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DBL%20Hendrix%20small.png College chemistry, 1983

Derek Lowe The 2002 Model

Dbl%20new%20portrait%20B%26W.png After 10 years of blogging. . .

Derek Lowe, an Arkansan by birth, got his BA from Hendrix College and his PhD in organic chemistry from Duke before spending time in Germany on a Humboldt Fellowship on his post-doc. He's worked for several major pharmaceutical companies since 1989 on drug discovery projects against schizophrenia, Alzheimer's, diabetes, osteoporosis and other diseases. To contact Derek email him directly: derekb.lowe@gmail.com Twitter: Dereklowe

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January 7, 2010

Extortion, Retractions, And More

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Posted by Derek

Now here's a strange tale, courtesy of Science magazine, about some retracted work from Peter Schultz's group at Scripps. Two papers from 2004 detailed how to incorporate glycoslylated amino acids (glucosamine-serine and galactosamine-threonine) directly into proteins. These featured a lot of work from postdoc Zhiwen Zhang (who later was hired by the University of Texas for a faculty position).

But another postdoc was later having trouble reproducing the work, and in 2006 he made his case for why he thought it was incorrect. Following that:

Schultz says the concerns raised were serious enough that he asked a group of lab members to try to replicate the work in Zhang's Science paper in addition to several other important discoveries Zhang had made. That task, however, was complicated by the fact that Zhang's lab notebooks, describing his experiments in detail, were missing. Schultz says that in the early fall of 2006, the notebooks were in Schultz's office. But at some point after that they were taken without his knowledge and have never resurfaced.

After considerable effort, Schultz says his students were able to replicate most of the work. The biggest exception was the work that served as the basis for the 2004 Science and JACS papers. "It was clear the glycosylated amino acid work could not be reproduced as reported. So we tried to figure out what was going on," Schultz says.

So far, so not-so-good. But here's where things get odd. Around this time (early 2007), Zhang started to get e-mails at Texas saying that unless he send $4000 to an address in San Diego, the writer would expose his "fraud" and cause him to get fired. The messages were signed "Michael Pemulis" - Science doesn't pick up on that pen name, but fans of the late David Foster Wallace will recognize the name of the revengeful practical joker from Infinite Jest.

That brings up another point: the e-mails quoted in the Science article are in somewhat broken English: "you lose job. ... Texas will fire you before you tenure. . ." and that sort of thing. But my belief is that no one who drops the second person possessive while writing would make it far enough into Infinite Jest to meet Micheal Pemulis and use him as an appropriate alias for an extortion plot.

At any rate, after the San Diego police got involved, they told Zhang that they had a suspect, but Zhang decided not to press charges. That fall, though, "Pemulis" dropped the bomb, with a hostile anonymous letter to everyone involved - officials at Scripps and UT-Austin, the editors at Science, etc. In 2009, Zhang was denied tenure. The postdoc mentioned above (now at Cardiff) has published a paper in JBC detailing the problems with the original work. (He denies having anything to do with the missing lab notebooks or the threats made to Zhang). And everyone involved is still wondering just what is going on. . .

I certainly have no idea. But I can say this: although I've spent a lot more time in industry than in academia, a disproportionate number of the people I've worked with over the years that I consider to have had serious mental problems are still from my academic years. Whoever "Pemulis" is, I'd put him or her into that category. Grad students and post-docs are under a lot of pressure, and some of them are at a point in their lives when their internal problems are starting to seriously affect them.

Comments (49) + TrackBacks (0) | Category: Biological News | The Dark Side | The Scientific Literature


COMMENTS

1. Yorick on January 7, 2010 10:12 AM writes...

What is the critical issue here? Is it the documented inability of a prominent research group to reproduce results in high-profile publications? Or is it a bizarre campaign of innuendo regarding putative threats and extortion?

I suggest we focus on the facts, and the science, at hand.

The truly appalling aspect of this tripe is the paltry sum allegedly being extorted. $4,000? That is just a sad indictment of the state of academic research. Perhaps we can learn from investment bankers, mortgage industry, etc.

