GrantRant VIII

January 19, 2013

Do not EVER spend so much time geeking away about the amazingly swell trees that you will be characterizing that you forget to convince the reviewer that the forest itself holds any interest. And I mean ANY interest…..Seriously dudes, I’m trying to help you out here but you are giving me absolutely nothing to work with. There is barely any point in me even reading your experimental manipulations….I can tell already there is no overall justification for doing them in the first place!

Via the New Zealand Herald:

A boy who almost died of tetanus before Christmas is home and on the mend, but his parents are desperate for others to vaccinate their children after they did not.

Auckland couple Ian and Linda Williams thought they had made an informed decision against immunising their three children because of concerns over adverse reactions.

But they regretted their decision when middle child Alijah contracted the potentially fatal disease just before Christmas, and was put in an induced coma on life support at Starship hospital.

They immediately immunised their other children and wrote to Alijah’s school to warn parents who had not vaccinated against the disease and others such as whooping cough.

“It was me that put my son in this situation,” Mr Williams said.

Yes, yes it was. Don’t let it be you who does the same, people. Vaccinate, vaccinate, vaccinate.

h/t: bengoldacre

I barely have to change the leadin for this reposting. Last time I said “Sports doping is in the news again this week.” It was a previous round of Lance-fest. Well, he’s finally confessed to doping through his 7 TdF wins and a lot more besides.

Doping has been with cycling since forever.

I put this up at the original DrugMonkey blog on 8/21/2007.

We’ll start off our discussions on sports doping with the classic psychomotor stimulants, the amphetamines. You know, good old “speed”. A class of drugs primarily considered indirect dopamine agonists because they bind to the dopamine transporter with good affinity (dopamine reuptake inhibitor) and also act to facilitate dopamine release from the terminal. As with similar compounds they also tend to have some affinity for other monoaminergic transporters and will thus modulate norepinephrine and serotonin. Nevertheless, the major action usually under discussion is to increase dopamine levels in the synapse. Read the rest of this entry »

Dump Journals

January 17, 2013

To be absolutely clear, I use the term “dump journal” without malice. Some do, I know, but I do not. I use it to refer to journals of last resort. The ones where you and your subfield are perfectly willing to publish stuff and, more importantly, perfectly willing to cite other papers. Sure, it isn’t viewed as awesome, but it is….respectable. The Editor and sub-editors, probably the editorial board, are known people. Established figures who publish most of their own papers in much, much higher IF journals. It is considered a place where the peer review is solid, conducted by appropriate experts who, btw, review extensively for journals higher up the food chain.

What interests me today, Dear Reader, are the perceptions and beliefs of those people who are involved in the dump journal. Authors who submit work there, the Editor and any sub-editors….and the reviewers. Do we all commonly view the venue in question as a “dump journal”? Or are there those that are surprised and a bit offended that anyone else would consider their solid, society level journals as such a thing?

PatheticImpFactorAre there those who recognize that others view the journal as a dump journal but wish to work to change this reputation? By being harsher during the review process than is warranted given the history of the journal? That approach is a game of chicken though…if you think a dump journal is getting too uppity for its current IF then you are going to just move on to some other journal for your data-dumping purposes, are you not? If a publisher or journal staff wanted to make a serious move up the relative rankings, they’d better have a plan and a steely nerve if you ask me.

This brings me around to my fascination with PLoS ONE and subjective notions of its quality and importance. What IS this journal? Is it a dumping grounds for stuff you had rejected elsewhere on “importance” and “impact” grounds and you just want the damn data out there already? That would qualify as a dump journal in my view. Or do you view it as a potential primary venue…because it enjoys an IF in the 4s and that’s well into run-of-the-mill decent for your subfield?

Furthermore, how does this color your interaction with the journal? I know we have a few folks around here who function as Academic Editors. Are you one of those that thinks PLoS ONE should be ever upping its “quality” in an attempt to improve the reputation? Do you fear it becoming a “dump journal”? Or do you embrace that status?

