Expectations for trainee publication output

A question arrived about publication expectations for trainees at the blog mailbox recently.

I was wondering if you would consider a blog post and perhaps encouraging discussion on a related topic, on how do you evaluate your student/postdoc performance and how common is the 1 paper/yr “rule”?

At the outset I was skeptical that much use would come of trying to answer this because the real answer is “It depends very much on subfield and ultimate career aspirations, therefore broad sweeping pronouncements are of little value.“. And this is true. But what the heck? I’ll give you my thoughts from my point of view, no doubt some others will go shitnutz about how it is clearly different and maybe we can hash out the space of useful answers.

Some detailed stuff that I thought about, but often are not discussed thoroughly include:
– I always assumed that when people talk about 1 paper/yr it refers to 1 first-author paper but not in a top-tier journal (usually “best in the sub-field” journal, e.g. Org. Lett., J. Med. Chem., etc.)

Yeah. I think one paper per year is a pretty good general starting point. Emphasis on general. For trainees, I think this average will be lower, ditto if you only count first-author papers. But it is a pretty good target expectation for the central tendency. One first author per year in a “top tier” journal is a ridiculously absurd expectation for postdocs. Even one per year in a “top tier” journal as senior author is only possible for the very top laboratories and is therefore not the expectation for everyone. If you can do it, good on you, but it ain’t typical. So if you are in a place where you think this is the standard for postdocs? please. I’m familiar with a lab that has probably one of the highest CNS counts ever and the postdocs do not hit one CNS pub per year as first author. They have not done so over the ~15 years I’ve been watching the lab’s production. So anyone who does this out there in the whole postdoc population is the rare exception.

– How do you factor in non-1st author papers? Ignoring the effects of journal IF, would one 1st-author paper = two 2nd-author paper?

There is no direct relationship, I would argue. Non-substitutable quantities. No amount of non-first author papers makes up for not having any first-author papers. They are just that important in the minds of many people, including me. Conversely, the existence of some 2nd-Xth author papers is better than not having any, because more is better when it comes to publications on the CV. I suppose at some point there would be a balance point in which too many Nth author papers starts to subtract from the credit generated by the first-author list. It would be related to the thought of “why doesn’t this trainee have more firsts if she is this experimentally productive?”.

– Do people even consider anything greater than 2nd-authorship (i.e. having 3rd authorship is basically useless or not counted)? If so, does the level of the prestige of the journal change this perception (i.e. having 3rd authorship in PNAS is equivalent to a 1st-author in some 2nd-tier journal like Biochemistry)?

In my view, no, the Nth author on an article in a higher IF journal doesn’t trump first-author in a lesser journal. See above, the Nth authorships count but I would say they are independent of the first-author credits. So within the sphere of Nth authorships, sure, the higher IF is better.

– How do you factor in the prestige or IF of the journal? Does publishing in Science/Nature/Cell count as having 2-3 1st-author papers in 2nd-tier journals?

Indubitably the CNS first-author counts more than several first-authors in lesser journals. One might even suggest that CNS first-author as a postdoc trumps infinity non-CNS first-authors. For some situations. There are those that assert that the presence/absence of very specific journals on the CV is the difference between round-filing an application for an Assistant Professor position and placing it on the long-list for consideration. I credit these assertions but would also point out that there are many perfectly acceptable jobs that would not have this absurd criterion.

– Do people take a time-average (i.e. as long as you get 5 papers in 5 years it’s fine), or is having a regular output more important (i.e. would prefer to have 1 paper every year as opposed to 2 papers in 1st year and 3 papers in 5th year but nothing in between)?

I would say that it is only once one becomes a PI that it is ever reasonable to look at consistency of output. This particular example would not even be noticed, I would say. And even then it sort of depends on the type of work you do. I know of multiple types of work in my areas of interest (particularly human studies) that have years of data collection followed by a flurry of papers.

