Demise of The Academic Jungle

GMP has taken down her blog, The Academic Jungle. In her final post she asserted that academic/science blogging (as she sees it) has little or no significance. That the disappearance of such blogging won't make any difference.*

Perhaps that's true for her, but not for me.

I am continually learning a lot from other blogs. Reading about the trials, tribulations and triumphs of tenure-track faculty as chronicled at Prof-like Substance, Professor In Training, Blue Labcoats, ChemBiLOLogy and The Prodigal Academic has no doubt had a positive effect upon my interactions with junior faculty at my institution. I've learned much about women in science from some of the same blogs, plus Isis and Zuska. Drugmonkey and Comrade PhysioProf have dispensed invaluable advice on obtaining funding, particularly from the NIH. And Janet Stemwedel's Adventures in Ethics and Science blog is always food for thought.

In addition, the interactions I have had with people in the comments sections of this and numerous other blogs have in general been a blast.

My own blog has allowed me to share frustrations and triumphs, dispense advice unasked, and generally blather and pontificate. Maybe not useful for others, but certainly cathartic for me.

Blogging and reading academic/science blogs have significance for me.








* Hopefully I'm not getting her comments wrong or out of context. Since her blog no longer exists I'm having to go by memory - I read the post last night.

What? But... Hang on a sec...

I go away on vacation (hmmmmm, vacation.... sun, beer, sand, beer, waves, beer, seafood, beer and beer...) and all hell breaks loose.

Well, maybe not hell. But a whole new blog collective just... appeared. Scientopia. And many of my favorite science bloggy types have moved there. I was going to list them but Bora over at A Blog Around the Clock has already done so here.

Tres cool.

Disordered ramblings

Of late I've become interested in so-called intrinsically disordered proteins (IDP's).* These are proteins that contain one or more "significant" regions of sequence that are unstructured. "Significant" can range from perhaps ten or so residues, up to the entire protein. There are experimental data suggesting that the disordered regions in some of these are vital for function. It is generally thought that disordered regions important for function might undergo a folding reaction when bound by another protein, or a nucleic acid, or even a small molecule.

I'm interested in IDP's** because two of my favorite proteins have disordered domains that are essential for function and that do undergo the kind of folding upon binding mentioned above. This makes these proteins more interesting to me intellectually (not that they would be boring without disorder), but can also make them significantly more difficult to study than your garden variety well-folded, globular protein.

The IDP field is populated by large numbers of bioinformaticists (spawning my last post). There are also experimentalists and computational biologists (of the molecular simulation kind), but much of the initial driving force in creating this as a field appears to have come from the bioinformaticists. A small group of them.

Who are seriously over hyping the field.***

The hype being based largely on predictions of disorder. Predictions. Not much data. A prediction is just a pointer to something that might (or might not) be interesting. It's pretty much meaningless without experimental verification.

This is a problem. Yes, we all need to sell ourselves and our research. We all need to convince others that what we do is important and should receive gobs of funding $$$'s. But what you're selling has to have some connection to reality. A track record. Data.

Right now the IDP field has all the appearances of an infomercial for some kitchen gadget that is promised to mix, knead, puree, blend, chop, slice, dice, julienne, fry, roast, bake, boil, steam, load the dishwasher, sweep the floors, put the children to bed, and polish your shoes. Only believable in the wee hours of the morning after a long evening consuming copious quantities of the alcoholic beverage of your choice.

For now I'm keeping my credit card in my pocket.










* There are many, many recent reviews on the subject. This one is okay (and free).

** I seriously dislike the name "intrinsically disordered protein." For a start, the majority of the IDP's that have been identified are mostly well-structured and only have a fraction of their sequences disordered. I saw someone use the term "intrinsically disordered region." That's an improvement.

*** Case in point: the many, many reviews. Many, many of which were authored/co-authored by this guy. Dude, enough already. Go spend some time in the lab generating new data.

Geekery

Thanks to the grant-making powers that be it looks like I might be getting a new toy. Makes me feel all warm and fuzzy inside.

Now I need to start planning how to get one of these... Or an equivalent.

I like fluorescence. Can you tell?

Another datum on why impact factors are useless

The latest newsy thing from the TheScientist.com just landed in my inbox. Top story today is titled "New impact factors yield surprises." In the short piece the reporter notes how the impact factor (IF) for Acta Crystallographica - Section A has jumped 20-fold since last year and is now the second highest for science journals (edging out NEJM). This apparently is all due to a single 2008 article, chronicling the development of the SHELX crystallography computer program suite, which garnered some 6600 citations.

Okay, so this is an extreme example of how IF's can be manipulated via review-type publications, but still...




On the other hand, if you're currently on the job market and have a publication in Acta Crystallographica - Section A, you just might want to make note of the current IF in your CV.

The captain has turned on the fasten seatbelt sign

Buckle up folks, we're in for a rough ride...


Apparently the NIH is concerned funding rates are going to fall off a cliff in 2011. Jocelyn Kaiser has a news piece this week in Science.


