Thought of the Day

(by drugmonkey) Mar 05 2015

This is about the cognitive dissonance involved with realizing your part in a collective action.

It is about the result of a slowly evolving cultural hegemony.

It is about the tragedy of the commons and the emergent properties of systems that depend on the decisions of individual self-interested actors.

It is not all about Snidely Whiplash figures intentionally committing egregious, knowing acts of thievery and sabotage.

We need to be very clear about this or it devolves into useless fighting about personal responsibility for things that are not the direct result of highly specific individual acts.

5 responses so far

Harold Varmus is stepping down from the NCI Director position

(by drugmonkey) Mar 04 2015

His letter to the NCI community is here.

Finally, when I return to New York City full time on April 1st, I will establish a modestly sized research laboratory in the Meyer Cancer Center at the Weill-Cornell Medical College...

Harold Varmus is 75 years old. I will be very fascinated to see if his idea of "modestly sized" accords in even the slightest with what I think of as a modest laboratory operation.

18 responses so far

Gen X will never live up to its scientific potential

(by drugmonkey) Mar 04 2015

The NIH Director, Francis Collins, was speaking to Congress this week and was widely quoted as lamenting the fate of junior scientists. As per this Sam Stein bit in HuffPo:

“This is the issue that wakes me up at night when I try to contemplate the future of where biomedical research can go in the United States,” Collins said. “They are finding themselves in a situation that is the least supportive of that vision in 50 years. They look ahead of them and see the more senior scientists struggling to keep their labs going and suffering rejection after rejection of grants that previously would have been supportive. And they wonder, 'Do we really want to sign up for that?' And many of them, regrettably, are making the decision to walk away.”

Obviously he is talking about trainees and perhaps the very newest of assistant professors, aka ESI qualified NIH applicants.

This goes along with a continued trend from the NIH. To wring their collective hands over those who are in their mid to late 30s and younger. To take some steps to help them out, most definitively with special paylines for the Early Stage Investigators who must be no more than 10 years away from the PhD award. To nod sagely about "eating our seed corn" as if they have the slightest clue what that might mean and whether it actually applies here (it doesn't).

It ignores another trend from the NIH, i.e. working busily to shore up the ability of the oldest guard of scientists to remain funded. You know about the Emeritus award they are considering. You have observed how well the very oldest slice of our PI applicant pool is treated at study section. And you have seen how NIGMS, the IC most serious about this workforce stability stuff*, put the oldsters at the front of the line with their MIRA initiative. Of course, the second in line (and in fact the only ones in line) for this little MIRA project are, you guessed it, ESIs.

We plan to issue a MIRA funding opportunity for early stage investigators as quickly as possible. We hope the first application due date will be sometime this summer.

As per usual, the demographic of the mid-career investigator is overlooked.

One of the comments on the NIGMS MIRA post is heart breaking and incredibly truthful. BioScientist wrote:

However, I have genuine concerns about the idea to roll it out first to either well-funded labs or early stage investigators. From what I can see, where it is most needed is in mid-career labs that do not have multiple R01’s, which in many cases are imploding in the present environment. These are the PI’s who are writing 10 grants to get 1 funded right now. The well-funded empires are doing just fine, and I have not found the PI’s of such labs to be the egalitarian types would would give up a dime so that someone else could keep a lab running.

For ESI’s, this could be an interesting experiment in how to launch successful careers. Many of us who endured the system of the last decade are discouraged and demoralized. Personally, I will never live up to my scientific potential after so many years of wasting time on failed proposals and preliminary results for projects that were never funded.

emphasis added. As if I have to do so.

Do you wonder why the current greybearded and silver haired people who remain powerful in science are so keen to cry over the poor, poor Millennial generation of scientists and wring their hands over the future of science, all the while doing nothing about the present of science?

Because the Boomers (and a few years' worth of pre-War folks) cannot acknowledge what they have done to the Gen X scientists. Some of the charges are as follows.

1) Extended graduate school training from 4 years to 6+. Sure they used all sorts of very truthy sounding excuses about mastering different domains, getting those three publications in CNS journals, the collaborative nature of vertically ascending science, etc. But they accomplished it...and their own successes prove it unneeded.