When I have recommended shooting for consistent output, being concerned with whether a manuscript submitted to Journal X at this point in the year will have a pub date from this year, etc it has to do mostly with motivation. Most of the time the pace of submission for a postdoc is not going to be easily controlled. The experiments have their own timeline. Things come up. New things need to be done to wrap up the paper. Then there are the many sources of delay in the review process. There is no reason to obsess about 2 in first year / 3 in fifth over meeting a strict rate of 1 per year for 5 years.

The clock is ever ticking, however and since one cannot go back and fill in missing publication-years, one is best keeping one’s eye on the prize. If you haven’t had a paper in a two year span, well maybe it is better to dump out a quick one, give up on hitting the highest possible IF, etc. You have to make this judgement thinkingly, of course. And no, there are no formulaic answers such as my correspondent seems to be seeking.

Balance. That is my best suggestion.

Sandy

Stay safe, friends in the path of Hurricane Sandy.

Hoping this turns out milder than anticipated…

Advice for new grant writers gets one thing wrong

The latest iteration is on the Twitts, launched by queries from @JacquelynGill. You can browse the #firstgrant hash tag if you want some background.

One of the sounder bits of usual advice to new grant writers is to get some examples from established scientists. The closer to your field and the closer to the agency you are soliciting, the better.

All true. I can’t imagine someone drafting a credible NIH application from the instructions alone.

Where I think the typical advice goes wrong is in emphasizing successful applications. As if this is all you need.

I think new grant seekers should ask their friends and senior colleagues for the losers too. With, preferably, the reviews.

There is much about the NIH review process and one’s likely success within it that can be gleaned best from comparing successful and unsuccessful grants.

UPDATED: A prior post on what is wrong with the NIAID sample grants.

NIAID and NIDDK are fond of the R56

The R56/Bridge mechanism of the NIH is called the High Priority, Short-Term award

will fund, for one or two years, high-priority new or competing renewal R01 applications with priority scores or percentiles that fall just outside the funding limits of participating NIH Institutes and Centers (IC). Investigators may not apply for R56 grants.

Sounds good right? It gets better:

The R56 award will help early career stage scientists trying to establish research careers as well as experienced scientists who can benefit from interim funding while they revise their applications.

Woo-hoo! Sign me UPPE!!!!

Except, sigh, they don’t fund very many of these. Or at least my ICs of interest never seem to be that interested in giving me a hand while I revise my awesome applications. And in fact I seem to see these things quite often awarded to year -2xA1 projects and fairly infrequently awarded to noobs. But that’s kind of subjective….

I took a search REPORTER for R56 awards since July 1. And sorted by the IC.

WOWSA. First thing I noticed is that my ICs of closest interest aren’t handing (m)any of these out right now. So, sucks for me. But at least I don’t have to whinge about fairness.

NIAID and NIDDK however clearly LOVE these things. Just LOVE the R56. I count 88 of the 1R56 awards out of 136 from NIAID and an additional 30 from NIDDK. The next biggest players are NIDCR with 5 and NIMH with 4, not even close.

I noticed something else interesting. 72 of 136 are for A1 versions of the proposal.

NIAID seems to be the ONLY IC to fund R56s for competing continuations, picking up 17 of them. Some for original submissions sure, but some for A1 revision.

I emphasize. The A1 version of applications are being awarded R56s. Which can’t be revised. And can’t be resubmitted except in clearly-different guise. Yet the announcement clearly says the R56 is for preparing a revision of a just-miss, meritorious proposal.

So what in the hell are these being awarded for? One might ask.

Now I didn’t delve down into trying to determine who was a new investigator versus and established investigator. Mostly I was hoping to complain about my favorite ICs where I could sort based on name recognition with this little exercise. But perhaps some NIAID mavens could review the list for us.

Here’s what I want to know. To what extent are these being used to give a break to genuine noobs and to what extent are they being extracted out of POs by long term investigators who haven’t managed to get a fundable score. To what extent are they letting Professor Bluehair keep her extra postdoc or technician around but completely missing the point that Assistant Professor Noob would like to get her first one of those, thanks.

To what extent are they propping up labs of PIs nearing the common (nonscience) retirement age and to what extent are they failing to sustain momentum for people more in my age bracket who have a fair bit of productive science ahead?