Some "lowlights":

The 2-year grants will run out in 2011, and when that happens it could cause a nasty shock. Barring a new windfall—and none is in sight—NIH's budget will drop sharply next year. Much of the work recently begun will be left short of cash. The result could be the lowest grant funding rates in NIH history, and the academic job market will suddenly dry up—especially for young researchers.


Ummm, duh.


"This is the cliff that people are talking about, " Collins said. "We are going to face a crunch" in 2011, he said. The success rate, or portion of reviewed applications that receive funding, which hovered around 30% a few years ago and 20% this year, "will be more like 15%."


20% this year? Really?

The cliff problem was the focus of a meeting of economists, academic leaders, and NIH officials last week at Cold Spring Harbor Laboratory on Long Island in New York. Economist Paula Stephan of Georgia State University in Atlanta expects trouble as a glut of postdoctoral fellows and graduate students who were hired or kept on with ARRA money will hit the job market. "There is going to be a huge backlog of individuals looking for jobs and fellowships in 2011 and 2012, " predicts Stephan.

One suggestion: persuade Congress to fund one-time "bridge" fellowships to give ARRA-funded postdocs more time to find academic jobs or switch careers. "It wouldn't take a whole lot of money, " says meeting organizer Richard Freeman, a labor economist at Harvard University.

What academic jobs is he talking about? Basically Freeman's suggestion boils down to giving "bridge" funding to ARRA-funded postdocs so they have time to bail out...

Harvard microbiologist and American Society for Microbiology President Roberto Kolter, who spoke at Cold Spring Harbor, says "there's a wait-and-see attitude right now" in his department, which didn't apply for much ARRA money. He and many of his colleagues won't need to renew their grants for 2 or 3 years. But then, he expects, "there will be some casualties."

Ain't that the truth...

Re that stolen iPhone...

The Daily Show With Jon Stewart	Mon - Thurs 11p / 10c
Appholes
www.thedailyshow.com
Daily Show Full Episodes Political Humor Tea Party

A haiku-like post

Lab in quandary

Protein expression zero

Bad ampicillin

Travel notes

A few observations after having returned from a meeting:

1) As someone in line before me found out, belligerently demanding airport security rush you through the screening process because you're late for your flight, and then becoming abusive when security politely informs you that you have to go through the same process as everyone else, is guaranteed to get you "special" treatment. And make you miss your flight.

2) There is an inverse correlation between the amount you pay for a hotel room and the chances of the stopper in the bathroom sink working.

3) The odds of the movie shown on my cross-country flight being watchable are slim to none.

4) The odds of the person sitting next to me on a cross-country flight having some hygiene issues are quite high.

5) Really bad talks get discussed far more than decent, but not quite kick-ass, talks. But not in a good way. The postdoc who gave a talk that very clearly demonstrated that he didn't know or understand basic physical properties of the kind we expect undergrads to know will be remembered for some time.

6) Not knowing how to set up, run and/or analyze experiments is not an impediment to giving a talk at a large meeting based on said experiments (n >> 10). And this is not correlated with career stage (student vs. postdoc vs. PI).

7) The best airport in the world is the one you land at at the end of your trip.

Write for your reviewers

There was an interesting discussion over at DrugMonkey recently regarding perceived and/or real issues with the grant review process. In particular there was some back and forth over what to do when you receive bad reviews from someone who clearly isn't an expert in your area. My first thought on reading some of this was...

Why on earth would you EXPECT the reviewers of your proposal to be experts in your field?????

It takes very little thought to come to the realization that the odds are very much against the roster of an NIH study section or NSF review panel actually having even one such expert. It is simply unrealistic to expect that to be the case. And even if it is, your proposal may not be assigned to that person for a variety of reasons (conflict of interest, reviewer already overloaded etc.).

Having your proposal reviewed is nothing like having a manuscript reviewed. Journal editors have access to a much, much larger pool of potential reviewers than program officers (PO's). Editors have the "luxury" of identifying and contacting reviewers who really do know the specific area of each manuscript.* PO's are stuck with the study section/review panel roster, plus maybe some ad hoc reviewers. And those ad hocs may not be experts in your area. Even if they do use ad hocs (very commonplace at the NSF**), your PO, and you as a proposer, want reviewers who are on the panel. No matter how good the ad hoc reviews, if someone, preferably two someones, on the panel isn't pushing hard for your proposal it won't be funded. Period.

So why would you write a proposal thinking it's going to be reviewed by an expert? Don't. You'd just be screwing yourself. Write it for reviewers with a general knowledge of your area. That's grantology 101.







* Getting them to agree to review is another matter.
**  At the NSF ad hocs submit reviews electronically and aren't present at the panel.

End of an (old) era

This week I sent three of these off to surplus.

A 13-year old Unix workstation...
Kind of cute really.

I had bought them out of my start up funds when I first started here. I hadn't turned them on for at least five years. I felt kind of sad getting rid of them.

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.

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.

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.

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.

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:

Background/Training/Education
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.

Publications
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.

Funding
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.

Awards
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.