Sandbox (4)

Sometimes very active discussions about peripheral issues overwhelm a thread, so this is a permanent home for those conversations.

I’ve opened a new “Sandbox” thread as a post as the new “ignore commenter” plug-in only works on threads started as posts.

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3,471 thoughts on “Sandbox (4)

  1. walto,

    Problem was file format, sorry. You can upload PDFs but only image files will display. I converted your PDF to an image file but it is poor quality. Hopefully people will follow the link to enable them to read the text.

    ETA I’ve added links to my comment with image.

    Oh, and congratulations on getting published.

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  2. Alan Fox:
    To be fair to phoodoo, he may be at real risk using the internet to discuss political repression in China.

    Blink twice, Phoodoo if that is true.

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  3. Do you guys remember that chinese scientist who claimed to have evidence that SARS-CoV-2 was engineered in a lab in China?
    A new paper is out: https://zenodo.org/record/4028830#.X1_IjRAzaHu

    The abstract suggests a conspiracy theory: “The alternative theory that the virus may have come from a research laboratory is, however, strictly censored on peer-reviewed scientific journals”

    Not promising. So it won’t be published for peer review apparently. It’s sponsored by an organization with a political agenda: https://rolsociety.org/

    Would the pros be interested in discussing the contents of the “paper”? Does it deserve it’s own thread?

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  4. dazz,

    Potentially, although the statement “… knowledge of the origin of SARS-CoV-2 and of how the virus entered the human population are of pivotal importance in the fundamental control of the COVID pandemic…” is one hell of an unpromising start.

    It could be a short conversation. I will try to be as cold-eyed as I can.

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  5. I can see Dr. Li Meng-Yan mentions the Nature paper in their introduction.

    A widely cited Nature Medicine publication has claimed that SARS-CoV-2 most likely came from nature. However, the article and its central conclusion are now being challenged by scientists from all over the world5-15. In addition, authors of this Nature Medicine article show signs of conflict of interests16,17, raising further concerns on the credibility of this publication.

    Wow, that’s kind of ironic, isn’t it?

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  6. Then they go on to cite 11 references about scientists from all over the world challenging the conclusions of the Nature paper

    5. Maiti, A.K. On The Origin of SARS-CoV-2 Virus. Preprint (authorea.com), DOI:
    10.22541/au.159355977.76503625 (2020).
    6. Lin, X. & Chen, S. Major Concerns on the Identification of Bat Coronavirus Strain RaTG13 and Quality
    of Related Nature Paper. Preprints, 2020060044 (2020).
    7. Bengston, D. All journal articles evaluating the origin or epidemiology of SARS-CoV-2 that utilize the
    RaTG13 bat strain genomics are potentially flawed and should be retracted. OSFPreprints, DOI:
    10.31219/osf.io/wy89d (2020).
    8. Segreto, R. & Deigin, Y. Is considering a genetic-manipulation origin for SARS-CoV-2 a conspiracy
    theory that must be censored? Preprint (Researchgate) DOI: 10.13140/RG.2.2.31358.13129/1 (2020).
    9. Rahalkar, M.C. & Bahulikar, R.A. Understanding the Origin of ‘BatCoVRaTG13’, a Virus Closest to
    SARS-CoV-2. Preprints, 2020050322 (2020).
    10. Robinson, C. Was the COVID-19 virus genetically engineered? (https://gmwatch.org/en/news/latestnews/19383, 2020).
    11. Robinson, C. Another expert challenges assertions that SARS-CoV-2 was not genetically engineered.
    (https://gmwatch.org/en/news/latest-news/19383, 2020).
    12. Sørensen, B., Dalgleish, A. & Susrud, A. The Evidence which Suggests that This Is No Naturally Evolved
    Virus. Preprint, https://www.minervanett.no/files/2020/07/13/TheEvidenceNoNaturalEvol.pdf (2020).
    13. Zhang, B. SARS-CoV-2 Could Come from a Lab – A Critique of “The Proximal Origin of SARS-CoV-2”
    Published in Nature Medicine. (https://www.linkedin.com/pulse/sars-cov-2-could-come-from-labcritique-proximal-origin-billy-zhang?articleId=6651628681431175168#comments6651628681431175168&trk=public_profile_article_view, 2020).
    14. Sirotkin, K. & Sirotkin, D. Might SARS‐CoV‐2 Have Arisen via Serial Passage through an Animal
    Host or Cell Culture? BioEssays, https://doi.org/10.1002/bies.202000091 (2020).
    15. Seyran, M. et al. Questions concerning the proximal origin of SARS-CoV-2. J Med Virol (2020).

