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Shoddy Coronavirus Studies Are Going Viral And Stoking Panic (buzzfeednews.com) 73

Posted by msmash from the how-about-that dept.
Scientists are rapidly posting findings about the new coronavirus outbreak online, accelerating the speed of scientific discoveries -- and of misinformation. From a report: Last Friday morning, after a week in which the coronavirus outbreak had been declared a global public health emergency, a group of scientists from India posted a paper online. A handful of genetic sequences in the new coronavirus matched those found in HIV, they reported, suggesting that this "uncanny similarity" meant the two diseases were linked. A scientist in India blasted out the provocative finding to his more than 200,000 Twitter followers: "They hint at the possibility that this Chinese virus was designed ['not fortuitous']. Scary if true." A Harvard researcher with tens of thousands of followers called it "very intriguing." The official-looking, highly technical paper whipped dozens of onlookers into a frenzy, declaring on Twitter and at least one blog that it showed the virus was "man-made" and "not natural" and "prob. not random." But that day and throughout the weekend, an army of scientists also tore apart its claims and pointed out there was no proof the matches were anything but a meaningless coincidence.

For the second time in as many weeks, a segment of social media was tfreaking out over a coronavirus study that hadn't been reviewed by experts or published in a journal. It was a "preprint," or a preliminary draft, published on BioRxiv (pronounced "bio-archive"), a free repository that hosts thousands of unvetted papers about the biological sciences. Preprint servers bypass the long, arduous timelines of traditional, peer-reviewed scientific publishing, and can lead to lightning-speed information sharing during outbreaks like this one. But the coronavirus is also bringing to light the pitfalls of this new system for the first time, as everyone from bad actors to naive ones grasp for new information in a panic-driven climate. The "uncanny" paper was withdrawn by its authors on Sunday, putting an end to an undeniably messy situation that spread misinformation about a little-understood virus that has so far sickened upward of 20,600 people and killed more than 420, the vast majority near the outbreak's epicenter in Wuhan, China.
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Shoddy Coronavirus Studies Are Going Viral And Stoking Panic More

Shoddy Coronavirus Studies Are Going Viral And Stoking Panic

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  • Move along, this information was not blessed by the priestly class. Disregard it immediately, or face the consequences.

    • So what you're saying is, you're gonna believe anything that any random fuckhead posts online as long as it's not from CNN, NYT or other mainstream (admittedly shitty) outlet. Gotcha. I have an anti-elite bridge to sell you!

      • Damn right, these fucking egg head scientists are all full of shit anyway. I get all my information from Twitter and dodgy right-wing blogs.

        • Dude. No. Just no. When mocking people nowadays you have to be more loony. I read your post above before I saw this and realized you were joking. You need to mention really crazy shit like Q or otherwise make it clear you are being sarcastic or it's literally impossible to tell.

          • "dodgy right-wing blogs" didn't give it away? That level of self awareness is beyond the reach of Q anon cranks.

            Fun fact, did you know that anyone can become a scientist. You don't need to be born to one of the 108 blessed families. And you don't need to swear allegiance to the dark lord. The only requirement is you show up to college for 4 years and go into a moderate amount of debt.

            Let those without student loans, mortgage payments, or maxed out credit cards throw the first stone!

            • No, it did in that post I replied to, but he posted above that with the less self-aware "oh sure, scientists are gods we must never doubt" line and no give-aways like "dodgy right wing blogs". It was 100% legit a talking point among conspiratards.

      • Re: (Score:3, Informative)

        by Shaitan ( 22585 )

        In fairness the paper did not come from random fuckhead posts online but from a highly credible and qualified source.

        On the one hand the sequences in common with HIV are in a highly variable region. On the other that is also where one might bio-engineer the sequences. On the one hand some of the sequences are short, with the longer sequences not being perfect matches. On the other all of those sequences are only found in this virus and HIV samples (though the shorter sequences are individually found elsewhe

        • Re: (Score:3, Insightful)

          by jeff4747 ( 256583 )

          On the other hand, there is a lot of your DNA matches a sea sponge. [sciencedaily.com]

          DNA similarity is extremely common. As a result, it's not only insufficient proof of this extraordinary claim, it's little-to-no proof at all.