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2. Anonymous on January 7, 2010 10:21 AM writes...

Save some opprobrium for the guy who built a career on factitious results!

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3. RB Woodweird on January 7, 2010 10:43 AM writes...

Notebooks are the bane of organic chemistry. I've been pushing for enotebooks and some sort of structure-based database here for two decades now. Ignoring the cost of duplication of mistakes and the nonduplication of successes you have in a large organization where chemists keep their records in a paper notebook, my demonstration of their weakness is simple. I stand next to a trash can holding one of our notebooks and do some estimation. Each book averages about 200 pages of work. Each page of work represents about a day's labor. The overhead cost to the corporation of a day of labor of a bench chemist is about $3000 (yes, really). So the notebook represents the investment of some $600K. Then I drop the book in the trash and ask where that money went.

I know some of the above does not apply in an academic environment, but the cost of implementing an electronic notebook system in academia is probably far less than in industry. Most software vendors give big academic discounts.

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4. gyges on January 7, 2010 10:59 AM writes...

"... although I've spent a lot more time in industry than in academia, a disproportionate number of the people I've worked with over the years that I consider to have had serious mental problems are still from my academic years."

Agreed. But is this a consequence of the individuals or the unhealthy atmosphere of academia? I tend to the latter explanation.

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5. PharmaHeretic on January 7, 2010 11:19 AM writes...

I cannot disagree either.. *S*

"... although I've spent a lot more time in industry than in academia, a disproportionate number of the people I've worked with over the years that I consider to have had serious mental problems are still from my academic years."

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6. Cloud on January 7, 2010 11:37 AM writes...

Perhaps the extortionist read Infinite Jest in translation?

RB Woodweird- the costs of implementing enotebooks go beyond the software license, as you no doubt are aware. But one thing you may not have thought about is the need to standardize record keeping practices if you are going to move everyone to an electronic system. In my experience, this is one of the most difficult aspects of any electronic data management roll out, and is the most common point of failure.

As for the problem with reproducing the experiments- you guys are always finding examples of biologists attempting to do chemistry and failing. I wonder if this is an example of a chemist attempting to do biology and failing?

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7. PharmaHeretic on January 7, 2010 11:44 AM writes...

How many of you have noticed that amoxapine, loxapine, clozapine, olanzapine and quetiapine have very similar structures but diverse pharmacological effects? Just curious..

http://pharmaheretic.wordpress.com/2010/01/07/finicky-sar-01/

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8. Anonymous on January 7, 2010 11:57 AM writes...


Just like Tiger Wood's fender bender, the retraction is really bad press for Peter Schultz (possible future Nobel Prize candidate) at Scripps.

We don't have TMZ to help us figure things out, but a simple google search brings you to this which was posted back sometime in June 2007:

Kyle Finchsigmate's blog
http://www.thechemblog.com/?p=585#comments

I'm not saying the retraction legitimizes the accusations, but it does have to make you wonder.
This may be another case of scientific fraud of a high-profile lab rather than a LaClair. Or this may be a case of bad science and some very late retractions....

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9. Tok on January 7, 2010 12:10 PM writes...

RB Woodweird - In our group we recently evaluated Cambridgesoft's e-notebook. Long story short, in order to print or export more than one page at a time from a notebook, one has to use the Enterprise version which is prohibitively expensive for a research group. We also found the support during this evaluation very lacking, likely because we made it clear we could not afford the Enterprise version.
Our network then went down for a day and nobody had access to their notebooks. Every person involved in the trial immediately switched back to paper notebooks. We now simply scan them in at regular intervals and back them up as pdfs on our externally backed up network drive.
I really liked the idea of e-notebooks, but the implementation was apalling.

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10. Archi Manning on January 7, 2010 1:36 PM writes...

Technology may come along someday to allow most of people use e-notebook. But as of right now, the best way we do, as mentioned by Tok, is to scan the notebook on quaterly basis and store them as pdfs on a bakup drive.

