More on "shitasse" journals

January 30, 2012

A bit of a Twittstorm was raised today by Jonathan Eisen (@phylogenomics) who posted a (Modest?) proposal that we should respond to Elsevier’s naughtiness over the Research Works Act by

stop helping promote articles published in Elsevier journals.  Don’t blog about papers in Elsevier journals.  Don’t tweet about them.  Don’t use Elsevier papers for journal clubs.  In essence, ignore them – consider them dead – make them invisible.  Not completely of course.  Any work should be considered a contribution to science or math or whatever your field is.  But there are LOTS and LOTS of things to do with your time.   

This is in strikeout because Dr. J. Eisen thought better of his snark. As I suggest above, perhaps he was making a Modest Proposal. At any rate, the original twittstorm was fanned by YHN.

My recent readers may have come to the conclusion that I am one of those Open Access wackanuts. I am not. I am, or have been, rather a skeptic of the more….excessively fervent OpenScienceELEV3NTY111!!!111!! types.

It is my position that the TruBeliever Acolytes of OpenAccess need a firm hand now and again to bring them back down to reality. Think of the responsibility churches have to keep the snake-handlers and speakers-of-tongues within reason. The way regular Christian folks need to point out that Pat Robertson is, in fact, pretty insane with his God’s revenge on the Hurricane-Belt stuff. You take my point.

Anyway, there is one core point that needs to be explicated in this because it segued from (J.) Eisen’s flipping of the bird to the overall notion that it is okay to dismiss / ignore research papers on the basis of where they are published. Some Twitt going by @lightsam1 is of the PhysioProffian opinion that there exist “shitasse” journals in which we will never find anything of any worth, scientifically, so there is every excuse to simply ignore them.

This is unscholarly in the extreme. The argument, in my view, is exactly the flip side of lauding papers that are published in GlamourMags as if they are something special. They are not.

In either case. The science is the thing. There should be no substitution, ever, for making a scientific judgment about the merits of a given paper based on association.

This was the essence of my objection to (J.) Eisen’s original post. No matter how pissed you may be at the publisher, it is not right to overlook the best, most relevant papers. It is not. Similarly, it is not right to overlook the best (or first, or most comprehensive) citation because it was not in a sufficiently Glamourous journal. This runs counter to good scholarship in academic science. I will entertain the debate over priority, if it is the best scholarship to cite the first report that touches on an issue simply because it appeared first. I happen to think an excess of this is a very large part of Glamour problem but…ok. It is always okay to have differences of opinion over what is the “best” or “most comprehensive” or “most elegant” demonstration of a much-replicated effect. Fine. That we can debate.

However. The notion that you are citing (or not citing) a paper based on where it is published is always wrong.

Consistent with what I was saying in a prior post, there was an excuse in the Pre-PubMed era to focus on a subset of the available journals because humans weren’t capable of keeping up with everything. In the PubMed era, however? No excuse whatsoever. Online databases and search engines provide readily available, simple and reasonably* comprehensive mechanisms to sort the literature.

If anything, you should be almost unaware of journal identity and IF and perceived “status” these days. It just doesn’t have any scholarly value.

*remember, not everything relevant to your work is indexed by your favorite search database. Who know when some odd economics paper might be really cool to cite, eh?

In the previous post on journal publishing, I observed that sub-sub-specialty journals were an anachronism of the era prior to the establishment of nearly comprehensive search engines and databases like PubMed. In that era, dividing the monthly output of scientific papers into journals made sense. First of all, it would be pretty hard to pick up a monthly issue of “The Omnibus Journal of Biomedical Science”. Second, it would be unduly laborious (and paper cut-y) to keep flipping around from some index or TOC to the abstracts you wanted to scan. So there were certain physical realities driving journal specialization.

Not to mention the fact that across the decades from 1886 to 1996 (PubMed established) there was a gradual and sustained addition of sub-specialty societies, narrower and narrower subfields of interest and an all around expansion of academic science. This came with a desire for yet another group of scientists to have selection of the studies they most wanted to read into a smaller number of journals.

I am not privy to all the details of the history of journals in academic science. Not even close. But what I do know is that a publisher such as Elsevier has a metric boatload of small sub-specialty journals at present time. Many of which are tied to an academic society. They continue to launch NEW ones. (Phew, I’m already link exhausted- Google “Official Journal Elsevier” and see what you get. The list is enormous.)

It is, or has been, in the interests of both Elsevier and the academic society to continue this arrangement. Occasionally societies will switch publishers. For example, Neuropsychopharmacology jumped from Elsevier to Nature Publishing Group in recent memory**. Occasionally you’ll be looking at the online site for a journal and notice a truncation in the archive..and have to Google around to figure out who used to publish the journal. Nevertheless, it is clear that Elsevier thinks these arrangements are good ones. Presumably because they get good return from libraries when they bundle a bunch of journals into a fixed price menu.

