MIRA Moaners

March 31, 2016

Jocelyn Kaiser reports that some people who applied for MIRA person-not-project support from NIGMS are now complaining. 

I have no* comment.


Some weaksauce low energy muppet just tried to shame me for being “easily amused”.

Is that supposed to be cutting?

The alternative is either that you are humorless or too dumb to get the joke, right?

Thought of the day

March 27, 2016

Personalized, artisanal trolling is the new twttr.

Don’t do this. Ever.

I “think” of doing experiments all the time. As do you, Dear Reader. Dreaming up an experiment is no particular feat for a scientist who has been in the business for awhile. The trick is accomplishing and publishing the study.

If you haven’t done that, then it just looks silly to go around telling people you thought of doing the work they just published.

H/t: You know who you are dude.

at RetractionWatch:

After the University of Texas postponed a hearing to determine whether it should revoke a chemist’s PhD, her lawyer has filed a motion to stop the proceedings, and requested the school pay her $95,099 in lawyer fees and expenses.

We have discussed individuals convicted of scientific fraud in the course of doctoral studies before and wondered if a University could or would attempt to retract the doctoral award. Well, looks like this is one of those cases.

The Austin Statesman reports:

In Orr’s case, UT administrators moved to revoke her degree after finding that “scientific misconduct occurred in the production of your dissertation,” according to a letter to Orr from Judith Langlois, senior vice provost and dean of graduate studies.

The dissertation committee concluded that work related to “falsified and misreported data cannot be included in a dissertation and that the remaining work described in the dissertation is insufficient to support the award” of a Ph.D.,” Langlois wrote. Orr was invited to submit a new thesis summarizing other work to earn a master’s degree.

This is interesting because the justification is not that she is being punished for being a faker, otherwise why would they invite her to submit a master’s thesis? The justification is that ignoring the allegedly falsified work leaves her short of a minimum qualification for the doctorate. Given the flexibility involved with doctoral committee requirements and the sheer scope of data usually involved in a thesis, my eyebrows are raising at this. Back to the RetractionWatch piece:

The motion for final summary judgment includes an affidavit from Phillip Magnus, a chemistry professor at UT, who argues that…

her dissertation consisted of two branches of work towards alkaloid natural products and a methodology project to generate novel structures. She characterized about 100 organic compounds in her dissertation. Even without completed syntheses of natural products, her research towards the natural products was significant, and provided her the training to become a skillful and passionate scientist. Being correct or incorrect is part of scientific research. Being correct, or synthesizing a particular molecule are not requirements for passing a course at the University, or obtaining a Ph D degree. Furthermore, the possibility of being wrong is not a justifiable reason to rescind a former student’s degree.

Yeah, this certainly points at a usual sticking point between the RetractionWatch types and me.

It is ESSENTIAL to differentiate between merely being wrong or mistaken (or even sloppy) and intentional fraud.

The Austin Statesman piece goes on to detail how the supervising PI and a subsequent postdoc wanted to build on Dr. Orr’s work and she told them to re-do certain work. They didn’t, published a paper (with her as author) and it was subsequently retracted for a chemical step being non-reproducible. Was her warning due to knowing she’d faked some results? Or was it due to her gut feeling that it just wasn’t as nailed down as some other results and she’d like to see it replicated before publishing? Did her own subsequent work cast doubt on her prior (valid but perhaps mistaken) work? Etc.

The Chronicle of Higher Education reports that some Universities are being more flexible on previous grant-related criteria for tenure. 

Interestingly, University representatives refused to identify faculty that have been tenured without major grants. 

I sure hope we don’t find out this is another source of bias for the traditionally empowered demographics.

An interesting retraction of an Editorial expression of concern hit the Twitts:

The Editors and publisher have withdrawn an Expression of Concern previously contributed by noted neuroscientist David Amaral, with his agreement.

