Paper Review Ponder

December 31, 2009

What’s up with these journal editing/reviewing systems that email the reviewers when the decision has been made but don’t append the reviews. Requiring the reviewer to go back and log into the reviewer site and make a few clicks decreases the numbers who are going to read over the other reviewer comments.
That’s bad. You should always read over the comments of the other reviewers as a continuing education / calibration of your own reviewing behavior. Plenty of journals just send you the Editor Decision and reviews as the notification. Easy. Peasy.

Funny how certain topics keep coming back to the table for discussion. I could just requote the first line of this repost, couldn’t I? The relevant current discussion comments are here, here and here. This post went up on the old blog Dec 11, 2007.


In a couple of comments to a recent post, people were exploring the concept of whether it matters if a particular individual is funded to do something since perhaps the other competing, well-funded labs will just do it anyway (start with this one). I would argue that this is wishful thinking. While there is some truth to the idea that only by accumulating a big pile of resources is one free enough to play around and take risks, established programs have a tendency to get conservative. So breaking up OldBoy type cronyism is a good goal.
As luck would have it, we have two RFAs (one doubles up for different mechanisms which is necessary with the new and idiotic grant packages) and a Program Announcement (with Set Aside Funding; “PAS”) from NIDA that let us pursue this a little more.

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This was originally posted June 4, 2007.


This is a picture of Eloria noyesi eating a coca leaf from Chen et al 2006, Gene, 366 (1): 152-160, Molecular cloning and functional characterization of the dopamine transporter from Eloria noyesi, a caterpillar pest of cocaine-rich coca plants
E.noyesi eats coca leaf

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This originally went up August 13, 2007.


Writedit notes:

Science has published an elegant posthumous article by Daniel E. Koshland, Jr. entitled The Cha-Cha-Cha Theory of Scientific Discovery … representing the 3 categories of discovery: Charge, Challenge, and Chance. In brief:
“‘Charge’ discoveries solve problems that are quite obvious … ‘Challenge’ discoveries are a response to an accumulation of facts or concepts that are unexplained by or incongruous with scientific theories of the time … ‘Chance’ discoveries are those that are often called serendipitous and which Louis Pasteur felt favored ‘the prepared mind.'”

I want to go a little beyond writedit’s point so I’ll quote more extensively from the article

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Merry Christmas, Dear Reader!

December 25, 2009

Here’s wishing a very Merry Christmas to all of my Readers who are celebrating! I do hope you are surrounded by friends and family- even if they are driving you mad.

It has been a couple of years since I wrote this one and I was wondering to myself if study sections have been de-clustered. If you have an odd moment (and really, what else would you be doing the next couple of days) scan through your favorite study sections’ funded grant output and see how clustered those sections are at present. This post went up Dec 7, 2007 on the old blog.


We’ve been discussing the degree to which insular sub-groupings of scientists protect and maintain themselves and their peers through the grant review process. We’re using “bunny hopping” thanks to whimple and the NIH CSR calls this “clustering“. Note upfront that this analysis and discussion does not necessarily require overt malicious intent on anyone’s part. The presentation at the recent PRAC meeting from Don Schneider identified the IFCN (Integrative, Functional and Cognitive Neuroscience) group of study sections as top suspects in the “clustering” phenomenon. Can we derive a little more information one wonders?

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ResearchBlogging.orgThere is an interesting paper that I just ran across which will possibly please a certain segment of my audience. You see, it provides a bit of a test of the hypothesis frequently bandied by my commenters that anti-drug messages backfire. That if you tell adolescents all sorts of bad things are going to happen to them if they try an illicit drug once, and it doesn’t happen, somehow you are actually encouraging them to try the drug again. This general area is an occasional interest of mine and you can read a few thoughts here, here, here, here and here. The paper itself is this one.
Skenderian JJ, Siegel JT, Crano WD, Alvaro EE, Lac A. Expectancy change and adolescents’ intentions to use marijuana. Psychol Addict Behav. 2008;22(4):563-569. [Free PubMed Central version]
This paper describes a secondary analysis of data collected under the National Survey of Parents and Youth which focuses on the efficacy of an anti-drug media campaign. This means that it is, necessarily, correlational in nature, not a prospective experiment*. The purpose of this secondary study was laid out as:

There are many possible reasons for [poor effect of anti-drug messages] including the possibility that the typical campaign often is designed to develop expectancies regarding marijuana use outcomes that may not be experienced by the initiate. Changes in expectancies regarding marijuana, and the effects of such changes on initiates’ intentions to continue use, are the focus of this investigation.

In short, if we deliver lies-to-children to adolescents, do we end up encouraging cannabis use?

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From writedit we receive the tipoff to a new initiative of NIH’s Center for Scientific Review. The Press Release says:

CSR is sending invitations to about 2,500 members of the scientific community with a strong commitment to peer review and experience serving as reviewers… Joining the college will allow reviewers who find it difficult to manage the travel and commitment of being a regular reviewer to remain engaged in peer review…College reviewers primarily will provide written or “mail-in” critiques and be involved in two-stage reviews, which have successfully assessed thousands of special sets of applications, such as the Transformative R01 and Challenge grant applications as well as groups of translational applications and small business applications.

Oh I think I will be taking this up a time or two. Initial observations:
-just when they were reducing the ad hoc participation on regular panels and increasing the load (thereby broadening the “fit”) of regular reviewers…this?
-all talk of impact and significance for regular review is rolled back, these initial reviewers will be expected to nitpick the design and methods, just like before!
-feedback from those who sat on the second stage of the Transformative and Challenge reviews this summer sure wasn’t all that positive..but then CSR seems to frequently steam forward with great enthusiasm on changes where I can’t seem to find anyone who is in favor of them.