[Sidebar: This is a bit of a fly in the ointment, btw. One thing I do laud the publishers for is when they’ve taken effort to PDF all of their back catalog…back to vol 1, issue 1 in the dark ages in some cases. When there’s a shift in the publisher that took place prior to the online age it seems to me that their motivation for putting up a back catalog for a journal they no longer publish is not very high.]

What do the societies get in return?

I am, shall we say*, somewhat informed about moves by at least two society level journals to switch their default member subscription from print to online. The response seemed to be overwhelming approval and lack of opting-for-print amongst the memberships. No surprise, almost all of us are complete and total converts to the benefits of online access to journal articles and personal PDF archives on our computers. Yes, even the rapidly emeritizing cohort. Still, it is nice to see the data, so to speak. Nice to see that if a society stops sending print issues to clog up faculty bookshelves collecting dust, nobody objects.

But……ego. Somehow I bet the existing societies would get their backs up a little bit if there was a suggestion that they simply give up their journal. Neuropolarbear asked what could be done about the assy position being taken by some publishers on the Research Works Act issue. This is the one trying to reverse the law demanding the deposit of all NIH funded papers into PubMedCentral (in peer-reviewed, accepted, manuscript form).

One thing we could do is to demand our society journals stop working with the jerky publishers.

This thought is what brought up all the above blathering. It is very likely that each and every small journal couldn’t make it on their own. Well, duh, of course not. As noted by the irrepressible Comrade Physioproffe

From what I understand, the other issue moneywise is that big publishers like Elsevier force institutions to pay subscription fees for shitteasse journals that no one reads by bundling them with their flagship journals. Those journals wouldn’t even exist if they had to survive on their own submission/publication fees.

But if all we’re talking about is a sort of virtual journal…why can’t some other umbrella journal publisher just kind of take up the slack? Why couldn’t a PLoS ONE type of outfit agree to provide all the publishing services and put some sort of tag on the article to group by academic society?

*christ that was priggish, wasn’t it?

**fascinating. In the case of Neuropsychopharmacology, the entire back catalog was transferred over to NPG so if you click on an article that your print copy insists was published by Elsevier, boom, you end up at NPG.

The Rock Talk blog of the NIH’s Office of Extramural research notes that a report (pdf) overviewing the responses to a prior RFI has just been released.

A few things that I’ve picked up on first skim.

Vote leveraging. They had 219 responses. That’s IT. 5% were from NIH staffe and 20% from official representatives so really that is only 164 comments from normal folk like us. If you responded (and I did) you get to be 0.6% of the response. Coolio. This is why I continue to urge you to participate in such things- apathy means that your efforts count for a lot more than just your own little opinion. You represent a much larger fraction.

Diversity. This particular RFI did not ask specifically about diversity to my recollection. But many people brought it up, no doubt because the Ginther et al 2011 report was published before comments were due. There were also lots of comments about the challenges faced by women who head laboratories.

Staff Scientists / nonPI stable careers. As you know, a topic on which I have opinions, DearReader.

Suppose something like this were made available for career Ph.D. scientists as essentially a fellowship. Without any requirement for a professorial appointment and minimal actual research component. The important point being that it is applied for, awarded to and evaluated for renewal by the career scientist with every expectation that this is a career award. There would be details of course. You’d have to have a host lab at most times- but allow for transition if one lab loses grant support or something. Nice and easy for the supported career scientist to find a new lab, don’t you think? “Hey, PI Smith, I have my salary supported and I’d like to come play in your lab…” would go over quite nicely. Progress could be evaluated just as with any other award, keeping the pressure on for the individual to publish

Well, this new report says:

There was much support among individual commenters to create permanent career staff scientists positions. They saw this as a way for all parties to reap the benefits of training support provided by NIH. Institution commenters where divided, some taking a cautious approach to the idea of utilizing staff scientist in the lab, citing possible adverse effects including potential loss of innovative ideas (currently provided by graduates) and the reduction in project budgets to cover the salaries for these positions.

and ends up with the “NIH Action Recommendation” of

Provide grant mechanisms and change the funding policy to increase project budgets to support the costs associated with permanent staff.

Emphasis added. I will be fascinated to see how closely the eventual initiative on this hews to my proposal. Fascinated.

I mean seriously. The original post over on @mbeisen’s It is NOT junk blog drew out a Elsevier flack Tom Reller who had a thing or two to say about the Research Works Act being peddled by New York CongressCritter Carolyn Maloney. In that last linked comment, Mr. Reller claimed:

When I say peer review process, I think you’re hearing just peer review. Peer review is exactly what you say it is, volunteer work in the name of academic science, and it never would have dawned upon me to have to say this, but of course we know peer reviewers aren’t paid. And we know that we, and our journals need them. If you ever reviewed for one of our journals, thank you, and we truly hope you continue to do so. I know all about the issues related to how difficult it is to find quality peer reviewers. You’re often paid by the government, and it is time consuming, we get it.

