4 ms·

They did share it with scientists. Here’s Francois Balloux saying he replicated the results, tried to find holes, couldn’t https://mobile.twitter.com/BallouxFr

by graeme 4y ago

They did share it with scientists. Here’s Francois Balloux saying he replicated the results, tried to find holes, couldn’t https://mobile.twitter.com/BallouxFrancois/status/1583165259799412737 https://mobile.twitter.com/BallouxFrancois/status/1583165259...

lamontcg 4y ago
Here's another blue check immunologist on twitter with a substantially different take: https://twitter.com/K_G_Andersen/status/1583252866394771456 https://twitter.com/K_G_Andersen/status/1583252866394771456
- mikeyouse 4y ago
  The authors of this paper are confused about the technology they're using... it's not a good sign about their conclusions.. https://twitter.com/matias_kaplan/status/1583235087067336704 https://twitter.com/matias_kaplan/status/1583235087067336704 https://twitter.com/NoahOlsman/status/1583275862442807299 https://twitter.com/NoahOlsman/status/1583275862442807299
  - lamontcg 4y ago
    Oh dear... Yeah, the author affiliations on the title paper made me wonder if they knew what they were doing at all.
    - tripletao 4y ago
      Their terminology would indeed seem wrong, but the WIV has apparently used a similar assembly strategy (leaving the sites in the final assembly) before: https://twitter.com/jbkinney/status/1583267221047869441 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.
      - mikeyouse 4y ago
        As far as I've been able to read, those sites aren't in the final assembly in Shi's papers - just in the primers. And even more worrying than the false discovery rate are all of the missing genomes they should be comparing. I fear they've left them off because they punch big ole holes in the theory... e.g. https://twitter.com/zhihuachen/status/1583258714340892672 https://twitter.com/zhihuachen/status/1583258714340892672
        tripletao 4y ago
        > As far as I've been able to read, those sites aren't in the final assembly in Shi's papers - just in the primers. 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.
        mikeyouse 4y ago
        Nope - the restriction sites aren't in the final assembly in that paper. These authors just don't understand the tools remotely well enough to have written their paper. It will never be published. https://twitter.com/alchemytoday/status/1583361758903013376 https://twitter.com/alchemytoday/status/1583361758903013376
        tripletao 4y ago
        Yeah, I think Kinney is wrong here. Someone else found a survey paper noting the theoretical possibility of using BsaI and BsmBI in a way that leaves the sites in the final genome, but I haven't seen anyone who actually did that. So I'm leaning to a false discovery here.
        lamontcg 4y ago
        Another good twitter thread on it this morning: https://twitter.com/acritschristoph/status/1583486403416969216 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.
  - mzs 4y ago
    or not: https://twitter.com/VBruttel/status/1583233001319956480 https://twitter.com/VBruttel/status/1583233001319956480
    - mikeyouse 4y ago
      It feels telling that when I click that link, the associated tweets are the kookiest of conspiracy theories about Pfizer execs, vaccine mandates and people screeching about things they clearly don't understand. I suspect in a few days, with Bloom and others reviewing the preprint they're going to be forced to pull it down and "rework" it.
- fsh 4y ago
  It's incredible that the only sensible comments on this thread are this far down. The HN audience really has a massive Dunning-Kruger problem when it comes to science topics (especially true for COVID conspiracy theories).
  - _Wintermute 4y ago
    As a pharmacologist reading the HN crowd arguing about hydroxychloroquine a year or so ago really highlighted 90% of this site regarding topics other than development or start-ups is at the same level as youtube comments, but with more arrogance.
    - salawat 4y ago
      Eh... That's why it's important to speak up and teach where you can. You never know who might learn something, and you may find yourself learning something in return. Nobody gains anything in silence however.
    - nil-sec 4y ago
      I had the same experience a couple of years back when people started discussing AI. I try to keep this in mind but somehow I keep forgetting. It’s genuinely difficult to filter good from bad takes without expert level understanding of a topic unfortunately.
- BlueTemplar 4y ago
z7 4y ago
Looks like he deactivated his account. I would guess the response to these tweets might have something to do with it.

