Archive for Research News

Supplemental Funding 2008 - and FY09 Budget Projections

From H.R. 2642 (Supplemental Appropriations Act, 2008 - signed into law by our very own Dear Leader on June 30):

For an additional amount for `Office of the Director’, $150,000,000, which shall be transferred to the Institutes and Centers of the National Institutes of Health and to the Common Fund established under section 402A(c)(1) of the Public Health Service Act in proportion to the appropriations otherwise made to such Institutes, Centers, and Common Fund for fiscal year 2008: Provided, That these funds shall be used to support additional scientific research and shall be merged with and be available for the same purposes and for the same time period as the appropriation or fund to which transferred: Provided further, That this transfer authority is in addition to any other transfer authority available to the National Institutes of Health: Provided further, That none of these funds may be transferred to `National Institutes of Health-Buildings and Facilities’, the Center for Scientific Review, the Center for Information Technology, the Clinical Center, the Global Fund for HIV/AIDS, Tuberculosis and Malaria, or the Office of the Director (except for the transfer to the Common Fund).

No word as yet from the Great Zerhouni as to how these funds might be distributed. I’m sure it will be transformative, though.

Now, the NIH is not the only agency celebrating Christmas (or your favorite giving holiday) in July. NASA receives “an additional amount for `Science, Aeronautics and Exploration’, $62,500,000″, while the Department of Energy gets “an additional amount for `Science’, $62,500,000, to remain available until expended.”

The NSF receives a split dividend: “For an additional amount for `Research and Related Activities’, $22,500,000, of which $5,000,000 shall be available solely for activities authorized by section 7002(b)(2)(A)(iv) of Public Law 110-69″ and “For an additional amount for `Education and Human Resources’, $40,000,000: Provided, That of the amount provided, $20,000,000 shall be available for activities authorized by section 10 of the National Science Foundation Authorization Act of 2002 (42 U.S.C. 1862n-1) and $20,000,000 shall be available for activities authorized by section 10A of the National Science Foundation Authorization Act of 2002 (42 U.S.C. 1862n-1a).”

Science provides a nice overview of these goodies as well as current House and Senate versions of the FY09 budget … which won’t see the light of day until well into 2009. For now, a 4% increase for the NIH, and a healthy 13% increase for the NSF. In addition to the big 4 noted above, Science also briefly reviews budget requests for NOAA, NIST, USDA, EPA, and the US Geological Survey.

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Nature on Misconduct

Update: As noted below in Brendan’s comment , open discussion of this issue continues at Nature Network. Please join in there! The Chronicle is also having a lively discussion of “the oath” … and JAMA has a nice summary of why even well-intentioned folks cannot overcome unconscious bias caused by conflicts of interest, and The Lancet notes this commentary in covering a plagiarism case in the UK. Links to The Gallup Organization report on which this commentary is based can be found at ORI and below.

Nature reports a survey conducted by the Office of Research Integrity that, not surprisingly, finds that most misconduct goes unreported. Sandra Titus et al. found that the “2,212 researchers we surveyed observed 201 instances of likely misconduct over a three-year period. That’s 3 incidents per 100 researchers per year.” (an average of only 24 institutional investigation reports are submitted to ORI each year).

Titus et al. contacted 4,298 scientists holding NIH extramural research funds at 605 institutions.

In 2006, we asked participants to indicate the number of times they had observed suspected research misconduct in their own department in the past three academic years (2002–05). 2,212 scientists provided complete responses to questions concerning research misconduct (51% response rate). Of these, 192 scientists (8.7% ) indicated that they had observed or had direct evidence of researchers in their own department committing one or more incidents of suspected research misconduct over the past three academic years. The 192 scientists described a total of 265 incidents.

Scientists were asked to indicate how they became aware of the possible misconduct and were told to report observations and not hearsay. … We used these descriptions to validate whether the observation met the federal definition of research misconduct [fabrication, falsification, plagiarism].

Two people independently coded and evaluated the 265 descriptions to determine whether each met the federal definition of research misconduct. In all, 64 reports (24% of the total) did not meet the threshold of the federal definition — which left 201 observations of potential misconduct made by 164 scientists (7.4% ). These 201 misconduct observations included fabrication or falsification (60% ) and plagiarism only (36% ).

According to our respondents, 58% of the observed incidents had been reported to officials at their institutions.

The authors go on to extrapolate that annually “approximately 1,350 would have been reported [compared with actual number of 24] whereas almost 1,000 could be assumed to go unreported to any official.”