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11. Michael Pyshnov on January 7, 2010 2:02 PM writes...

When the turn of the University of Toronto comes? Are they untouchable? There is a huge material, 50 documents, waiting to be exposed: www.universitytorontofraud.com
Michael Pyshnov

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12. RB Woodweird on January 7, 2010 2:12 PM writes...

Tok and Archi Manning -
Good points. The last sticking point here blocking implementation of any enotebook system has always been the price. Regular as clockwork, we have a vendor come in every five years and present the product. We demo it. Everybody loves it, then the estimate reaches management, who say: Wait a minute, what is really wrong with the way we do things now? DC al Fine.

So I made my own half-assed version of electronic record keeping, and I have not written in a notebook since August 19, 2005. Here it is, free of charge: For lot records, I use a Word document. Stuctures are embedded ChemDraw. NMR, MS, UV, HPLC data is printed to pdf and stored in a folder with the lot record. TLCs and other non electronic data is scanned on a cheap HP desktop scanner or our copier/fax/scanner and stored as images. I title each piece of data with a lot number and compound name and any other appropriate identifier and keep it all in a lot folder. I haven't filed a manila folder in a filing cabinet for 5 years.

So all the work is on the network drive(s), which are backed up every night. The beauty of the system comes in when you have to search. I use Copernic desktop search. (Someday we will have the wisdom to implement an enterprise search appliance.) If I need to know when the last ten times I used borotritide were, Copernic finds all the instances of the word in the whole volume in a flash. Of course, I can't search structures, but at least all the data is in one place, pretty much indestructible, searchable, and shareable.

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13. Tok on January 7, 2010 3:37 PM writes...

RB Woodweird - It's funny you mention Word because pasting the fids and other files into a Word tab in enotebook was the only way I found to insert those data into a notebook entry. Their built in software to handle those spectra was unusable.

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14. milkshake on January 7, 2010 4:44 PM writes...

The Schultz lab story writeup is painful to read.

Whoever sent these anonymous denunciations and blackmail e-mail acted like a complete jerk: If he(she) had any real grievancies or troubling misconduct to report - and for whatever reasons could not go to Pete Schultz - he should have acted through the appropriate channels like a professional.

The Scripps institute has a "Reseach Education and Compliance" office which now accepts even anonymous submissions through ethicspoint.com webpage.

For the most extreme cases there is a federal agency called Office of Research Integrity and they investigate everything in the most thorough way - and if misconduct is found this has stark consequences for federal funding of the responsible parties, and outright fabrications which used federal research funding actually do get prosecuted as a criminal offense.

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15. mikeymedchem on January 7, 2010 4:57 PM writes...

Re: eNotebooks -- we purchased the Cambridgesoft eNotebook, hosted (ie they handle the infrastructure), and got a really good price for it for our academic institution. We had some bumps in getting it up and running, but the have clearly seen the light and have introduced a cheap(er) academic version than they may have hawked a while back.

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16. Biobrit on January 7, 2010 8:23 PM writes...

@RB Woodweird

Kudos for you for trying your own ELN solution. I'm sure that you've realised this, but there are 2 major issues with this, which are or are not relevant depending on how you see the role of an ELN. Namely 1) Your method makes it very difficult to share information eg people have to come to you to access your notebook, and more importantly 2) you lose the time-stamp protections that support first to invent based patents, and the ability to add witnesses which also help protect any invention of yours.

As a general comment on ELN in academia..... IMHO, and ignoring the cost issues, an ELN is perfect for academic labs. But those making the decision tend to see them in the paradigm of trad notebooks, as mere repositories of information. The ability to easily search for methodology (and to avoid repeating others failures), copy/paste methods, build templates of common methods, share information and even use the ELN to generate ideas adds significant value. Having said that, academic labs tend to need more of a cultural shift than industrial labs, where, IMO, scientists are less protectionist of their notebooks and enforce higher (or more patent friendly) standards of notebooking.

