January 19, 2011

Linear, sigmoidal, arc and exponential.

I’m certain you can find career paths of biomedical research PIs that can be so described. You can think of the dependent variable as a conglomerate measure of lab size- people, funding, space, collaborations and vigor.

I used to see a lot of sigmoids in my subfield peers.

A slow start, struggling to land that first major funding. Hard to find or hard to fund postdocs so making do with techs, undergrads and maybe a grad student who don’t know any better.

Eventually things click, the grant clouds pour down direct costs rain and the postdocs come a-running.

A successful career launch.

It feels as though I’m seeing a lot more interruptions lately. Peeps who I thought were, and should be, on the steep part of the curve suffering an interruption of some sort. Not always sure why…after all it’s kinda rude to front your colleagues about perceived slowdowns. Unless you are the Chair, I suppose. I tend to assume it is because the grant dice just aren’t coming up. And there is very little room for error in the current funding environment. Very different from when I was just getting started in my independent phase.

Watching the people that I like take a hit in what should be a time of scientific vigor in their career path is unpleasant.

This moment

January 19, 2011

We have some great stuff in the hopper.

Immediate data flow is rocking, I get PI crack updates every few days that are fun and fascinating.

Middle term, the projects themselves are on track and doing what they are supposed to be doing, I.e. turning up unexpected leads for more studies. Moar! I say!

Long term we have almost a programmatic effort going on at least two things I’ve been working on for a couple, three years.

The last is my *job*, of course. That’s what the PI is supposed to be doing. Getting the several year plan harmonized into a program of investigation. Lining up the people, of course. And the funding. And wrangling the local institution into doing what you need it to do.

The data-crack is undeniable. It is a powerful and immediate reinforcer. So are new hypotheses and unexpected results that need to be figured out, investigated and nailed down with more data.

But the *programmatic* successes?


I like my job quite a lot today.

There are certain things I have recently been informed that it is improper to discuss in mixed company.
So I’ll put the rest of the discussion after the jump.

Read the rest of this entry »

as is our wont, the CPP and I had a recent email exchange…

Your Humble Narrator: honestly sometimes I get commenters that make so little sense I question whether I am getting demented- because I cannot for the life of me make out what they fuck they mean….

Comrade PhysioProf: I am having trouble reconciling this d00d’s illiterate paranoid ravings with his claim that he is funded by [some institute].

Your Humble Narrator: just like [that dude] over at writedit’s it is amazing to me that people with such wackadoodle paranoid outlooks could ever write a revised grant that is anything other than ranting.

Comrade PhysioProf: I’m sure people read some of the shitte we write and thinke the same thinge!

Your Humble Narrator: touché!

Holy crapoli on a cannoli!

I missed the webcast of Harold Varmus’ recent townhall and it doesn’t appear to be up yet on the web. [UPDATE: Here’s the videocast] But a commenter named lula over at writedit’s pad says:

Although not is as many words, Varmus said that there will not be a payline for the NCI in FY2011. He indicated that funding selection will be made in a case by case basis with input from program leaders, and taking into consideration programmatic priorities, etc. The only number that he put out there was 7%, by means of suggesting that grants within this or lower percentiles would be funded; honestly he sounded unconvincing (and unconvinced) about the whole process and a bit at loss on how to explain it. He also reiterated the NCI’s commitment to NI/ESI but without any specifics.

This was affirmed by another commenter.

Have we sunk down so far that there is no point in having a payline? Will Program staff be making their priority decisions for *everything* at NCI?

The thinkin' chair

January 11, 2011

This question is mostly for the PIs in the audience. Now, I know about your trips to the coffee shop to hide out from your lab member’s quotidian interruptions that can blow your day if you aren’t careful. Not talking about that. When you are in your office do you ever sit elsewhere than in front of your computer workstation?

I need to do that more. Sit across the room with a document, manuscript, paper..or even nothing. Just sit and think quietly.

I don’t do enough of that.

