I am motivated to once again point something out.

In ALL of my advice to submit grant applications to the NIH frequently and on a diversity of topic angles, there is one fundamental assumption.

That you always, always, always send in a credible application.

That is all.

Percent Effort

January 30, 2015

Times I have made critical progress in conceptualizing experiments, grant proposals and manuscript language this past month or so.

-exiting lab on way to get in my car
-riding a chairlift
-sitting at my desk putzing on Twitter
-the shower
-lingering at coffee shop
-during random PI blathering to technician

Blogrolling: Grant Slave

January 30, 2015

Check it out.

Things that I actually have to say to some people.

yes. it is bad news that there is yet another way for people to fuck themselves the hell up on stimulant drugs. yes.

BikeMonkey Post

One inexorable rule of the jungle…err, savannah, is that the predatory carnivore that takes out the old, the slow and the weak members of the herd is actually doing a favor for Wildebeest kind.

Somewhere in there is a lesson for the study section reviewer.

Read the rest of this entry »

The latest version of the query was on the Twotts:

My advice, of course, is to do both of these things. Start up a new line of attack right away as well as do a good job with the line of work that your R00 is for, with the thought of converting that into an R01 project later.


Before anyone gets to that they need to sit themselves down for a little pondering.

This advice that I give (go big right from the start) has to be modulated by two critical factors. What kind of scientist you want to be and what kind of scientist you are expected to be.

So, first question that you need to ask yourself is what you see as your ideal lab operation both right now (next 2 yrs) and into the future (say, year 10). What do you prefer? What is going to make you happy both scientifically and mental-health wise? How much can you handle? How much can you handle five years from now (because, dear n00b PI, what seems overwhelming in year 2 is much easier in year 4 or 8)?

This has to be your starting point. If you can’t see your way to a sustainable, desired future operation of your little cottage industry of science……well you aren’t going to be happy. What do you want to do? This is critical for deciding how to go about attaining your goal and for deciding what strategy to pursue right now.

The second question has to do with what you are supposed to be doing given your job category, University type, subfield, etc. Are you expected to be a two-grant lab? Are the sorts of production rates that are expected of you only possible with more support than one R00 can provide? Look around you. What are your peers in your Department, in your School of X and in your subfield doing?

Do you have a huge teaching burden? Do you get a lot of free undergraduate labor for your sciencing or do you need to be able to hire technicians and postdocs?

There was a followup…

Which implies that local advice was to focus on the one project, then ask for more money later.

Danger, Will Robinson.

This could be the answer to the local expectations question. Could be. But it could also be the voice of long outdated, or generationally privileged, experiences talking.

Older colleagues may think you young pups are in the same era that they enjoyed. An era when the expectations of renewing a funded project (that was reasonably productive) were very high. Those expectations are not high anymore. It is career suicide, imnsho, to assume that you can submit a new application in the final year of your current single-grant support and get refunded immediately. Suicide, that is, assuming that you are in a place which demands essentially continual funding. Now, of course, if all the people around you have gaps in funding all the time, and it never seems to perturb tenure chances, then this changes the equation for your individual situation.

R00-holders, and those who have managed to acquire major funding in the first 1-2 years, face another strategic consideration. A little bit ago, someone was proposing a “twins” strategy of simultaneous submission so as to game the ESI designation. It’s worth a read. There is another consideration for the first couple of years of appointment. The study section sympathy for lack of independent productivity (read, papers) from your own lab diminishes quickly with time. In year 1-2, the sane reviewers are not going to expect that you have generated substantial amounts of data or published papers “from your new lab” yet. They will review you accordingly. Once you start into year 4? Well, you will be hard pressed to find any reviewers being sympathetic. So this gives you a sort of grace period to send up grant proposals with very minimal supporting data and without a Biosketch filled with your senior-author pubs.

So, as always, you need to do your career research and some hard introspecting about your plans. Nobody can hand you the answer. You need to collect relevant evidence, determine what is the best path forward for you given your situation and select the best course of action.

Kind of like doing the science itself.

The PR headlines are breathless and consistent:

Researchers Identify Brain Circuit That Regulates Thirst

Brain’s On-Off Thirst Switch Identified

The paper is here.

Yuki Oka, Mingyu Ye & Charles S. Zuker Thirst driving and suppressing signals encoded by distinct neural populations in the brain Nature (2015) doi:10.1038/nature14108

The takeaway punch message from the Abstract:

These results reveal an innate brain circuit that can turn an animal’s water-drinking behaviour on and off, and probably functions as a centre for thirst control in the
mammalian brain.