Training Future Surgeons…or Scientists

Teacher Ms. S. has requested support for her science class to learn basic vertebrate biology with the time honored dissection lab.

This grant will provide our science classroom with the equipment necessary to complete two laboratory dissections with 100 students. After an in depth study of the circulatory system and the chambers and structures of the heart, we will dissect a sheep heart. I selected a sheep heart since they are almost identical in size and structure as a human heart. We will continue with our anatomical studies of the other human organ systems, including the respiratory, digestive, excretory, reproductive, muscular, and skeletal systems. As a final culminating project, we will dissect a large bullfrog to develop a much deeper understanding of how the organs work together in the human body.

The REALM Charter school in Oakland California has an admirable goal

MISSION
The mission of Realm Charter School is to cultivate resiliency, develop critical thinking skills, advance knowledge through rigorous studies, and equip students to serve our communities and the world in the 21st century. Realm Charter School will serve diverse urban students in grades 6-12 using a student-centered model that features project-based learning, an emphasis on technology, research and action on concerns in the community and activities that develop emotional resiliency.

and is described further by Ms. S.:

The REALM Charter School student body consists of 80% students of color living in Richmond, Berkeley, and Oakland. Approximately 60% of our students are Latino, and the remaining 40% are African American, Asian and White. We are a project based design school. We teach students to tackle problems and seek solutions through creative ingenuity.

As my longer term readers know, I’ve had my eye out for the dissection projects for a few years now because I think they are some of the most memorable primary and secondary school experiences when it comes to scientific education. This has been recently reinforced because one of my children was afforded the ability to do several dissections in a summer program that my spouse and I could happen to afford. Not every child in America is so lucky, as you well know, and this is a High Poverty school.

This is not a cheap project, the remaining balance sits at $1,089 as of this writing. This makes it a steep hill to climb, but I think we have a shot at making it a reality. So please, if you can, donate. Even just a little bit, $5 or $10, chips away at the total and creates momentum.

If you cannot, please consider forwarding the link on your Twitter, on your Facebook and even by email to your friends and families.

I am already humbled by the generosity of the Readers of the DM blog and of the Scientopia Collective. Thanks to everyone who has already pitched in.

Your Republican Party thinks quite a lot about rape

Via brain wrap at DailyKos

Obama has a better approach

A query on your publication practices

This one is mostly for the PIs in the audience but I’m sure trainees will have experiences to share as well.

What fraction of the people who have spent time in your laboratory have ended up with authorships on published papers?

(Including students and techs)

Donor's Choose Time!!!

Yes, folks, it is that time of year. You get to open up your wallets, even $5 helps people, to help little kids’ school classrooms. It is no secret that public education has been enduring a long downward slide in the ranks of things that are important to voters/taxpayers in the US. But you probably didn’t know just how bad it has gotten. Peruse these projects, see the things that you remember as having been the expected value (like dissection in 10th grade Biology) and wonder that this is no longer the case.

Then give. The kids will benefit.

The purpose of writing GrandeTheorye scientific review articles

The sole purpose of generating a review article that lays out your GrandeTheoryeEleven in the biomedical sciences is so that you can try to take sole credit for ideas that occur to many members of your subfield who are following the same literature that you do.

Please note that Nobel Prizes in Physiology or Medicine are not generally handed out for review articles.

The conversation is not about whether or not the guy is a sexist; it is about what he said

siiigh.

that is really what I find so distasteful of this whole affair. The witch-hunt being carried out by some of these commentators reeks of McCarthyism like persecution to seek out “impure thoughts” and destroy those who may harbor them. There is ZERO EVIDENCE that DM is actually sexist, other than an idiotic comment he placed on facebook.

There is no better way to address this than with illdoctrine

Repost: I Am…

There was a blogpost responding to the Maestripieri comment that noted a tendency for more mainstream outlets to emphasize the complaints of women over those of men. I rush to disagree since it happens that Isis and Janet Stemwedel are eloquent and quote worthy. My post was little more than a “don’t do this”.

