A new paper claims SARS-CoV-2 bears signs of genetic engineering
economist.com
economist.com
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.
The "completely crazy" strategy was state-of-the-art and published by the WIV in 2016 https://twitter.com/R_H_Ebright/status/1583868000888795137
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/acritschristoph/status/15834864034169692...
That information did exist at one point.
What I've tried repeatedly to impress upon people here is that most routine cloning strategies leave pretty clear signatures, and the idea that a lab would go so far as to eliminate these signatures for such mundane virology work is tantamount to a much more elaborate conspiracy theory.
I don’t need to be a biologist to call your assumptions out as junk science.
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.
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.
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.
Could you please show a single example you feel demonstrates this thing you describe as "trust me bro, im a scientist" stance?
"As someone who was a genetic engineer for a long while, watching HN talk about dodgy papers like this is painful."
Understand: "as a great scientific with long career, i feel depressed to see so much stupidy."
Trying to attract my sympathy for his "painfull feeling", therefore trying to positively bend my opinion in his favor.
"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."
Im not a specialist here, but this babbling just suggest me someone unable to think out of the box, restricting all possibles to only what he can master.
"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."
"would leave" - "it would" - To me this is legalist wording. A way to suggest something without actually affirming it. cause the dude is not sure at all in fact.
So may be the core idea of his message is scientifically groundede and valid, but the way he expresses it is far more closer to the 'trust me bro' stance than critical neutral scientific phrasing.
This is a prime example of Asimov's quote: "Anti-intellectualism has been a constant thread winding its way through our political and cultural life, nurtured by the false notion that democracy means that 'my ignorance is just as good as your knowledge.'"
first the guy claims he is a scientist and continue with some obfuscated babbling mixing emotional tone and hazardous outcome. Which at first and second read, isnt a scientific neutral analysis and critics.
Therefore it left only the "trust me bro" posture. Which is far from beeing efficient at all.
Just because you’re unfamiliar with molecular biology doesn’t make it obfuscated babbling.
They're not looking for the existence of the sites they're looking at the distribution of them. Their paper shows that in natural viruses the distribution is distinct from synthetic viruses.
The proposed classifier is how uniformly distributed these sites are, not that the sites exist.
> circular argumentation
Can you elaborate? They select a site based on commonly used it is (and maybe also the fact that Baric and WIV published on it). Then they found evidence of it being used. What's "circular"?
> great depth about how ridiculous this paper is
The crux of his argument (and yours) is tweet 10/ in that thread -- "You CAN actually do it like that, but why should you?" which is pretty weak.
Often, if not most, of the time the engineering I come across hasn't been done in the slickest most optimal way. The fact that there's a better way to do something isn't proof that everyone's been doing that the whole time.
For example, WIV was using non-seamless cloning in 2016 https://twitter.com/R_H_Ebright/status/1583868088524541953
> pretty tired of debating people who don't know biology
I started my PhD in math biology but for whatever reason I just couldn't get along with the PI or any of the postdocs. I don't know what it was. I eventually switched to just math. Oh well.
I used to second guess my decision but in the nearly two decades of research since I've never come across the level of smugness and credentialism that I now see coming from that field. Every disagreement is met with remarks about "kindergarten molecular biology" or referring to other researchers diagrams as "cartoons". Now I don't second guess anymore.
Perhaps if you're so bothered by the people here you should keep your posting to virological.org or simply talk with the biology profs on Twitter directly.
https://virological.org/t/the-comparative-recency-of-the-pro...
Horseshoe bats are the likely reservoir of sarbecoviruses (1), including SARS-CoV-1 and SARS-CoV-2 (2–4). Since the emergence of SARS-CoV-1 in 2002 and SARS-CoV-2 in 2019, there has been an increase in the sampling of sarbecoviruses in bats, which can reveal how recently SARS-CoV-1-like and SARS-CoV-2-like viruses sampled in bats shared a common ancestor with, respectively, SARS-CoV-1 and SARS-CoV-2 (jointly referred to as SARS-CoVs)
It may lie to one side of a debate about "engineering" but I take heart from the virologists doing the ongoing detective work to unpack what we can know about this disease and its vectors.
(I posted this to HN directly before. It got very little traction which I doubt means very much)
If the paper in the article is correct then what really needs to be done is a ban on gain of function research.
https://en.wikipedia.org/wiki/Wuhan_Institute_of_Virology#ci...
I imagine getting the balance of R value and virulence just right would be difficult; I didn't include that in my estimate.
Pandemics come along every hundred years or so, so this will happen again unless we hurry up and exterminate all mammals (humans included).
Alternatively, people could stop panicing. As pandemics go, Covid was extremely mild, and tools like contact tracing and mRNA vaccines will help us reduce the impact of the next one.
Citation from year 2025 needed
Why? This is like saying all car repairs should be done in the same clean room that the Webb telescope was assembled in.
Because most car repairs don't have a non-zero outside chance of ending the human species?
"A new controversial paper claims SARS-Cov-2 bears signs of genetic engineering"
Thats a good sign.
I cannot render a percentage number to this probability but in my mind it’s close to certainty.
the title of this article is not clickbait. not any kind that is manipulative, anyway.
it is a headline designed to get you to read an article, yes, and in that way most headlines are "bait" for someone, but clickbait headlines specifically use manipulative techniques to both avoid telling the nature of the article at all, and still prey on a reader's curiosity, both of which encourage the reader to load the article page, often to see that the article itself isn't something the reader cares about. clickbait headlines and articles are both designed solely to create revenue from advertisement impressions.
this article headline is accurate and complete, and the article is exactly what the headline said it would be.
so, not clickbait at all. not even close.
When I Google “What is click bait?” I get this definition: “(on the internet) content whose main purpose is to attract attention and encourage visitors to click on a link to a particular web page.”
This article kinda does actually fit that definition. Not with manipulative wording in the title, but with choice of topic and (to parent’s point) highlighting an outlier and lacking representation for the general trends.