As a fan of work on procedural and distributive justice by Brian Martinson, Melissa Anderson, et al., I was particularly pleased to see the accompanying editorial, Solutions - not scapegoats, address the need to examine the environment as well as the individual:

Meanwhile, misconduct investigations all too often focus solely on an individual offender, and fail to diagnose the environment that has allowed misconduct to flourish. Instead, institutions should seize the opportunity to learn from the experience, and to address the bigger questions. For example, did the atmosphere in the lab create the pressure to cut corners? Or did the intensity of the tenure chase contribute? One way to address such questions might be through internal departmental discussions, in which everyone is free to admit mistakes, and discuss how to fix the problems instead of apportioning the blame.

Indeed, the authors suggest 6 strategies for championing research integrity at an institutonal level:

Adopt zero tolerance: “Social responsibility to the academic community and to the public who fund the research will be strengthened when it is apparent that an institution has a real commitment to integrity.”

Protect whistleblowers: “more than two-thirds of whistleblowers, in a Research Triangle Institute study, experienced at least one negative outcome as a direct result of their actions. Plus, 43% reported that institutions encouraged them to drop the allegation.”

Clarify how to report: Establish “a reporting system that clearly identifies the individuals to whom allegations should be brought, and establishing clear policies, procedures and guidelines related to misconduct and responsible conduct.”

Train the mentors: “Mentors specifically need to become more aware of their roles in establishing and maintaining research rules and minimizing opportunities to commit research misconduct. An institutional investment in building better mentors is an important vehicle to promoting research integrity.”

Use alternative mechanisms: “Auditing research records would be one such means. Mechanisms of review are needed to reduce deficient record keeping, improper protection of human or animal subjects or the utilization of questionable research behaviour.”

Model ethical behaviour: “Institutions successfully stop cheating, for example, when they have leaders who communicate what is acceptable behaviour, encourage faculty members and staff to follow the policies, develop fair and appropriate procedures for handling misconduct cases, focus on ways to develop and promote ethical behaviour, and provide clear deterrents that are communicated.”

In this same issue, Nature also cites the decision of the Ottawa Health Research Institute to suspend Kristin Roovers, whose case ORI closed and reported on last year.

Of course, the lively discussion of the Hellinga retraction is just that - a discussion of the retraction and the science involved, though I suspect we will eventually be discussing more formal issues of misconduct.

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VCU-Philip Morris Agreement Researched

Although the NYT has not printed a correction, clarification, editor’s note, retraction, or any other indication that the veracity of Mr. Finder’s reporting has been called into question, they did offer, rightly, the opportunity for VCU to respond in the form of a letter to the editor from President Trani. This letter, although more thoughtfully articulated than his prior memo, continues to downplay the real problems of any university engaging in research service agreements and the even greater ethical problems with this particular research service agreement, setting aside the sponsor for now.

As part of my commentary on this, I disclose that I have been sent a copy of the agreement obtained by a third party through a Va FOIA request (details below) and will quote verbatim a few critical points omitted by Trani in his letter and overall response to this story.

For example, secrecy (from the agreement itself):

”19. Neither party shall, without the prior written approval of the other party, (i) advertise or otherwise publicize in a written manner the existence or terms of this AGREEMENT or any TASK ORDER or any other aspect of the relationship between SPONSOR and VCU … If at any time a third party, including without limitation any news organization, contacts VCU concerning SPONSOR, VCU shall make no comment and shall notify promptly SPONSOR of the third party.”

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CTSA Consortium Expanded

So, last October I had a little fun working out the logic for my office pool picks for the next CTSA sites. Today we learn that 14 new sites have joined the consortium:

Albert Einstein College of Medicine of Yeshiva University (New York City)
Boston University (Boston)
Harvard University (Cambridge, Mass.)
Indiana University School of Medicine (Indianapolis)
Northwestern University (Chicago and Evanston, Ill.)
The Ohio State University (Columbus, Ohio)
The Scripps Research Institute (La Jolla, Calif.)
Stanford University (Palo Alto, Calif.)
Tufts University (Boston)
The University of Alabama at Birmingham (Birmingham, Ala.)
University of Colorado Denver (Aurora, Colo.)
The University of North Carolina at Chapel Hill (Chapel Hill, N.C.)
The University of Texas Health Science Center at San Antonio (San Antonio)
The University of Utah (Salt Lake City)

I only missed Scripps, but they have a heck of a lot of collaborating sites (including, interestingly, the Center for Applied Genomics at CHOP - Children’s Hospital of Philadelphia …)

Only 22 spots remaining in the Consortium. Who’s left?

UCLA, UMd, UMinn, Georgetown, Medical College of Wisconsin, NYU, SUNY Stony Brook, U Cinncinati, U Florida, U South Florida, U Tennessee, Baylor, Penn State, UCSD, U Vermont , U Illinois-Chicago , MUSC , U Missouri, UNM, Dartmouth, LSU, U Arkansas, U Hawaii, U Kansas, U Kentucky, U Louisville, U ND, U Oklahoma, UVa

Plus, I’m sure, at least a dozen or so not named here, such as an Arizona contingent, U Nebraska, a Mountain State rep, (never mind - the KY & TN sites would cover Appalachia), et al. (and then there is VCU with their corporate partner Philip Morris USA)

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Secret Smoke-Filled Agreements

Update: I’ve discussed President Trani’s letter to the NYT above. And perhaps this NYT article explains how this all could have happened.