    • Re:Nothing to see here folks (Score:5, Informative)

      by coastwalker ( 307620 ) <acoastwalker@NospaM.hotmail.com> on Wednesday February 05, 2020 @10:41AM (#59693132) Homepage

      The best rebuttal I have read is this one.
      from the comments on the paper so you can all calm down:
      Alex Crits-Christoph

      All four of the identified amino acid insertions are extremely short and are found in the genomes of many other organisms, not just HIV. In other words, the primary finding of this work are entirely a highly expected coincidence.

      All organisms contain a DNA code that has the genetic instructions for development, functioning, and growth - this is known as the "genome". You can imagine each genome as a book of instructions. What these authors did is look in the genome book of the 2019 novel coronavirus and identified 4 sets of letters that aren't found in the genome book of SARs, a related coronavirus. They then compared these letters to the genome book of HIV, and found some places where they looked somewhat similar - but not even identical. However, because these sets of letters were so short, they are often found in many genome books by chance - they way you might search for the phrase "can be there" in Google Books and find that thousands of books contain those words - but this is not an example of plagarism.

      Note here: We call these sets of letters "insertions" because they are in one genome, but not in a close relative - "insertion" does not imply human interference or engineering - it is an evolutionary term and refers to a natural evolutionary mutation.

      Here are the four insertions:

      TNGTKR

      HKNNKS

      RSYLTPGDSSSG

      QTNSPRRA

      These four insertions are protein sequences, that are encoded by a DNA sequence (which you may know uses molecular "letters" of A, G, C, and T to encode for proteins, which uses 20 molecular amino acid "letters").

      You, dear reader, do not have to take anybody's word for it that these letters are a concidence - you can do the bioinformatics yourself!

      If you would go to: https://blast.ncbi.nlm.nih.gov... [nih.gov]

      You will arrive at a search engine for these genome books, kind of like the Google of biology. Click on "Protein Blast", because are going to search for these protein sequences.

      Under where it says "Enter accession number", you can paste any one of the four sequences above.

      And then you can hit the "BLAST" button at the bottom of the screen. In a few minutes you will get a set of results.

      Let's go through the results for the longest sequence, "RSYLTPGDSSSG", together.

      Under the "Description" field you can see resulting hits. The first hit you see is to "spike glycoprotein [Wuhan seafood market pneumonia virus]" - this is good, because we know that this sequence came from this genome. Under "Per. Id" you can see the similarity of this sequence to other hits - in this case, you can start by seeing that this sequence is also found in Bat coronavirus, so isn't actually novel at all! And there are many comparative hits that as equally as good, or often better, than the HIV comparison.

      Let's then take a look at the second sequence, "HKNNKS", together.

      If you go through the same search process for this sequence and look again at the results, you can see hundreds of perfectly identical matches. Maybe you see Sipha flava - that's an Aphid, or Tetrahymena - that's an Amoeba. Drosophila is a fruit fly. Clearly this sequence is found in thousands of genomes.

      Fortunately, the search has a built in way of answering the question "How likely was this result to have occurred by chance?". It is called the E-value, or Expect Value - the number of times we'd expect to see this result purely by chance. As you can see here, many of the E-values listed on this page are greater than 7829 - so we'd have expected to see 7829 instances of matches like these completely by chance! This is not evidence for gene transfer or gene similarity - it's simply a coincidence. As you now search for the other insertions described by this paper, you'll see that all of them hit hundreds of other genomes simply by chance. It is no surprise at all that they could have matches with some similarity in the HIV genome.

      Congratulations! You are now a more careful and proficient bioinformatician than the authors of this paper.

    • No, it really is a bad paper.

      You share a lot of DNA sequences with sea sponges [sciencedaily.com]. That doesn't mean you're engineered from sea sponges, or sea sponges are engineered from humans.

      DNA similarity is extremely common. By itself, it is not evidence of engineering by humans.

