Is this going to be yet one more of those “will be withdrawn after peer scrutiny but by then it is too late because the false meme has been injected into the public consciousness” things?
https://mobile.twitter.com/BallouxFrancois/status/1583165259...
https://twitter.com/matias_kaplan/status/1583235087067336704
https://twitter.com/jbkinney/status/1583267221047869441
I'd worry about their false discovery rate, for the same reason I worry about the large number of parameters in Pekar's epi model. It's still an interesting result, though.
Where did you read that? Kinney explicitly asserts the opposite, but I can't figure out what he's referring to. Someone else linked to Figure S9 from their 2017 PLOS Pathogens paper, which indeed seems not to contain the site in the final assembly. I've edited my other comment here to reflect that.
https://twitter.com/acritschristoph/status/15834864034169692...
This is the real kicker to me:
> What about missing sites? The authors propose that someone made a bizarre combination of additions and deletions of cut sites. RecCA matches SARS-CoV-2 at all missing sites because other viruses do. E.g. this one: similar to RpYN06 not just at the mutation, but the entire region.
Clear evidence of recombination across the whole region and not just mutations to manipulate the cut site.
And Francois Balloux seems to have deleted his twitter account this morning.
Jesse Bloom said he'd try reproducing with a wider range of natural viruses and potential synthetic assembly strategies. Unless and until that still gets an interesting p value, I'd agree this is oversold.
Nobody gains anything in silence however.
"Scientists publish papers not because the paper is the end of science, but because it is a unit of research that is valuable to share with others so that others can use this brick of knowledge and either build with it… or find its weakness and break it down...We wrote our entire analysis in R and shared our code with the world. I tried SO hard to check every single line of code and make our pipeline clear & easy to reproduce. However, despite nearly giving myself stomach ulcers checking every line and stressing about these findings, it’s possible someone finds a mistake in our work. We don’t share this work happily - this is the saddest paper I’ve ever written. We’ve shared our code precisely for that reason: we want you to see exactly what we’ve done, and if we’ve done something wrong we are open to hearing it."
As to your original concern, it is a valid one. I wrote this is response to pre-prints popularized via the press earlier this year:
-> Make bold, unjustifiable claims in the preprint; -> Ensure widespread coverage in the science press; -> Walk back those claims during peer-review; -> Get published; and then -> Watch blue checks tout original claims as "Fact!"
They only get withdrawn if they go against the narrative. Any kind of paper that says masks work, lockdowns work, or any paper suggesting Covid is worse than any virus ever… it’s totally cool to share publicly. Doesn’t even matter if it is poorly constructed or turns out to be false.