half years I've blathered on about politics, spam, making tenure (or not), teaching, obesity, grants, vending machines, ipods, plagiarism, research, and a plethora of other nonsense. There are plenty of clues sprinkled throughout as to whom I am and where I work. It wouldn't take much to find me.

    And so I've been considering shutting things down. After all, who needs the hassle that would follow from my colleagues and superiors figuring out I was blogging about them? Just not worth it.

    Thus dear readers, I bid you adieu.

    Screw that. I have almost 10,000 hits. You didn't really think I was going stop now did you?

    Monday, May 04, 2009

    Dear Reference Letter Writer

    Thank you so much for your letter of reference for the student who applied to our NSF REU program. It was so very informative. Knowing that the student's favorite activity is reading will truly aid our decision process. So much more than the information we requested, such as their research potential, ability to work with others, or even classroom performance. I can fully understand why you have given them the "strongest possible recommendation."

    And of course you clearly understood that no apologies were necessary for sending in your reference letter two months past the deadline.

    Thursday, April 16, 2009

    Off I go then

    I'm off on vacation for the next two weeks. Woo hoo!

    It starts with my little brother's wedding this weekend where I'm expecting something along these lines:

    See you all in a couple of weeks!

    Monday, March 30, 2009

    Twitterererer.. er

    Twitter has been getting all sorts of publicity recently. Which has got me wondering. What do you call someone who uses twitter?

    Applying to an NSF REU site [Updated]

    There's an interesting discussion going on over at Isis's palace regarding the personal statement essays required by many REU sites as part of an application. I run such a site. Following are some thoughts on how (and perhaps how not) to apply to REU sites.

    A summer spent at an REU site can be a wonderful experience that can help you decide whether a career in scientific research is for you. Or a career in science in general. That's what the REU program is all about. It's not for padding your CV. Only apply if you're serious about working through the Summer. Working hard. At the end you will have learned a lot. And maybe earned a stellar reference letter or two that will help get you into grad school or where-ever you want to be next.

    Keep in mind these sites get a lot of very good applications. It's very competitive. Here the acceptance rate is below 10%.

    Choice of Sites
    There are oh so many sites to choose from. Choose carefully. Don't spam them with applications. We can see right through that kind of thing.

    Apply only to those sites you are truly interested in. And have the background for. Majoring in mediaeval music probably won't be seen as a big plus at that physics site you've applied to.

    And don't think you need to attend a site at an Ivy league school. I'm at a state school. Former participants from the site I run have ended up grad students at some of the best schools in the country.

    Criteria Used

    First, you MUST be a U.S. citizen or permanent resident. That's an NSF rule. Can't be bent or broken. Don't bother applying just because you have work authorization. It's not enough. If you're not a citizen you need a green card. Nothing else will do.

    Have a decent GPA. I'm afraid anything under 3.0 just isn't looked at. If you're below 3.2 you need a really good explanation for why this doesn't reflect your true potential. We get a lot of applications with GPA's greater than 3.8. It's very, very competitive.

    That pesky personal statement essay thingy needs to be good. Truth is, if everything else is stellar you might get away with a poor essay. But by stellar I mean so good every site you apply to calls to offer you a slot with double the stipend of everyone else. Plus accommodations in a five star hotel. That good. You're best bet here is to a) avoid the long list of relatives who have died of assorted diseases you wish to cure, b) avoid the cutsey story about falling in love with the chemistry set you got on your third birthday, and c) tailor your letter to the site you're applying to. Tell us why you want to spend your summer HERE. And read Isis's advice.

    Prior research experience. Had a whole bunch? Great! Good for you. Too bad we probably won't take you. The REU program is aimed at giving research experiences to students who have few, if any, opportunities to do research. A little prior research experience is okay. A lot means you might not get an offer. Not all sites conform to this approach, but I have been assured by other REU PI's that not doing so can have serious consequences for the site. For example, not getting the grant that supports it renewed...

    And then there are the...

    Letters of Recommendation

    I cannot overemphasize the importance of your letters of recommendation. These can easily make or break your application. They need to be good. They need to be sent on time (this year I received one a month to the day after the deadline - way after we had sent out offers). They need to be good (did I say that already?). They need to be substantial - two sentences saying you're the best student since the last one they wrote a letter for won't cut it. And they need to be from people who can really say something about your potential in science. Not from relatives (yes, had one of those... Mom was very proud of her little boy). Not from your favorite English professor (I've received many - they're mostly useless*). Not from the manager of the store you've been working in part-time (okay, those are a bit better than useless, but still not great). You will be accepted into an REU site based on your scientific potential. That is what these letters must address. And most of all, they need to be good.

