Right, I'm off then.

Okay, so you probably realized from my last post that the blog is moving. I'm off to LabSpaces.net. 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.

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.

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?

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.

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.

My 2.5 week old nephew's favorite song

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

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.

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.

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.

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

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.

Kickass or kickarse science?

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




or, kickarse?




Discuss.

Your science is not enough

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

Assertiveness.

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

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

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

Something to think about and work on.

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

New Year

2010 already. How did that happen?

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

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



Odyssey's research project has a minor setback.


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



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

And now my project has...

a son!!!!



Doesn't Dad look proud?

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


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


Life is good.

May this be a good year for all of us.

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.

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.

Mistake?

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