Update: Outstanding Blog Entry by an VCU Adjunct Professor summarizing the many (& snowballing) unethical activities going on in Richmond (and a great follow-up commentary here as well).

The NYT today reports on an astoundingly unethical and outrageous research agreement between VCU (Virginia Commonwealth University) and Philip Morris USA. The need to deny existence of this agreement if asked by the press … the ability of Philip Morris to remove everything but prepositions from journal manuscripts and any other form of dissemination … the pre-assignment to the company of intellectual property generated. Jiminy Crickets.
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Cont’d Hellinga Fall-Out (May 2008)

Ugh. Nature summarizes the continued (& spreading) negative repercussions of the retracted Dwyer et al. papers discussed here and throughout the scientific community. An excellent Nature feature article by Erika Check Hayden covers the entire saga in detail.

Earlier, our man-on-the-spot David added a nice summary of an article in the May 5, 2008 issue of Chemical & Engineering News, including a bit more insight from John Richard in Buffalo and Hellinga’s dismissive reply (thanks so much, David, for all your contributions).

Nature notes that Richard and his group “wasted seven months and tens of thousands of dollars failing to reproduce the results from Hellinga’s lab” and that Mary Dwyer’s scientific career is over before it started. The editors also observe the questionable rationale in Hellinga’s accusing her of scientific misconduct: “As Dwyer’s adviser, Hellinga was responsible for training her. If she made mistakes, they are ultimately his responsibility.”

And, Nature spreads the wealth by noting that Duke itself owes something to the scientific community, and indeed, one hopes they are not holding their breath and hoping this will blow over so Hellinga can get back to the business at hand: bringing in research dollars to the University.

Earlier discussion can be read first here (initial Science retraction and detailed comments on problems with the science involved) and then here (The Scientist blog coverage, Chemical & Engineering News synopsis, et al.).

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Bridge Over Troubled Waters

The Scientist discusses a case study of a budget-crunch-induced lab closure, the personal and professional fall-out, and the concept of intramural bridge funding. In this case study, the PI (at Man’s Greatest Hospital) received a couple of Type 1 R01s during the NIH budget doubling that were not scored (article refers to them being returned without review - I assume she means without discussion/score) as Type 2s, resulting in funding loss … personnel loss … job changes … the works. Very interesting & engaging series of comments in response as well.

Historically, Type 2 R01s (competing renewals) enjoy roughly twice the success rate of Type 1s: 49.1% vs 24.5% in 2002 … 42.1% vs 20.0% in 2004 … 33.5% vs 16.3% in 2006. Hence the encouragement to pursue R01 vs R21 or R03 funding if possible (since the latter non-renewable mechanisms cannot take advantage of this higher success rate for Type 2s). In 2007, the gap narrowed a tad, with 36.1% success rate for Type 2 vs 19.2% for Type 1. As The Scientist points out, this meant 4,108 Type 2 applicants ended FY07 with out an award in hand.

I was pleased to see The Scientist feature institutional bridge funds. I strongly feel no research institution with a shred of integrity can get by operating without such a mechanism in place and transparent criteria for evaluating requests and distributing funds (distributive & procedural justice). These institutions gladly take the indirect costs their investigators bring in (70% at Dana Farber! and when I left another HMS teaching hospital in the late 80s, it was at … 92.3%!!! compared with a paltry 49% here at Baby It’s Cold Outside). In a cut-throat climate, they also dangle the damnedest recruitment packages to lure/buy funded researchers from other institutions. They better be ready to step up to the plate when the loyal productive PIs need help weathering the storm.

Apparently the Dana Farber will help those with scores within the 15th percentile that still weren’t funded. Baby It’s Cold Outside gives some weight to the percentile but just as much to the summary statement (some scores are outliers due to easily fixable application weaknesses rather than lack of productivity or scientific significance), the PI’s response to the critiques, and other funding sources. Budget requests must be prioritized, with students who need support in that particular lab for that particular project to finish up experiments for their thesis or dissertation receiving the highest priority. Maintaining a specialized animal model/pedigree or ensuring data collection continuity for a clinical cohort rank up there as well. Explicit reviewer requests for specific data to include in the amended application can qualify as bridge worthy. So, some strategies to consider for those of you trying to make a case for internal bridging monies at your home institution.