Sacrifice means you too.

December 22, 2009

“Do it to Julia! Not me! Julia!” –Winston Smith


BikeMonkey Guest Post
I have been reading over the minor tempest that the DM has been trying to stir up with respect to the NIH grant as a “gift” to the PI. It strikes at deeper chords of tension that we have in NIH-funded science, chords that emerge most strongly every time there is a budget crisis. Or the appearance of a budget crisis in the NIH, anyway. It amuses me to match the identification of “the real problem”, the prescription offered as a solution and the career status of the person making the comment.
Older PIs complain about all the junior reviewers on study section and want to replace them with people more established, just like themselves.
Junior PIs complain about the rich-getting-richer and the OldBoys/Girls club and want caps on the total amount of funding a PI can hold.
Middle career PIs complain about OldBoys/Girls and Early Stage Investigator affirmative action…and propose a variety of creative cures that seem custom fit to benefit their own exact situation.
But the selfishness hardly begins and ends with NIH funded scientists. Not by half.

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Authorship Wackaloonery

December 22, 2009

This shit cracks me the fuck up:

Carbonic anhydrases are upstream regulators of CO2-controlled stomatal movements in guard cells
Honghong Hu1,5, Aurélien Boisson-Dernier1,2,5, Maria Israelsson-Nordström1,3,5, Maik Böhmer1,6, Shaowu Xue1,4,6, Amber Ries1, Jan Godoski1, Josef M. Kuhn1 & Julian I. Schroeder1
* * *
5. These authors contributed equally to this work.
6. These authors contributed equally to this work.

Three co-first authors and two co-fourth authors!?!? I am trying to imagine the negotiation between the Schroeder, Bohmer, and Xue:
Schroeder: Xue, where are those fucking PCRs!?!?
Xue: I’m not giving them up unless you make me fourth author!!! Fifth authorship is for fucking LOSERS!!!
Bohmer: No fucking way!!!! I’M FOURTH AUTHOR!!111!!!ELEBVENYT!!111!!
Schroeder: Ah, you fucking guys are a pain in my fucking ass! OK, how about this? You can be co-fourth authors. Happy now?
Xue: Ok, boss.
Bohmer: Ok, boss.
Schroeder: Great. Now get the fuck out of my office, you ridiculous fuckwads.

Following our little discussion of whether or not NIH grants should be viewed as largesse or something a little more…professional, our good blog friend Anonymoustache teed off:

Not to be framing anything here, but I believe the best analogy for NIH grants is investment capital, and it would serve us all well to look at it and think about it in that fashion. Think about the NIH as a venture capital firm that has a really large portfolio. It makes calculated bets on a really large number of projects with a view to a two-fold return on investment: i) Increasing the body of scientific knowledge, and thereby ii) Generating advances in healthcare and medicine.

Go read the rest.

Age 32, cardiac arrest….

December 21, 2009

Sigh.
Le Sigh.
A young actor is dead at 32 of cardiac arrest. At least that is what the early reporting is saying. Also that Brittany Murphy collapsed in the shower. Some additional reporting indicates that she’d lost a great deal of weight recently, some photographs that have been published seem to confirm that impression. Some suggestion of her being on multiple prescription drugs for multiple unnamed ailments.
Dammit.
’cause you know what is coming next. My only questions are “Which drugs?” and “In what combination?”.

For those of you that haven’t been following along, Oklahoma State University President Burns Hargis unilaterally blocked a project on anthrax vaccine development from going forward. The project was IACUC approved and NIH funding had been allocated (OSU’s end was a subcontract on the project). The reasons given by President Hargis were less than convincing. It boiled down to an assertion that the work was “controversial” and “not in the interests of OSU”, combined with a rejection of the speculation that he had caved in to demands from one of OSU’s biggest donor couples (the wife of the couple is a noted AR activist and well beloved by extremist organizations). Did I mention the project included baboons as research subjects?
[ A great summary is here at Speaking of Research. ]
In all the explaining coming from President Hargis and OSU spokespeople, we have a continued assertion that the University is not against all animal reseach and has not been swayed by AR activists. Well, one of the Oklahoma state legislators isn’t buying this line of bullpockey anymore than I am.
Representative Phil Richardson:


“I bleed Orange as much as anyone, but I am deeply concerned by the actions of OSU officials, which appear designed to cater to animal-rights fanatics instead of providing a sound education in agricultural sciences,” said Richardson, a Minco Republican who received his Doctor of Veterinary Medicine from OSU in 1967.

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Repost: The Big Bucks

December 18, 2009

For some reason or other the recent discussions around here on the way we should view NIH grant money (largesse, fee-for-service) made me think this issue was worth raising again. While we’re looking all….entitled you know. This post originally appeared Jan 15, 2008 on the old blog.


A recent reader discussion touching on scientist compensation has blown up on a prior post. Bill (no, not that Bill) and whimple have been leading the charge. To add another data point we have the current NIH Notice on Salary Limitation on Grants, etc. The money quote is as follows:

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I had a very fascinating comment pop up in a prior thread following a post which described the relationship between Congressional budget passing and the ability of the NIH to fund grants. This was motivated, I will remind you, by a comment at writedit’s place from a trainee who was holding a 3%ile score (i.e., well within any likely payline) and anticipating a NIH fellowship award on Dec 1.
A couple of commenters described NIH grants as “FREE money” or “gifts“..and I took exception to this characterization.
There were a couple of exchanges until finally another (?) commenter laid down enough rotten egg to merit another post. It started with:

Bitter much?

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