Are you involved with another journal that some might consider a dump journal for your field? Do you think of it this way yourself? Or do see it as a solid journal and it is that other journal, 0.245 IF points down, which is the real dump journal?

Good one Francis!!!

January 16, 2013

NIH Director Francis Collins was discussing sequestration and the impact of the past many years of flat budgets with POLITICO:

“For people who are in the early stage of their career to just miss the pay line once, twice, three times is pretty demoralizing,” he said. “And they are getting demoralized.”

Three times? THREE?????????!!!!?????

Your are damn right that is “demoralizing” but people are going to have to miss the paylines upwards of SIX times holmes! You said it yourself.

…only about one in six of those who apply actually receives a grant. The chances used to be one in three, Collins said.

When we are sitting around an 18% success rate, well, three straight misses had better not put you off your effort. Not if you want to get funded. You had better hit 6 applications before you start thinking about another line of work. Because that is what it takes to meet the odds.

are offered by Bashir.

Even if these recommendations were enacted tomorrow, and worked exactly as hoped, the gains would be slow and marginal. #1 seem to more address the problem of under representation.

Go play over there.

From an ASM Forum bit by Casadevall and Fang:

An example of a rejected descriptive manuscript would be a survey of changes in gene expression or cytokine production under a given condition. These manuscripts usually fare poorly in the review process and are assigned low priority on the grounds that they are merely descriptive; some journals categorically reject such manuscripts (B. Bassler, S. Bell, A. Cowman, B. Goldman, D. Holden, V. Miller, T. Pugsley, and B. Simons, Mol. Microbiol. 52: 311–312, 2004). Although survey studies may have some value, their value is greatly enhanced when the data lead to a hypothesis-driven experiment. For example, consider a cytokine expression study in which an increase in a specific inflammatory mediator is inferred to be important because its expression changes during infection. Such an inference cannot be made on correlation alone, since correlation does not necessarily imply a causal relationship. The study might be labeled “descriptive” and assigned low priority. On the other hand, imagine the same study in which the investigators use the initial data to perform a specific experiment to establish that blocking the cytokine has a certain effect while increasing expression of the cytokine has the opposite effect. By manipulating the system, the investigators transform their study from merely descriptive to hypothesis driven. Hence, the problem is not that the study is descriptive per se but rather that there is a preference for studies that provide novel mechanistic insights.

But how do you choose to block the cytokine? Pharmacologically? With gene manipulations? Which cells are generating those cytokines and how do you know that? Huh? Are there other players that regulate the cytokine expression? Wait, have you done the structure of the cytokine interacting with its target?

The point is that there is always some other experiment that really, truly explains the “mechanism”. Always.

Suppose some species of laboratory animal (or humans!) are differentially affected by the infection and we happen to know something about differences in that “mediator” between species. Is this getting at “mechanism” or merely descriptive? How about if we modify the relevant infectious microbe? Are we testing other mechanisms of action…or just further describing the phenomenon?

This is why people who natter on with great confidence that they are the arbiters of what is “merely descriptive” and what is “mechanistic” are full of stuff and nonsense. And why they are the very idiots who compliment the Emperor on his fine new Nature publication clothes.

They need to be sent to remedial philosophy of science coursework.

The authors end with:

Descriptive observations play a vital role in scientific progress, particularly during the initial explorations made possible by technological breakthroughs. At its best, descriptive research can illuminate novel phenomena or give rise to novel hypotheses that can in turn be examined by hypothesis-driven research. However, descriptive research by itself is seldom conclusive. Thus, descriptive and hypothesis-driven research should be seen as complementary and iterative (D. B. Kell and S. G. Oliver, Bioessays 26:99–105, 2004). Observation, description, and the formulation and testing of novel hypotheses are all essential to scientific progress. The value of combining these elements is almost indescribable.

They almost get it. I completely agree with the “complementary and iterative” part as this is the very essence of the “on the shoulders of giants” part of scientific advance. However, what they are implying here is that the combining of elements has to be in the same paper, certainly for the journal Infection and Immunity. This is where they go badly wrong.