    [Update] How We Choose

    I forgot to talk about this bit. It's kind of important.

    So given the above, how do we choose which applicants to make offers to? I can't speak for other REU sites, but here we try to take a balanced approach. Setting aside criteria like belonging to an under-represented group (a big deal for the NSF), our perfect candidate would be the following: someone with a 4.0 GPA, from a small college, no research experience, professing a unquenchable desire to attend grad school, with stellar letters of recommendation.

    We've only ever had a few applicants like that (we've had many come very close). So how do we choose? Well, someone with a 3.8 GPA from a small college would be ranked higher than a 4.0 from an R1 institution (plenty of potential research opportunities). High grades in science courses are more important than high grades in non-science courses. Stellar recommendation letters will trump GPA's to a point. Lack of research opportunities will also trump GPA's to a point. A clearly expressed desire to pursue a scientific career (research or otherwise) ranks high. In the end, it's somewhat subjective. It has to be.

    Contacting the Site

    It is perfectly okay to contact the REU site you've applied to to make sure all your materials have arrived. Or to find out where they are in the sorting/ranking/making offers process. It is not alright to have someone else contact the site on your behalf. Especially not your Mom. Trust me, that leaves a very, very bad impression.

    Declining an Offer

    Finally, let's say you're one of the chosen few and receive an offer from one or more REU sites. But you've already committed to another site (or internship). Please, please, please don't wait to decline. As noted by FSP recently, too many (i.e. more than zero) students leave declinations until the last minute, or worse, "forget" to decline offers. If you do this you may well be screwing another student. Someone who really, really wanted to get into site A, but had to accept an offer from their second or third or fourth choice because the acceptance deadline arrived before they received an offer from site A. Even if you're not screwing someone else (and you'll never know if you did), it's just plain common courtesy.

    * The letters, not the English professors.

    Friday, March 20, 2009

    Wednesday, March 18, 2009

    The NIH wants to be the NSF!

    New announcement from the NIH - apparently they're going to use some of their stimulus money to fund...

    Wait for it...

    Undergraduate students for the summer!

    The announcement reads remarkably like one for the NSF REU program. The application doesn't look too onerous. And it's on paper, not (I wonder why? <--- sarcasm). If you have some enthusiastic undergraduates who want to work for you, here's your chance to get them paid for ($10/hour - a bit below the NSF going rate of $10.60/hour). Just keep in mind that they can be a lot of work up front. And a lot of fun.

    Tuesday, March 17, 2009

    Gratuitous self citation

    I'm currently reviewing a manuscript where 38 of the 65 cited papers were written by the senior author. And ~30 of those are at best tangentially related to the manuscript under review... I have never come across such a egregious case of gratuitous self-citation. Have you?

    Somehow I don't think this manuscript will see the light of day. At least not in its current form.

    Tuesday, March 10, 2009

    Happiness... a full and productive lab.

    So far this year I've snatched supertech from the jaws of dysfunction, picked up a very good grad student, started a new and talented undergrad, and am working with a very bright high school student.

    The lab is humming along.

    So much so that I've had to suspend the weekly beatings.

    Friday, March 06, 2009

    That's my boy!

    We went to a family event at my girls' elementary school last night. While there I was in the corridor with my son who wanted a drink from the water fountain. After he had finished drinking a teenage girl walked up to get a drink. Without missing a beat my son, with an impish grin, asked her where she lives...

    Did I mention my son is two-and-a-half? The future will be interesting.

    Wednesday, February 25, 2009

    Oh dear...

    As of this moment, my blog is the top hit for Google searches using:

    "how many papers needed for tenure"
    "papers needed for tenure"
    "papers for tenure"

    and number two for:

    "how many papers for tenure"

    Not that I care that people find my blog that way (I get 4-5 hits a day from people using those searches - and might even get more now with this post). It's more concerning that there are that many people who think they can find the answer on the internet.

    Oh, and for those who find this post using such a search, read this.

    Tuesday, February 17, 2009

    Judging presentation skills scale [UPDATE 2]

    It's been a while since DrugMonkey reposted this meme, but the seminar I had to endure today reminded me of it and inspired me to invent my own scale for judging presentation skills. Not the science being presented, but the skill with which it is presented.