2) Extended postdoctoral "training". The moved us from where even two years as a postdoc prior to professorial appointment was slightly suspicious (in the early to mid 1970s) to a situation in which two sequential 3-5 year postdocs are viewed as the necessary minimum (just a few years ago, prior to the ESI foofraw). The oldest generation oversaw this.

3) Even during the NIH doubling, they grabbed all the grants and kept beating up the newly appointed GenX scientists with Stock Critiques, sent them around the airport traffic pattern in endless revisions and with "good scores" that were clearly unfundable. Anything to delay entry and preserve their expanding empires.

3) The R29 FIRST was dismantled** but was replaced by a NI check box. It supposedly took the oldster power brokers 10 years to realize was to the benefit of, you guessed it, themselves. I.e. those highly established scientists that simply didn't have NIH funding yet. It took me about 3 hours of my first study section meeting to see this.

4) ...aaaand what do you know? By the time the old guard power brokers "realized" this NI problem, they were able to fix it with a time-limited ESI designation tagged to the time of PhD award, instead of the time of Asst Prof appointment. This conveniently skipped right over the Gen X scientists.

So what did this accomplish? Well, on the trainee end of the screw-job this just meant more time in which a venerated or even hard charging mid career lab head could benefit from the intellectual contributions of the Gen X scientists. Pretty much like intellectual vampires. The crediting system whereby author lines expanded and the senior author got all the glory was refined and elaborated from the 1990s through the Naughties as the NIH budget doubled. The number of "postdocs" supported on research grants soared through the roof. And the new models, conceptual breakthroughs and new theoretical approaches continued to give subsequent grant largesse and subsequent paper / finding laurels to the lab head. While the Gen X scientists continued as postdocs, or were shelled out of the system or manged to get a job but couldn't get funded very easily.

I was there. I know who did the actual work in the labs in my fields of interest. I know the way a finding or paper or model resulted in the lab head having copious funding for a decade and a half, verging on two decades now. I know which of those scientists of my generation failed to make it big. There are a lot of them that will never achieve their promise. A lot who had to bail entirely on the career after what would have been a career-making paper as a trainee, if they were just a generation older. I can point to very few of the Gen X people in my fields of closest interest who have hit mid career with anything like the funding, verve and accomplishment of even some of the more, shall we say, pedestrian*** members of the generation just prior to mine****. Actually, come to think of it, I am hard pressed to point to a single one.

I am not suggesting the older folks who benefited had no right to do so. I am not saying they didn't deserve any credit, nor am I claiming they didn't contribute intellectually.

At all.

I am saying that they (as a generation) arranged things so that they got ALL OF the credit and benefit of the collaborative breakthroughs. And this is not right. They did not suffer a similar fate at the hands of their more-senior colleagues because times were very different. Expansive. Lab sizes were smaller and the trainees were more consistently encouraged to fly away and shine on their own. This is what happened through the 70s and 80s when they were transitioning. And yet they have the nerve to call us riff raff. To question our commitment to science in oh so many ways. To continue to credit themselves for breakthroughs and advances that rested on the intellectual labors of a younger generation that they now disparage.

Some of us are surviving. Yes. This is obvious. Some of us are thriving. Some of us squeaking by on fumes and prayers. Some Most of us yo-yo between these extremes.

As the comment said, however, we will never reach our potential as scientists. Not in the way we witnessed the generation or two before us reach theirs. Not as a generation and not as the vast majority of individuals. Ever. It cannot be recovered.

Do you wonder why we are angry at each and every NIH initiative that comes down the pike that is explicitly designed to skip over our generation of scientists, yet again?

This is why.

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*yeah. This is as good as it gets.

**for good reason, it had problems

***to be clear, I count myself in this category

****Who managed to get past the noob-abuse and hazing ritual juuuuuuust as the doubling hit stride. This is the generation that managed to land the last few R29s, for reference*****.

*****In truth, those who were never eligible for either R29 or ESI designation makes a much better and tighter demarcation than Gen X versus the Boomers and Millennials when it comes to this stuff. But it is pretty damn inside baseball to use such terms....

Related Reading: Does anybody want to be president? Anyone?

