What does a retracted paper mean?

I’ve been having a little Twitt discussion with Retraction Watch honcho @ivanoransky over a recent post in which they discuss whether a failure to replicate a result justifies a retraction.
Now, Ivan Oransky seemed to take great umbrage to my suggestion in a comment that there was dereliction in their duty to science to intentionally conflate a failure to replicate with intentional fraud. Per usual, we boiled it down to a fundamental disagreement over connotation. What it means to the average person to see that a paper is retracted.
I rely upon my usual solution, DearReader. Select all choices that apply when you see a retraction or that you think should induce a retraction.

A retracted paper meansonline survey

Direct link to the poll in case you can’t see it.
My position can be found after the jump….

IOM Committee on Chimpanzee Research

The Nature News Blog has a bit on the recent meeting of the Committee on the Use of Chimpanzees in Biomedical and Behavioral Research. The NIH commissioned the Institute of Medicine to:

Explore contemporary and anticipated biomedical research questions to determine if chimpanzees are or will be necessary for research discoveries and to determine the safety and efficacy of new prevention or treatment strategies. If biomedical research questions are identified:

Describe the unique biological/immunological characteristics of the chimpanzee that make it the necessary animal model for use in the types of research.
Provide recommendations for any new or revised scientific parameters to guide how and when to use these animals for research.

Explore contemporary and anticipated behavioral research questions to determine if chimpanzees are necessary for progress in understanding social, neurological and behavioral factors that influence the development, prevention, or treatment of disease.

I was struck by a comment reported by the Nature News blog from a participant who objected to the scope of the study.

Repost: An Honor Codes’ Second Component and Research Science

This post originally appeared at the old site Oct. 4, 2007.

---

Many academic honor codes boil down to two essential statements, namely “I will not cheat and I will not tolerate those who do“. For “cheat” you may read any number of disreputable activities including plagiarism and research fraud. My alma mater had this sort of thing, I know the US military academies have this. Interestingly a random Google brings up some which include both components (Davidson College, Notre Dames, Florida State Univ (which as been in the academic cheating news lately), and some which do not (CU Boulder, Baylor); Wikipedia entry has a bunch of snippet Honor Codes. The first component, i.e. “don’t cheat” is easily comprehended and followed. The second component, the ” I will not tolerate those who do” part is the tricky one.

On Conflicts of Interest

There’s a quote that will show up on the rotator over there on the left that I found at Ed Brayton’s place. It reflects the confusion that the reasonable heterosexual man typically feels over the (US) right-wing idealogue talking points about “making” people gay. You know, by extending them rights, admitting that they exist, refusing to bash them, etc, the social fabric is apparently constructing gay people out of heterosexual cloth. This rejoinder is pitch perfect.

I’m not going to say that all homophobes are closeted homosexuals. I just want to point out that anyone who thinks social pressure is all that keeps straight men from forsaking women to pursue other men has no idea what it’s like to be a straight man.

I have a similar response to people like Psi Wavefunction who write:

That is, your results should probably be of a kind that would encourage further funding in your field. Presumably, if you get funding for environmental topics, you’d be better off with results stating your Cute Fluffy Animal is on the brink of extinction rather than ‘oh it’s doing fine’. In that particular case, who the hell is going to dump more money into Cute Fluffy Animal research if it’s not under some sort of threat? Conflict of interests much?

What? Okay, beyond the point of whether scientists might actually believe that Cute Fluffy Animals are on the brink of extinction based on their research and that of their subfield, we have the usual bullshit allegation that scientists just go out and “prove” what their funding agencies want to hear.
It makes me wonder, if a person really believes this, whether they have any idea what it actually means to be a scientist. Now in the case of my usual opponents from the legalize-eet perspective, agreed, they don’t know what it means to be a scientist because they are not scientists. No worries, we should probably shoulder the task of explaining to them how our lives work. For someone who appears to fancy themselves a science blogger though? hmm.