Scanning notebooks achieves almost none of the benefits of ELNs, except that the notebooks can't be lost/stolen/destroyed. But still just a hole for information rather than a database.

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17. BioBrit on January 7, 2010 9:31 PM writes...

@Tok @Archi Manning

Your experience isn't unique, in academia or industry. The software is generally pretty great, but the implementation mostly is awful. The institution generally assumes that the system will pretty much run itself with minimal configuration or support, while the truth is that you need someone responsible for running it, bridging between the scientists and IT/legal/vendor, training, bug fixing, writing documentation, changing the culture and just being a point person when people have problems. In academia, who would do that? A postdoc/PhD student who leaves after x years (and has to decide between spending time working on the ELN and doing research)? You also need a budget to make things better, once you've rolled out your 'it will do for now' version.

The institutions are interested in bringing in the systems, but not in making sure they run smoothly when they are there. Industry isn't always any better mind. And the vendors don't generally stress that this is needed.

As a point of reference, I'm an industrial med chemist, but have also implemented an ELN. It took a long time and a lot of effort to get it runnign smoothly, but a lot of the barriers were, in truth, self-inficted.

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18. S Silverstein on January 8, 2010 12:00 AM writes...

The politics, machinations and craziness especially in Ivy academia were in my experience far worse than in the industry I worked for in the beginning of my professional career: the municipal transit authority in a large eastern city.

20+ labor unions, some militant, constant labor-management strife, workers comp fraud, attacks on the Medical Department like the cartoon in the union newspaper seen at the middle of this post.

Ivy academia was worse.

(Non-Ivy is much better.)

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19. Silverstein again on January 8, 2010 12:16 AM writes...

Biobrit writes at #17:

"the truth is that you need someone responsible for running it, bridging between the scientists and IT/legal/vendor, training, bug fixing, writing documentation, changing the culture and just being a point person when people have problems. In academia, who would do that?"

Whoever would do it would best need a background in both biomedicine and IT, plus cultural issues at the interface of these areas.

One possible answer: people who've trained in this:

http://www.nlm.nih.gov/ep/GrantTrainInstitute.html

and similar programs internationally.

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20. dearieme on January 8, 2010 7:18 AM writes...

My industrial experience is much shorter than my academic experience. Allowing for that,
hearing a colleague say of another colleague "I think he's mad" seems to me to have been noticeably commoner in academic life.

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21. RB Woodweird on January 8, 2010 7:36 AM writes...

@BioBrit

The data is all on a network volume which is reachable by anyone in the company anywhere on the planet. They do have to know where to look or have a method of searching it, but it is there for all to see.

I guess there are features in Word that allow one to track creation and changes to documents, time stamp them, even allow electronic signatures. One could cobble up an acceptable, patent-friendly template, I suppose. I would be surprised if others haven't done this already.

But management only sees money spent, not money saved. There will come a day when legal goes to operations and tells them that they lost the corporation actual money by not having ELNs. Then and probably only then will one show up on my desktop.

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22. S Silverstein on January 8, 2010 9:41 AM writes...

I received some anonymous email excoriating me for my comments about Ivy academia compared to a transit company. Here is an example of what I was referring to. Ivy league in all its glory.

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23. J-bone on January 8, 2010 11:01 AM writes...

Woodweird, I ran into the same issue about timestamping as BioBrit, both at my grad school and now at my postdoc. I started using Word to type up procedures much like yourself, but was quickly told by my PI to cease and desist due to patent obligations that required handwritten procedures. Fortunately for him, I was never clever enough to invent anything patentable. I asked about electronic lab notebooks at my postdoc and was told I needed to write everything, again for patent reasons.

Silverstein, I can't speak on Ivy League vs. non-Ivy League politicking and bureaucracy, but I can say that the non-Ivy League version sounds similar to your transit authority analogy. What makes it more infuriating is that people have Ivy League sized egos without the Ivy League sized accomplishments.