All we’re saying is that there is a peer review process, and there is more to peer review than just the peer reviewers themselves. Our systems track it, our publishers support it, then there’s what we do to print and preserve the outcome. Michael granted as much.

We call final published articles private sector information products because we (the private sector) have added value, as before mentioned, to the articles.

I find my self searching for this “added value”. By listening and reading what the publishers and their representatives have to say, perhaps we can find some clues to this mysterious value that they add to the scientific paper.

One Graham Taylor, flack for the UK Publishers Association, has an opinion bit up in the Guardian (in response to something written by Mike Taylor). Mr. Taylor opines:

We need a flow of accessible funds through the scholarly communication system to finance what we do. Hitherto these funds have flowed through academic library budgets, the “old” subscription model, which Dr Taylor describes as “a useful service in pre-internet days”. In future they will likely flow from research funding agencies (and a few charities and foundations) looking to enable open access.

Well, yes and no. We do need to continue to finance the distribution of scientific papers / scientific information. For sure. What we don’t need is Mr G. Taylor’s “we”. The publishers are a classic middle man, standing between the producer and consumer. Sometimes that brings value, sometimes it brings blood sucking leechery that adds cost but no value to the system. The real question at hand is determining whether the traditional publishers are starting to veer from “adds value” into “leeching off the system”.

Publishers pursue the goal of universal access through whatever means are practically available.

HAHAHAHAH! Where “practically available” means “We, the publishing middle man get paid.” Right? If their goal was universal access they’d be whittling down their profits to the unmentionable, cutting salaries down toward the public sector salaries, etc. Ever seen the publisher representatives in a typical editorial board meeting? Yeah, you can pick them out by the nice clothes. Ahem.

It is widely acknowledged that there is not an access problem for researchers based in universities, research institutes or the corporate sector.

Absolutely and completely false. The smaller institutions, colleges, etc do not have anywhere near the access to the breadth of journals available. And oftentimes they are forced to make tough choices because of journal “bundle” options offered by, e.g., Elsevier. Companies large and small have to decide how to fund securing the literature- some do it on a one-off basis because it is cheaper. Many folks at smaller biotechs hose off the local University in one way or another- through their spouses employment, through their old access from when they were a postdoc, friends..or just stopping by the University campus and using the wifi. Either way, people are having to cobble together their “access” to the entirety of the academic literature. With variable success.

Pub Med Central changed all that. All the subsequent research was available to anyone, from community college to small private college to biotech startup. All right there. Easy, peasy from the desktop.

Public funds have not paid for the peer-reviewed articles that are based on research supported by agencies such as the National Institutes of Health (NIH). They have only paid for the research itself and whatever reports the researchers are required to submit to the agency.

Another falsehood, wrapped up with a disingenuous misdirecting belittlement. “Only” for the research? ONLY????? These publishers seem universally unaware that the VAST, VAST majority of the value of an academic article is the bloody research. The damn content. That is what has value. The fancy layout? That’s nice and all but we can do without that. The science is the thing. Trying to dismiss this as a minor contribution is…well…..that takes some serious chutzpah.

There is another, more serious misdirection here. The public does in fact “pay for” the entire article at present. By way of library access fees and the other ways that articles are obtained. Money is fungible so one way or another, the public contribution in NIH grants, public University support, student tuition and probably even the health care system (hospitals need access, yo) pays for these articles.

Public funds are already paying the middle man “for the peer reviewed article”. The question is, once again, can we make this process more efficient (yet equally effective in distributing science) by eliminating the middle man?

The journal article based on the research has been the subject of significant extra investment that must somehow be recovered if scholarly communication as we know it is to survive.

I am still trying to get my head around this claim because it is the cornerstone of the publishers’ argument. What “significant extra investment”? The reviewers themselves work for free*. For real journals, with academic, real-scientist editorial staff, the editors are maybe paid a little and the administrative person who works in the Editor in Chief’s office gets paid as well. Sure. But this is penny ante stuff. There are not 5 to 10 full time people with the sole job of being editor. Suppose the NIH decided to run it’s own journals…think they couldn’t just take over the salary lines? Of course they could.

This brings me to the online peer reviewing software systems, such as ScholarOne Manuscripts or Editorial Manager. Sure, maybe some publishers have developed their products in house. But there are lots of options. These are not functions that we require the big publishers to provide either.

