5 ms·

As someone who was a genetic engineer for a long while, watching HN talk about dodgy papers like this is painful. This paper posits a completely crazy cloning

As someone who was a genetic engineer for a long while, watching HN talk about dodgy papers like this is painful. This paper posits a completely crazy cloning strategy that makes no sense (ie doing something far more convoluted than typical bsaI/bsmbi seamless cloning workflows that breaks the whole point of "seamless" workflows), and then tries to use that to make a case for a genomic signature that we could look for. They then look at a handpicked set of viral genomes, but leave a bunch out and duplicate others (I think WIV04 and WHu are the same), and largely seem to be observing without realizing it that yes, recombination occurs among these viral lineages. This isn't even getting into the fact that a restriction-ligation based cloning strategy would leave glaringly obvious fingerprints behind in the form of the hundreds of nucleotide differences that are present outside the cutsites across the lineages... it would be blindingly obvious if someone just cut-and-pasted sars-cov-2 from other studied genomes.

rcpt 4y ago
They "handpicked" those because they're some of the most common. This is discussed in their paper. The "completely crazy" strategy was state-of-the-art and published by the WIV in 2016 https://twitter.com/R_H_Ebright/status/1583868000888795137 https://twitter.com/R_H_Ebright/status/1583868000888795137
- alevskaya 4y ago
  I'm pretty tired of debating people who don't know biology here. Using seamless cloning methods is super common - but they don't work like the paper authors suggest they do. I misspent my youth doing reactions and workflows like these for over two decades. What they're observing is homologous recombination between strains - all the sites they're claiming are found in nature. Again - there would be a genetic signal the strength of the noonday sun burning your eyes out if sars-cov-2 was made by cut-and-paste at these sites. You wouldn't need this ridiculous circular argumentation to prove that point. If we're linking to tweets, these two go into great depth about how ridiculous this paper is: https://twitter.com/Friedemann1/status/1583519970902048768 https://twitter.com/Friedemann1/status/1583519970902048768 https://twitter.com/acritschristoph/status/1583486403416969216 https://twitter.com/acritschristoph/status/15834864034169692...
  - iancmceachern 4y ago
    Thank you, this is why I come to HN (facts). Keep fighting the good fight.
  - jmeister 4y ago
    >I'm pretty tired of debating people who don't know biology here Too bad. This is a matter that affects every citizen in this country, and the experts lost their credibility a couple of years ago at least. The rubes will keep shouting their barbaric yawps over the roofs of the world.
    - ggm 4y ago
      No, they didn't loose their credibility. To political debate they were never granted it, and between themselves as peers it hasn't been lost. Your perception and reality diverged and your claims they lost credibility lacks a crucial qualifier: 'to me' -which I and many many others discount, even at the volume of American science scepticism. You actually aren't a majority, anywhere and you don't define scientific credibility any more than politics does.
      - tetris11 4y ago
        It is weakening somewhat. The sheer volume of papers that pass in high impact journals, and then are later pulled after X years with minor repercussions, seems at least to me to be an alarming trend. That, paired with the cronyism I've personally witnessed between editors and professors... as someone entrenched in the field, I have to say, I'm surprised more people aren't jaded.
    - simplotek 4y ago
      > This is a matter that affects every citizen in this country, and the experts lost their credibility a couple of years ago at least. I don't agree. What we did see is ignorance and completely absurd conspiracy theories taking the center stage while experts were being sidelined or even completely removed from the discussion.
drpixie 4y ago
Yeah - Covid seems to be one a few topics that bring out "special" opinions. It's a pity, and not confined to HN, but seems to be a sign of the times.

rcpt 4y ago

They "handpicked" those because they're some of the most common. This is discussed in their paper. The "completely crazy" strategy was state-of-the-art and published by the WIV in 2016 https://twitter.com/R_H_Ebright/status/1583868000888795137 https://twitter.com/R_H_Ebright/status/1583868000888795137

alevskaya 4y ago
I'm pretty tired of debating people who don't know biology here. Using seamless cloning methods is super common - but they don't work like the paper authors suggest they do. I misspent my youth doing reactions and workflows like these for over two decades. What they're observing is homologous recombination between strains - all the sites they're claiming are found in nature. Again - there would be a genetic signal the strength of the noonday sun burning your eyes out if sars-cov-2 was made by cut-and-paste at these sites. You wouldn't need this ridiculous circular argumentation to prove that point. If we're linking to tweets, these two go into great depth about how ridiculous this paper is: https://twitter.com/Friedemann1/status/1583519970902048768 https://twitter.com/Friedemann1/status/1583519970902048768 https://twitter.com/acritschristoph/status/1583486403416969216 https://twitter.com/acritschristoph/status/15834864034169692...
- iancmceachern 4y ago
  Thank you, this is why I come to HN (facts). Keep fighting the good fight.
- jmeister 4y ago
  >I'm pretty tired of debating people who don't know biology here Too bad. This is a matter that affects every citizen in this country, and the experts lost their credibility a couple of years ago at least. The rubes will keep shouting their barbaric yawps over the roofs of the world.
  - ggm 4y ago
    No, they didn't loose their credibility. To political debate they were never granted it, and between themselves as peers it hasn't been lost. Your perception and reality diverged and your claims they lost credibility lacks a crucial qualifier: 'to me' -which I and many many others discount, even at the volume of American science scepticism. You actually aren't a majority, anywhere and you don't define scientific credibility any more than politics does.
    - tetris11 4y ago
      It is weakening somewhat. The sheer volume of papers that pass in high impact journals, and then are later pulled after X years with minor repercussions, seems at least to me to be an alarming trend. That, paired with the cronyism I've personally witnessed between editors and professors... as someone entrenched in the field, I have to say, I'm surprised more people aren't jaded.
  - simplotek 4y ago
    > This is a matter that affects every citizen in this country, and the experts lost their credibility a couple of years ago at least. I don't agree. What we did see is ignorance and completely absurd conspiracy theories taking the center stage while experts were being sidelined or even completely removed from the discussion.

drpixie 4y ago

Yeah - Covid seems to be one a few topics that bring out "special" opinions. It's a pity, and not confined to HN, but seems to be a sign of the times.