Thursday, August 05, 2010

Right, I'm off then.

Okay, so you probably realized from my last post that the blog is moving. I'm off to This is a homegrown science news site run by Brian Krueger. Brian invited me to set up shop over there. He already has an impressive (and young) group of bloggers - go check them out. My new home is here. I'll continue to blather on incessantly about the things that interest me, while simultaneously raising the average age of the bloggers at LabSpaces.

Later today I'll be changing the RSS feed on this site to point over to the new blog. This site will remain and I'll pop over to check on things every now and then. But all new posts will be at my new home.

See you on the other side!

And Blogger, thanks for all the fish.

Wednesday, August 04, 2010

Wanted: good moving company.

Must be good at moving glass without breaking it. Especially glass filled with a variety of beverages. Mostly beer.

Tuesday, August 03, 2010

A successful brainwashing

I have had an exceedingly bright undergrad working in my lab over the summer. This week is her last before heading off to her home institution. Today she told me she didn't want to leave. She wants to stay and try to figure out what the enigmatic protein she's been working with really does.

Yes!!!!!!!!!! (Odyssey pumps fist in air)

Of course, she'll head back to her home at the end of the week. Maybe she'll come back next summer...

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.

Monday, August 02, 2010

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.

Tuesday, July 20, 2010

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.

Monday, July 19, 2010

Data mining talks

As a molecular biophysicist I often hear talks (and see posters) given by bioinformaticists.* I am struck by how these are almost uniformly abysmal. I'm not necessarily referring to the data, but rather the presentation as a whole. This has reached the point where I don't think I can bring myself to sit through another bioinformatics talk (or poster presentation) for at least the next three months.

Why has the quality of the now dozens of such talks I've suffered through been so low?

In the majority of cases I posit it's a combination, in varying degrees, of a lack of imagination and a disconnection from the underlying biology. Too many of these presenters regale their audiences with interminable laundry lists of how property X is over-represented in sequences of class A, and under-represented in sequences of class B. Ummmm... So what? Why should I care? Often such presenters either don't know or are too lazy to spend the time connecting their data with known biology. As an example, I recently sat through a talk where the speaker made a big deal about the prevalence of glutamine-rich sequences in proteins involved in transcription. Not once did he refer to the fairly substantial body of experimental data on these very same sequences. In fact, when asked, he couldn't offer up any explanation for this observation.** Major fail.

I can't explain why this happens. Obviously it shouldn't. Perhaps it's a function of the relatively immature nature of bioinformatics as a field. It's still at a stage where method development trumps method application. Application of the intelligent kind.

I remember when macromolecular crystallography talks suffered from similar issues. They would often be these long detailed descriptions of the structure(s) just solved by the crystallographer. No connection to the biology, just the details of the structure. Listen, I don't give a rat's arse that there's a type VIIb turn between helices 7 and 8. What I want to know is what the structure tells us about the biology. Nowadays most crystallographers do make the connections. One can't get a grant for simply solving structures any more.***

I've heard through the grapevine that getting a grant to do bioinformatics has become increasingly difficult. More so than would be expected from the downturn in science funding. Perhaps we'll see the field forced to mature more rapidly and presentations improve.

* By "bioinformatics" I mean the data-mining thing. A colleague once defined it thusly: "Bioinformatics is the mining of biological databases for profit (not necessarily of the monetary kind)." This is distinct from computational biology which, at least at the molecular level, tends to employ an energy function of sorts.

** Glutamine-rich regions can be involved in DNA binding - the glutamine side chain is quite good at making hydrogen bonds with nucleic acids.

*** Not when I'm reviewing the grant. :-)

Friday, July 09, 2010


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?

Monday, June 21, 2010

Another datum on why impact factors are useless

The latest newsy thing from the 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.

Cook out!

Why are there only seven hotdogs in a Hebrew National packet?* Packets of hotdog buns contain eight buns. I'd have to buy eight packets of Hebrew National hotdogs and seven packets of buns to even things out. Fifty-six hotdogs!

But then I'd need fifty-six beers - one per hotdog - to go along with that. Beer comes in six- or twelve packs, or cases of twenty-four... So I'd need to buy twenty-four packets of Hebrew National hotdogs, twenty-one packets of buns and seven cases (or twenty-eight six-packs) of beer. Now we're up to 168 hotdogs.