NIGMS has released their annual update on the review outcome for NIH R01 applications directed their way for potential funding (see bottom of this post for prior Fiscal Year links). The most salient figure is the histogram of percentile ranks arising from the initial review, identified by whether they were selected for funding or not.
As far as I’ve ever seen, NIGMS is the only NIH Institute or Center that does this. As you can see from the figure, one of the most interesting features here is that we can identify how many “skips” and “exceptions” are in their pool of applications.
Skips refer to grant applications which appeared to score well within the apparent (or published) payline and did not get funded for one reason or other. Exceptions refer to those applications which did not score within the apparent payline but were selected for funding anyway. The latter are substantially more common than the former, of course. We’ve talked about these exceptions (i.e., “pickups“) before.

Read the rest of this entry »

Remember when Nature offered us a completely objective and unbiased review of PLoS?

Public Library of Science (PLoS), the poster child of the open-access publishing movement, is following an haute couture model of science publishing — relying on bulk, cheap publishing of lower quality papers to subsidize its handful of high-quality flagship journals.

drdrA alerts us to the fact that Nature Publishing Group seems to have changed their minds about dirty, gutter, bulk publication of lower quality papers.

Nature Scientific Reports

Commentary from Martin Fenner over at PLoS blogs and from Bjorn Brembs.
This is why NPG cracks me up. Totally unembarrassed to say whatever, whenever no matter how inconsistent with their supposed other goals (see goals for robust online discussion of published papers) or with their prior statements or with their other actions (see hand wringing about Impact Factors). Just like a good business should, I suppose.

This one is for some folks I’ve been engaging with on the Twitts about Uncle Siggy…

Link to Youtube

Don’t forget DrZen’s comment:

Freud was a comparative neuroanatomist who made significant discoveries:

Remember the $100 Spike folks? Who went on to launch a startup company called Backyard Brains to create cheap electrophysiology devices for the kid-education market?
They have launched a KickStarter drive to raise some cash for the next development cycle. They are looking to reach $5,000 and you have until Jan 9 to participate if you are so inclined. Here’s the overview:

Our goal is to develop a production version of the ‘SpikerBox’, an inexpensive, easy to use, bioamplifier for neuroscience experiments. It will be used by students in junior highs, high schools, and undergrad universities. We intend to make the teaching tools user-friendly enough that students of all ages can understand how to experiment with the nervous system of insects.

and here’s what they plan to use the KickStarter dough to accomplish:

We currently make the enclosures for our boxes by hand. While wood looks esthetically pleasing, it takes a lot of time and labor to manufacture. Our goal is to make our SpikerBoxes as cheap as possible. We are raising money to build a CNC acrylic or plastic based enclosure. Our goal in the enclosure is to make it low cost, easy to get access to the insides (we want kids to open it!) and ideally be transparent so that the electronics become a part of the experience.
Your investment will be spent to design and build several acrylic-based prototypes. This will allow us to bring these prototypes into high school classrooms and get direct feedback from the students and their teachers. The winning prototype will become our new enclosure. All because of you. Let the NeuroRevolution begin!

If you’ve never heard of KickStarter before, the FAQ will give you an idea of what it is all about. In essence you pledge a donation. If the pledges total the $5,000 threshold by the deadline, you are charged for your pledge but if it fails to reach enough pledges you are not charged (you have to use Amazon Flexible Payments Services, which permits this).
As far as I can tell there is no upside for the donor beyond being an angel. No tax deduction unless the entity to which you are eventually donating is a qualifying entity. No intellectual property or other interest in the company accrues to you, this is not an investment. So it may not appeal to everyone…
You can look through some of my prior posts, linked at the start, for why I like these guys and their effort so much. They are doing some creative stuff to try to get kids interested in neuroscience. They’ve been legging it out, doing some kids’ camps and generally putting on a traveling demo show during the year and, of course, continue to entertain at the SfN annual meeting. This past year’s bit of SfN Theme H fun was hooking their model (the cockroach leg) up to the head of a turntable and recording LP-induced spike activity. They also were trying to demo up a cheap way to wire up a toy remote control to the antenna sockets of a roach so as to be able to control the direction of movement. Fun stuff if they can get it to work and I assume all of this will eventually be put into a set of lab kits.

