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Lesley Sitter's avatar

Full transparancy isn't even enough, as journals and ethic commitees and sometimes reviewers are just as complicit in my experience. I've been involved with three cases, two obvious, one less so.

One of these wrote about an outbreak of disease A, but genome data shows it to be a more common organism B. I first mail the authors, no response, then I express this to the editor of the paper, who escalates to the head editor of the journal, it dissapears for 3 months, and comes back with a ethics committee referral. They thing that me and the original authors should write a letter, let the audience decide, i.e. shifting the burden of proof off the journal and onto the reader, essentially making a case that journals aren't actually usefull for publishing factual data.

Second case, a bit more nuanced. A partial genome is presented that is statistically impossible. It presents 30% of a genome that coincidentally has 98% of all critical diagnostic loci. Secondly, it has reads that are identical to high coverage samples in their study, suggesting cross-talk or spiking. We were not allowed to raise this problem to the journal, because collaborators were involved. So we are shielding "friends" from clearly dubious data that is the foundation to their paper.

Last, a paper publishes a disease A from region B. They also show several other signals in region B, but only partial genome recoveries for disease A. It only took a day to identify that they used the wrong software to identify the partial genomes, and the wrong software to visualize the accuracy of the calls, because in fact, there was bo signal, just incorrect use of software (like throwing darts, and everything lands on the wall around it, and still calling it bullseye). Secondly their sample with full genome recovery has human DNA. Mapping that human DNA revealed it is not from region B at all, but from the other side of the world. Given that their entire story hinged on the presence of disease A being in region B, its in their title, intro and conclusion, you'd expect the authors to acknowledge the issue or the journal to pull it. However first we wanted to included it in a supp for our own paper, and were told by the chief editor to remove it. Then we wanted to submit a matter arising, but were told that they didn't see value in it. After a second group identified the same issue and raised it with the chief editor, we were asked to quickly send our matters arising manuscript. After that, we were left in the dark for more than a year. This year we finally got a response, one reviewer argued that the humand DNA waa likely just contamination, even though it contained a fully covered 18x mitochondrial genome, but then suggested the disease was valid. Another reviewer was hesistantly agreeing with us but essentially asked for months of additional work from our end to prove we were correct. The authors themselves redid their libraries and now did find human DNA from region B, mixed with region C, so they could not determine the validity. They also redid the low coverage ones, and were only able to obtain 600 reads, across the 3 samples, an all of them were in conserved genes. Yet somehow argued that this did not at all matter, because we didn't have an ethical agreement with the native population of region B to even be allowed to look at the human DNA. Lastly the journal gave us a week to respond, and that was a hard deadline. Now it is going to be published as an opinion piece rather than a document attatched to a retraction.

Overall, i see no accountability at any level. I see protectionism from top to bottom. I strongly doubt that a system like this will last much longer and only see a way forward with a fraud database. Something that funding bodies can just type a name in, and see how many red flags an author has. Because the system doesn't seem to be able to self correct. The fraudulent authors want to save face, the supervisors don't want the scandal, the uni doesn't want the lawsuit, the funders don't want the label of being unable to see the difference between good and bad projects (plus they need to fill their quotas), the journals don't want to lose their income and status despite not fulfilling their core function, and no one indirectly involved wants to be associated with drama and therefore no one will stick their necks out to say anything.

Milkshake Goodman's avatar

Gather round kids and grab your muskets, the Qui Tam Clan ain't nuthin' to fuk wit.

Qui Tam prosecution is a little-known provision still available in some jurisdictions (notably the US) which allows private individuals to file charges and prosecute a criminal case themselves on behalf of the government. It is sometimes referred to as "private prosecution".

The relevance here is that you can skip over all the challenges of getting the police (or some other agency) to understand and prosecute scientific fraud by just directly prosecuting scientific fraud yourself.

Even better, if your prosecution is successful, you win a cut of whatever civil penalties are recovered.

The one caveat is that this provision only lets you prosecute people defrauding the government, not fraud in general. But given that practically all research is funded (in part or in whole) on government grants, pretty much any fraudulent paper you identify likely has standing.

At some point, you fosci / sleuths / whatever are going to realize there's an upper bound on the effectiveness of any system based on reporting things to an authority. Doesn't matter if its a research integrity office, a district attorney, a regulatory body, etc.

At a fundamental level the premise of an office where "you report it, we do something about it" has pretty much never worked well in any context. Anyone who attempts to navigate such a system either gives up or ends up learning so much along the way just to get marginal success that they've effectively studied a law degree without getting one.

What I'm saying is, some of you are going to unwillingly become fake lawyers along your journey. You should embrace that fact now. Living in denial about it just means being willfully blind to a whole world of highly effective levers you could be pulling.

The court registry is a path to certain abilities some consider unnatural.

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