But what about the paper plates? Do they come in packs of 168? Or six? or seven? Eight? Twenty-four? And how about napkins?


Steak anyone?

* According to that repository of all things true, Google, seven is a lucky number in Judaism. Hence seven hotdogs.

Monday, June 14, 2010

Targeted reviewers?

There's been some discussion on various blogs about the "OMG! NSF is Completely Broken and the World is Going to End!" forum headed up by the disgruntled "Aureliano Buendia." See Prof-like Substance and DrugMonkey for some interesting comments.

Something mentioned in that forum and in a comment at DrugMonkey's piqued my interest. QoQ over at DM's asserted that the NSF is indeed broken and noted in support:

First, the identity of the reviewers is not public and changes from submission to submission -- so you can't target a grant.

You can't target a grant.* I'm not entirely sure what QoQ means by this, but I suspect they want to write their proposals for specific reviewers on the panel. Perhaps so they can try to "butter up" the reviewers by citing their work favorably and often, or to avoid having to write a proposal in more general language that reviewers not experts in the sub-sub-field can understand. Or maybe even both. Or neither.

It doesn't matter really, because targeting reviewers on the panel is WRONG, WRONG, WRONG!!!!!!!


'Cos there ain't no guarantee that the reviewers you are targeting will get your proposal.

In fact the odds are not in the least bit favorable. Review panels at the NSF (and study sections at the NIH) cannot have experts from every sub-sub-field on them. Unless you want either panels with many dozens of members, or many, many more panels than currently exist (and there are already a lot). So the odds are there may be one reviewer at most who is an expert in your particular sub-sub-field (and that person is likely a competitor...).

Targeting panel members would be a particularly stupid thing to attempt (if you could) at the NSF where you could have anywhere from three to ten people reviewing your proposal. Usually three or so on the panel, and the rest as outside, "mail in" reviewers. Even if there is an expert on the panel you could target, one good review isn't even close to being enough to land funding. And let's be realistic - a panel member might be somewhat flattered by some "buttering up" in a proposal, but they're generally smart enough to recognize it for what it is.

Write your proposals for people only somewhat conversant with your corner of the field (and cite all the relevant literature, and none of the irrelevant). If you can't do that, chances are, you won't stand a chance of being funded.

* Actually, the NSF does let you do a form of targeting that a proposer would be foolish not to take advantage of. When you submit your proposal you are given the chance to suggest reviewers. In my experience NSF PO's do actually use some of these suggestions as outside reviewers. Obviously these need to be reasonable suggestions...

Friday, June 11, 2010

If you're going to say no, at least do it quickly

I'm on the editorial board of a journal in my field. I am often assigned manuscripts as managing editor. This means finding reviewers. Of late I've noticed a disturbing trend (ANECDOTE ALERT!!!). People I ask are taking an unreasonably long time to decide whether or not they will review a manuscript. Days. A week even. If this were just one or two people you could explain it away easily enough. They're traveling, for example. But it's not one or two. It's approaching 30-40%. Given that I'm managing two to four manuscripts at any given moment, that's a lot. And when they eventually get back to me (those that do...), they invariably say no they can't review the manuscript.

Why are you taking so long? Read the abstract (which we send in the email), think about what else you have to get done in the next couple of weeks, and decide whether or not this is a review you want to do. Then get back to me by reply email. Not a hard process. The longer you take to decline the invitation, the longer the whole process takes. Is that what you want to happen with your manuscripts? Didn't think so. So if you're going to decline, get off your rear end and say no quickly.

Monday, June 07, 2010

An open letter...

To the rabbit that ate all the leaves off the cucumber plant in my vegetable garden:

You may be cute and furry, but let me just remind you of something-

you are also edible.

Friday, May 07, 2010

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...

Wednesday, May 05, 2010

Building bridges

Based on the comments to my previous post, albeit a small sample size, there does seem to be support for requiring recipients of, or applicants for, bridge funding to demonstrate their worthiness. While I have the attention of a larger than normal audience (thanks to DrugMonkey), let me ask how bridge funding is handled in your department. Do you have set criteria/expectations, or is it handed out seemingly arbitrarily? If there are criteria, what are they?