So what do the publisher’s add to the “peer review” of journal articles? I really don’t know. Keep in mind that I categorically reject the notion that we need GlamourMag style professional editors to get this job done.

It often appears to me that their only unique role in this process, given modern internet technologies and tools, is to figure out ways to keep sucking money out of the system, but providing “value” that we really don’t need.

many do object to a mandate that appropriates their material without compensation.

Now this is just gobsmacking. Since the vast majority of their “material” consists of the academic research, writing and peer reviewing services that they get for FREE, it is really frigging rich for the publishers to cry about appropriating material without compensation. I mean do they even listen to themselves? Ever?

Finally, the dinosaur sinking in the tar pit part:

Such journals are on the whole by their very nature tailored and adapted to the needs and interests of specific research communities. This is a complex and nuanced system that needs time to adapt to new methodologies.

Dedicated journals are an anachronism held over from before the advent of PubMed, pure and simple. Partitioning scientific research into field journals of different emphasis and focus was necessary for humans to find the most relevant work. Now we have search engines and online databases. The function served by subspecialization of print journals is entirely unnecessary at present. If you need it for organizational means in the (virtual) editorial offices of a general “Journal of the NIH” or “Journal of all US Science funded by the Taxpayers”, there is no reason that we couldn’t have subsections partitioned off.

Dr [M] Taylor’s assumption that this can somehow all be routinely accommodated on a “service” basis is to misunderstand the nature of publishing. Publishers invest at their own risk and quality standards are essential to manage that risk. We need a market to organise such a high volume of transactions. Take that away and we would be left with a Stalinist nightmare.

No, you misunderstand that we don’t give a rat’s patootie about “the nature of publishing”. We care about the distribution of scientific results! Print or even online “Publishing” as an industry is irrelevant. We just need the lower-case-p version of publishing. We do NOT need a “market” to organize any such thing. Does the “market” get involved in the peer review of NIH grants? No? Then why do we need it to publish the results? We do not.

And dude. Seriously. The “Stalinist nightmare” bit? Get a grip.

*UPDATE: Neuromusic emphasized a very important point in a comment. Peer reviewers work at no charge to the publisher. Their time is not “free” however, since this is considered to be part and parcel of their job. Whether it be “service” of a hard money faculty member or as part of time allocated on grant awards, it is expected that scientists will contribute to the review of manuscripts. This raises an interesting point. Consulting fees in industry vary, of course, but for a fairly new Assistant Professor the expected rate in my fields of interest is about $100 / hr or $1,000 / day. If publishers are going to act graspy about their “compensation” then they are going to have to start budgeting at least a couple of hundred smacks per reviewer for each manuscript. Hey, look at the plus side- going to be a lot easier to get papers reviewed if the invitations come with a $200 carrot.

Commenter Adriana suggests something very interesting on a prior post addressing NIH grant funding policies, the change to only a single revision, etc.

Some of this seems counter productive. People that have spent maybe 15 or so years setting up model systems and generating hypotheses (paid for by NIH) are getting cut off right at the time their projects are starting to produce high yields. In a lot of cases the funds are diverted to new investigators with worse priority scores to set up more new models systems. Just when they get going they will probably get cut off too.

My first reaction was “whoa!” Bad optics, homes! Telling the grant funders that “well, give me 15 years of full funding and then see what I really produce!” sounds a bit like vapor ware. A confidence racket of some sort.

But I’ve also mentioned something about the trendlines of scientific careers. And sure, I’ve often seen PIs experience a huge surge in productivity during the middle career years after an initial interval of struggle. The grants come in, the postdocs come buzzing around and all of a sudden the lab is a serious player. It can take 5-8 years, easy. Several of my most salient examples match this sort of timeline. Fifteen years though? Fifteen years from the start of the lab to the acceleration phase?

That is a little more unusual to me. I”m not saying there are not people that have ups and downs throughout their careers, sure there are. I know plenty. So a downturn in year 10 is not necessarily predicting a lasting decline and yes, when grants come back the lab starts roaring again. But usually, this is not from a lab that has been in the doldrums for the prior 10 year interval. Usually, from what I see, that lab has had prior indications of the potential.

Let us leave specific predictors of timeline aside for a moment however. It doesn’t really matter if we’re talking early-mid or mid-mid career, some of the implications of the current NIH policy-making still apply.

I think I’ve tried a time or two to get into the “cry me a river” post for people like…..well, me. I don’t feel sorry for me. Okay, that’s a lie, I do feel very selfishly sorry for myself if I cannot obtain the grant funding that I desire and think that I, in some way, deserve.