I was alerted to an article published in The New York Times on “Keeping Women in Science on a Tenure Track” by dr becca and drdrA. Don’t worry, it was written by a man so you can take it seriously and all. Heh. Actually, this is just a distillation of an interesting report entitled “Keeping Women in the Science Pipeline,”. From the NYT bit:

women Ph.D.’s with young children are 27 percent less likely than men with children to receive tenure after entering a tenure-track job in the sciences. The report notes that single women without young children are roughly as successful as married men with children in attaining tenure-track jobs.

According to the report, plans to have children affect women postdoctoral scholars more than their male counterparts. Women who had children after becoming postdoctoral scholars in the University of California system were twice as likely as their male counterparts to shift their career goals away from being professors with a research emphasis — a 41 percent shift for women versus 20 percent for men.

Go read, there’s more.

Anyway, I have a new favorite plan to help with this little problem, thanks to Cath of VWXYNot who commented:

The CIHR (Canadian equivalent of the NIH) and some of our other funding agencies have CV formats that include a dedicated “Interruptions and Delays” section.

This is brilliant! The NIH needs to adopt this right away as a required line on their Biosketch. Don’t worry, they have several other line items that are supposed to be included even if the response is Not Applicable. The point is to make it default and a part of every application so that the applications of those who feel it necessary to use it will not stick out as unusual.

There are a number of upsides. First, it will be a subtle and insidious statement that it is expected that NIH applicants will have had delays in their career progress or scientific projects due to certain personal and family-related factors. The CIHR does specify a number of obvious scenarios beyond just childbearing, see Cath’s comment. Expected and therefore accepted. From the point of view of the funding agency. And, as we’ve noted on occasion, the NIH reviewer is supposed to be working for the NIH to help with their priorities. Not the reviewer’s personal and idiosyncratic viewpoints, but to help with the job that is expected of them by the NIH. They don’t always do this, of course, but having expectations laid out relatively explicitly can’t but help.

The second upside is a bit more specific. My usual advice for these types of delays is that it is dangerous to bring it up in your application before anyone has criticized you for it. Since in the old days you got two rounds of revision and at least one round of revision was pretty much necessary, no biggie. You submit your app, take your criticisms for apparent delays (if any, they are not inevitable) and come back with your response in the revised application. As always, the point is to explain, not to excuse. The advocating reviewer can then use your supplied reason to beat back criticism from anyone else. Yes I have seen this work very favorably on more than one occasion. Something along the lines of “My productivity was reduced in the past five years because I bore two children in that interval” or similar as a response to a criticism about productivity. Trouble is, now that we’re down to a single revision and ICs are steepening the paylines for even the A1 revision, this isn’t a great strategy anymore. I think you have to face it head on in the original application if you judge your “Delay” to be so obvious as to entail a good chance of drawing reviewer fire.

Wouldn’t it be nice if there was a nice custom made section (which didn’t take away from your precious 12 pages) for this?

I think so.

And I would think that on a NIH-wide basis it would result in a few more meritorious grants being funded despite the apparent “Delay” introduced by a woman PI bearing children, a PI of either sex undergoing a health crisis or caring for a sick family member…or even a lab experiencing a natural disaster.
Erratum: the original version mistakenly referenced the Chronicle of Higher Ed as the source rather than the NYT.

Professor David E. Nichols is a legend for scientists who are interested in the behavioral pharmacology of 3,4-methylenedioxymethamphetamine (MDMA, aka, ‘Ecstasy’). If you look carefully at many of the earlier papers (and some not-so-early) you will see that people obtained their research supply of this drug from him. As well as much of their background knowledge from publications he has co-authored. He has also worked on a number of other compounds which manipulate dopaminergic and/or serotonergic neurotransmission, some of which are of great interest to those in the recreational user community who seek (ever and anon) new highs, particularly ones that might be similar to their favorite illicit drugs but that may not currently be controlled. Those who are interested in making money supplying the recreational consumer population are particularly interested in the latter, of course.