Nevertheless it would be bad if there were any impression generated that only women thought the remarks of Maestripieri were out of line. Men object too.

Although this is only part of a complex reason, I was reminded of this previous observation of mine.

---

I am a friend. A friend to women who I met when I was 5 years old, ones I met in high school, college, grad school. Women I met as a postdoc, as a faculty member, as an inhabitant of my community. They work in any number of professions from publication to politics to public health to scientific research to mainstream media to education, etc, etc. Many different walks of life. Many of them experience uncomfortable moments, sustained toxic work environments and/or flagrant discrimination in their working lives. I like my friends. Their continued happiness and well being is important to me.

Gaining clarity on the pharmacology of the bath salt MDPV

There are two new pharmacological investigations on the substituted cathinone drugs that have been discussed here on occasion.

Each of

Baumann MH, Partilla JS, Lehner KR, Thorndike EB, Hoffman AF, Holy M, Rothman RB, Goldberg SR, Lupica CR, Sitte HH, Brandt SD, Tella SR, Cozzi NV, Schindler CW.Powerful Cocaine-Like Actions of 3,4-Methylenedioxypyrovalerone (MDPV), a Principal Constituent of Psychoactive ‘Bath Salts’ Products. Neuropsychopharmacology. 2012 Oct 17. doi: 10.1038/npp.2012.204.

and

Simmler LD, Buser TA, Donzelli M, Schramm Y, Dieu LH, Huwyler J, Chaboz S, Hoener MC, Liechti ME.Pharmacological characterization of designer cathinones in vitro. Br J Pharmacol. 2012 Aug 17. doi: 10.1111/j.1476-5381.2012.02145.x.

report very similar findings for MDPV, the cathinone that appears most frequently in US newspaper reports.

As a very general rule, the amphetamine class stimulants do a couple of things to enhance the neuron-to-neuron chemical communication that occurs in the brain. The most common and significant effects tend to involve the transporter mechanisms that remove dopamine, norepinephrine and / or serotonin from the synapse, the gap between two neurons. These transporter molecules are an integral part of terminating a signalling event which has been caused by the release of one of these three monoamines from one of the neurons in question. Interfere with the operation of these transporters and a drug can potentiate the magnitude or duration of a given signalling event (i.e., release of one of the dopamine (DA), norepinephrine (NE) or serotonin neurotransmitters).

The amphetamine class stimulants have these properties. As does cocaine. As do therapeutic drugs such as methylphenidate (Ritalin) and Prozac. The term selective serotonin re-uptake inhibitor, SSRI, for Prozac-class antidepressant drugs refers to the transporter, obviously, and also indicates a key thing with the term “selective”. Drugs which have the ability to interact with one of the monoamine transporters tend to interact with the other ones as well. Substantial differences in effect can be associated with differences in the relative ability a specific molecule has to attach to the DAT versus the NET versus the SERotonin transporter (SERT). As one clear example, methamphetamine and MDMA differ in their relative ability to inhibit the SERT….this property of MDMA is associated with many of it’s stimulant-atypical properties relative to other amphetamine-class drugs.

The new studies both show that MDPV blocks all three transporters with much more potent effects at the DAT and NET relative to SERT. As Baumann and colleagues note, MDPV is 50 and 10 times more potent than cocaine (not an amphetamine, we’ll come to this) at DAT and NET respectively. Simmler and colleagues similarly indicate that MDPV is much more potent at DAT than cocaine or methamphetamine which did not qualitatively differ from each other.

So to this point, MDPV looks like a high-potency traditional stimulant. Most effective at the DAT, fairly effective at the NET and with less ability to block the SERT.

Cocaine and the amphetamines diverge at this point because the amphetamines act as a substrate at the transporters. Instead of only interfering and blocking them from doing anything, the amphetamines actually substitute for the neurotransmitter in question and are taken up into the cell. In so doing, they also cause an exchange to happen whereby the transporter moves some neurotransmitter from inside the cell back into the synapse. This transporter mediated efflux contributes to any “regular” release of neurotransmitter mediated through the merging of intracellular sacs (called vesicles) with the cell membrane.

