Tuesday, December 01, 2009

You lost WHAT?!?!?!?!?

I was waiting for the lads over at Drugmonkey to tackle this since CPP would no doubt do a better job. But since they haven't as yet, here goes...

In the November 26 issue of Science there's yet another retraction. This time it's from the group of Peter Schultz. For those who aren't in the know, Schultz has made a name for himself developing ways to trick the translational machinery into inserting non-natural residues into protein chains. The retracted paper (Science 303, 371 (2004)) dealt with the insertion of residues with an attached sugar, the idea being this could be used to study glycosylated proteins in a more controlled manner.

For those without access to Science, here's the retraction in full:

Retraction


We wish to retract our Report (1) in which we report that β–N-acetylglucosamine-serine can be biosynthetically incorporated at a defined site in myoglobin in Escherichia coli. Regrettably, through no fault of the authors, the lab notebooks are no longer available to replicate the original experimental conditions, and we are unable to introduce this amino acid into myoglobin with the information and reagents currently in hand. We note that reagents and conditions for the incorporation of more than 50 amino acids described in other published work from the Schultz lab are available upon request.
Zhiwen Zhang,1 Jeff Gildersleeve,2 Yu-Ying Yang,3 Ran Xu,4 Joseph A. Loo,5 Sean Uryu,6 Chi-Huey Wong,7 Peter G. Schultz7,*


* To whom correspondence should be addressed. E-mail: schultz@scripps.edu
1 The University of Texas at Austin, Division of Medicinal Chemistry, College of Pharmacy, Austin, TX 78712, USA.
2 Chemical Biology Section, National Cancer Institute, Frederick, MD 21702, USA.
3 Rockefeller University, New York, NY 10065, USA.
4 6330 Buffalo Speedway, Houston, TX 77005, USA.
5 Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095–1569, USA.
6 University of California, San Diego, CA 92121, USA.
7 The Scripps Research Institute, La Jolla, CA 92037, USA.

Reference
1. Z. Zhang et al., Science 303, 371 (2004).




Let's break this down...

Regrettably, through no fault of the authors, the lab notebooks are no longer available to replicate the original experimental conditions...


Say what?!?!? You LOST the lab notebooks???? And it's not the fault of any of the authors???? Okay, I can imagine a number of circumstances where this could happen. A fire for example. But if it's something like that why not give the details???? I'm all for the assumption of innocence and all that, but come on, this smells worse than a bucket of shrimp in the sun.

...and we are unable to introduce this amino acid into myoglobin with the information and reagents currently in hand.


They can't reproduce their own experiments. Now call me old school, but I always go by that tried and true rule that the Materials and Methods section of a paper should contain enough detail that the experiments can be reproduced by someone else. Someone not in the lab that did the work. And the retracted article does have two pages of supplementary material, most of which is the Materials and Methods... But the lab (and presumably the authors) that originally did the work still can't reproduce it even with the combination of the lab's collective knowledge and memory plus the published Materials and Methods. Smell that bucket of shrimp yet?

We note that reagents and conditions for the incorporation of more than 50 amino acids described in other published work from the Schultz lab are available upon request.


We lose our lab notebooks and can't reproduce our own experiments, but everyone should still trust us...


I need to open a window or two.

17 comments:

Arlenna said...

Hmmmmmm... yeah, see, synthetic rather than biosynthetic incorporation IS useful for something. Those glycosylated amino acids probably are not very metabolically stable, so somebody must have pushed their data interpretation a little too far there.

And yeah... lost the notebooks????

Anonymous said...

I completely agree, although I am also disappointed that Science didn't require the authors to either omit or explain the notebook "loss". That is totally unacceptable and sets a horrible precedent. The paper below is yet another piece of the puzzle (From a former Schultz lab member) that explains in detail why the Schultz and coworkers’ experiments did not “work”. Basically, E. coli lack the non-specific esterase activity required to free the sugar-amino acid from its per-O-acetylated form (While you might not guess it from the title, this paper is directly related to the retracted papers). Well done Tippmann!

A critical examination of Escherichia coli esterase activity. Antonczak, A.K., Simova, Z., Tippmann, E.M. J. Biol. Chem. Vol. 284, Num. 42, pp. 28795

Samia said...

Whoa.

JollyRgr said...

Holy sh*t......that sort of talk would make you a 'prime suspect' in my job!!!

Goose said...

Oh dear...!

Dr. Jekyll and Mrs. Hyde said...

Holy bejeezus. Can't believe they got away with that. What, "We gave them to the secretary to photocopy and they flew out her open window"?? And yeah, not being able to replicate your own work, in your own lab, with the people who originally did the work...seems as though the lab books are the least of the problem.

biochem belle said...

I'm in agreement with many points made here. A couple additional comments:

- A related paper from Schultz and Wong was retracted from JACS. No mention of missing lab books there (http://pubs.acs.org/doi/abs/10.1021/ja906705a) What is said: "for the isolated case of glycosylated amino acids we are unable to incorporate them under these conditions or those originally described (and note complexities with nonsense suppression and cellular availability)."

- Among other things, Schultz is known for having an ultra-competitive mega-lab. By mega, I mean 40 people. At a time. Still no excuse for this sort of "regrettable" event.

Anonymous said...

I have a reason and it is a good one - the dog ate it.

I used that when I was a kid. Anyone else used it before?

Anonymous said...

The strange thing is that the lab books “went missing”, they worked for 2 years afterwards to no avail to get this work; given the size and resources of groups like the Schultz lab and their endeavours to repeat the work, it shouldn’t have taken 5 years to generate a retraction. They published not 1 but 2 papers supporting their claims (this would suggests that each paper contained new results) that had to be retracted. And finally, they retracted the papers 5 years after their original publication and only when another group published work that provided evidence their approach didn’t work (which was not mentioned in the retraction I note). May be it was this new paper that meant the Schutlz lab were required to retract the paper and not because of his moral duty to scientific truth. If this was the case, then this isn’t as simple as someone making an innocent mistake. They should have retracted this work several years ago when it was found they could not repeat this work. Therefore, there may be more to this than meets the eye. How much man hours and cash have been wasted trying to repeat this work?

Anonymous said...

missing notebook=fraud, period.

How do you explain two pieces of data in the original Science paper to support the incorporation of glycosylated serine: MALDI-MS and Lectin binding? Fraud is the only explanation.

Odyssey said...

Obviously something very strange is going on here. Fraud?I think you would need a full Investigation to be able to decide that.

Anonymous said...

Tippmann is a hero.

Science needs whistle-blowers like Tippmann. It can't have been easy to declare to the world that your old boss has some dodgy/fraudulent papers. Pitty it took this paper to precipitate the retraction as I suspect Tippmann and other lab members knew of the problem when working for Schultz. I think a more thorough explanation from Schultz would help the community understand how and why this has happened.

GPhilly said...

I'm coming to this blog a bit late, but I just have to ask: has anyone looked into whether this fraudulent work benefited in some way one of Schultz's companies? Like maybe Ambrx? Losing academic integrity is one thing, but if Schultz perhaps criminally bilked investors out of their money, that's something else entirely.

Odyssey said...

Everyone should take a deep breath and step back from this for a moment. Schultz has not been shown to be guilty of fraud. As far as I know he's not under investigation. And I'm not accusing him of fraud. I just found his explanation for withdrawal of the paper lacking.

Anonymous said...

Whistleblower

Anonymous said...

whistleblower

Odyssey said...

Whistleblower

???