NIH Director Collins went to Kenya and all I got was

(by drugmonkey) Aug 04 2016

...a picture he took with the 0.2%.

9 responses so far

More politico professional parallels

(by drugmonkey) Aug 03 2016

Is the RealSolution to the stresses of the NIH grant system best described by the tone of the RNC or the DNC convention?

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(by drugmonkey) Jul 29 2016

The other lesson to be drawn from recent political events and applied to science careers is not to let toxic personalities drive the ship. 

Yes this means not giving them control over anything that is really important. 
But it also means not letting them control you to the extent you are reacting to them, more than doing your thing. 

It applies to grant and paper revisions. It applies to the science you do, how you do it and who you choose to work with. 

It means you need to wall the toxic actors off in their own little silo, only dealing with them at need or desire. 

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I should really post something science related

(by drugmonkey) Jul 28 2016

Really I've been meaning to, Dear Reader.

I've been distracted by a couple of work related things.

But I do want to draw together a thought from the Democratic convention speeches this week and the profession of science.

We are stronger together. Science works best when it is collaborative...we all parrot this truthism at one time or another. And we do collaborate. Within our laboratories if nothing else.

There is also competition. No doubt, no doubt. Very pointed in some ways. We've talked about the long odds of making it through to the professor chair, of getting the grants funded and of getting the paper published in just the right journals.

It's tempting to go low.

Michelle Obama says she always goes high when they go low.

She's right, you know? In the short term it may cost you a bit. Missing that opportunity to do dirt to your professional competition may let them advance in some small way beyond you. Maybe a not so small way.

I'm convinced, however, that taking the high road tends to work out better in the long run.

My confidence in this was wavering a tiny little bit in recent times. It's nice to be reminded that people who act the ass eventually are going to pay a price. You can get by for a little while but eventually, eventually, you are going to run out of those willing to give you a benefit of the doubt. Run out of friends and supporters. Run out of collaborators.

Because when it comes right down to it there are many scientific collaborators out there to work with. If you develop a bad reputation, they will choose others.

It took until this week to see a full slate of unreserved admiration and respect for the political life of Hillary Clinton on display. To my recollection anyway. It took a long time for her. I don't know that she always took the high road but she sure didn't take many low ones, especially given the vitriol directed at her over the years.

So I'm not saying take the high road because it will lead to immediate recognition and reward. It may take some time. It may never occur.

But hey, at least you can look yourself in the mirror every day without flinching.

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Political observation

(by drugmonkey) Jul 25 2016

When pressed, the more mainstream supporters of Donald Trump in the Republican party insist that they believe that Trump does not really mean the full import of his wildest statements. He doesn't really plan to block all Muslims from entering the country, he doesn't really mean to deport all undocumented immigrants, he doesn't really mean to.... etc. So, as I understand their thought process, it is okay to support his candidacy and this doesn't mean that you support all that crazy stuff.

Interestingly, these self-same people have a burning hatred (or at least a profound irrevocable mistrust) of Hillary Clinton because they believe that she doesn't really mean what she says during the campaign or in her prior political activities. They are positively obsessed with conspiracy-level accusations about her alleged insincerity, dis-ingenuity and secret machinations. And completely and utterly unable to take her policy statements, and descriptions of her reasons for her prior actions, at face value. And to be clear, it is not just that they criticize her actions. They are worked up to an absolute frenzy about their beliefs about her alleged insincerity, far more than they are about the actual policies or actions.

It's fascinating. On the one hand Republicans support Trump because they believe he is a liar. On the other hand, they absolutely hate Clinton because they believe that she is a liar.

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I oppose H8

(by drugmonkey) Jul 22 2016

Sometimes just shaking your head isn't enough.

One of the things that I've believed is the very essence of the American Dream is the aspiration to own your own little home, live in a nice neighborhood, raise your kids as best you can and live happily ever after with your spouse.

NBC Philadelphia reported on the American Dream of one couple as it is right now in 2016.

The couple said they bought the house in 2014 and moved there for a fresh start — a place where their boys, now ages 8 and 13, could play in the yard with the four family dogs and leave behind the hurt of their biological parents’ struggles with drugs and crime.

But, the pair said, they found only discrimination and hate. First, they said, in the form of the frivolous lawsuit, and later during a months-long campaign of repeated vandalism to their home that included someone using the cover of night to scrawl the slur onto their garage, breaking their security sensors on numerous occasions and twice taking a hacksaw to the white fence that supposedly sparked it all.

There's a gofundme set up to pay this family's legal bills.

I'm going to suggest that this is a great opportunity to give even as little as $5 just to register a vote of protest against hatred and in support of decency. Or as the lighting of a candle in the darkness.

Or maybe, as I do, you think that this could easily be you, your family or the family of people that are really close to you. The specifics may vary. Maybe it is not your sexual orientation but the color of your skin. Maybe it is your religion or the clothes you choose to wear. Maybe it is your chosen profession or perhaps a health or ability condition. Whatever it may be, you might be unlucky enough to end up in a neighborhood with people who hate you for what you are, not for who you are. And some of these sick individuals may be feel it is perfectly acceptable to persecute you because of their hatred.

