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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, Eric Tippmann, 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. Eric Tippman (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'.

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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 study?

-- SS

[1] Tensions and Paradoxes in Electronic Patient Record Research: A Systematic Literature Review Using the Meta-narrative Method. Greenhalgh, Potts, Wong, Bark, Swinglehurst, University College London. Milbank Quarterly, Dec. 2009. Available at: http://eprints.ucl.ac.uk/18821/

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35. J-bone on January 11, 2010 8:40 AM writes...

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)

This sounds similar to a situation I dealt with in grad school. I was working on a methodology and ran a reaction that once gave spectacular yield/ee and he got excited. Then he told me to try using a new modified reagent that had been showing some promising results and it bottomed out. Over the course of 6 months he told me every day (not hyperbole, he was a nightmarish micromanager) that I wasn't doing that reaction correctly and that I got great results on the first reagent so there was no reason for the 2nd one not to work (despite the fact that they were DIFFERENT REAGENTS). No matter how many times I ran the reaction with the 2nd reagent and got the same results he would tell me to keep running it.

I finally put my foot down and told him to stop wasting my time, which he solved by having a different grad student run the reaction. I'm sure you can guess the results and his response.

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36. DC on January 11, 2010 9:54 AM writes...

J-bone, next time you should tell him to try the reaction himself, lol

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37. Anon on January 11, 2010 9:56 AM writes...

#35 J-bone

Although not knowing the individual involved, a saying from one Albert Einstein may apply:

Insanity is doing the same thing over and over again and expecting different results.

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38. Eric M. Tippmann on January 11, 2010 3:49 PM writes...

When I arrived at Scripps, I knew nothing of molecular biology, having come directly from completing a PhD in Physical Organic Chemistry. Very few other labs could have afforded me the time, or leeway, necessary to cut my teeth in a completely new research area. In this regard, I am very pro-megagroup. In regards to the Science and Nature articles that followed up on the Schultz retractions, they gloss over several key facts that I insisted should be included. The first fact was that Merck’s nearly $500 million acquisition of GlycoFi in 2006 means that there are still viable alternatives to the production of glycosylated proteins; and therefore reason to remain optimistic about the field in general (i.e. fund grants). The second fact was that at least two other Scripps’ post-docs, as well as an undetermined number of biomedical companies, began working full-time on reproducing the now retracted papers already in 2004. The third fact is that I never worked on the glycosylation papers directly. My analysis came completely from published papers. When I presented my analysis of the now retracted papers back in the autumn of 2006, I did so against the accumulated backdrop of a minimum of 5-10 vacuous post-doc years from my fellow friends and coworkers. And by vacuous, I mean that their attempts to reproduce the original works did not simply mean that these workers failed a “faithful� or verbatim reproduction of the original works, it means that they failed to accumulate 1% of the original claims. I am often asked how was I so smart to be able to figure out a problem that escaped so many other, much smarter, people. The answer, as with many scientific breakthroughs, was one of serendipity. While recovering in the hospital, two pages from two disparate reports ended-up next to each on my hospital bed. A child would have noticed the similarities. When I did go and present my analysis, I did so repeatedly, and I did so to no fewer than 30 former and current Scripps co-workers. These individuals would go on to tell other individuals. By my assessment, the flaws in these two retracted papers were already pervasive in the community by the end of 2006. I would continue to present the same analysis at international conferences over 2007-08. In regards to the JBC paper that we did eventually get published, the manuscript began its life as a communication to The Journal of American Chemical Society, which was submitted on February 7, 2009. This initial manuscript was rejected without review. Similar treatment would befall our manuscripts at 6 other journals. I would have also hoped that the key scientific aspects of my 2006 analysis, or our 2009 JBC paper, would have been found to be more in-line with Nature's mission of reporting “…issues concerning science.� This is because few other retracted papers can lay claim to monetary values approaching half a billion dollars, and therefore it is my opinion that Science and Nature’s readers, many of whom referee important papers, would have benefited more from an in-depth analysis of these retracted papers. Specifically, what was the key evidence offered that the referees from two of our top journals found so seductive. Since this has not been the case, it seems only right to again attempt to resolve such scientific issues in the scientific literature.

