Faked Crystallography
science.org
science.org
What it turned out they had done is optimize a predicted structure of their molecule using density functional theory (DFT), then draw it like a crystal structure would be displayed (a 3D plot with error ellipsoids at each atom, with probable bonds shown) and tried to pass it off as a true crystal structure. My advisor missed this when he reviewed it first - if you're reading quickly, you just see a crystal structure and accept it for what it is. So I wonder how many like this slip through the cracks every year. Apparently a lot, if the CCDC identified ca. 1000 of them.
Maybe there should be a bounty on uncovering these?
This shit has to stop. If publish or perish is going to continue to be a thing, maybe just switch to publishing negative results. It's not sexy, but it's valuable too.
I had an argument recently about why fundamental research was important. The other person insisted that money should only be spent on endeavors where the outcome is known to benefit humanity. They couldn't accept, despite not having any science or math training, that sometimes we study things that start off seemingly useless and become important, or that we sometimes stumble upon things. (And this is why we should spend money on science in general).
Think about all the scientifically illiterate politicians who control money and funding who probably have similar views.
I can totally understand how we let things get this bad. If you don't provide a positive result, you might be facing unemployment. It's not about advancing our knowledge anymore.
If we are to be allowed to publish papers from negative results then I should go and dig out my PhD notes and get writing!
Seriously, though, I started noticing the many broken incentives early on, after a explanation about "impact factor" from an older PhD student in our lab.
This was one of (and unfortunately not the only) reason I decided to leave academia after my Ph.D., leaving my field entirely and going into software engineering rather than taking a postdoc position. Academia isn't for everyone, and neither is industry... but wow, I sure am happier where I am now.
What often happens though is that the paper will get retracted but then the authors play hot potato in blaming different people for faking it and it turns into a whole mess where you don't always know (i.e. cannot prove) exactly who did the faking.
"Someone else faked it and I missed it, just like all the reviewers!!"
Why does a low residual electron density prove the model? What is electron density anyway? And how do we measure it?
Anyway it seems like this whole conversation is out of your depth currently. There are many good X-ray crystallography texts available if your interest continues.
why not just publish this instead. surely an optimized model is still valuable.
In my field (small inorganic molecules used as catalysts), I typically calculated the structure along the way to calculating the molecular orbitals for describing the electronic structure (important for understanding many properties of the catalyst and its reactivity) and predicting the infrared and visible spectra (useful for comparison with experiment and for explaining the electronic and magnetic properties of the molecule). It's the whole picture that's valuable, not just the structure - and the more experimental properties you include, the harder it is to fake the whole thing.
ANy time you have a 3D structure (model) you can run the equations in forward mode to create the structure factors of the crystal that would have created that model.
That is not what fake data is. It might be a misrepresentation is the author tries to pass it out as experimental results, but it is not fake, i.e. it came from a real study and actually has some meaning (though not much if it is indeed an unstable structure that can just be observed in a computer, and it is ground for rejection depending on the journal).
I mean, I don’t have much patience with people over-hyping their results, but fake data of the common sort is either photoshopped graphs, re-used spectra coming from other studies or compounds, or things like that. And this definitely happens. But the “it came from a simulation, therefore it’s fake” argument is very unhelpful in general.
A spectrum from a simulation is not fake, it’s just a simulation result.
This is also not what the article is about. The problem they face is completely fabricated data, not DFT structures in a poorly worded paper.
Of all places, this is probably the last one where I would expect this argument.
https://bmcresnotes.biomedcentral.com/articles/10.1186/1756-...
https://www.science.org/doi/10.1126/sciadv.1600192 """ Textbooks and teaching classes still emphasize that hydrogen atoms cannot be located with x-rays close to heavy elements; instead, neutron diffraction is needed. We show that, contrary to widespread expectation, hydrogen atoms can be located very accurately using x-ray diffraction, yielding bond lengths involving hydrogen atoms (A–H) that are in agreement with results from neutron diffraction mostly within a single standard deviation"""
I’ve observed something sociologically fascinating about China. In multiple fields, gaming, research, academics etc, the proportion of the population likely to cheat seems to be higher in China. Examples include,
https://www.theatlantic.com/education/archive/2016/03/how-so...
https://www.ign.com/articles/2018/02/16/99-of-pubgs-banned-c...
https://www.reuters.com/investigates/special-report/college-...
https://www.nature.com/articles/d41586-021-02587-3
There are cheating scandals everywhere, but, as an outsider, it seems to be somewhat more endemic in China. The anomaly begs the question, why.
Being born in China doesn’t radically wire your brain in a different way. People seem to cheat everywhere, but more people are more likely to cheat here, in this specific environment, why is that? What’s causing them to adopt this behavior as an acceptable strategy?
I can’t seem to find any interesting research on the topic beyond idle speculation. Does anyone know of anyone investigating this?
Note - this comment is not meant to be denigrating nor a judgement, but an observation and a question. The question begs a deeper attempt to ascertain a) if it’s true and b) the factors driving it.
Same goes for academia I suppose. When incentives for academia are aligned towards publishing, and if there is minimal or no enforcement of cheating at an organizational level, you’re at a disadvantage if you don’t cheat.
I don’t think Chinese academic institutions have robust academic integrity and enforcement policies and unless that changes, you’re likely to see Chinese academics stuck in a Nash Equilibrium.
When we got his part of the paper it had just been copied wholesale from academic sources; the professor had already been prewarned. We all got an "F", and the one student was put on probation, and lost his funding. It really sucked. The rest of us were given a chance to rewrite the term paper.