79 responses so far

The plot thickens...

(by drugmonkey) Mar 03 2015

for those of you poor souls who do not understand Twitter. like PP.

5 responses so far

Neuroscientists: Start Electing Advocates

(by drugmonkey) Mar 03 2015

NamasteIshIconThe following is a guest post from Namaste. Ish. Previously known as the bluebird of happiness, My T. Chondria. Stuff happened. The kitten walked away. Deal with it.


WANTED: Outspoken advocates for neuroscience research who is not afraid to ruffle a few feathers, call Congress Critters out on the current implosion of science funding and opportunities for trainees.

QUALIFICATIONS: Membership in the Society for Neuroscience.

JOB DESCRIPTION: The Society seeks “Leaders who best represent the interests and needs of the membership.”

SFN-NamasteishFig

With over 40,000 members, I look at the presidents of the SfN and wonder; do these people represent my interests and needs? I mean, do I have common struggles with folks in the National Academy, with HHMI status who have unfettered access to top tier journal editors and members of NIH Council? The answer is no, as I imagine it is for most of you.

Admittedly all of the people have made extraordinary contributions to neuroscience research, and have mentored countless outstanding scientists but this is not the job. The job is advocacy and I’m unimpressed.

I did a little experiment and searched Google News for 10 of the last presidents and came up with a rather unimpressive 40 events in which the lot of them had touted science (other than their own work) in any mainstream media outlet. These folks are putting out their semi annual newsletters and gaining ZERO traction in the real world. We can’t afford to preach to the choir any longer. We need people who will use a broad array of social media, PR and outreach tools to get the message across immediately.

I don’t know a single event around the SfN meeting in which the President or Counselors talk openly with the public, invite lawmakers to the meeting and chaperone them thru the day highlighting our biggest and most exciting stories as well as our most personal struggles as a community. We need these things to survive. We do not live in a culture that embraces science and education and where rational thought is valued. I know for sure we won’t get there by sending newsletters to ourselves. I would go so far as to argue that some of the past presidents are part of the problem we currently have in science. There are past SfN presidents in their late 70’s and beyond who still hold faculty appointments, are getting grants, holding onto research space, dollars and trainees when the market has a glut of young talent and few job vacancies.

NIH cannot petition Congress for money. So your society presidents and counselors need to be doing this and facilitating ways for us to do it as a group. We can no longer afford to be handing out these jobs as yet another feather in the caps of BSDs. Anyone who thinks we should need look no further than the ASBMB who ended up with Steve McKnight as a president who promptly used his column to tell the wee folks of science they are not worthy of performing NIH reviews or judging his work.

Nominate someone who will do better and represent you here. By Friday.

30 responses so far

The Journal of Neuroscience needs to explain the author ban

(by drugmonkey) Mar 03 2015

I agree with the following Twitter comment

Insofar as it calls for the Editorial Board of the Journal of Neuroscience to explain why it banned three authors from future submissions. As I said on the prior post, this step is unusual and seems on the face of it to be extreme.

I also said I could see justification for the decision to retract the paper. I say that also could stand some explanation, given the public defense and local University review decision.

5 responses so far

For anyone sick of all the jackclammery of their profession today. You know who you are.

(by drugmonkey) Mar 02 2015

No responses yet

The Journal Ban Hammer: Nastier implications

(by drugmonkey) Mar 02 2015

There is one thing that concerns me about the Journal of Neuroscience banning three authors from future submission in the wake of a paper retraction.

One reason you might seek to get harsh with some authors is if they have a track record of corrigenda and errata supplied to correct mistakes in their papers. This kind of pattern would support the idea that they are pursuing an intentional strategy of sloppiness to beat other competitors to the punch and/or just don't really give a care about good science. A Journal might think either "Ok, but not in our Journal, chumpos" or "Apparently we need to do something to get their attention in a serious way".

There is another reason that is a bit worrisome.

One of the issues I struggle with is the whisper campaign about chronic data fakers. "You just can't trust anything from that lab". "Everyone knows they fake their data."

I have heard these comments frequently in my career.