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39. milkshake on January 11, 2010 9:02 PM writes...

Eric, you were incredibly brave and it probably did not serve to improve your career - by making yourself unpopular with a number of establishment people (whom you perhaps did not even get face-to-face). After all this is not some bogus-institute group like LaClair's, and you are not a famous and tenured man yourself - Why do you think no-one has pointed it out publically before you? There was clearly a damage control and you were making it more difficult...

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40. Archii Manning on January 12, 2010 8:56 AM writes...

With Eric's effort, the problem (academic fraud and possibly cover-up by big fish and how the so called academic community treats the whistle-blower) still may not change at all. But without people like Eric, the problem will never change. Thanks Eric!

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41. Mr. Gunn on January 13, 2010 3:52 PM writes...

Rob Day from Rescentris says above that a ELN such as his company provides would have solved the problem. I'm not so sure. It might have been easier for an insider to delete the material from an ELN than to physically steal the notebooks.

Scanning the pages of a physical notebook is crazy, though.

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42. Biobrit on January 13, 2010 6:27 PM writes...

@Mr Gunn
Assuming it is set up correctly, you can't delete data from an ELN, that why its so popular. Unless you have admin rights on the server and delete the entire database of course, but that would be kind of obvious. Of course, the sort of half-way house solution, where data is stored locally on a PC harddrive is much more open to such deletions.

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43. TMWTD on January 14, 2010 7:55 AM writes...

I think that Schultz hid the notebooks. It's better to say "oops, lost the notebooks, I guess we have to retract it" than "we don't do very careful work in my group".

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44. Rob Day on January 14, 2010 3:23 PM writes...

@ Mr Gunn & BioBrit..
BioBrit is correct. Data cannot be deleted from a modern ELN. It can be hidden, but not deleted. hidden data is still viewable by administrators. In addition, any attempt to modify the audit trail or hide activities in a 21CFR11 compliant ELN can be detected. The actual data is obfuscated in ways that make it impossible for anyone to access it directly, even if the hard drive is removed from the server machine. Best practices such as multiple access roles, digital signatures, controlled access to server hardware and secure, integrated offsite backup to a third party archive service (such as Iron Mountain) add even more security by making access to the finalized version of the data virtually impossible. The whole point of ELN solutions is that they add security, authentication and audit capabilities that are incomparably more secure than traditional pencil and paper.
Also, BioBrit, I am a UK national living in the US. Send marmite!

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45. milkshake on January 14, 2010 3:59 PM writes...

All fans of electronic documents please consider this: Notebooks are above all a tool for doing research. In science the research and the result publication is based on trust. (There is review process and then there are research misconduct investigation mechanisms - including government agencies like ORI.) It would be perfectly doable to put in place a record-keeping system that would prevent theft of research records or their alteration. But look at the trade-offs: People write into their notebooks the unvarnished notes of research in progress. They append comments on margins, they cross the sentences. They should be able to do this on the bench rather then going to their office and type stuff into computer.

Electronic notebooks are not good. They take more time to keep and more difficult to browse through - also, I was once trying to reproduce experiments after from a colleague who prepared some pretty useful materials and then left, and all his records were in electronic notebook - and pretty much most of the experimental details was missing.

I think xeroxing or scanning the notebooks is a preferable way of dealing with the data preservation problem. Scanning one notebook can be done in 20 minutes, and in synthetic chemistry people complete about two notebooks per year.

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46. BioBrit on January 25, 2010 6:27 PM writes...

@Rob Day - I just had my Marmite stash topped up again. And no, I won't share. (I'm in the US too).

@ Milkshake. I'm forced to disagree. Writing on margins, crossing out sentences? Not sure what the difference is to editing an open ELN experiment. Want to write down some ideas? A good ELN provides for that, and makes it much less likely your idea is lost. Your example of the scientist with bad records - did he really keep immaculate records when using paper? People with good record keeping techniques tend to keep them when moving onto ELN, we found quality generally went way up, not the reverse.
I'll give you that access is important, give the scientists tablets or laptops to take to their benches and its easier for them to update real time. And cuture is too, people take some time to adjust to the increased visibility of their work.