Professor Nichols has published a recent viewpoint in Nature in which he muses on the uses to which some of his work has been put:

A few weeks ago, a colleague sent me a link to an article in the Wall Street Journal. It described a “laboratory-adept European entrepreneur” and his chief chemist, who were mining the scientific literature to find ideas for new designer drugs — dubbed legal highs. I was particularly disturbed to see my name in the article, and that I had “been especially valuable” to their cause. I subsequently received e-mails saying I should stop my research, and that I was an embarrassment to my university.

I have never considered my research to be dangerous, and in fact hoped one day to develop medicines to help people.

As with most scientists, I have little doubt. And ultimately, I agree with his observation that

There really is no way to change the way we publish things, although in one case we did decide not to study or publish on a molecule we knew to be very toxic. I guess you could call that self-censure. Although some of my results have been, shall we say, abused, one cannot know where research ultimately will lead. I strive to find positive things, and when my research is used for negative ends it upsets me.

It is unfortunate that Professor Nichols has been put in this position. Undoubtedly John Huffman of JWH-018 fame (one of the more popular synthetic full-agonist cannabinoids sprayed on herbal incense products) feels much the same about his own work. But I suppose this is the risk that is run with many lines of basic and pre-clinical work. Not just recreational drug use but even therapeutic use- after all off-label prescribing has to start somewhere. And individual health (or do I mean “health”) practices such as high-dosing on blueberries or cranberries, various so-called “nutritional supplements”, avoiding certain foods, exercise regimes, diets, etc may be based on no more than a single scientific paper, right?

So we should all feel some bit of Professor Nichols’ pain, even if our own work hasn’t been mis-used or over-interpreted…yet.

UPDATE: Thoughts from David Kroll over at the cenblog home of Terra Sigillata.

ok, not really. But I think we’re going to look back and say that this is when scientific blogging started being mainstream activities. I view it through the blog collective lens.

Prior to 2010, Nature Network and Scienceblogs sucked up all the air. Which was cool and all but it didn’t leave a lot of room. Or there wasn’t enough of a market, so to speak.

So what happened?

Discover magazine got serious by acquiring Ed Yong and Razib and by so doing created a third-way of collectivized scienceblogging.

Then, Scienceblogs and Nature Network had major (the former) and minor (the latter) assplosions. Talent departed with various levels of spleen being vented and rancor being…rancored.

This led, inevitably perhaps, to the formation of Scientopia and Occam’s Typewriter from a core group of emigres from each of the large collectives, respectively.

In parallel Wired magazine tried the Discover Magazine blogs model and Scientific American at least laid the groundwork (i.e., hired Bora Zivkovic as community manager) for what I suspect will be another instance of the Discover Magazine blog collective model.

PLoS blogs launched…unclear to me under which model but I bet it will eventually look more like the Sb / Nat Net / Scientopia / Occam’s Typewriter type of model.

In the breech, the wily upstart LabSpaces pulled a fast move by emulating the path buried in the origins of They pulled together a healthy number of existing privateer blogs, created a great deal of enthusiasm and really went to town. I’d say they easily won the enthusiasm and energy title for new blog collectives.

Along with this, the model of blog collective organized by scientific topic expanded as well. The all-geo site is currently just Highly Allochthonous but going by the Twitter energy of recent geoscience meetings I see a lot of upside future. Perhaps more interestingly, The Gam joined oldtimer Deep Sea News as a second Oceans blog collective. Strong work.

So science blogging continues to grow and, more importantly, become more formalized into go-to collectives and organizations. Some commercial, some not.

I can’t help but think this is related, perhaps not causally but as a reflection of the same trends, to a growth in recognition of

The Society for Neuroscience continues to tip toe but the Twitter chatter at the 2010 meeting was much more substantial. Even the tiny (and, let us admit, conservative) College on Problems of Drug Dependence started a blog.