Even blogging about research papers is sensitive, especially within your own field. You have to balance opinion, factual accuracy and style without offending the authors. Some bloggers find it perfectly sensible to unleash a tirade against some paper they don’t like, but I’d prefer not to sever potential relationships with people I’ve never met, even if I do think their paper is a piece of crap. Primarily for selfish reasons: at this point, I’m in no position to start collecting enemies in academia. Or anywhere, really.
If I were a truly independent blogger, that wouldn’t fucking matter, and I’d probably make a point of devouring every crappy paper I come across for shits and giggles.

So 1) speak for yourself and 2) what is UP with these people who assert what nasty nefarious behavior they would get up to if only they had some cover? Seriously?
This ties into the usual allegations from out-bloggers about pseud-bloggers. This unproven assertion that all this nasty id-based behavior is almost impossible to resist, save the social embarrassment of providing one’s own name.
If this is what you really believe then you have no idea what it means to have an intrinsic professional, moral and ethical center.

Conflict for NIH Funded Bloggers

Greg Laden raises a decent question* amid the PepsiBlogs kerfuffle what with his reflexive need to take potshots at his perceived blog enemies and all .

Somewhere in the middle are blogs written by scientists at MRU’s who are mostly funded by some major single source (NIH, Big Pharm, … maybe even Pepsico???) but who, since they are either indy or pseudo, are different than a corporate sponsored blog.

I’m pretty sure I’m the blogger that takes the most heat for NIH funding conflict of interest, because of my topic domain. I’ll have to dredge up the links later because they are not overwhelmingly common.
The charge comes from people who don’t like my comments about the possible health risks of recreational drugs, most typically when I am talking about cannabis. It comes in two basic flavors.

More evidence that the NIH has no interest in curbing real COI

At all.
ScienceInsider overviewed a dismal story being reported by The Chronicle of Higher Education. It involves a tale I’ve discussed before with a new twist. ScienceInsider:

In 2008, a Senate investigation found that Nemeroff failed to report at least $1.2 million of more than $2.4 million that he had received for consulting for drug companies. NIH suspended one of Nemeroff’s grants, and in December 2008, Emory announced that it would not allow Nemeroff to apply for NIH grants for 2 years.

As I was just saying, this is the scope of the real problem. Changing the reporting rules from $10K per year to $5K per year does absolutely nothing about a guy who fails to report some or all of his outside activity.
Still, a 2 year suspension sounds like something, doesn’t it?

Why NIH tightening financial rules will do absolutely nothing about real COI

NIH has been touting their new and improved reporting rules which are intended to keep their grantee PIs on the straight and narrow. A news bit in Nature has the highlights.

The proposed rules state that a “significant financial interest” exists when the combined value of an investigator’s equity holdings in, and payments from, a publicly traded company exceed US$5,000 in any given year. Under current rules, the reporting threshold is $10,000.

Got it. Somewhere between $5,000 and $9,999 per year in consulting or stock cashout or dividends or whatnot we have a big group of PIs out there doing bad things for the money. And we’re going to fix that.
Please.

A ballsy play indeed

From Female Science Professor we learn:

In an article on May 18 in The Globe & Mail, the results of the program are described, including the fact that Canada was able to “poach” leading researchers from other countries and lure them to Canada with the millions of research $$ associated with these Chairs. The article effuses about the aggressive program of luring top researchers:
For Ottawa, it was one of the biggest bets on scientific research in a generation. But for the man at the centre of Canada’s worldwide drive to recruit top scientists, it was a “ballsy” play that at times resembled a bidding war for NHL free agents.
These CERC chairs are referred to by the following terms: star researchers, renowned scientists, foreign researchers, and, more generically, as “individuals”, or simply “these people”.
Two days later, The Globe & Mail realizes that it might want to mention that “these people” are all men.