The two papers agree in finding that MDPV has no ability to cause transporter-mediated efflux of dopamine and is therefore best categorized neuropharmacologically as a “pure” blocker (like cocaine) rather than an amphetamine-like transporter substrate.

The Simmler paper adds an in vitro model of blood/brain barrier penetration…in very simple terms the degree to which a molecule is fat-liking versus water-liking can alter the speed at which it can cross cell membranes and get into the brain. This paper used an in vitro preparation of human capillary endothelial cells (that form the blood-brain barrier) to show that MDPV is likely to cross the blood-brain barrier very rapidly, consistent with high lipophilicity predicted from its structure.

The upshot of the two papers is that MDPV shows pharmacological properties consistent with classical stimulants. It shows relatively high selectivity for DAT over SERT and high potency relative to drugs such as methamphetamine or cocaine. In vivo neurochemistry in the Baumann paper confirm that MDPV has potent effects on dopamine levels in the nucleus accumbens, a hallmark of drugs (beyond the stimulants even) which have substantial risk for compulsive use. The only somewhat discordant note for the structure-activity nerds is that MDPV looks so much like the rest of the amphetamines and cathinones that it will be interesting to discover why it doesn’t act as a transporter substrate (Simmler et al included a number of other cathinones and showed that many of them do act as transporter substrates.)

Together these papers suggest that MDPV has high abuse liability with a use pattern characterized by frequent re-dosing much like one sees with cocaine. This is consistent with many self-reports that are emerging from people who use MDPV and therefore, despite the relatively brief time on the “market”, we can predict a cocaine-like dependence problem to emerge for MDPV in the near future.

The upside of scientific meetings

It’s quite possible that the full-throated value of a scientific meeting for your science is only realized once you are a PI.

It is not infrequent that I come back from scientific meetings all in a tizzy to do one of three things.

1) Put the hurry up on pumping out some data that we’ve been collecting.

2) Start new experiments! Several. We gotta get on this right now people so let’s moooooove!

3) Write two or three new grant proposals.

The reasons are varied but it all comes down to the constellation of encouragements you get at a conference through talking with various people about your data and their own data.

This is why we do this. Because the science is exciting. And meetings put a thick underline below this experience.

SfN 2012: Professors behaving badly

I don’t actually know Dario Maestripieri although I have read some of his scientific work now and again over the years. His areas of interest include primate social behavior as well as mating systems and reproductive strategies. Apparently his interest extends to the human primate.

Professor Maestripieri has posted a rather idiotic observation about the Society for Neuroscience meeting and his apparent disappointment in the lack oI eye-candy available for his personal enjoyment. Now yes, he posted this on Facebook which is nominally private-ish. But clearly he has enough “friends” that someone was offended and saw fit to screen capture and send it around.

There is a very simple response here. Don’t do this. It’s sexist, juvenile, offensive and stupid. For a senior scientist it is yet another contribution to the othering of women in science. In his lab, in his subfield, in his University and in his academic societies. We should not tolerate this crap.

Professor Maestripieri needs to apologize for this in a very public way and take responsibility for his actions. You know, not with a nonpology of “I’m sorry you were offended” but with an “I shouldn’t have done that” type of response.

UPDATE: I have now heard this tale from about a half dozen independent directions. Several people expressed thanks to me and mentioned their channel on the info hesitated to publicize for fear of some sort of retaliation. Well, the cat is well and truly out of the bag and there are multiple lines of revelation on this. If you are one of the original sources, you have company. I thank you all for bringing this behavior to light.

As always, feel free to sock up in the comments, use something other than your usual in the email field though.

See Janet’s post here.

And Isis’ post.

And Jezebel.

Return of the A2 revision for NIH Grants?

According to a blog entry at Nature the NIH is reconsidering their policy limiting applicants to a single revision of an unfunded grant proposal.

Good. They should do so. Unless, as I’ve said repeatedly, they can show that the increase in the percentage of grants funded on the first try is driven by genuine “first” tries. Rather than being driven by ideas which have been previously reviewed, in different guise.