> We all got an "F"
> The rest of us were given a chance to rewrite the term paper.
That seems really unfair. Why didn't the rest of you just get a grade based on the quality of the rest of the paper?
e.g. https://eric.ed.gov/?id=EJ1178415
which describes cultural differences in cheaters
These PhD papers were apparently the easiest to quickly edit from someone else and push past the uninterested reviewers.
Anyways they reported a structure of a very important protein, the pump involved in exporting antibiotics from a bacterium. But none of the data made sense, there were known mutations that changed activity that were in strange places in the molecule. He chalked it up to "allosteric interactions".
The problem with crystallography is that we can't directly measure the phases of the diffraction pattern (we can measure the intensities) and as anyone who does Fourier transforms knows, the phases contain more information than the intensities. So we typically bootstrap a guess of the phases using a similar protein, then calculate a rough structure, then assign more detailed locations for specific atoms based off of chemical constrainst, then recalculate phases of the model, then apply these fake phases to the known intensities to get a refined electron density, and so on iteratively.
The risk is you can think your shit smells like roses, and use math to support your claim .
Anyways someone didn't bite the bs, and actually redid all of the phases using three orthogonal methods (xenon soak, gold soak, selenomet) and showed that three transmembrane helices were totally misassigned. The original pi wrote an apology, chalking it up to his python script he'd written hastily flipped the signs of some of the rows.
This is bullshit. I cannot imagine how flipping some of the signs could have resulted in this error. What is more likely is that the PI bootstrapped with a premature model of the protein, that made the threading errors, where he threaded the sequence through the electron density completely wrong, as a guess, to beat competitors to the punch.
Anyways the pi, Geoffrey Chang, was never called out on this bullshit or his toxic workplace. He's still a professor in academia, at a highly ranked institution.
http://xray0.princeton.edu/~phil/Facility/Guides/ABCtranspor...
I'm not 100% sold that it was malicious, but imo that doesn't change much. Chang's job was to be a PI and vet these things and whether he failed in his duties intentionally or unintentionally, he should lose his job.
The Xray data and model bias and handedness is so complex and hard to deconvolute that since that incident I've always wondered if we are doing enough to vet the huge amount of xray structures on deposit. I'm very glad to be primarily in cryo instead...
Ok, downvoted. Can someone explain to me how a centrosymettrically inverted structure will get some of the helices correct?
Now, sure, if you can prove that there was deliberate misconduct on the part of the PI, then you can go through channels and hopefully get an investigation opened. There was an article on HN recently (linked in another comment here) where this happened/is happening with Alzheimer's research. But it's often not so clear cut, as you've pointed out - you leave enough room for ambiguity, then "apologize" and retract the paper. There's no (significant) negative consequences for the retraction if you're already an established leader of your field (and you can still use your influence over the peer review process to shape the field to continue favoring your research). Meanwhile, the accuser is all but guaranteed to be blacklisted from their field for the same reasons - and if they don't have tenure yet, then game over, hope you had a backup career in mind.
The current incentives in academic research are broken. Sometimes I wonder if the tenure system is partly to blame - does it go too far in creating these protected positions of power that can be abused? Then again, tenure exists for a very good reason - to protect dissenting voices by being pushed out by these same forces. It seems more and more however that tenure is no longer sufficient to protect against this (or maybe it never was), and we need broader reform of the peer review system in order to foster healthy and open discussion in the research community.
This is the result of mandatory publication requirements placed on the Chinese medical professionals. Gaming the system with paid fake publications is just another industry that popped up to meet this requirement.
I'd say there's 2 reasons one might pollute the datastream:
1. Obfuscate competitor's data queries
2. Use "approved" articles as a tool to trick regulators in a grander series of fraud.
It's particularly difficult with most proteins and other biomolecules. [0] But even for small molecular compounds, it isn't always easy. I'm not sure about growing high quality crystals of metal-organic frameworks, but they could easily be limited by defects. Some compounds might be too waxy if there are long aliphatic chains involved.
Even if you do get decent-looking crystals, they might be twinned. If you are working with air or water sensitive compounds, they need to be handled with extreme care and might degrade before the data collection is complete. Some might also have temperature sensitivity, such that they need to be kept at -20 C to prevent melting or another phase transition.
Overall it can be a real make-or-break issue for someone engaged in chemical research.
[0] Check out this PDF of a PowerPoint on the topic: https://hamptonresearch.com/uploads/documents/ramc/RAMC2011_...
Also, it looks like they are changing the topic each year to follow the current fashion, and they are publishing like 200 papers per year, so $50K is like $250 per paper. My (totally unsupported) guess is that they are charging a few hundred bucks per paper, so using a real diffractometer to make a new unique fake image for each paper would duplicate the price of each paper.
Behind the scenes I imagine journals are finding it increasingly difficult to find people to review papers from inside China.
There should be some border between an obviously fake paper and obviously real one.
Fake papers could be used by someone to remove and cancel a real papers together with them if no good criteria is used to separate them. Chinese author name or address does not seem to be a good one.
It would be really interesting to see an equivalent model trained to predict these structures. The physical chemistry of transition metal complexes, especially when multiple metals are in close proximity to each other and connected by shared ligands, is much more complicated than proteins. The reason is because of multireference effects - essentially the quantum entanglement of multiple possible electron configurations. These are exceedingly difficult calculations to perform - common approximations are O(n^8) or worse and require highly specialized knowledge to apply correctly - so an ML model that can efficiently make predictions in this space would be a major transformative breakthrough.
Probably the thread is interesting enough to deserve a merge, so we'll move the comments thence hither.