    Herein I present Odyssey's

    Presentation Impact Scale Summing Offending Factors Factor*,

    hereafter shortened to PISSOFF.

    It's very simple really,

    PISSOFF = sum(Offending Factors)/(Total Number of Slides)

    where Offending Factors are determined by, but are not limited to:

    • Total number of slides exceeding number of minutes allotted for presentation (Offending Factor = [Total Number of Slides - 0.9*(Minutes Allotted)]2)
    • Number of slides in presentation speaker skips over during presentation
    • Number of figures the speaker does not refer to/explain
    • Number of tables (or other sections) with text too small to read
    • Number of tables with too much text to read
    • Number of times speaker flicks backwards and forwards through slides in order to find the one he wants to talk about
    • Number of slides that have nothing to do with the topic being presented
    • Not addressing the audience (+10 to 20 depending upon severity)
    • Mumbling (+10 to 20 depending upon severity)
    • Assuming everyone in the audience is familiar with the background of the topic (+10 to 20 depending upon severity)
    • Presenting more than one story (+20 for the first additional story, +40 for the second, +1000 for the third and subsequent stories)
    • Speaker waving the laser-pointer around like a madman (+5 to 10 depending upon severity)
    • Use of yellow on a white background (+10 per instance)
    • Use of red text on a blue background (+10 per slide)
    • Using canned Powerpoint backgrounds (+10 for simple backgrounds up to +40 for complex backgrounds)
    • Use of canned Powerpoint background that is animated (+200)
    • Excessive use of animation (+10 to +50 depending upon severity)
    • Speaking with their back to the audience (+20)
    • Number of "in case they ask that question" slides appended to the end of the presentation
    • Running over the allotted time (add 10x[Number of Minutes Over]2/(Minutes Allotted))
    • Speaker appears bored (+100)
    • Use of the phrase "this is really fascinating work, but I don't have time to tell you about it", or anything similar (+20 per instance)
    • Figures/movies that don't work because the speaker didn't bother to try them out beforehand (+10 per instance)

    Feel free to suggest more Offending Factors. I know there are many, many more - I'm too brain-dead to think of them right now.

    The PISSOFF scale runs from zero for an excellent speaker to greater than one for a speaker who should never, ever be asked to present again.

    I estimate yesterday's speaker would have a PISSOFF score of about 0.9...

    * Yes, yes, I know it sounds horribly redundant etc.

    Monday, February 02, 2009

    Tuesday, January 27, 2009

    Global time wasters

    My, my there are a lot of you, and from all over!

    Figure 1: Map denoting where the visitors to this blog hail from (red dots).

    Don't you have anything better to do?

    Thursday, January 22, 2009

    How Many Papers for Tenure?

    The title of this entry comes from a Google search a recent visitor to my blog used.

    Good question.

    I can't answer it.

    The only people who can give you some kind of answer to this are senior faculty in your department (and possibly college), and yourself.

    But you absolutely must know the answer very early in the tenure-track process. Preferably before you officially start your position. At the very latest six months in.

    So how do you find out how many papers you need? You need to do two things:

    1) Ask. Ask early and often. Ask the senior faculty in your department. If you've met some, ask senior faculty in related departments within your college (e.g. within medicine, or within arts and sciences). You may not get a straight answer. You may get several different answers. Hopefully you will get some kind of answer.

    2) Look it up. Find out how many publications the last few people who made tenure in your department had. No one tenured in the last few years? Look up the publication totals of recently tenured people in related departments within your college.

    Once you've done both of the above, take the largest of the answers you've found (they may not match up).

    That's the absolute minimum number of publications you are aiming for.

    Absolute minimum. You want more. You may need more.

    The answer to the question "how many papers needed for tenure?" is not set in stone.

    [UPDATE] Do apply some common sense to the above. Let's say your senior colleagues provide you with a consensus estimate of X publications, and the last three people to get tenure in your department had (X+1), (X+2), and (X+10) publications. Take (X+2) as your minimum goal.

    Tuesday, January 20, 2009

    Dear Future Applicant for Tenure and Promotion

    Your time on the tenure track is thundering its way towards the big decision. Soon you are going to have to put together that thick wad of documents known as your tenure packet/dossier/file. All of the documents in that packet are important, but some are more important than others. None are more important than your curriculum vitae. This document, your c.v., is a summary of almost everything needed to evaluate you for tenure and promotion. The other documents just provide the details.