Somebody like me immediately thinks to himself “subfornical neurons control drinking behavior? This is like the fifth lecture in Psych 105: Introduction to Physiological Psychology.”

Let’s do a little PubMed troll for “subfornical drinking“. Yeah, we’ve known since at least the 1970s that the subfornical control of drinking behavior is essential, robust and mediated by angiotensin II signalling. We know how this area responds to blood volemia and natremia and how the positioning relative to the third ventricle and the function of the circumventricular organ vis a vis the blood-brain barrier permits this rapid-response. We know the signalling works through AT1 receptor subtype to excite subfornical neuronal activity via electrophysiological recording techniques and genetic deletions. Cholinergic mechanisms have likewise been identified as critical components via pharmacological experiments. Mapping of activated neurons has been used to identify related circuitry. The targets of subfornical neurons are known and their involvement in drinking behavior has likewise been characterized. Extensively. We know that electrical stimulation of these neuronal populations activates drinking in water sated rats, for goodness sake! We know there are at least three subpopulations of SFO neurons involved and something about the neurochemical signalling complexity.

There are review articles that you can read if you want to get up to speed.

The new work by Oka and colleagues simply repeats the above-mentioned electro-stimulation experiment from 1983 using optogenetic stimulation. Apart from this, maybe, we have an advance* in that they identified ETV-1 vs VGAT (GABA transporter) markers of two distinct subpopulations of neurons which have opposite effects on the motivation to consume water.

That’s it.

This paper is best described as a very small, incremental advance in understanding of thirst and drinking behavior, albeit tarted up with the pizzaz of optogenetic techniques.

Yet it was published in Nature.

Someone really needs to introduce the editorial staff of Nature to PubMed.
*BTW, a Nature editor confirms this microscopic incremental advance is what is new about this paper.

via retraction watch we learn:

A Bijan Ahvazi has been working at the USPTO since at least 2008, and today a source confirmed that it was the same person who was the subject of last October’s ORI report. Ahvazi was found to have faked five different images in three different papers, two of which have been retracted.

The Notice of ORI finding appeared in October of 2014.

Based on the report of an investigation conducted by the National Institutes of Health (NIH) and additional analysis by ORI in its oversight review, ORI found that Dr. Bijan Ahvazi, former Director of the Laboratory of X-ray Crystallography, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), NIH, engaged in research misconduct in research supported by the Intramural Program at NIAMS, NIH.

The Notice shows that the offenses for which Ahvazi was convicted date to 2004 and 2006. One doesn’t have to assume that much to figure out that he was busted and then had to look for a new job somewhere between 2006 and 2008. It took until 2014 for his fraud to come to light via the official ORI mechanisms. Presumably, although we don’t know for sure, the investigation was confidential up until it reached its formal conclusions which may have permitted him to avoid telling the US Patent and Trade Office about his little whoopsie? I dunno, do you think the USPTO would hire a data fraud as a patent examiner if they knew about it? One thinks not.

p.s. apparently a co-author of this data faker died under bizarre circumstances in 2003.

Odyssey is pondering review articles today. That led to a question from Dr. Becca about the ideal ratio of reviews and primary research articles.

I am not a fan of authors publishing essentially the same review in multiple journals. Nor am I a fan of the incrementally updated review published every year or two. And I am really not fond of burgeoning subfields where everyone spits out a me-too review which then outnumber the primary research articles!

So, my views on this question are likely more negative than average.

Winter Brain vs GRCs

January 25, 2015

The winter “ski meeting” is about as junkety as it gets in science. It looks bad to spend the Federal grant dollars attending an academic meeting at a ski area. Especially when sessons are planned in a way to carve out plenty of daylight hours for skiing.

And yet your standard GRC does the same thing. Except you replace skiing the Rockies with hiking in the Appalachians.

Somehow the latter seems less like an elite and frivolous activity.

But really, it is about the same thing.

H/t: a certain troll

Open Thread

January 23, 2015

Whatcha got today, folks?

Good Gravy.

One David Korn of the Massachusetts General Hospital and Harvard Medical School has written a letter to Nature defending the indirect cost (IDC; “overhead”) rates associated with NIH grants. It was submitted in response to a prior piece in Nature on IDC which was, to my eye, actually fairly good and tended to support the notion that IDC rates are not exorbitant.

But overall, the data support administrators’ assertions that their actual recovery of indirect costs often falls well below their negotiated rates. Overall, the average negotiated rate is 53%, and the average reimbursed rate is 34%.

The original article also pointed out why the larger private Universities have been heard from loudly, while the frequent punching-bag smaller research institutes with larger IDC rates are silent.