The original version of this Comment ‘Expression of Concern’ published by D. Amaral has been withdrawn by the Publisher in relation to the paper: ‘Organization of connections of the basal and accessory basal nuclei in the monkey amygdala’ by Eva Bonda, published in Volume 12, pp. 1971-1992 (doi: 10.1046/j.1460-9568.2000.00082.x). The review carried out at the University of California at Davis in December 2001 (brought to the publisher’s attention in February 2016) concluded that the allegation against Eva Bonda described in the commentary ‘Expression of Concern’ by D. Amaral did not meet The Office of Research Integrity’s definition of research misconduct, and was not pursued further.

That November 2000 Expression of Concern read, in part:

It has recently come to my attention that Eva Bonda has published a paper in the European Journal of Neuroscience entitled, ‘Organization of connections of the basal and accessory basal nuclei in the monkey amygdala’ ( Bonda, 2000). The data described in this paper were produced by my students and me at the University of California, Davis. Support for carrying out the experiments that produced these data was provided by the National Institute of Mental Health, through grant MH 41479 for which I am the Principal Investigator.
..The publication of this single-authored paper was totally unauthorized. Eva Bonda was a postdoctoral fellow in our laboratory.

Ok, so PI asserts ownership of data collected in his lab. Fine, fine… Typical story of postdoc who thinks that she owns and controls her data? And the PI was blocking publication for reasons unknown. We all have been down the various roads of he said/she said often enough to imagine a variety of scenarios where we might alternately side with the trainee or the postdoc.


She had access to the preparations that were described in the paper. However, she did not carry out any of the experimental procedures involved in making the tracer injections reported in this paper. These injections were made by other students in the laboratory and by me. Moreover, other than processing the tissue from a small minority of the reported cases, it was the technical staff of our laboratory rather than Eva Bonda that carried out the histological processing of the reported experiments.

Ah. Well that sounds bad. This suggests it is a little more like theft of credit from more people than just the PI. I happen to disagree with the not-infrequent pose of postdocs on the internet that they own and control “their” data that they generated in the laboratory of a given PI. But that is much more of an arguable position than is taking data generated by many people other than one’s self and asserting control/ownership from a position that is not the PI.

Amaral finishes by making the charge of academic misconduct against Bonda very explicit:

In my view, the appropriation and publication of these data is a serious breach of scientific ethics. I have asked the Editor of the European Journal of Neuroscience to take appropriate action including publication of this Expression of Concern. Upon consultation with the Office of Research Integrity, Public Health Service, US Department of Health and Human Services, the agency responsible for protecting the integrity of NIH funded research programs, the UC Davis campus has agreed to initiate a review of the allegations of research misconduct. Based on the outcome of this review, further actions, including request for full retraction, may be taken concerning this.

Of course, the recent retraction of the Expression of Concern indicates that Bonda, the postdoc, was exonerated of misconduct charges in 2001!

Wow. Why did it take Amaral 15 years to retract his accusations? This seems spectacularly dickish to me.

And given the fact that the postdoc was not found guilty of misconduct by the University, it really questions the factual basis of his assertions in the original Expression of Concern. If I were the postdoc in question, I might have launched a counter accusation of professional misconduct. Depending, of course, on the details of the inquiry and what each party did and did not do. The exoneration of the postdoc may simply have been a lack of proof of intent, rather than any disagreement over the facts.

I notice, however, an interesting poll put up by an individual who both was RTing the tweets that alerted me to this situation and apparently co-published with Amaral.


Gee, I wonder what the nature of the dispute was between Amaral and Bonda?

The subject of this poll is the juxtaposition of “good data” with “high quality standards” of the PI. Given what Amaral does, I’m going out on a limb and assuming we are talking about how pretty the immunohistochemical images are or are not (the Bonda paper is nearly all immuno-staining pictures).

Reviewer mindset 

March 22, 2016

I was just observing that I’d far rather my grants were reviewed by someone who had just received a new grant (or fundable score) than someone who had been denied a few times recently. 