January 15, 2013

Of all superpowers to have, I’d pick “kill at a thought”. No question.


Damaged Goods

January 14, 2013

Have you ever had a manuscript severely damaged by the process of peer review?

by way of example, I can recall one time where the Editor demanded I chop off two experiments..and I did so*.

Otherwise, I’m generally of the opinion that peer review has a positive impact on the manuscript.

*Those figures have yet to see the light of day and may never get published. A shame, but then, we got the paper published and the main point was one of the other figures.

As you know, I have a morbid fascination with PLoS ONE and what it means for science, careers in science and the practices within my subfields of interest.

There are two complaints that I see as supposed objective reasons for old school folks’ easy complaining bout how it is not a real journal. First, that they simply publish “too many papers”. It was 23,468 in 2012. This particular complaint always reminds me of

which is to say that it is a sort of meaningless throwaway comment. A person who has a subjective distaste and simply makes something up on the spot to cover it over. More importantly, however, it brings up the fact that people are comparing apples to oranges. That is, they are looking at a regular print type of journal (or several of them) and identifying the disconnect. My subfield journals of interest maybe publish something between about 12 and 20 original reports per issue. One or two issues per month. So anything from about 144 to 480 articles per year. A lot lower than PLoS ONE, eh? But look, I follow at least 10 journals that are sort of normal, run of the mill, society level journals in which stuff that I read, cite and publish myself might appear. So right there we’re up to something on the order of 3,000 article per year.

PLoS ONE, as you know, covers just about all aspects of science! So multiply my subfield by all the other subfields (I can get to 20 easy without even leaving “biomedical” as the supergroup) with their respective journals and…. all of a sudden the PLoS ONE output doesn’t look so large.

Another way to look at this would be to examine the output of all of the many journals that a big publisher like Elsevier puts out each year. How many do they publish? One hell of a lot more that 23,000 I can assure you. (I mean really, don’t they have almost that many journals?) So one answer to the “too many notes” type of complaint might be to ask if the person also discounts Cell articles for that same reason.

The second theme of objection to PLoS ONE is as was recently expressed by @egmoss on the Twitts :

An 80% acceptance rate is a bit of a problem.

So this tends to overlook the fact that much more ends up published somewhere, eventually than is reflected in a per-journal acceptance rate. As noted by Conan Kornetsky back in 1975 upon relinquishing the helm of Psychopharmacology:

“There are enough journals currently published that if the scientist perseveres through the various rewriting to meet style differences, he will eventually find a journal that will accept his work”.

Again, I ask you to consider the entire body of journals that are normal for your subfield. What do you think the overall acceptance rate for a given manuscript might be? I’d wager it is competitive with PL0S ONE’s 80% and probably even higher!

For some reason the response on Twittah to the JSTOR downloader guy killing himself has been a round of open access bragging. People are all proud of themselves for posting all of their accepted manuscripts in their websites, thereby achieving personal open access.

But here is my question…. How many of you are barraged by requests for reprints? That’s the way open access on the personal level has always worked. I use it myself to request things I can’t get to by the journal’s site. The response is always prompt from the communicating author.

Seems to me that the only reason to post the manuscripts is when you are fielding an inordinate amount of reprint requests and simply cannot keep up. Say…more than one per week?

So are you? Are you getting this many requests?

Sure enough:

A 65-year-old South Carolina woman was mauled to death by the family pit bull in a gruesome attack that unfolded as she babysat her three young grandchildren Tuesday.

oh, and I’m sure the 12 year old will totally not be fucked up for life over this

When the girl discovered the dog mauling Betty Todd, she attempted to stop the animal, but could not do it, so she gathered her younger siblings and took them to another room before calling her father for help.

UPDATE: Chra-heist. Another one!

SPARTANBURG COUNTY, S.C. —A 44-year-old Upstate woman is in serious condition after she was attacked by pit bulls overnight, according to Spartanburg Public Safety Capt. Art Littlejohn. Littlejohn said that at about 2 a.m. police were called by someone who said they heard a woman being attacked by dogs.
The incident report said an officer saw two or three dogs “biting/eating” a woman who was lying on the ground.

and another?