Cripes. I was just drafting up something responding to Bob O’Hara on spousal hire policy and wrote an aside that fits much better here.
In discussing affirmative action hiring (a thing Bob called discrimination-and-therefore-unethical in a comment), he admits that he is okay with “discrimination” to deal with existing “disparity” which is a result of “past discrimination”.
Nice framing.
I mean seriously dude, c’mon. Read how you framed that stinker. Try it this way- Affirmative action hiring policies exist to make current discriminatory hiring policies that favor white guys slightly more fair, equitable and ethical for candidates who are more meritorious but have lost out to undeserving white guys.
This CERC thing that FSP pointed to is totally past-tense, right?
Go read her post, especially those of you who frame this nonsense the way Bob O’Hara does in your own mind.

Spousal Hiring is Unethical? Puhleeze.

I recently read over a bit in the Chronicle of Higher Ed that seemed to me to be a very thoughtful take on the practices of spousal hires in academia.
The author, David Bell, was a dean at Johns Hopkins University at one point and had gained some experiences of the advantages and disadvantages of policies which resulted in the hiring of the spouse of an academic that was the target of the primary recruitment.
Most of the issues are familiar to my readers. Academics who are married to another academic professional face special challenges on the job hunt. Our employment often requires a move to a geographically distant location. Frequently the hiring University or college is the only academic jobsite within reasonable commuting distance. Dual-academic-career couples are highly motivated to find two jobs at the same place.
Universities and colleges have long recognized this and have instantiated various ad hoc solutions. The goal, of course, is to be able to land their primary recruit who just happens to be part of a dual career couple. The recruitment cost to the University, in addition to the salary, labspace and other demands of the primary recruit, includes opening up another academic job, tenure track or otherwise. Big deal.
Personally I think this is a great solution to the modern reality of academic folks married to others in the business. [Discl: I'm in one such partnership]
But hoo-boy. The comments after that bit in the Chronicle just went nuts.

Love the idea that you can give my job away because I don’t have a spouse/partner you want. Isn’t it terrific that the profession hires, according to David Bell’s article here, more than a third–a third!–of its faculty because of whom they sleep with. Damn this is a prescription for the meritocratic society I had been told I was being raised in.

Eight retractions…so far.

I first saw the story break in a retraction notice published in PNAS.

The authors wish to note the following: “After a re-examination of key findings underlying the reported conclusions that B7-DCXAb is an immune modulatory reagent, we no longer believe this is the case. Using blinded protocols we re-examined experiments purported to demonstrate the activation of dendritic cells, activation of cytotoxic T cells, induction of tumor immunity, modulation of allergic responses, breaking tolerance in the RIP-OVA diabetes model, and the reprogramming of Th2 and T regulatory cells. Some of these repeated studies were direct attempts to reproduce key findings in the manuscript cited above. In no case did these repeat studies reveal any evidence that the B7-DCXAb reagent had the previously reported activity. In the course of this re-examination, we were able to study all the antibodies used in the various phases of our work spanning the last 10 years. None of these antibodies appears to be active in any of our repeat assays. We do not believe something has happened recently to the reagent changing its potency. Therefore, the authors seek to retract this work.”

Although curious as to who was the bad apple, given that all authors signed the PNAS retraction, I have to admit that “10 years” thing really got my attention. I have been waiting for the other shoe to drop…turns out it was a closet full of shoes.

A Scientific Misconduct Oddity

A recent notice (NOT-OD-10-095) of scientific misconduct from ORI has a curious twist I’ve not seen before.