    • Now I know what freaking out is, but what is tfreaking out? Bad Slashdot editors? A new word?

  • We are related to every living thing (Score:4, Interesting)

    by AndyKron ( 937105 ) on Wednesday February 05, 2020 @09:57AM (#59692970)
    I'm pretty sure a handful of genetic sequences in the new corona virus will match DNA in every human body. We are, after all, related to every living thing on this planet

    • Re: (Score:2)

      by baenpb ( 1343241 )
      It's not like we evolved from viruses, but viruses can insert their DNA into the human DNA. It's kind of their thing. So I completely agree.

    • Re: (Score:3)

      by Zocalo ( 252965 )
      Pretty much. I think there are a few things like specific extremophiles and other exotics that are borderline, but so far at least it does appear that every form of life on Earth likely had a common root ancestor, and there is a considerable DNA/RNA overlap between most eukaryotes and bacteria. Viruses may have DNA and/or RNA as well, but again they are more than likely mutations that branched off the same tree, so again significant levels of common structures should be assumed by default. The CoronaViru

    • How does that preclude genetic engineering? "BuzzFeed" has put an impossibly high bar on the authors to prove that it was engineered. In reality the authors simply said the sequences in this coronavirus were unlikely to occur in nature and they left it at that.

      • How does that preclude genetic engineering?

        it doesn't. What it does do is preclude DNA similarity alone as evidence of genetic engineering.

        First, you need to know how common that similar sequence is. If it's already in an enormous number of genomes, it's very unlikely to have been engineered. If the sequence is only found in one completely unrelated animal, then you'd have to figure out if it's co-evolution or engineering. Lots of almost-unique sequences from non-relatives would point towards engineering, but you can't rule out co-evolution.

        This

      • Evidence of genetic engineering would be something like finding an actual gene encoding some known function from the other virus.

        Coronaviruses have about 30 kilobases of RNA, HIV something like 10kb. Finding a shared sequence of six bases is analogous to comparing two books and finding out that the word "nonsense" is included in both. It's only a tiny fraction of a gene and meaningless without context.

    • Probably not. [sciencealert.com]

      Unless you want to pull back the supposed common origin of life to basically an unfalsifiable "we're all related because we all come from atoms". And, naturally, propose there was only one abiogenesis event, because it's certain but so improbable that it only happened once, type of incoherent naturalist position.

      And, in the case of an engineered organism, "related" is a rather tenuous descriptor.
  • But the virus itself was patented: patent link [google.com]
    "The present invention also relates to the use of such a coronavirus in a vaccine to prevent and/or treat a disease." i.e. It's a bioweapon they create in the classic fail-west devils advocate pre-emtive problem for a solution that is destroying our very civilization. Quacks!
    Thai Doctors have had success treating the virus with HIV drugs lopinavir and ritonavir along with flu medication oseltamivir [pharmaceut...nology.com]
    Who really knows, but I know one thing: only a sucker wou

    • But the virus itself was patented: patent link [google.com]

      Yes, a completely different member of the (very large) coronavirus family, one that has not much to do with the current 2019-nCov and affects animals not even humans, has been patented for a procedure to make vaccine use a weakened variant of that specific coronavirus.

      How does this serve as an argument that the completely different 2019-nCov is a bio weapon ?

      Thai Doctors have had success treating the virus with HIV drugs lopinavir and ritonavir along with flu medication oseltamivir [pharmaceut...nology.com]

      0. "success treating". Nope. Read the actual interview: it's not a cure but it helps slow the progression and diminish symptoms.
      1. It's based on an int

  • A "hint" to scientists simply means "we might have stumbled upon something that may warrant further exploration."

    • That is very non-committed. The paper with the HIV link hypothesis has nothing to say and will only cause stupid speculation so why publish it?

      • It's fine to publish it - we are not their intended audience and never should have even heard of this article. Blame the media for grasping at straws trying to scoop a story that isn't there.