And if so perhaps you hope, as I do, that if you had uncharitable neighbors like these poor people do, that the rest of the country would rise up and register a small vote of support for you.

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Personal jihads and distinguishing better/worse science from wrong science

(by drugmonkey) Jul 22 2016

This is relevant to posts by a Russ Poldrack flagellating himself for apparent methodological lapses in fMRI analysis.

The fun issue is as summarized in the recent post:

Student [commenter on original post] is exactly right that I have been a coauthor on papers using methods or reporting standards that I now publicly claim to be inappropriate. S/he is also right that my career has benefited substantially from papers published in high profile journals prior using these methods that I now claim to inappropriate. ... I am in agreement that some of my papers in the past used methods or standards that we would now find problematic...I also appreciate Student's frustration with the fact that someone like myself can become prominent doing studies that are seemingly lacking according to today's standards, but then criticize the field for doing the same thing.

I made a few comments on the Twitts to the effect that this is starting to smell of odious ladder pulling behavior.

One key point from the original post:

I would note that points 2-4 were basically standard practice in fMRI analysis 10 years ago (and still crop up fairly often today).

And now let us review the original critiques to which he is referring:

  • There was no dyslexic control group; thus, we don't know whether any improvements over time were specific to the treatment, or would have occurred with a control treatment or even without any treatment.
  • The brain imaging data were thresholded using an uncorrected threshold.
  • One of the main conclusions (the "normalization" of activation following training") is not supported by the necessary interaction statistic, but rather by a visual comparison of maps.
  • The correlation between changes in language scores and activation was reported for only one of the many measures, and it appeared to have been driven by outliers.

As I have mentioned on more than one occasion I am one that finds value in the humblest papers and in the single reported experiment. Often times it is such tiny, tiny threads of evidence that helps our science and the absence of any information on something whatever that hinders us.

I find myself mostly able to determine whether the proper controls were used. More importantly, I find myself more swayed by the strength of the data and the experiment presented than I am by the claims made in the Abstract or Discussion about the meaning of the reported work. I'd rather be in a state of "huh, maybe this thing might be true (or false), pending these additional controls that need to be done" then a state of "dammit, why is there no information whatsoever on this thing I want to know about right now".

Yes, absolutely, I think that there are scientific standards that should be generally adhered to. I think the PSY105: Experimental Design (or similar) principles regarding the perfect experiment should be taken aspirations.

But I think the notion that you "can't publish that" because of some failure to attain the Gold Plated Aspiration of experimental design is stupid and harmful to science as a hard and fast rule. Everything, but everything, should be reviewed by the peers considering a manuscript for publication intelligently and thoughtfully. In essence, taken on it's merits. This is much as I take any published data on their own merits when deciding what I think they mean.

This is particularly the case when we start to think about the implications for career arcs and the limited resources that affect our business.

It is axiomatic that not everyone has the same interests, approaches and contingencies that affect their publication practices. This is a good thing, btw. In diversity there is strength. We've talked most recently around these parts about LPU incrementalism versus complete stories. We've talked about rapid vertical ascent versus riff-raff. Open Science Eleventy versus normal people. The GlamHounds versus small town grocers. ...and we almost invariably start in on how subfields differ in any of these discussions. etc.

Threaded through many of these conversations is the notion of gate keeping. Of defining who gets to play in the sandbox on the basis of certain standards for how they conduct their science. What tools they use. What problems they address. What journals are likely to take their work for publication.

The gates control the entry to paper publication, job appointment and grant funding, among other things. You know, really frickin important stuff.

Which means, in my not at all humble opinion, that we should think pretty hard about our behavior when it touches on this gate keeping.

We need to be very clear on when our jihadist "rules" for how science needs to be done affect right from wrong versus mere personal preference.

I do agree that we want to keep the flagrantly wrong out of the scientific record. Perhaps this is the issue with the triggering post on fMRI but the admission that these practices still continue casts some doubt in my mind. It seems more like a personal preference. Or a jihad.

I do not agree that we need to put in strong controls so that all of science adheres to our personal preferences. Particularly when our personal preferences are for laziness and reflect our unwillingness to synthesize multiple papers or to think hard about the nature of the evidence behind the Abstract's claim. Even more so when our personal preferences really are coming from a desire to winnow a competitive field and make our own lives easier by keeping out the riff raff.

9 responses so far

Group effects. or "effects".

(by drugmonkey) Jul 22 2016

How many times do we see the publication of a group effect in an animal model that is really just a failure to replicate? Or a failure to completely replicate?

How many of those sex-differences, age-differences or strain-differences have been subjected to replication?

10 responses so far

Thought of the day 

(by drugmonkey) Jul 15 2016

I was joshing with the spouse about coups, Trump and the ready availability of pseudo-combat firearms today and a thought later occurred to me.

I'm actually pretty confident in the trigger pullers in my household.