I see many more local Universities and research institutes using Twitter and Facebook…and even establishing blogs as part of their PR mission. PR as institutions, sure, but part of that is to brag about the science their investigators are conducting and publishing.

Last but not least, Jeremy Berg, Director of the National Institute of General Medical Sciences used blogging with skill and enthusiasm to advance his agenda.

A comment from williams on a prior post intrigues me. S/he asserts:

My opinion is that reviewers should assess the scientific merit of a grant in itself (impact/significance/ PI’s scientific potential). Period. If an investigator has had an interval of no support that is irrelevant to the science she/he is proposing to do at this time in point.

In theory, I would agree. In theory.

The trouble is that this sort of assumes “all else equal”. And I just don’t see anything other than vanishingly rare circumstances meeting this standard.

Now to sidetrack for a little bit, the discussion was mired down by the term “failed grant” which to me means an interval of funding that has resulted in some less-than-productive outcome. arzey had said

You can almost always learn more about how to do an experiment from a failed experiment than from a successful one. Or to paraphrase: all happy grants/PI’s are alike, every unhappy grant/PI has lots to teach us.

The commenter williams, however, seems to be obsessed with failed grant applications, i.e., those which do not win funding. A different matter, in my view and somewhat less interesting. Of course we should learn from our applications that fell short. With the comment I started with, we perhaps reach a happy middle ground.

The Investigator component of grant review looms large. Despite the fact that formally speaking the NIH award is to a University and that PIs and other staff could be swapped around willy-nilly in theory, the participating investigators are a huge factor. A large part of the assessment of Investigators is the publication record of the participating staff. Not just mere publications, either, but oftentimes an assessment of how publications fit in with the prior and ongoing research support. If you have relatively little research support, well then reviewers are going to extend more latitude for a publication record that is less than expected. If you have a huge amount of funding, these expectations can rise.

Now let us acknowledge that williams is correct that grant review is supposed to focus on the qualities of the current plan. A good grant score on a new application (i.e., not a continuation of an existing project) is not supposed to be an award for doing well in a prior interval of funding. It is supposed to be an informed prediction that the current proposal will be successful if funded. Likewise, an excellent grant application should not be penalized for apparent deficits in the past work of the participating investigators under a different award.

Herein lies the trouble. Most people assume that past performance of an investigator is a good predictor of future performance, leaving the specifics of a given scientific plan aside. So there is an overwhelming tendency to view a wildly successful prior interval of funding (aka, “track record”) as a good predictor that the current application will result in similar success…..just because of the PI. Similarly, there is a tendency to view a lack of success in a prior interval as a prediction that the current application will not go well.

Favorably disposed reviewers will be looking for some reason to excuse what looks like dismal past performance, I hasten to reassure you. In fact, I have recommended before that if there is some apparent deficit in your own track record, you do what you can to provide an explanation in the application. Subtly. The advocate reviewer needs something to work with. I have personally seen all sorts of explanations, not excuses, explanations in grants. They can go down pretty well. Everything from trailing spouse issues to health conditions to child bearing to local weather disaster to local institutional screwage. If the reviewers like your proposal, they are looking to come up with reasons why your past interval of suboptimal performance does not hold as a predictor of your future performance leading the project.

All this does, however, is confirm the validity of the more general assumption that past performance predicts future performance. Right?

So how would we view an interval without funding? Here we are talking a mid to late career investigator who has had prior support, say, and then has gone for some serious interval (say 2+ years) without a grant. Should the Investigator criterion take a hit? Is this any different from going too long without any scientific publication? Does it, at some level, say something about an investigator if s/he is unable to keep the lab funded*?

I think it has to be a consideration. It is as much a part of the assessment of Investigators as any other traits and credits, in my view.
* to be clear I am talking relative to expectation. There are going to be some job categories for which continual funding is not an expectation. And some for which it is something more than an expectation. Let us not get distracted yelling about subfield differences and job types.

The DM Blog iPad Case

How did those good folks at CafePress know? Look what they’ve come up with the protect my latest technological obsession. Awww.
And never fear, there are cases for the 3G and 4 iPhones as well.