        • Re: (Score:2)

          by kqs ( 1038910 )

          Oddly, I looked but didn't find this story at any media outlet I trust, though I found a few "shoddy study makes morons panic" stories. So I'm not sure why you blame the media, unless you are reading and trusting media which would print tripe like this. And if so, then I'm pretty sure the media is not the problem.

  • So the paper says this coronavirus contains sequences that are not likely to have occurred in nature. Obviously with the advent of CRISPR it's now pretty straightforward to splice genes around in a lab. Then good old BuzzFeed comes to the rescue and ridicules the paper by claiming that because the authors can't prove it was engineered it could well just be a coincidence. The paper never claimed it was engineered, it just pointed out that these sequences were unlikely to occur in nature. Idiots.

    • The author on social media where he pushes his preprint paper very much does make a claim it was engineered. Which is a moronic thing to do, he is nuking his career with it. He'll be forever known as a guy who made a simple research mistake and turned himself into a conspiracy nutter over it.

    • So the paper says this coronavirus contains sequences that are not likely to have occurred in nature.

      And this is false. The sequences already occurred in nature, in other things. Some are in other coronaviruses, some are in other viruses, and some are in everything from humans to fruit flies to amoebas.

      DNA similarity isn't in-and-of-itself proof of anything. Genes are pretty heavily conserved, and when they're not conserved, similar evolutionary pressure results in similar gene sequences (co-evolution).

      To put it another way, the outside of mammalian mucous membrane cells are all pretty similar (conserve

  • First off, reading the papers, the authors are speculating about some sort of in-situ exchange between the SARS virus and HIV. Not engineering, that was added on by media reporters.

    Second, even withing the papers there's no formal analysis of the probability of the mutation given the suspected heritage, they just say, oh, that's unlikely

    Third, the genetic record of coronavirises is far from complete, and that the actual ancestors were likely never in the record.

    Forth, there's methodological problem for usin

  • OMFG! I just saw video out of China of a patient trying to eat the brains of a doctor! It totally happened! Panic!! Actually, true story - my wife in Home Depot yesterday saw someone buying cases of face masks that they said they planned to put up on Ebay and gouge a profit. Aren't we a lovely and yet dumb as paint species?

  • As usual. It generates clicks, it generates revenue, so let's create a panic.

    I'm done with idiots who believe those bullshit peddlers. Go sit in the corner with the religious and keep giving your money to the assholes that keep you dumb, ignorant and panicky.

  • Not that batshit insane profit-through-panic "news" media system.

    Riiight.

    (Hypothesis: Without the media putting a spotlight on them, neither SJWs nor Trump would even be a thing.)

  • Most of the people, the large majority that died were over 60, high blood pressure and/or diabetic or cancer survivors or other pre-existing conditions.

    • Re: (Score:1)

      by rldp ( 6381096 )

      Yeah I mean more people die in car crashes than in 737 crashes, so why all the hubbub over some sensor?

      I think people are clearly just racist against Boeing.

    • It's hype. The coronavirus is literally one of the causes of "the common cold" and has been for a very long time - which has a 3% mortality rate. This strain of coronavirus comes in around 2.01%, so it's not even a severe strain of it. Does this mean the Chinese didn't try to cross the cold virus with HIV? No, they probably did that given those markers have been found AND the outbreak started in a town in China with a BSL4 lab designed by a Harvard engineer who was arrested for selling the secrets of ho

    • Re: (Score:1)

      by AHuxley ( 892839 )
      The sick need to be detected as they make other people sick...
      The options are:

      1. Temp, illness starts and they can go to hospital well before they infect others.
      ie isolated, prevented from making others sick..
      The numbers go down. The better math.

      2. But if they feel fine and wonder around for days/week before seeking treatment?
      Dont worry about self isolation as they still "feel" ok..
      Shopping, education, walks, travel, tourism... for a week..
      Thats the complex math of how many other people did t

  • China government has it all under control this is no big deal

    Please bow down to Winnie the Flu and accept your medical information from a country that believes you can heal yourself by sticking pins into the magical power points on your body.

  • Comment removed based on user account deletion

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