This is a story of a very strange and scientifically confusing stealth correction for a 10 year old paper in Science, but let’s first bring some perspective.
Just when 2020 began, the Nobel prize winner and US-American chemistry professor Frances Arnold retracted her Science paper, published in the same year she received her Nobel prize: 2018. She announced it in a tweet:
“After publication of the Report “Site-selective enzymatic C‒H amidation for synthesis of diverse lactams” (1), efforts to reproduce the work showed that the enzymes do not catalyze the reactions with the activities and selectivities claimed. Careful examination of the first author’s lab notebook then revealed missing contemporaneous entries and raw data for key experiments. The authors are therefore retracting the paper.”
Every scientist can become victim of coauthor’s research misconduct, and it takes exceptional decency and research integrity to retract your own paper voluntarily. Arnold should be applauded for that, as should be other scientists who retracted their works without being asked or, as it almost always happens, forced to.
Instead, the media jumped on the story, BBC even addressed the academic as “Ms Arnold” with the undertones of “Woman gets Nobel, fails in Science”, which presumably will be used by certain characters as argument for why women so rarely get Nobel Prize in chemistry, physics or physiology / medicine.
Here a female Nobelist took responsibility for her lab member’s likely research misconduct which she did overlook initially, but eventually uncovered herself, and then acted most exemplary. Yet no media was interested to compare her actions to those of certain other Nobelists.
How about Louis Ignarro, who coauthored many papers with massively fake data, while peddling phony health supplements and magic pomegranate juice? How about Sir Martin Evans, who teamed up with some notorious liar and struck-off dentist to offer miracle cures to heart attack patients using fraudulently-patented cells of very questionable origin, free of any scientific background? Both Ignarro and Evans are Nobel Prize winners in physiology or medicine and highly respected by every science journalist. Which brings us to another case, that of chemistry Nobel prize winner Sir Fraser Stoddart and a paper he and his coauthors recently stealthily corrected in Science. Nobody writes about that either, because these are all successful men of science after all.
This is the Science paper, from the lab of Omar Yaghi in Berkeley, University of California:
Qiaowei Li, Wenyu Zhang , Ognjen S Miljanic, Chi-Hau Sue , Yan-Li Zhao , Lihua Liu , Carolyn B Knobler , J. F. Stoddart, Omar M Yaghi Docking in metal-organic frameworks Science (2009) doi: 10.1126/science.1175441
On 14 March 2019, a comment was posted on PubPeer:
“Figures 4A and D show MOF-1001 before and after docking of PQT2+, a single crystal–to–single crystal transformation.
The process from A to D is described as “MOF-1001 crystals were introduced into a saturated solution of PQT·2PF6 in acetone”. The supplementary video also shows that shaking is involved. The bottom part of Figure 4A and D shows that the crystals have moved. I thus wonder how the crystals can be unaffected by the washing process, as they do not move at all between the two pictures.
Are Figures 4A and D for illustrative purposes? Were crystals fixed onto a substrate for the purpose of those pictures? I welcome clarification on this experimental aspect.“
Indeed, it is very confusing. The article was accompanied with an online video showing how a large volume of paraquat solution was added to a flask with MOF-10001 crystals, which was then shaken. The added fluid at least doubled the total volume (also the photos in Figure 4A and D prove it), which is bound to have caused much turbulence, with a mystery remaining how this would have left all crystals unmoved. And the video even showed the flask being shaken. Maybe the authors made a mistake, and accidentally used a colour-adjusted placeholder picture twice?
On 31 August 2019, an anonymous reader approached the journal Science with their concerns:
“I thus wonder how the crystals in the top of Figures 4A and 4D can be unaffected by the washing process, as they do not move at all between the two pictures. There is, in fact, not a single pixel displacement of any of the crystals, between the uncomplexed and complexed crystals in Figures 4A and 4D. I do not understand how that could be physically possible, and wonder: Are Figures 4A and D for illustrative purposes? Were crystals fixed onto a substrate for the purpose of those pictures?“
Science editor Jake Yeston immediately replied:
“This paper was published too long ago for us to pursue a formal data request. You are free to contact the authors directly.“
The reader forwarded this exchange to me, and I wrote to Yeston, asking why Science deems a 10 year old paper suddenly too old to bother about its data integrity. Yeston replied citing “poor judgment on my side” and explaining:
“After further discussion, we have contacted the authors to request an explanation for the concern expressed in the PubPeer comment, notwithstanding the time elapsed.”
Common sense would let you expect an upcoming corrigendum, where the authors would apologise for an inadvertent mistake, replace the images in Figure 4 and remind everyone that all conclusions remain unaffected. Instead, something much stranger happened.
In late October 2019, Yeston and the then-Editor-in-Chief Jeremy Berg announced to issue a clarifying correction. Because, according to the editors, the two images were actually perfectly correct as the authors explained. Yeston clarified:
“Just to be clear, their claim is that the sample was under the microscope the entire time, the same sample of crystals in a solvent suspension. They introduced the paraquat reactant slowly and carefully so as not to perturb the crystals. That’s what they clarify is being shown in the image—not a dry sample of crystals that they spilled out of a vial twice in order to take two different photographs. I was initially confused too about how the latter interpretation could be physically possible, but I think the clarified experiment does indeed seem feasible. I corresponded and talked with three of the authors extensively, and I believe they made a thorough case for the integrity of the experiment.“
The anonymous reader remained unconvinced:
“To be frank, that you can introduce a reactant in the solution and the image does not move at all, not one of the crystals by a single pixel, is a feat I would not be able to achieve, nor anyone in my group.