    One from Authorea (which is a doc repository, not a scientific journal, as far as I can tell) a bunch of preprints, some articles from online magazines, and one in the Journal of Medical Virology that is published as a letter to the editor, but no peer reviewed papers, if I’m not wrong.

    ETA: And #13 (Zhang, B) supposedly published in Nature, doesn’t show up in searches. Is that a made up reference?

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  7. There are too many problems with this to bother listing them.
    The throwing of shade on E. Holmes and I. Lipkin is beyond ironic, given the authors’ employer. Likewise the import attached to Shi and Li engineering EcoRI-BstEII fragments, right down to the incorrect citation number (should be #48, not #47, near the bottom of page 17; this leaves a casual reader with the impression that EcoRI-BstEII fragment swaps were published in 2008 — that would be evidence of malfeasance, if it were true.).
    Regarding the science, there’s a lot of “well look, it could have been engineered” without ANY suggestion of evidence that it WAS. I did look at the bit about the furin cleavage site, and speaking as someone who HAS engineered a furin cleavage site into a protein, [heh], they are talking shite.

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  8. dazz: And #13 (Zhang, B) supposedly published in Nature, doesn’t show up in searches. Is that a made up reference?

    That’s B Zhang’s self-published critique of the paper they are trying to diss, which is: Nat Med. 2020 Apr;26(4):450-452.

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  9. DNA_Jock: That’s B Zhang’s self-published critique of the paper they are trying to diss, which is: Nat Med. 2020 Apr;26(4):450-452.

    Oops, I’m a bit slow, hehe. Thanks.
    The Linkedin link to Zhang’s article is broken though. Kinda sloppy, isn’t it?

    ETA: I take it you agree that none of those references belong in the scientific literature, right?

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  10. dazz: I take it you agree that none of those references belong in the scientific literature, right?

    Well 5 thru 13 are unreviewed.
    I am not sure about #15: Seyran; I don’t have a subscription to J. Med Virol.
    On the other hand #14: Sirotkin & Sirotkin is kosher, but given that they are pointing out that serial passage in a lab is not distinguishable from serial passage in a poultry farm, and they reckon that is sufficient to explain the origin of SARS-CoV-2, they actually deep-six much of the “Rule of Law Society” tin-foil-hattery.
    Oh vey.

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  11. DNA_Jock: I am not sure about #15: Seyran; I don’t have a subscription to J. Med Virol.

    I believe that’s the one submitted as a letter to the editor, and it seems to be an open letter: https://onlinelibrary.wiley.com/doi/epdf/10.1002/jmv.26478

    Please, correct me if I’m wrong.

    ETA: Source: https://onlinelibrary.wiley.com/doi/10.1002/jmv.26478

    DNA_Jock: On the other hand #14: Sirotkin & Sirotkin is kosher, but given that they are pointing out that serial passage in a lab is not distinguishable from serial passage in a poultry farm, and they reckon that is sufficient to explain the origin of SARS-CoV-2, they actually deep-six much of the “Rule of Law Society” tin-foil-hattery.

    Is there a way to access the peer review process on that one,please?

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  12. dazz,

    Thanks, I didn’t look hard enough for Seyran. Contrary to what Li-Meng et al claim, Seyran is supportive of Andersen et al’s argument, specifically the “if you were going to engineer the spike protein, this isn’t the sequence you would come up with” aspect. Highlighting how unlike other human tropic viruses SARS-CoV-2 is is an argument against man-made origin.
    Li-Meng is apparently seeking asylum in the USA.
    Sirotkin & Sirotkin is a little weird.
    Karl Sirotkin appears to have had an unremarkable career in bioinformatics, whereas Dan Sirotkin appears to have a more chequered career after Harvard and the NSA.
    Served 3.5 years, apparently.
    I recommend Carl T Bergstrom for a saner view.