“I saw the generation just prior to me hit the sigmoidal acceleration phase when I was a late postdoc and early faculty member. That is my model of expected value in the NIH-funded career path. If I do as well as they did in the early phase, dammit, I deserve my chance to shine. I’ve struggled to build not just a lab, not just a few projects but a scientific program. And now, just as I’m getting to the point where things should be relatively comfortable and highly productive..this. The NIH budget goes south, those extra grants are harder to come by, the renewals much, much less certain and I’m still struggling. Dammit.”

Sound familiar my mid-career friends?

Of course, our “struggle” much of the time is not the struggle just to stay alive. We have a grant or two to last us through the bad times. When things get really rough, heck, we can finally get around to writing up old papers to keep productivity smooth. We have endless amounts of technical preliminary data on which to base new applications, maybe even some pilot data that supports a hypothesis. We know a lot of folks on study sections personally and some of them are, at last, kinda junior to us. Junior enough that they might, gasp, actually see our applications as coming from “a well established and accomplished scientist”.

Things could be worse.

This is why my sympathies for people like me continue to be muted when it comes to different policy points over there in NIH land. Yes, I would for sure like to see the next generation ahead of me suffering the same conditions that I seem to experience. See the old guard be treated as harshly as everyone else in the granting system. You know what? It may be happening, much as we think the grass is greener. How will we know until after the fact? After all the data emerge in 8-15 years showing what happened in this time of stress.

Will the NIH system really experience investigator dropout in serious numbers? Will we come to find that the major effect was on the amount of funding over 10yrs of PI time, but not on the number of total investigators? Will we find that my generation, the mid-career types, pay a specific toll….as is being hypothesized by Adriana?

I will say that the NIH ignores the winy, selfish complaints of the current crop of mid-career investigators at their peril. These are the very people who are putting in the long hours on study sections reviewing grants. If they feel that ESI folks are getting too much in the way of assistance, regardless of whether they are or not on some objective measure, they are going to push back. And continue to punish ESI applications. Subconsciously perhaps, but it will be there. Actually, it has always been there.

Mid-career folks have probably always been tremendously to blame for the fact that every initiative of the NIH to help the newly independent secure grant funding has fallen short. Because NIH is in a reinforcing cycle of pecking order.

Driven by the nearly inescapable, hindbrain driven, emotional, fierce belief of mid career scientists that dammit, they deserve their chance for an explosive phase in their labs.

I don’t have any answers for the NIH.

I feel this way about my own laboratory and research program.

I bet a million dollars you do too.

And help keep his attention on this possible throw-away from the State of the Union address.

I was heartened by several observations from the US President that seemed to suggest he understands that investment in basic research (no, not just targeted development) was the key to sustained economic growth into the future. But you need to help keep him on task. And get Congress on board.

I noted a few months ago that a petition has been launched to collect signatures favoring minor increases in funding for the NIH. There are 3,931 people as of this writing.

Are you one of them? Have you passed the link around your lab, department or Uni? How about to your academic socities? Have you posted it on your Facebook and Twitter feeds?

Please do.

As you know there are diverging viewpoints across the wide swath of traditions in the ginormous tent of biomedical science regarding academic credit based on where one’s articles appear. You know that Impact Factor of a journal (average number of citations for articles published in a 2 yr period, roughly) is important to many. Where the higher the IF of the journal you publish in, the better. Regardless of the number of citations garnered by the actual paper. So if you happen to work an article into a IF 15 journal and that is only cited 8 times in two years, that’s way better than the one you fought into a IF 4 journal that turns out to be field shaping and gets cited 20 times, 50 times or 100 times in the first two years.

This led me some time back to speculate that what we really needed was a measure of how your article performed relative to expected value for the journal in which it was published. I proposed a z-score, I think.

Today, Odyssey has me thinking about a few things related to this topic.

The most directly appropriate one is the notion of whether it is a matter of differential credit if you consistently get your papers cited more than the IF of the journals in question, less than the journal IF or a random selection. I argue today that since IF is more universally valued, if you are getting papers into journals of higher IF than the articles actually secure themselves, you are winning. Conversely, if you consistently get more cites than the IF of the journals you publish in, you are not being credited as much as you should be.

OTOH, my prior, more personal view is that if you are kicking butt with more citations than the IF of the journals into which you fight your papers, it shows that your work is more valuable than the peer review system “predicts” on initial review and therefore you are the awesome.

(Oh yes, that is exactly what the Byzantine IF chase of modern biomedical science is doing, btw. Trying to predict the number of citations your paper will get in the next two years. Deal with it.)

Of course, this is contaminated by the presumption that the authors of each paper actually care to participate in the IF chase system. Not everyone does….

As you may be aware, I exist in a field that still has a bit of OldSkoole authenticity to it. Folks for whom the IF chase is not the be-all, end-all it is for many spheres in academic science today. Not that they don’t have their little opinions about what type of publication record reflects “the best kind of scientist”. Not at all. It is just that IF is a lesser player.