Scott J. Brodie, DVM, Ph.D., University of Washington: Based on the findings in an investigation report by the University of Washington (UW) and additional analysis conducted by ORI in its oversight review,
ORI found that Scott J. Brodie, DVM, Ph.D., former Research Assistant Professor, Department of Laboratory Medicine, and Director of the UW Retrovirology Pathogenesis Laboratory, UW, committed misconduct in science (scientific misconduct) in research supported by or reported in the following U.S. Public Health Service (PHS) grant applications:
1 P01 HD40540-01 (National Institute of Child Health and Human Development [NICHD], National Institutes of Health [NIH])
5 P01 HD40540-02 (NICHD, NIH)
1 P01 AI057005-01 (National Institute of Allergy and Infectious Diseases [NIAID], NIH)
1 R01 DE014149-01 (National Institute of Dental and Craniofacial Research [NIDCR], NIH)
2 U01 AI41535-05 (NIAID, NIH)
1 R01 HL072631-01 (National Heart, Lung, and Blood Institute [NHLBI], NIH)
1 R01 (U01) AI054334-01 (NIAID, NIH)
1 R01 DE014827-01 (NIDCR, NIH)
1 R01 AI051954-01 (NIAID, NIH).
Specifically, ORI made fifteen findings of misconduct in science based on evidence that Dr. Brodie knowingly and intentionally fabricated and falsified data reported in nine PHS grant applications and progress reports and several published papers, manuscripts, and PowerPoint presentations. The fifteen findings are as follows:
1. Respondent knowingly and intentionally falsified a figure that was presented in manuscripts submitted to the Journal of Experimental Medicine and the Journal of Virology and in several PowerPoint presentations that purported to represent rectal mucosal leukocytes in some instances and lymph nodes in other instances.
2. Respondent knowingly and intentionally falsified portions of a three-paneled figure included in several manuscript submissions, PowerPoint presentations, and grant applications.
3. Respondent knowingly and intentionally falsified a figure included as Figure 1N in American Journal of Pathology 54:1453-1464, 1999, three NIH grant applications, and several PowerPoint presentations.

PowerPoint presentations?
What the hell are those doing in there?
Don’t get me wrong, data faking is data faking. I’m not down with that at all. But given the length of the accusation findings in the Notice (there were 15 total listed) throwing in the extra bit about PowerPoint presentations is odd.
What’s next?
“Respondent knowingly and intentionally falsified a figure included in several manuscript submissions, grant applications, PowerPoint presentations, and described in email exchanges with collaborators, conversations in the hallway at meetings and private conversations with his graduate students”

How many retractions does a PI get?

I was sort of kicking the latest journal article retractions around with a colleague. The Hellinga case. The Buck retraction. A few more in each of our respective spheres.
The question came up.
How many retractions can a lab survive?
I think one is a given. There’s the usual muddying of blame, accuse the postdoc or grad student, beg off on a mistake. For the first one.
What happens if there is a second one? Does it matter if it is 2 years apart or 15 years apart? Is that it, buh-bye, kiss of death? Or does it just depend on how good the excuse making is?

Do Appearances Indicate Anything About the Quality of the Data?

I’m mired in an effort to respond to a recent post of drdrA’s over at Blue Lab Coats on the deceptively simple issue of a manuscript rejection. This post is apparently a rich vein of blog fodder because PhysioProf already responded to the issue of pleading one’s case with the editor and I am trying to follow up on BugDoc’s request to expand on a comment I posted at Blue Lab Coats. That effort is bogging down so I thought I’d take care of one little nugget.
The part of drdrA’s post which made the most steam come out of my ears was the following point advanced by one of the paper reviewers:

“poorly performed gels and western blots which need to be improved.”

Should NIH Program Staff Scoop Their Own Investigators?

As purely entertaining as it is to watch PhysioProf troll the Open Access Nozdrul, these discussions always raise at least six interesting avenues for further thought. For example a comment from bill touches on the notion that private “ownership” of one’s ongoing (less than publication quality) data is bad for science. The specific example being that results that may be annoying “noise” to one scientist might be gems to another scientist, if she only was aware of those data. To me, anyway, this links to a more interesting consideration of the back-and-forth between our scientific ideal of collaborative group effort and the reality of personal ownership of “ideas” and “results”.
In this area I want to talk about the “ownership” of our scientific effort that might be asserted by NIH Program staff within the individual ICs to be used in ways that act against the interests of individual scientists.