It strikes me that this may not be universal logic.


 Is the disgruntled-applicant reviewer going to be sympathetic? Or will he do unto you as he has been done to?

Will the recently-awarded reviewer be in a generous mood? Or will she pull up the ladder? 

via comment from A Salty Scientist:


When you search for papers on PubMed, it usually gives the results in chronological order so many new but irrelevant papers are on the top. When you search papers on Google Scholar, it usually gives results ranked by citations, so will miss the newest exciting finding. Students in my lab recently made a very simple but useful tool Gnosis. It ranks all the PubMed hits by (Impact Factor of the journal + Year), so you get the newest and most important papers first.

Emphasis added, as if I need to. You see, relevant and important papers are indexed by the journal impact factor. Of course.

Just remember this graph when you are being told about the service requirements of your job and how “good it will look to the P&T committee” if you say yes to the next demand on your time.

In fact, you know what? Just go ahead and print this out and slip it under your Chair’s door.

Diversity and the Ivory Ceiling by
Joya Misra and Jennifer Lundquist at Inside Higher Ed.

Strategic advice

March 21, 2016

Reminder for when you are submitting your manuscript to a dump journal.

Many of the people involved with what you consider to be a dump journal* for your work may not see it as quite so lowly a venue as you do.

This includes the AEs and reviewers, possibly the Editor in Chief as well. 

Don’t patronize them. 

*again, this is descriptive and not pejorative in my use. A semi respectable place where you can get a less than perfect manuscript published without too much hassle**.

**you hope.

This is funny
Right wing anti-science nuts in Congress are not going to stop attacking research grants just because the Abstracts are expressed in less technical language. Their political agenda is at work and poor understanding of the project  has nothing whatever to do with their motivations. 

On whitening the CV

March 18, 2016

I heard yet another news story* recently about the beneficial effects of whitening the resume for job seekers.

I wasn’t paying close attention so I don’t know the specific context. 

But suffice it to say, minority job applicants have been found (in studies) to get more call-backs for job interviews when the evidence of their non-whiteness on their resume is minimized, concealed or eradicated. 

Should academic trainees and job seekers do the same?

It goes beyond using only your initials if your first name is stereotypically associated with, for example, being African-Anerican. Or using an Americanized nickname to try to communicate that you are highly assimilated Asian-Anerican. 

The CV usually includes awards, listed by foundation or specific award title. “Ford Foundation” or “travel award for minority scholars” or similar can give a pretty good clue. But you cannot omit those! The awards, particularly the all-important “evidence of being competitively funded”, are a key part of a trainee’s CV. 

I don’t know how common it is, but I do have one colleague (I.e., professorial rank at this point) for whom a couple of those training awards were the only clear evidence on the CV of being nonwhite. This person stopped listing these items and/or changed how they were listed to minimize detection. So it happens.

Here’s the rub. 

I come at this from the perspective of one who doesn’t think he is biased against minority trainees and wants to know if prospective postdocs, graduate students or undergrads are of Federally recognized underrepresented status.


Because it changes the ability of my lab to afford them. NIH has this supplement program to fund underrepresented trainees. There are other sources of support as well. 

This changes whether I can take someone into my lab. So if I’m full up and I get an unsolicited email+CV I’m more likely to look at it if it is from an individual that qualifies for a novel funding source. 

Naturally, the applicant can’t know in any given situation** if they are facing implicit bias against, or my explicit bias for, their underrepresentedness. 

So I can’t say I have any clear advice on whitening up the academic CV. 

*probably Kang et al.

**Kang et al caution that institutional pro-diversity statements are not associated with increased call-backs or any minimization of the bias.


I’m right here. On the blog.

Nothing is (seriously*) wrong with me.


*i.e., beyond the usual.

**and yes, I am touched by all y’all’s concern for my well being. Thank you for that.