On the one hand, I am a big believer in innocent-until-proven-guilty and therefore this kind of crap is totally out of bounds. If you have evidence of fraud, present it. If not, shut the hell up. It is far to easy to assassinate someone's character unfairly and we should not encourage this for a second.

Right?

I can't find anything on PubMed that is associated with the last two authors of this paper in combination with erratum or corrigendum as keywords. So, there is no (public) track record of sloppiness and therefore there should be no thought of having to bring a chronic offender to task.

On the other hand, there is a lot of undetected and unproven fraud in science. Just review the ORI notices and you can see just how long it takes to bust the scientists who were ultimately proved to be fraudsters. The public revelation of fraud to the world of science can be many years after someone first noticed a problem with a published paper. You also can see that convicted fraudsters have quite often continued to publish additional fraudulent papers (and win grants on fraudulent data) for years after they are first accused.

I am morally certain that I know at least one chronic fraudster who has, to date, kept one step ahead of the long short and ineffectual arm of the ORI law despite formal investigation. There was also a very curious case I discussed for which there were insider whispers of fraud and yet no findings that I have seen yet.

This is very frustrating. While data faking is a very high risk behavior, it is also a high reward behavior. And the risks are not inevitable. Some people get away with it.

I can see how it would be very tempting to enact a harsh penalty on an otherwise mild pretext for those authors that you suspected of being chronic fraudsters.

But I still don't see how we can reasonably support doing so, if there is no evidence of misconduct other than the rumor mill.

5 responses so far

Banning authors once a paper is retracted from the journal?

(by drugmonkey) Mar 02 2015

A post at Retraction Watch alerts us to to a paper retraction at the Journal of Neuroscience. The J Neuro notice on this paper reads:

The Journal of Neuroscience has received notification of an investigation by the Perelman School of Medicine at the University of Pennsylvania, which supports the journal's findings of data misrepresentation in the article “Intraneuronal APP, Not Free Aβ Peptides in 3xTg-AD Mice: Implications for Tau Versus Aβ-Mediated Alzheimer Neurodegeneration” by Matthew J. Winton, Edward B. Lee, Eveline Sun, Margaret M. Wong, Susan Leight, Bin Zhang, John Q. Trojanowski, and Virginia M.-Y. Lee, which appeared on pages 7691–7699 of the May 25, 2011 issue. Because the results cannot be considered reliable, the editors of The Journal are retracting the paper.

From RetractionWatch we learn that the Journal has also issued a submission ban to three of the authors:

According to author John Trojanowski ... he and Lee have been barred from publishing in Journal for Neuroscience for several years. Senior author Edward Lee is out for a year.

This is the first time I have ever heard of a Journal issuing a ban on authors submitting papers to them. This is an interesting policy.

If this were a case of a conviction for academic fraud, the issues might be a little clearer. But as it turns out, it is a very muddy case indeed.

A quote from the last author:

In a nut shell, Dean Glen Gaulton asserted that the findings in the paper were correct despite mistakes in the figures. I suggested to J. Neuroscience that we publish a corrigendum to clarify these mistakes for the readership of J Neuroscience

The old "mistaken figures" excuse. Who, might we ask is at fault?

RetractionWatch quotes the second-senior author Trojanowski:

Last April, we got an email about an inquiry into figures that I would call erroneously used. An error was made by [first author] Matt Winton, who was leaving science and in transition between Penn and his new job. He was assembling the paper to submit it, there were several iterations of the paper. One set of figures was completely correct – I still don’t know what happened, but he got the files mixed up, and used erroneous figures

Winton has apparently landed a job as a market analyst*, providing advice to investors on therapeutics for Alzheimer's Disease. Maybe the comment from Trojanowski is true and he was in a rush to get the paper off his desk as he started the new job**. Maybe. Maybe there is all kinds of blame to go around and the other authors should have caught the problem.

Or maybe this was one of those deliberate frauds in which someone took shortcuts and represented immunohistochemical images or immunoblots as something they were not. The finding from the University's own investigation appears to confirm, however, that a legitimate mistake was made.

...so let us assume it was all an accident. Should the paper be retracted? or corrected?

I think there are two issues here that support the Journal's right to retract the paper.