But back to the original story, I did enjoy reading about this on The Chemblog back when the story first broke. Any sense of dysfunctionality in an institution besides my grad school made me feel better, because then I knew it wasn't just us did things the wrong way.

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24. BioBrit on January 8, 2010 11:27 AM writes...

@RB Woodweird
The timestamp issue is one of authenticity of the timestamp, the Enterprise versions generally have the timestamp encrypted on the server, and although not impossible, it would be prohibitively difficult to adjust the times. If you are just working off of your desktop then you are just timestamping from the PC clock which is easily altered.

"But management only sees money spent, not money saved." Oh, so very true.

@J-bone: Handwritten vs typed doesn't matter for patents. A verifiable signature (ink or e-) is important. But, having things loose-leaf is an issue. I think your PIs are probably only getting or giving half the truth.

@Silverstein again: Probably true. But my background was pure chemistry, then industrial medchem. I didn't even own a computer until 6 or 7 years ago. The configuration side isn't so difficult, you just need to spend the time on it. More challenging is the cultural changes you need to achieve.

Given that I've spent the last 9 months looking for new medchem work, perhaps I should suggest that TSRI really do need an ELN and need me to run it for them :-)

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25. Hap on January 8, 2010 1:54 PM writes...

Could the extortion have been an instance of teamwork (the person naming the blackmailing entity and the person writing the emails would be two different people)?

I'm sure the professor might be interested in the Infinite Jest reference, too - if his grad students were reading it in grad school, that's time they should have been in lab. Slackers!

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26. Cloud on January 8, 2010 2:11 PM writes...

Silverstein: " Whoever would do it would best need a background in both biomedicine and IT, plus cultural issues at the interface of these areas."

You have just stated why I have a job. I have pretty much built a career bridging between biomedical research and IT, with some project management training and experience thrown in. I am not the only person doing this, but in my experience companies don't realize they need someone like me until they have been burned by a few scientific IT projects that go up in flames. So, when I'm looking for jobs I either get "why would we need someone like you? Go away." or "OMG, do we need someone like you. Can you start tomorrow?" And I am almost always applying for a position that emphasizes only part of my background (the science, the IT, or the project management).

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27. MedInformaticsMD on January 8, 2010 3:10 PM writes...

Cloud writes at #26,

"in my experience companies don't realize they need someone like me until they have been burned by a few scientific IT projects that go up in flames"

Sometimes not. Merck (or Merck Schering or whatever they call themselves now), for example, still does not seem to understand this, even after people got burned to "Crispy Critters" clinical trials information system in the failed CRISP project of the 1990's, for example.

Read this book: “Understanding And Communicating Social Informatics” by Kling, Rosenbaum & Sawyer, Information Today, 2005 (look up on Amazon). You will undoubtedly find many familiar themes in it.

An introductory essay entitled “Learning from Social Informatics” Kling at the University of Indiana can be found at the link here (.doc format). The book was based on this essay.

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28. Rob Day on January 8, 2010 5:08 PM writes...

Oh dear. What a mess. If only the Scripps group had deployed an enterprise grade ELN to protect, manage and authenticate all research performed in that lab, they probably could have avoided all this unpleasantness.

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29. Sili on January 8, 2010 7:20 PM writes...

Dr Silverstein,

Do you have any casestories that aren't depressing? This is the second (very interesting and wellwritten) bit I've read by you, and I'm once again growing scared of 'the real world'.

Permalink to Comment

30. S Silverstein on January 9, 2010 9:44 AM writes...

#29 Sili

Sili, also that last story should not be depressing. It is a case study of what can be accomplished by scientists regarding bullies in 'the real world.' It also suggests one should carefully interview and do due diligence on anyone one considers reporting to, since prevention is the best medicine. -- SS

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31. Tyrone Slothrop on January 9, 2010 4:44 PM writes...