Although non-profit institutes command high rates, together they got just $611 million of the NIH’s money for indirect costs. The higher-learning institutes for which Nature obtained data received $3.9 billion, with more than $1 billion of that going to just nine institutions, including Johns Hopkins University in Baltimore, Maryland, and Stanford (see ‘Top 10 earners’).

Clearly Dr. Korn felt that this piece needed correction:

Aspects of your report on US federal funding of direct research costs and the indirect costs of facilities and administration are misleading (Nature 515, 326–329; 2014).

Contrary to your claim, no one is benefiting from federal largesse. Rather, the US government is partially reimbursing research universities for audit-verified indirect costs that they have already incurred.

Ok, ok. Fair enough. At the very least it is fine to underline this point if it doesn’t come across in the original Nature article to every reader.

The biomedical sciences depend on powerful technologies that require special housing, considerable energy consumption, and maintenance. Administration is being bloated by federal regulations, many of which dictate how scientists conduct and disseminate their research. It is therefore all the more remarkable that the share of extramural research spending on indirect costs by the US National Institutes of Health (NIH) has been stable at around 30% for several decades.

Pretty good point.

But then Korn goes on to step right in a pile.

Negotiated and actual recovery rates for indirect costs vary across the academic community because federal research funding is merit-based, not a welfare programme.

You will recognize this theme from a prior complaint from Boston-area institutions.

“There’s a battle between merit and egalitarianism,” said Dr. David Page, director of the Whitehead Institute, a prestigious research institution in Cambridge affiliated with MIT.

Tone deaf, guys. Totally tone deaf. Absolutely counter-productive to the effort to get a majority of Congress Critters on board with support for the NIH mission. Hint: Your various Massachusetts Critters get to vote once, just like the Critters from North and South Dakota, Alabama and everywhere else that doesn’t have a huge NIH-funded research enterprise.

And why Korn chooses to use a comment about IDC rates to advance this agenda is baffling. The takeaway message is that he thinks that higher IDC rates are awarded because His Awesome University deserves it due to the merit of their research. This totally undercuts the point he is trying to make, which is presumably “institutions may be private or public, urban or rural, with different structures, sizes, missions and financial anatomies.“.

I just don’t understand people who are this clueless and selfish when it comes to basic politics.

Thought of the Day

January 22, 2015

On the resetting of the date of original submission:

One thing it does is keep a lid on people submitting a priority place holder before the study is even half done. I could see this as a positive step. Anything to undermine scooping culture in science is good by me.

Skeptic noted the following on a prior post:

First time submitted to JN. Submitted revision with additional experiments. The editor sent the paper to a new reviewer and he/she asks additional experiments. In the editor’s word, “he has to reject the paper because this was the revision.”

This echoes something I have only recently heard about from a peer. Namely that a journal editor said that a manuscript was being rejected due to* it being policy not to permit multiple rounds of revision after a “major revisions” decision.

The implications are curious. I have not yet ever been told by a journal editor that this is their policy when I have been asked to review a manuscript.

I will, now and again, give a second recommendation for Major Revisions if I feel like the authors are not really taking my points to heart after the first round. I may even switch from Minor Revisions to Major Revisions in such a case.

Obviously, since I didn’t select the “Reject” option in these cases, I didn’t make my review thinking that my recommendation was in fact a “Reject” instead of the “Major Revisions”.

I am bothered by this. It seems that journals are probably adopting these policies because they can, i.e., they get far more submissions than they can print. So one way to go about triaging the avalanche is to assume that manuscripts that require more than one round of fighting over revisions can be readily discarded. But this ignores the intent of the peer reviewer to large extent.

Well, now that I know this about two journals for which I review, I will adjust my behavior accordingly. I will understand that a recommendation of “Major Revisions” on the revised version of the manuscript will be interpreted by the Editor as “Reject” and I will supply the recommendation that I intend.

Is anyone else hearing these policies from journals in their fields?
*having been around the block a time or two I hypothesize that, whether stated or not, those priority ratings that peer reviewers are asked to supply have something to do with these decisions as well. The authors generally only see the comments and may have no idea that that “favorable” reviewer who didn’t find much of fault with the manuscript gave them a big old “booooooring” on the priority rating.

Over at Rock Talk, by a Joel MacAuslan:

It isn’t about whether to fund only the “best” science: I really DON’T want only Isaac Newtons and Louis Pasteurs to be competitive, and to be able to spend their careers on this research. That’s because I don’t want to wait 200 years for all that “great” science to trickle through society. Fund lots and lots of very good science, and cure heart disease in 40 years, instead!