Monday, April 12, 2010

A haiku-like post

Lab in quandary
Protein expression zero
Bad ampicillin

Wednesday, April 07, 2010

To the author...

...of the poster I saw yesterday.

Red text on a green background. Really? Did you even think about that for one moment? Aside from the fact it's really, really hard to read for those of us with decent eyesight, what about the ~8% of the population who are colorblind? Most of whom have red-green colorblindness?

Oh wait. It was a public service thing, right? A test for red-green colorblindness for those in the poster session! How clever...

Odyssey's red-green color blind test.

Or maybe you're just a moron.

Monday, April 05, 2010

Can one reviewer make a difference?

I am occasionally asked to review manuscripts for a journal in my field that has a storied past, but over the last decade has fallen out of favor. It's impact factor (for what little that's worth) is now down below 2.5. This is not a journal I have ever published in, but I feel compelled to accept an invitation to review every now and then for two reasons. One is that I know a number of people on the editorial board and would like to stay on good terms with them. The other, lesser reason, is more altruistic and likely misguided. In the back of my mind I have this little voice saying that maybe this journal can be restored to its former prominence if submitted manuscripts were reviewed more rigorously. Judging from the dross that is regularly published I would say rigorous review is not a common occurrence at this journal.

I've been quite content to review two or three papers a year for this journal for the above reasons. Until recently. Much to my surprise I was asked to review a revised manuscript that I had rejected. Rejected just two weeks before the revised manuscript was submitted. Rejected for what I believed were fundamental flaws of the kind that make pretty much all of the work described in the manuscript worthless. Turns out neither the other reviewer, nor the editor (someone I don't know) spotted the same flaws or agreed with me. I can deal with that. Perhaps I was wrong - it can happen. So I read the revised manuscript and the authors' cover letter. Turns out the authors didn't think my perceived flaws were a problem. Again, I can deal with that. But here's the thing. The flaws I had identified were related to very, very basic solution thermodynamics. The kind you are taught in general chemistry. Or even high school. Okay, I could be wrong, so I consulted a physical chemistry textbook. Nope, I was right according to that. I asked a colleague*, who interrupted me before I could get half way through my explanation to tell me that the solution thermodynamics couldn't be right. For the same reasons I had identified.

So the authors are misguided wrong deluded idiots. Fine, it happens. Apparently the other reviewer either didn't read the manuscript carefully or is in the same category as the authors. Not so fine, but again, it happens. The editor? Now that's where I have a real issue. It would have taken him no more than 15 minutes to have read my review and checked the original submission to find I was right, leading to rejection of the manuscript. Instead he apparently looked at the two reviewer scores, one reject and one (very) minor revisions and split the difference. Lazy bugger.

So I ask you, what's the point? Apparently my efforts to be more rigorous as a single reviewer are wasted in this case. The reality is a journal cannot raise its standards via a "grassroots" effort on the part of the reviewers. I know that and have done for some time.

The moral here is I have to stop listening to those voices in my head.

Oh, and I rejected the manuscript again. And sent the editor in question a short lesson in basic solution thermodynamics. Perhaps not very tactful, but what do I care? I won't be reviewing for him again.

* Staying within the limits of reviewer/author confidentiality of course.

Thursday, February 25, 2010

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.

Thursday, February 18, 2010

Calling all chemistry types

Apparently the NSF Division of Chemistry is having trouble finding enough qualified reviewers. This would be a great opportunity for any chemistry types on the tenure-track out there. There is nothing like reviewing proposals to teach you how not to write one.

Wednesday, February 17, 2010

Live blogging

I know there has been some discussion on the 'tubes about live blogging from meetings, so I thought I'd pass this along. The Biophysical Society has selected four bloggers to live blog from the upcoming annual meeting in San Francisco. Apparently the Society is embracing blogging - not only did they call for volunteers they are apparently giving the selected bloggers iPod nanos as incentives. Cool.

Go check out the bloggers:

Sukriti at Eureka!
Matt at insingulo
Casey and company at Haverford
Fabian at science:biophysics//NBI prereflexive cogito

Monday, February 15, 2010

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.

Friday, February 05, 2010

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.

Friday, January 22, 2010

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?


Thursday, January 21, 2010

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...


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.

Tuesday, January 05, 2010

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.

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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.

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

And now my project has...

a son!!!!

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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.