So there are some folks that just don’t seem to give a damn about IF and they keep publishing in the same handful of society level journals that they have always favored. People who I would be happy to argue have had a sustained and fundamental impact on the world’s understanding of addiction, biological actions of recreational drugs, neuropharmacology and, hell, pharmacology in general.

So there is a pocket of the world of drug abuse science, which sits in evaluation of YHN btw, which seems to value a record of publication in certain journals of a less than Glamourous IF level. Often this is because the journal is indeed the journal which is tied to a specific society. And one’s participation in that society is viewed as a GoodThing to do. So if you belong to the society, perhaps you’d better publish in their journal now and again. Actually, perhaps you should do so frequently.

There are, however, examples of folks who seem to take this a wee bit too much to heart, in my view. And herein lies my pondering of the day. Why do I see diversity in the journals in which one publishes to be a good thing? Why does the appearance of a high density of pubs in a single journal (again, we’re talking IF levels where there is plenty of competition on that metric) make my eyebrow raise? Why am I drawn to an appearance of US/Norteamericano versus OldEuro bias in the selection of journals? (or is this latter merely a reflection of the aforementioned academic-society-journal captivity I’ve mentioned above? Why do I think to myself “Hey, we’ve never published in [Insert modifiers] Journal of [-ology] before, let’s give it a go” instead of sticking with a handful of the most-frequent suspect journals?

How’sabout you folks? Do you have a handful of normal journals that you consider using? Is there a strict hierarchy/search path that you descend in your attempt to get as high an IF possible for each submission? Are you topically distributed such that one set of projects in your lab goes to one journal and other projects have their own target journals?

I’ll let you speculate in the comments about the source of the quote that heads this entry. Grad student? Young scientist? Aging greybeard? From a small town grocer background/lab or a major playah?

On blogging

January 24, 2012

You know you are doing your proper job as a blogger when SiteMeter shows you a bunch of folks on the site for 20-40 min plus, just waiting around to enjoy the comment fireworks.

It is well established that approximately 85.473% of the battle when it comes to NIH Grantsmithing is making it easy for the reviewers to grasp your point[2].

Really easy.

Many bloggers have described the fact that you need to think about your audience. The grant reviewer in my mind’s eye is an overworked, grant-stressed, paper-decision-major-revision, lab disaster supervising PI who has finally cracked your grant open at 10 pm after putting his kids to bed, throwing some laundry in, running the dishes and making lunches for tomorrow’s schoolday. . Plus, she may have an infant squirming and latching on poorly at the same time. Still licking wounds from the last disappointing summary statement from his or her own grant application.That’s if you are lucky.

If you are unlucky she is getting serious about reviewing your grant while crammed in coach on the way to Bethesda for the actual meeting. And is planning on submitting the written critique the moment she hits the free wifi at the airport….

Then, should your application be so lucky as to be discussed, realize this, Dear Reader. The three assigned reviewers may have had the time, if they had the inclination, to pour over your application at leisure.

The rest of the panel? Not so much.

It is the rare reviewer who has read through the entire panel’s worth of applications in detail. And if there appears to be a disagreement between the three assigned reviewers during discussion, these other reviewers have something on the order of 10-15 minutes to scan through your application to attempt to resolve matters in their own mind.

You want their job to be as easy as possible. This is why I hammer away at the creation of blank space, headings, clear figures and direct writing. You know this. What many people don’t seem to realize is that your selection of citation style matters as well.

A lot.

Some folks seem to think that it doesn’t matter[3] or that the NIH insists on numbered citation styles[4].

[As a bit of a sidebar, before I go too deep, there is absolutely nothing about grant review that is fixed in stone. So if you know people who always use the numbered citations and get funded[5], bully for them. But realize they got the award despite a lapse in grantsmithing[6], not because it is unimportant.]

Back to our story, it appears some of this confusion may be attributable to Endnote, as one authority claims that the Endnote style for “NIH” is numbered[7,8]. I have recently tested this on my Endnote X4 for Windows and I find this assertion to be untrue. My style for NIH (default installation) is Author, Date style, not numbered.

but still. If you have some version of Endnote that has a particular style for “NIH” don’t you think you’d better check to see what the rules say? I mean, you could have a template grant from some idiot that uses Georgia font but you know to put it in the Arial, no? Or if your sample page is in 12pt font, you go and see what the rules actually say, right? So why would you take what some non-NIH entity says about the style for citation? I mean, you could ask the Twitts[8a]…but why not check the source [9].

Provide a bibliography of any references cited in the Project Narrative. Each reference must include the names of all authors (in the same sequence in which they appear in the publication), the article and journal title, book title, volume number, page numbers, and year of publication.

emphasis added- no reshuffling of “co-contribution” authors permitted!