It was a mess and highly stressful for those of us there at the time. It was initially surprising to see the work of some former super-star lab members come under such scrutiny. It became less surprising after a few bodies were uncovered, more so after more bodies were uncovered. A few former group members were clearly negligent and depending on what they knew and when they knew it, fraudulent. A situation like that could make students who wasted years trying to build on those experiments quite upset, especially when the bar for a successful Schultz group member was already set very high. When someone cannot reproduce results, ones scientific ability and skill are drawn into question (a la the sames group members who were fired) before repeated attempts to reproduce the results in question fail. The Schultz group is filled with high performing and exceptional students, whom when presented with the situation of years of nothing and their scientific prowess called into question reacted poorly. While their outrage may be justified, the audacity and the repeated antics became absurd after a while and does not excuse their behaviour. It is unfortunate when the students left in the wake of these people make the situation worse by threats, extortion, and craziness. We have seen these cases of fraud before and will probably see it again (Hendrik Schon, UAB, and Bengu Sezen).

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32. milkshake on January 9, 2010 5:18 PM writes...

#31: I wanted to ask you whether there was any implied pressure or confirmation bias coming from Pete Schultz, like in Dali Sames case, leaning onto his group members to produce the results that agree with these dubious papers?

I don't have any inside scoop in the Schultz case but I worked for a famous man in the grad school and he also had few "irreproducible" methodology papers published over his long and highly illustrious career. I noticed there that one postdoc across the bench was fudging the yields a bit and covering up the purities in his tot.synthesis/methodology work so that he could finish his molecule as soon as possible and move onto an industry job. The problem with our old Chief was that he took no for an answer and once he became convinced that something works (or ought to work) he would keep asking you about it in a highly suggestive way - and one would not make himself popular by pointing out the actual problems (it would only make him look like being incompetent and making excuses)

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33. tyrone Slothrop on January 9, 2010 10:09 PM writes...

Milkshake,

Confirmation bias; in short, Yes. But I think that is a bias we all share; mind you these are published papers in peer reviewed, reputable journals from professors now. I believe most of us would by default accept what is in the literature as true, especially considering the reputation of the publishing parties. Underscoring the difficulty of the situation for a dissident. Nobody is happy when valuable time and money need to be spent confirming old results; its not publishable or fundable.
I think you are highlighting the issue. Your buddy “fudging” his purity and yield, wasn’t taking the time to do a proper study of the reaction methodology or properly purify the products. Now he is able to devote more time to not doing proper methodology and purification on other projects. Carried out to the appropriate number of years, he has been quite productive. The person who suffers is the one who needs to use the methodology or pure product to do the SAR study, make the analogue, or different natural product. Not only can’t this person reproduce the results but must now do what wasn’t done in the first place, and they don’t get the publication because its already been published. Depending on the specifics this could take a while. Meanwhile, these people are being compared to each other; by the PI and by colleagues. The schultz group, being a collection of over-achieving high performers, don’t take well to doing what somebody didn’t do in the first place and then being judged against current and former colleagues in terms of production (especially “fudged” results/publications). Understandably so, they are trying to do the right thing and understand what went wrong to clean up the mess. It is a tough pill for the unlucky soul that was placed on the project. Pete didn’t apply the kind of implied pressure that you are suggesting. The intense pressure was to get results not specific results, and most of the pressure came from your colleagues and yourself. However, prospective schultz group members would be wise to study Worstward Ho (“All of old. Nothing else ever. Ever tried. Ever failed. No matter. Try again. Fail again. Fail better.”), Sisyphus, and possibly Prometheus depending on the project.

Tyrone

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34. MedInformaticsMD on January 10, 2010 9:21 AM writes...

#33 tyrone slothrop

In line with the link to the detailed case account of academic mayhem I posted in #22, perhaps a similar account of what sounds like a very educational situation would be useful?

In fact, as recommended by Greenhalgh et al. [1] in my field, who called for "eschewing sanitized accounts of successful projects" and instead recommending studies of clinical IT in organizations that “tell it like it is” using the de-identified critical fiction technique, perhaps someone could take on writing a de-identified case