But you underestimate what an ELN is. Sure, it's a good place to store information. But its a great database of info too, info you just won't even know is there when its in a book on the back of someone's shelf, or deep in the PIs office. And when used properly, when you build templates and have good libraries of reagents, it saves time **IF** you keep good records anyway.

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47. SS on July 7, 2010 3:54 AM writes...

Whistleblower perhaps? Sounds like Eric Tippmann's just a whistleblower.

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48. Niceguy on August 13, 2011 9:13 PM writes...

wow someone is really full of themselves, genuine critique and review is needed in the academic world. If Eric Tippmann didn't resort to extortion and illegal tactics, this issue could have been resolved earlier but some people dwell on drama. It is obvious Tippmann is the equivalent of an academic troll and receiving his due justice. A TIPpmann to all, DON'T FEED THE TROLLS!

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49. Eric M. Tippmann on April 13, 2012 9:17 AM writes...

Niceguy,

On the contrary, the facts show that I have only ever engaged in genuine critiques and reviews.

For example, as soon as I discovered the error in mid-2006, almost a year (!) before claims of harassment surfaced, I discussed openly and publicly with my supervisor and dozens of other colleagues in and around Scripps the fallacies in their papers. I frequently engaged in candid discussions on the topic of the flawed papers with probably close to 50 scientists. Each of these people would have discussed them with a few other people and so on. Because, let's face it, people at Scripps gossip. So already by the end of 2006 there were easily 100's of scientists whom would have known that I had blown the whistle. I had direct threats to stop talking about the matter and decided to leave the country.

And if there were any doubt in my initial analysis, the obvious experiments to determine if the papers were as flawed as I said, would have taken all of month to perform; I know because my group did them in 2008 and we published the results in JBC in 2009, well prior to the retractions. These exceedingly simple exps. were never performed at Scripps, nor were they cited in the retractions even though they were aware of the work.

It's very important to note the timeline. Because if someone had been going around publicly for nearly all of 2006, widely disseminating the data that led them to conclude some research was clearly flawed, then it does not make any sense to then, at some later point, try and ask for payment to keep the information private. For example, a paper can't run a revealing article or picture of some actress and then turn around and seriously demand money to keep the info private. Any thinking person wouldn't care because the info has already been made public! However, this is exactly the sort faulty logic that was offered about me and some, such as niceguy, unfortunately gobbled it up.

Another important fact was that I was never burned by trying to reproduce the faulty work, as I didn't waste one day trying to follow the techniques reported in the retracted papers. You know who might have been perturbed? I believe the 10 or so scientists that dedicated as much as 3 years of their lives trying to make the techniques work probably cared a bit more that the premise of their wasted effort might have been fraudulent work. As an added note, it would not have made any sense for me to send anonymous letters to Scripps for at least two reasons: first, I had already established a very public profile as the person repeatedly calling for the retraction of two high profile papers, it again doesn't make any sense to try and then hide, that's not my MO. Secondly, such letters almost certainly caused ever greater examination of the glycosylation work by those at Scripps. I would think the more attention on the issue, the more likely the papers might be retracted. Simply put, a retraction at any point up until the publication of our 2009 JBC paper would have obviated the need for our paper. Therefore, we really didn't want them to retract at that point because our work would have been unpublishable, meaning all my team's hard work would have been wasted.

The second thing I did was that I sat back, endured personal attacks, all the while working on yet another open, public, and genuine critique of their work. Since the authors failed to offer any scientific reason for their retractions, we provided it last year in PNAS:
2011, 108, 1320-1325.
http://www.pnas.org/content/108/4/1320 vol. 108 no. 4 1320-132

In this paper we performed some basic experiments to show that the glycosylation work failed not because of lost notebooks or anything, but simply because the enzymes reported were essentially wild type. As an added bonus, we issued a caveat on a third paper, involving the same people, that has flaws identical to the retracted papers, but has yet to be retracted. Maybe niceguys could read our genuine critique of this third paper and post something on its merits rather than posting nonsense.

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