When citing articles that fall under the Public Access Policy, were authored or co-authored by the applicant and arose from NIH support, provide the NIH Manuscript Submission reference number (e.g., NIHMS97531) or the PubMed Central (PMC) reference number (e.g., PMCID234567) for each article. If the PMCID is not yet available because the Journal submits articles directly to PMC on behalf of their authors, indicate “PMC Journal – In Process.”

That’s it though. No mention of a required citation style or of a bibliographic style, so long as the pertinent information is included.

Now, I know why you are tempted to use the gawdawful numbered citations. You think you are saving space and can squeeze yet more blabbedy-blah text in there to overhwhelm the reviewers.

Resist the urge.

It is hard to read academic text with numbered citations if you are actually using the citations to create the argument in your mind. Now maybe I am weird. But for me, especially in my subfields of interest, Name, Date for a paper citation is sufficient cueing to dredge up any number of details about the paper in question. With a mental image of the findings, interpretations, etc. Call me crazy, but your random schema for numbering the references doesn’t do the job.

Even if I flip back and forth between my place in the text and the reference list, I’ve probably forgotten what the hell [254] refers to a paragraph later. There is a prayer that (Schmelmitz et al, 1968) will trigger me to remember the paper without any need to flip to the citation list at all. And I’ll likely remember which one you mean, if I’ve flipped back to check the full citation, for longer than a few sentences.

Oh, and speaking of flipping to the Bibliography. Much easier to do with hardcopy grant applications. Much harder to do when reading the PDF on a computer. Maybe there are some fancy double pane views but I sure as heck don’t use them…are you gambling your average reviewers knows some way to do this?

So numbered citations are a clearly inferior way to cite an academic work. In fact, when I am the boss of science, whomever came up with this or perpetuates it as a good way to cite papers is going to be in the second group up against the wall[10]. They make it hard for the reader to figure out what work you are citing. Let’s face it, you aren’t wasting the space to explain the prior finding, either, are you? You are using the mere citation itself in hopes that it makes the point for you! Why would you want to make it hard on the reviewers? It’s only going to annoy them.

[1] Drugmonkey, 2012

[2]DrugMonkey, 2012

[3]Dr Zen, 2012

[4]Luminescer, 2012

[5]Luminescer, 2012

[6]Drugmonkey, 2010

[7]ericsuh, 2012

[8]ericsuh, 2012

[8a]Namnezia, 2012

[9]Application Guide for NIH and Other PHS Agencies

[10]Unless they are also a GlamourMag editor, then they go with their regular group[11].


Project Ownership

January 20, 2012

GMP has a good discussion going over at the Scientopia GuestBlogge.

I don’t want to be a petty, selfish project-hog advisor, but it’s not free for all; I don’t think that all the projects that I currently work on or plan on working on are fair game to claim as your own.

Get on over there and play…

SciAm bloggers get pizzaid!

January 19, 2012

A tweet from one @robinlloyd99 indicates that the pay structure worked out for the Scientific American blogs runs a fixed $200 per month.

.@BoraZ: some networks pay more to those who bring more traffic. @sciam network doesn’t. same monthly pay for every blogger. $200

Not too shabby. I may have reached that in one or two big months at but for the most part the paystructure there was running maybe $100-$150 per month for the DM blog, which was right around 20% or so down the traffic list. So the vast majority of Sb bloggers were not making anything near what SciAm blogs is paying. Including Sb escapees such as Myrmecos, SciCurious and Aunt Janet.


This is fantastic.

The case is from Bangor, ME. The initial report quoted an emergency room doctor as saying at least three people in the Bangor area had died from “bath salts”. As per the DEA emergency scheduling action in September, there are at least three synthetic cathinone derivative drugs of concern:

The Administrator of the Drug Enforcement Administration (DEA) is issuing this notice of intent to temporarily schedule three synthetic cathinones under the Controlled Substances Act (CSA) pursuant to the temporary scheduling provisions of 21 U.S.C. 811(h). The substances are 4-methyl-N-methylcathinone (mephedrone), 3,4- methylenedioxy-N-methylcathinone (methylone), and 3,4- methylenedioxypyrovalerone (MDPV). This action is based on a finding by the Administrator that the placement of these synthetic cathinones into schedule I of the CSA is necessary to avoid an imminent hazard to the public safety.

I had a prior post (lost in the Sb hole, reposted) discussing a bit of frustration with the conflation of two different drug molecules under one street name. Particularly when it comes to the sensationalized media reports.

This is why I’m happy the most recent report is a confirmation from the medical examiner that MDPV was involved in this case in Maine.

The state medical examiner’s office has determined that a man who took bath salts and died at Eastern Maine Medical Center last July overdosed on the synthetic street drug.