Deputies were told by the attending physician that the boy’s nose had been bitten off at a home off Highway 136 West. The pit bull had apparently eaten the nose after biting the child.

All just a complete coincidence I’m sure.

GrantRant VII

January 10, 2013

Everyone is going to hate you, pretty much.

Think about it. You have 7-10 grants assigned in your pile on a typical study section these days. Odds are good that at best one or two of these is going to be good enough to be in the hunt for funding. The rest of the panel is in the same boat, so it really doesn’t matter that the applicants don’t know precisely which of you* on the panel reviewed his or her proposal.

80-90 % of the applicants are going to be mad at you.

Since you have been selected for expertise in the relevant field…these are people who you know. You know their work and you probably like and cite it. They know you. They know your work.

And for at least a while after they see their disappointing score, and for another while after the pink sheets are posted, they cannot help but hate you a little.

Maybe even a lot.


*If you were triaged you do know for absolute sure that every member listed on that panel roster stood by and refused to pull your application up for discussion.

Back in the distant past, younguns, the US was involved in a struggle with the Soviet Union that many felt was an existential threat to our continuation on this planet. Among other features, this Cold War (perhaps better termed Ongoing Proxy War) featured the buildup of ecosphere destroying megaweapon bombs.

The fuzzy blankie we used to keep from going insane was the thought that since both sides could destroy huge amounts of the other side’s population, render much of its territory uninhabitable, and could do so should the other side move first, we were safe.

Since we were mutually assured to destroy each other, the logic of starting some serious beef was an insane one. Nobody in their right mind would actually do such a thing. So this kept certain behaviors (like the hilariously NewSpeak “pre-emptive counter-strike” with nuclear weapons) off the table.

In discussions of NIH Grant review, there is often a certain paranoia voiced that members of the review panel use this position of tremendous power to screw over their scientific rivals. Sounds plausible, does it not? After all, this grant stuff is a zero-sum game and the “peers” of peer review are after the same pool of money that each applicant is eying. These days it is a good bet that the reviewer has her own application under review elsewhere in the CSR…or has one pending funding in this self-same Fiscal Year.

That’s before we get to scientific competition to publish papers in some research area first. We all know that first is best and all others might as well go home, right? And any rational grant funding agency (don’t laugh) like the NIH should diversify their portfolio such that if they fund grant on a topic, the chances of another one on nearly the same topic should be lesser.

Naturally, the closer the reviewer expertise is to the grant in question, the closer this reviewer is to being in direct conflict of interest at some level.

My first approach to comforting the distraught Assistant Professor is to emphasize that our peers are professionals, with some degree of ethical centeredness who are for the most part attempting to do the job as asked.

This doesn’t comfort everyone. So today I offer the Mutually Assured Destruction theory for your consideration.

One of the most surprising things I found about study section service is the rapidity and surety with which payback opportunity was provided. During the early days of my study section service it was the appearance of many grants in my piles to review that were submitted by PIs who had previously appeared on study section panels reviewing my own proposals. After I’d been reviewing for a little bit, it was remarkable how quickly people who’s grants had appeared in study sections that I was on (and in some cases apps to which I had been assigned) were now in a position on panels reviewing other grants of mine.

I came away from all of this with the understanding that what goes around comes around VERY quickly in NIH grant review.

So for the paranoid types…do consider this additional source of pressure on the reviewer. If you don’t trust their professionalism, trust in their self-interest. This Mutual Assurance tends to suggest that reviewers would be crazy to screw with applicants out of pure self-interested bias.

It’s been awhile that we’ve been rolling as a blog collective and I am curious what you think. If you are a reader of any of these blogs that predates the collective, have you missed a beat? Are there things that you dislike (or like better) about your favorite blogs?

For everyone, what do you like and dislike about Scientopia? What would you see as a way to improve?

Open thread, so go nuts.