Don't get me wrong, we're not a gun nut family- very likely I'm the only one who has so much as touched a firearm. But if they had to..... 

I was thinking about their respective ages and peers and what not and I'd pick them every time. 

I didn't know I had that particular confidence in my spouse and kids. 

Funny thought to occur. 

6 responses so far

Columbia University busted for taking too much overhead on NIH grants

(by drugmonkey) Jul 15 2016

From the Manhattan branch of the US Attorney's Office charged:

The United States’ Complaint-In-Intervention (the “Complaint”) alleges that from July 1, 2003, through June 30, 2015, COLUMBIA impermissibly applied its “on-campus” indirect cost rate – instead of the much lower “off-campus” indirect cost rate – when seeking federal reimbursement for 423 NIH grants where the research was primarily performed at off-campus facilities owned and operated by the State of New York and New York City. The Complaint further alleges that COLUMBIA failed to disclose to NIH that it did not own or operate these facilities and that COLUMBIA did not pay for use of the space for most of the relevant period.

...and Columbia University admitted:

COLUMBIA has admitted that it applied the on-campus indirect cost rate to the 423 NIH grants even though the research was primarily performed in space not owned or operated by Columbia, and that it submitted to NIH certified reports that used the on-campus indirect cost rate to calculate the indirect cost amounts claimed by the university.

Ah, those tricky accountants.

Oh. cool. paging down on the complaint we get some specifics:

From July 1, 2003, through June 30, 2015, COLUMBIA’s On-Campus F&A Rate was approximately 61 percent, its Off-Campus F&A Rate was 26 percent, and its Modified Off-Campus F&A Rate was 29.4 percent. The Modified Off-Campus F&A Rate was to be applied to research conducted off-campus but within a certain proximity of the COLUMBIA campus.

Y'know. When I first read this my first thought was that I know some Columbia folks that work off campus at.... oh shit. It's them. It's the drug abuse folks.

COLUMBIA has a collaborative relationship with the New York State Psychiatric Institute (“NYSPI”), a clinical research facility administered by the New York State Office of Mental Health. COLUMBIA faculty perform research in two off-campus buildings owned by the State of New York and operated by NYSPI (the “NYSPI Buildings”). COLUMBIA faculty also perform research in another off-campus building owned and operated by the City of New York (the “City Building”).

For most of the relevant period, COLUMBIA did not pay the State of New York for use of the NYSPI Buildings, and therefore did not incur indirect “facilities-related” costs with respect to the medical research performed in these buildings. Similarly, COLUMBIA did not pay the City of New York for use of the City Building.

Presumably my friends who are the PIs on these grants had no idea. I have no idea what my institution actually charges the NIH as overhead on my grants, all I look at is my direct cost expenditures and balances. But still, sorry to see that it was their research grants that were involved. If nothing else it means that NIDA [Update: I found some details and 22/423 total grants were driect listings from NIDA, although there are what look like subaward identifiers (that may or may not involve other NIDA grants.)] was the entity being ripped off. The settlement was for $9.5 million. It doesn't say how much of this is direct recovery for the fraud and how much is court costs or punishment.

oh, wait. Damn. This looks bad.

COLUMBIA did not state on the applications for the NIH Grants that the research would be primarily performed off-campus, as required. Instead, Columbia frequently included the main address for the College of Physicians & Surgeons in the section of the application that was supposed to list the primary performance location. Even where the NYSPI Buildings or the City Building were listed in that section of the grant application, or mentioned elsewhere in the application, COLUMBIA failed to disclose that these buildings were not owned and operated by the university.

Starting in fiscal year 2009, in lieu of paying rent for use of one of the NYSPI Buildings, the Department of Neuroscience paid NYSPI a portion of the inflated indirect cost recoveries it received from NIH for research projects performed in that building.

This smells a lot more like highly intentional fraud and less like a mistake that someone should have caught. In the pre-award review of the grant, if you ask me. Especially when CU was clearly negotiating the rental arrangements with NYSPI. Someone pretty high up in the office of grants and contracts had to be doing this whole charade intentionally and with planning. There are a handful of other regulatory issues that I don't want to get into which very likely pointed a spotlight on the "performance location" too. This had to be intentional.

Turns out that this was a whistleblower case.

In connection with the filing of the lawsuit and settlement, the Government joined a private whistleblower lawsuit that had previously been filed under seal pursuant to the False Claims Act.

Good for that brave person for bringing this to light.

Final thought: I bet you that Columbia University is not the only NIH funded University out there that pulls some shenanigans like this. Now, you would think that there would be some sort of broad and universal alert sent to the Signing Officials of each University that has an on- and off-campus rate. Telling them to get their act together on this or any future investigation that busts them will automatically have the fines tripled. But going by at least one narrow similar area that I've followed over the past couple of decades (the anti-lobbying / grant writing thing) apparently this does not happen. So keep your eyes peeled for the next decade. I bet there will be more of these and that in each case it will again be figured out only via whistleblower.

43 responses so far

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