    So, dear applicant, please take the time and spend the effort to make your c.v. a document that will help those evaluating you come to the right decision. Because we really do want to see you be promoted with tenure. (Unless of course one of us is an obnoxious dickwad.)

    You can ease our task by making all the information we need easy to find and read. Put the important stuff up front, and leave out the truly unnecessary.

    And please don't use your c.v. to demonstrate your artistic nature. Please. Don't.

    Do have a neat, logically organized c.v. And spell check it. A sloppy, disorganized c.v. makes you look... well, sloppy and disorganized. Not really what I want in a colleague.

    Here are some further thoughts on some (not all) of the basics:

    My personal preference is for this to be in reverse chronological order, going from your current position back to your undergraduate schooling. Leave out where you went to high school* - really, we don't give a rat's rear end. And those perfect SAT/GPA/GRE scores you're so proud of?* Not of any interest to us when it comes to tenure decision time.

    Reverse chronological order please. That Journal of Biological Chemistry paper you published while in elementary school? Very impressive, but not going to count towards tenure. Put the papers you've generated as an independent PI first. Those are the only ones that count. And do us a favor. Make it very clear what papers came out of which positions - I personally like subheadings denoting "Papers arising from my postdoctoral work", "Papers arising from my graduate work" etc. It's important to include these because they establish your history. But they won't count towards tenure.

    And those manuscripts on your postdoctoral work you published while on tenure track? Sorry, they don't count towards tenure. They belong in the "Papers arising from my postdoctoral work" group. No, really, they don't count. Ever.**

    What about papers "in preparation"? Not going to count. Don't bother with them.

    Okay, if you really, really must. One "in preparation". Two at the very most. They still won't count. Three or four "in preparation"? That's asking for trouble. Unless you've published a gazillion papers while on tenure track - but they still won't count. If you're a little short on published papers and list three or four "in preparation"?* You've just given me the impression you have trouble finishing things, even with the tenure guillotine hanging over your head.

    Ten "in preparation"?* You're a delusional fool. Granted, I've met some tenured delusional fools, but to a person they hid their delusional foolishness until after they got tenure.

    Start with current/active funding. That's the most important by far. Actually it's really all that counts. Then list pending. If you have a revised grant pending that got a good score the last time it was reviewed, give us the score. Expired/previous funding comes last. Within each subgroup, reverse chronological order please.

    You won a trophy for badminton at high school? How nice. Doesn't count. Please just list the relevant stuff. Preferably in reverse chronological order.

    Professional Society Membership
    Listing this doesn't count for much, but not listing it looks... odd.* It suggests that you're not involved in your field outside of your own research program.

    Internal Service
    Please indicate what level each committee is. A Graduate Curriculum Committee at the University level is a very different beast to one at the Department level. President of your undergraduate chemistry club? Doesn't count.

    External Service
    You do have some, right? List the journals you reviewed manuscripts for and the agencies you reviewed proposals for. Editorial boards. Professional society activities. These are important. To get tenure and promotion you need to demonstrate that you have national standing. Recent national standing.

    Bottom line: Put the stuff that counts up front. You do know what counts at your institution, right?

    * Yes, I have seen this in a c.v. within a tenure packet.
    ** This topic deserves a post all of it's own.

    Monday, January 12, 2009

    Writer's block

    Anyone know a good cure?

    I'm trying to write what should be the last paper from my old, almost dead research program, but just can't raise the enthusiasm to get it done. I need to get this off my desk for a bunch of reasons, not the least of which being that one of my former undergrads worked her butt off collecting the data for this paper. She deserves the first authorship. She is now off at med school, so the writing is up to me.

    I'd rather be writing about my new research...

    Monday, January 05, 2009

    It's a New Year!!! Woohoo!!!

    Most years in early January I waste time bemoaning the fact that I didn't achieve everything I wanted to in the previous year. Not this year. Did I get everything done I wanted to last year? Hell no. I fell about two manuscripts and one grant submission short of my goals. So what? I managed to rebuild my dying research program and renew my NSF funding. IMHO, a good year.

    This year seems somehow more exciting and full of new possibilities. My new research project is up and running (albeit slowly), I'm laying the groundwork for a second, equally exciting new project and I'm restocking my lab with new personnel. Right now, the academic life is good.

    What about the funding downturn and failing economy? Not gonna let that stop me. Uh uh. Wouldn't be prudent. Someone's getting funding. Might as well be me. Besides, bitching and moaning about such things is not only a waste of time, but also makes you a less than desirable colleague. I'd rather be working on my kick-ass science.

    How about you?