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I remember in grad school a principal investigator that was notorious for driving his grad students and postdocs hard: he had set up a cot for them to sleep on
by throwawaymaths 4y ago
I remember in grad school a principal investigator that was notorious for driving his grad students and postdocs hard: he had set up a cot for them to sleep on in the office, if the bioreactors we're turning making protein he would ask wtf was going on (got to keep the pipeline filled)
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.
- opticfluorine 4y agoThat's unfortunately all too common of a story. And with the way peer review works - where the leaders of any niche topic are the ones who will be asked to peer review articles in the same area - the system makes it very easy for an established professor to shoot down dissenting voices. 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.
- throwawaymaths 4y agoI don't think it's tenure. Chang did not have tenure at the time.
- COGlory 4y agoHere is a link to some commentary on the ABC transporter debacle. http://xray0.princeton.edu/~phil/Facility/Guides/ABCtransporter.html 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...
- throwawaymaths 4y agoJust to be clear: I don't think it was malicious, I just think the excuse he gave was bs. I could be wrong -- I'm not a crystallographer, just a nonprofessional expert (I have given talks) at the Fourier transform. I just can't see how a centrosymettrically inverted structure would get some of the helices correct Ok, downvoted. Can someone explain to me how a centrosymettrically inverted structure will get some of the helices correct?