I don’t doubt the science reported in the paper, and the authors provide ample evidence and characterization of the compounds obtained. But I believe they cut corners on this particular subfigure. I guess everyone will be able to draw their own conclusion once all this is clarified.“
On 5 November 2019, Science issued a stealth correction. It has no DOI, it is not available as separate article and it can not be googled or accessed freely. There is no mention at the paywalled abstract page that the article was corrected. Not really the way a Corrigendum is supposed to be published, but the journal told me that they see if differently.
To get to the correction, you must log in, either via Science subscription or a free AAAS user account, which lets you read papers older than 1 year. Once you did that, you will probably search for the correction notice in the full text, but there is nothing. Instead, you must scroll to the bottom of the full text page to find a link to Supplemental Online Material. It is a new supplementary file, with some new revelations in it. After following that link, you will find, among other things, this text:
“Correction (5 November 2019): After the publication of this Report, the authors have provided a supplementary addendum to incorporate further technical details on the experiment monitoring the paraquat inclusion process in MOF-1001 without disturbing the crystals in Section S1. Figure S0 and accompanying paragraphs explain the experimental setup.
The original version is accessible here.”
To find the new addendum, you must download the updated supplement file and proceed to page 20. There, you will find a new section, and now we see it was not just a small spot where the crystals did not move, no, it was the entire bottom of the flask. A large field of crystals there remained perfectly immobile after a large volume of fluid was gently added, as if they were all glued. Except that they were not:
“Monitoring paraquat Inclusion without Disturbing Crystals:
To prove that the MOF pseudorotaxanes were obtained in a single-crystal to single-crystal transformation, rather than the dissolution and recrystallization manner, several MOF-1001 single crystals were placed at the bottom of a 20-mLvial in 5 mL acetone solvent, and drops of paraquat solution were added gently using pipet without disturbing the crystals. The whole process was monitored under optical microscope, and snapshots were taken at 0, 1, 2, 25, and 30 mins after adding paraquat. Partial pictures of the crystals at 0 and 30 mins were presented in the upper panels of Figs. 4A and 4D in the main text.”
Now, it may sound like kindergarten-like behaviour, but no, this is elite science on the highest level imaginable, Nobel Prize and all. It is worth noting that nowhere in the main text did the authors discuss the relevance of their experimental setup, neither previously or even now. It most obviously only became somewhat important after the journal reached out to the authors 10 years later regarding the PubPeer comment. The word “microscope” was not mentioned once before, not in the main text nor in the old supplement, which never bothered to explain the impressive paraquat addition technology in this regard. A technology which we now learn manages to keep every single crystal in its place despite these crystals not having been immobilised in any way as the authors admit.
And as for “drops of paraquat solution were added gently using pipet without disturbing the crystals“, how does one do that if the volume of paraquat solution added is (according to all information in the paper) at least twice the volume of the MOF-1001 crystal suspension? In the normal world, adding even one drop would have moved some crystals. But not here.
The only reasonable answer is: magic. Or the Infinite Improbability Drive. This is exactly why the Nobelist Fraser Stoddart will never retract a paper, while Frances Arnold retracted hers.
The new Science Editor-in-Chief Holden Thorp announced maximum transparency in corrections and retractions with his new 2020 editorial which accompanied the Arnold retraction. But for Yaghi and Stoddart, the journal decided against too much openness. I understand it, the correction is too embarrassing and plain weird, best to be hidden where nobody will find it. Reminds me of the Hitchhiker’s Guide to The Galaxy:
“But the plans were on display…”
“On display? I eventually had to go down to the cellar to find them.”
“That’s the display department.”
“With a flashlight.”
“Ah, well, the lights had probably gone.”
“So had the stairs.”
“But look, you found the notice, didn’t you?”
“Yes,” said Arthur, “yes I did. It was on display in the bottom of a locked filing cabinet stuck in a disused lavatory with a sign on the door saying ‘Beware of the Leopard.”
If such magic crystal technology really does exist in this universe, Stoddart deserves another Nobel Prize. To the very least, he and Yaghi should be lauded by some Vogon poetry.
Readers pointed me towards this interesting article in the ACS magazine C&EN from 2017. Right after he won the Nobel Prize, Stoddart, together with a business partner, set up a business called PanaceaNano, offering nanotechnology-based skin ointments: “Noble” line of antiaging cosmetics including a $524 formula described as an “anti-wrinkle repair” night cream”. This is how it works, as advertised by ACS:
“The nano-cubes are made of carbohydrate molecules known as cyclodextrins. The cubes, of various sizes and shapes, release ingredients such as vitamins and peptides onto the skin “at predefined times with molecular precision,” according to the Noble skin care website. […]
Stoddart himself declares, “It is an exciting moment to witness the birth of commercial products that improve the quality of life of people based on renewable, safe, organic, biodegradable functional nanomaterials.”
Anyone still mistrustful towards Sir Fraser’s scientific claims?
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