by graeme 4y ago

lamontcg 4y ago

Here's another blue check immunologist on twitter with a substantially different take: https://twitter.com/K_G_Andersen/status/1583252866394771456 https://twitter.com/K_G_Andersen/status/1583252866394771456

mikeyouse 4y ago
The authors of this paper are confused about the technology they're using... it's not a good sign about their conclusions.. https://twitter.com/matias_kaplan/status/1583235087067336704 https://twitter.com/matias_kaplan/status/1583235087067336704 https://twitter.com/NoahOlsman/status/1583275862442807299 https://twitter.com/NoahOlsman/status/1583275862442807299
- lamontcg 4y ago
  Oh dear... Yeah, the author affiliations on the title paper made me wonder if they knew what they were doing at all.
  - tripletao 4y ago
    Their terminology would indeed seem wrong, but the WIV has apparently used a similar assembly strategy (leaving the sites in the final assembly) before: https://twitter.com/jbkinney/status/1583267221047869441 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.
    - mikeyouse 4y ago
      As far as I've been able to read, those sites aren't in the final assembly in Shi's papers - just in the primers. And even more worrying than the false discovery rate are all of the missing genomes they should be comparing. I fear they've left them off because they punch big ole holes in the theory... e.g. https://twitter.com/zhihuachen/status/1583258714340892672 https://twitter.com/zhihuachen/status/1583258714340892672
      - tripletao 4y ago
        > As far as I've been able to read, those sites aren't in the final assembly in Shi's papers - just in the primers. 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.
        mikeyouse 4y ago
        Nope - the restriction sites aren't in the final assembly in that paper. These authors just don't understand the tools remotely well enough to have written their paper. It will never be published. https://twitter.com/alchemytoday/status/1583361758903013376 https://twitter.com/alchemytoday/status/1583361758903013376
        tripletao 4y ago
        Yeah, I think Kinney is wrong here. Someone else found a survey paper noting the theoretical possibility of using BsaI and BsmBI in a way that leaves the sites in the final genome, but I haven't seen anyone who actually did that. So I'm leaning to a false discovery here.
      - lamontcg 4y ago
        Another good twitter thread on it this morning: https://twitter.com/acritschristoph/status/1583486403416969216 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.
- mzs 4y ago
  or not: https://twitter.com/VBruttel/status/1583233001319956480 https://twitter.com/VBruttel/status/1583233001319956480
  - mikeyouse 4y ago
    It feels telling that when I click that link, the associated tweets are the kookiest of conspiracy theories about Pfizer execs, vaccine mandates and people screeching about things they clearly don't understand. I suspect in a few days, with Bloom and others reviewing the preprint they're going to be forced to pull it down and "rework" it.
fsh 4y ago
It's incredible that the only sensible comments on this thread are this far down. The HN audience really has a massive Dunning-Kruger problem when it comes to science topics (especially true for COVID conspiracy theories).
- _Wintermute 4y ago
  As a pharmacologist reading the HN crowd arguing about hydroxychloroquine a year or so ago really highlighted 90% of this site regarding topics other than development or start-ups is at the same level as youtube comments, but with more arrogance.
  - salawat 4y ago
    Eh... That's why it's important to speak up and teach where you can. You never know who might learn something, and you may find yourself learning something in return. Nobody gains anything in silence however.
  - nil-sec 4y ago
    I had the same experience a couple of years back when people started discussing AI. I try to keep this in mind but somehow I keep forgetting. It’s genuinely difficult to filter good from bad takes without expert level understanding of a topic unfortunately.
BlueTemplar 4y ago

z7 4y ago

Looks like he deactivated his account. I would guess the response to these tweets might have something to do with it.