As discussed here last spring, NIH R56 bridge awards are also available, not via direct application by the affected PI but by recommendation of program directors and ICs. Last January, the Great Zerhouni reissued official notice of the NIH Director’s Bridge Awards. Usually program officers nominate their best & most worthy PIs without saying anything to said PI (so as not to get hopes up, especially when people’s careers are at stake in many cases) … but they shouldn’t mind if you send a quick e-mail reminding them that your A0 was really close and you could sure use a funding safety net until the A1 or A2 is awarded. Now, if your application was more than 10 percentile points above the current payline, probably not much they can do (don’t even think about asking about R56 support for an unscored application).

As I type this, it occurs to me that the case study in The Scientist was unscored but still received $50K a year for 2 years from the MGH as bridge fund grants, so clearly they have more liberal standards than the Dana Farber … or the NIGMS … as well.

Next week, I check out Life on Mars. Maybe it will look better on the red planet.

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How to Succeed in Science: a Concise Guide

In Nature Reviews Molecular Cell Biology, NIAID’s Jonathan Yewdell invites those looking for research career advice in the biomedical sciences to “take a study break, grab a cup of coffee and read on.”

He offers his series “How to succeed in science: a concise guide for young biomedical scientists” in 2 parts.

In the May issue, Part I: taking the plunge, where he provides “unvarnished [not as unvarnished as PP's though] advice for young biomedical scientists on the difficulties that lie ahead and on how to find the right laboratories for training in the skills that you will need to succeed.”

In the June issue, Part II: making discoveries, where he provides “practical advice to young scientists on choosing a research topic, designing, performing and interpreting experiments and, last but not least, on maintaining your sanity in the process.”

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Fixing Near-Miss Grant Applications

So you have that priority score that is frustratingly close but no cigar. In fact, your program officer may have held out hope for last minute Council support … but no. What to do?

Case Study:

R21 receives a priority score of 138, 11th percentile (think about this a moment folks - 138 … 11th percentile?) … concerns are incredibly minor, including a quibble over word choice (discussed!). Think, use of sex vs gender appropriately. Not relevant to the science at all. However, this A0 is not funded.

The PI takes the Neuro-conservative zen view on resubmission (First, Do No Harm), including a clean, simple apology for the errant word usage. Remember, this is an R21 with only a 1-page introduction.

The A1 receives a priority score of 107, 0.1st percentile, with the following comments in the summary of discussion: “The proposal is significantly bolstered by the thorough responsiveness to minor concerns from the previous review and with the addition of new preliminary data. … the committee was unanimous in their high enthusiasm for this outstanding application.” Obviously.

So, the PI kept collecting data, did not change anything in the Specific Aims or, that I can recall, in the Background & Significance … did streamline one set of experiments thanks to a recent innovation in the lab.

In this case, I don’t think the program officer was a fount of insight, but I would recommend starting there if not enough guidance for the resubmission is communicated in the resume & summary of discussion. Hopefully your program officer heard or heard of the discussion and can offer pointers for what to address. I’ve seen scores of summary statements for just about every grant mechanism and IC, though, and usually the opening discussion paragraph (for scored applications) throws the PI a bone for preparing an amended application.

Certainly a pristine, laser-focused introduction sans color commentary is critical. Citing new reports in the literature as appropriate (especially by study section members) and of course tying in new data (even better, a new manuscript accepted/published) you have will show reviewers you are committed to seeing this work through in a sound, scientific manner. Appropriately integrating new data from the literature and/or your lab in the research design and methods (additional rationale for your approach, consideration as an alternative approach, insight into potential pitfall or divergence in outcome, etc.) will further increase reviewer enthusiasm. If your IC (institute/center) has a new strategic plan or programmatic priority in line with your proposal, point this out as well. The key is not to open yourself up for potential target practice with the insertion of a new theory or premise or methodology. And, of course, not to get in a pissing match with the study section.

I’m sure comments from yuns will add a battery of great suggestions. I find it difficult to offer blanket advice on this sort of situation without knowing the application and its history. Grantsmanship instruction is available freely everywhere … the key is to get good input on your application specifically rather than try to fix it in a vacuum, no matter how many grant-writing workshops you’ve attended or Websites you’ve clicked through. An army of one was never less likely to succeed as in the battle for grant funding.

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Hellinga Retraction Update

Latest Discussion can be read/joined here.

I wanted to thank David for his many comments in the ongoing discussion of the Dwyer et al. retractions, including his pointing out that the 2007 Journal of Molecular Biology article from this group was also formally retracted and, most recently, two enlightening electronic letters to Science (particularly the one from Dr. Richard at SUNY Buffalo) on this case.

And yet another update via David in the main thread on this retraction:

“One very interesting section of Andrea’s [Gawrylewski, The Scientist] blog entry that has not appeared online before is that “Shortly after the original paper appeared in Science in 2004, Hellinga went to give a seminar in Berkeley to present his new findings. [Jack] Kirsch said he brought up the issue with the Km and asked to see Hellinga’s data but never received it.” Yet another lesson to learn from this whole fiasco.”

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