We cannot ignore that publication of a finding first has tremendous currency in the world of academic publishing. So does the cachet of publishing in one Journal over another. If a set of authors are sloppy about their manuscript preparation, provide erroneous data figures and they are permitted to "correct" the figures, they gain essentially all the credit. Potentially taking credit for priority or a given Journal level away from another group that works more carefully.

Since we would like authors to take all the care they possibly can in submitting correct data in the first place, it makes some sense to take steps to discourage sloppiness. Retraction is certainly one such discouragement. A ban on future submissions does seem, on the face of it, a bit harsh for a single isolated error. I might not opt for that if it were my decision. But I can certainly see where another scientist might legitimately want to bring down the ban hammer and I would be open to argument that it is necessary.

The second issue I can think of is related. It has to do with whether the paper acceptance was unfairly won by the "mistake". This is tricky. I have seen many cases in which even to the relatively uninformed viewer, the replacement/correct figure looks a lot crappier/dirtier/equivocal than the original mistaken image. Whether right or wrong that so-called "pretty" data change the correctness of the interpretation and strength of the support, it is often interpreted this way. This raises the question of whether the paper would have gained acceptance with the real data instead of the supposedly mistaken data. We obviously can't rewind history, but this theoretical concern should be easy to appreciate. Maybe the Journal of Neuroscience review board went through all of the review materials for this paper and decided that the faked figure sealed the acceptance? For this concern it really makes no difference to the Journal whether the mistake was unintentional or not, there is a strong argument that the integrity of its process requires retraction whenever there is significant doubt the paper would have been accepted without the mistaken image(s).

Given these two issues, I see no reason that the Journal is obligated to "abide by the Penn committee’s investigation" as Trojanowski appears to think they should be. The Journal could accept that it was all just a mistake and still have good reason to retract the paper. But again, a ban on further submissions from the authors seems a bit harsh.

Now, I will point out one thing in this scenario that chaps my hide. It is a frequent excuse of the convicted data faker that they were right, so all is well. RetractionWatch further quotes the senior author, Lee:

...the findings of this paper are extremely important for the Alzheimer’s disease field because it provided convincing evidence pointing out that a previous report claiming accumulation of intracellular Abeta peptide in a mouse model (3XFAD) is wrong (Oddo et al., Neuron 2003), as evidenced by the fact that this paper has been cited by others for 62 times since publication. Subsequent to our 2011 J. Neuroscience paper, others also have found no evidence of intracellular Abeta in the 3XFAD mice (e.g. Lauritzen et al., J. Neurosci, 2012).

I disagree that whether the figures are correct and/or repeatable is an issue that affects the decision here. You either have the correct data or you do not. You either submitted the correct data for review with the manuscript or you did not. Whether you are able to obtain the right data later, whether other labs obtain the right data or whether you had the right data in a mislabeled file all along is absolutely immaterial to whether the paper should be retracted.

The system itself is what needs to be defended. Because if you don't protect the integrity of the peer review system - where authors are presumed to be honest - then it encourages more sloppiness and more outright fraud.

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*An interesting alt-career folks. One of my old grad school peeps has been in this industry for years and appears to really love it.

**I will admit, my eyebrows go up when the person being thrown under the bus for a mistake or a data fraud is someone who is no longer in the academic science publishing game and has very little to lose compared with the other authors.

22 responses so far

Is your NIH PO a little....grouchy?

(by drugmonkey) Feb 27 2015

Another one, paraphrased from multiple correspondents:

Dear DM: 
is it just me or are all the POs getting increasingly grouchy and unhelpful?

A. Reader

I am not certain, since I hardly have a representative sample. But I'd say no, this is probably just a bad run for you.

When encouraging you to interact with your Program Officer(s) I tend to emphasize the useful interactions that I have experienced. Consequently I may fail to convey that most of the time they are going to be unhelpful and even discouraging.

Try to see it from their position. They hear from dozens of us, all complaining about some dirty review deed that was done to our application and looking for help. Round after round, after round.

They cannot help everyone.

So take it in stride, as best you can, when you get a seemingly dismissive response. This same PO may become your best advocate on the next one*.

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*and then treat you like effluvium again after that. It's happpened to me, I can tell you.

36 responses so far

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