Ralph E. Willis, 32, had consumed “a toxic level” of methylenedioxypyrovalerone, or MDPV, a key ingredient of bath salts, Mark Belserene, administrator of the medical examiner’s office, said Wednesday.

I am even more happy that the journalist, Nok-Noi Ricker, requested even more information:

Willis had 150 nanograms per milliliter of MDPV in his bloodstream, a body temperature of 103 degrees and an erratic heartbeat when he got to the emergency room — all side effects of the hallucinogenic stimulant — the report states.

This is great. Usually we have to comb through a very slowly developing and erratic Case Report literature to determine anything at all about real-world, in situ, drug levels, combinations and identities that lead to medical emergency and death. Nice to see a reporter tenacious enough to do the followup beyond the original (and sadly typical) level of “Person dead, Cops say it was [insert drug name here]”.

I am also happy that the journalist includes the caveats. This guy was combative and agitated, from the reporting. So, as another quoted expert mentions, we can’t necessarily conclude that this is all down to a simple equation between plasma levels of the drug and the resulting cardiac complications.

“There are so many factors that go into [a bath salts] death that have nothing to do with the level” of drugs ingested, Karen Simone, a toxicologist and director of the Northern New England Poison Control Center in Portland, said Tuesday. “Maybe it killed him, and maybe it didn’t.”

Physically restraining bath salts users who are severely agitated and in a state of excited delirium can be harmful and even life-threatening because they usually have increased heart rates and high blood pressure, Simone and Dr. Jonnathan Busko, an emergency room doctor at Eastern Maine Medical Center in Bangor, have said.

As I have been mentioning in the case of mephedrone/4-methylmethcathinone, the academic literature has been slow to develop. There are now three pretty interesting papers which take a look at neurochemical, toxicological and behavioral effects of 4-MMC including Kehr et al 2011, Baumann et al, 2012 and Hadlock et al, 2011.

All I’ve been able to drum up* with respect to MDPV is Fuwa et al (PDF). The abstract is in English and the Figures are pretty easy to work out but…any of my readers fluent in Japanese and want to give translation a go?

*generally available. There were two adjacent posters at the recent ACNP meeting although I couldn’t really get a feel for whether they are close to publication or not. Stay tuned, there will eventually be some more data I would think.

This originally appeared on the version of DrugMonkey and fell into the gap when we closed up shop over there.

The New York Times had a piece up Sunday that was entitled “An Alarming New Stimulant, Legal in Many States“. I was alerted to this by David Kroll who reposted some prior comments at his Take as Directed blog. I’ve been getting some traffic from a BoingBoing linker from Maggie Koerth-Baker to an older post from me so I thought I’d better address a couple of points that jump out at me.
First and foremost, the reader should be extremely cautious whenever there is conflation of two different drugs under one purported street name. Even if they are structurally quite similar and some human reports have overlapping properties. In the case of “bath salts”, there is quite a bit of confusion over whether a news account is referring to 4-methylmethcathinone (4-MMC), methylenedioxypyrovalerone (MDPV), sees no difference between them* or doesn’t know if there is any difference.

Read the rest of this entry »

eli rabett observed in a comment to a prior post about reading the literature that

Graduate training is designed to pass lore from advisers to students. You learn much about things that didn’t work and therefore were never published [hey Prof. I have a great idea!…Well actually son, we did that back in 06 and wasted two years on it], whose papers to trust, and which to be suspicious of [Hey Prof. here’s a great new paper!… Son, don’t trust that clown.] In short the kind of local knowledge that allows one to cut through the published literature thicket.

This is true but one can’t take it too far. Lab lore can be another term for superstitious behavior. It is possible that “the way it works” is really just one of many ways to get something to work…and perhaps not even the best, most efficient or most clearly interpretable way.

There is another realization that comes along with time and reinforces the suggestion to ask senior professors things but not to actually take their angle on the matter.

As you move into early and middle independent career you may find yourself asking the senior Professors why X finding was never followed up on when you run across a fascinating bit of data in the old literature. Or perhaps you will ask whether Y was ever observed after having a “gee that’s not supposed to happen” moment in your own studies. Maybe you will need to inquire why the field does it like Z instead of the way that makes most sense to you.

This can turn into a research program or two if you are paying attention. Sure, if you ignore collective wisdom that doesn’t necessarily appear in the published literature, you run the risk of wasting much time re-inventing the wheel. I’ve done that too. And I will admit that there are several of the most curious leads that I have run across that I simply have not managed to turn into a research program yet.

However. There are ideas such as these that have turned into at least a R01 level funded project and resulting papers.

So don’t necessarily take the good Professor’s word that “I think Professor Schmoe did that back in ’68 and didn’t get anything” as being the end of your inquiry.