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  13. DNA_Jock: Contrary to what Li-Meng et al claim, Seyran is supportive of Andersen et al’s argument, specifically the “if you were going to engineer the spike protein, this isn’t the sequence you would come up with” aspect.

    That’s hilarious. So the one legit peer reviewed reference they have, actually contradicts their thesis. You can’t make this stuff up.

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  14. I’m curious about the covid mode of transmission.

    In March, when the panic began, everyone was recommending hand washing, but I am unaware of any evidence that the virus spreads via surfaces.

    Purely anecdotal, but in March, my local food market requires gloves in addition to masks. Other stores offered, but did nor require hand sanitizer.

    Now this store offers hand sanitizer, and takes your temp.

    Temperature taking seems to be the thing now. A few months ago it seemed settled that the virus was spread by asymptomatic people. Now it doesn’t seem so certain.

    Anecdotally, people no longer appear to be afraid. In March, grocery shopping was like living in a zombie apocalypse movie. Now, people go about their business, and masks are the only weird thing.

    The second wave is anomalous. I’ve been watching Spain, France, and UK. They have lots of new cases, but few associated dearths. This is true even if you allow a three or four week lag between Infection and death. I haven’t seen a geographical region have a major second wave of deaths.

    On the other hand, Florida, Texas, and California are all in their first wave, and deaths are not dropping as rapidly as the decline in new cases.

    I would appreciate someone checking my numbers, but covid does not seem nearly as deadly as the 1918 flu. My sources say the 1918 pandemic killed one percent of the world population. So far, covid seems on track to kill 0.02 percent. At the moment, it’s about 0.014 percent.

    The usual annual death rate is around 730 per 100,000. Covid should add two to that number. The number varies more than that from year to year.

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  15. petrushka: In March, when the panic began

    March? Is that when the orange idiot was lying his ass off?

    And you were blaming the mayors?

    BTW, they didn’t have phone tracking apps and 2 dollar masks available in 1918.

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  16. petrushka: I would appreciate someone checking my numbers, but covid does not seem nearly as deadly as the 1918 flu. My sources say the 1918 pandemic killed one percent of the world population. So far, covid seems on track to kill 0.02 percent. At the moment, it’s about 0.014 percent.

    The usual annual death rate is around 730 per 100,000. Covid should add two to that number. The number varies more than that from year to year.

    Your numbers are wrong and, additionally, your math is wrong.

    Even if your 0.02% number were reasonable, it would correspond to 20 per 100,000, not two.

    But 20 per 100,000 seems to be either optimistic, or missing the point, or both.
    US, UK, Spain, Italy, Sweden, Brazil, Mexico all have rates over 50 per 100,000

    In other news, mask-wearing, hand-washing and temperature-taking do not eliminate CoViD (or flu) transmission: they significantly reduce it.
    That’s the goal.

    Requiring gloves is a bad idea, since most people do not know how to take them off.

    But hey, if your sole criterion is “Not as bad as the 1918 flu”, cool beans. CoVid isn’t as bad as the Chicxulub impact, either, I guess.

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  17. DNA_Jock: Requiring gloves is a bad idea, since most people do not know how to take them off.

    Well, how do you take them off? Peel off inside out, so any putative contamination stays inside the glove?

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  18. Alan Fox,

    Actually, it’s pretty easy. Just imagine that the outside of both gloves is covered in shit/vomit/fluid of your choice…

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  19. DNA_Jock:
    Alan Fox,

    Actually, it’s pretty easy. Just imagine that the outside of both gloves is covered in shit/vomit/fluid of your choice…

    Drumpf apparently pays money for that.

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  20. I think I need to follow Carl T Bergstrom religiously.
    Just picked up an interesting factoid from his twitter feed:
    Dodd et al 2020 looked at the rates of SARS-CoV-2 reactive blood in blood donations.
    Sensitivity is 90%.
    953,9216 blood donations were tested.
    Reactivity was
    In first-time donors: 2.99% (# reactive =4,786)
    In repeat donors: 1.58% (# reactive = 12,550)
    The proportion of first-time donors sky-rocketed from 11% to 17% when testing was publicized, so there’s a significant effect of “people donating blood in order to get tested” — that’ll even be true among repeat donors too (such as my wife).
    So these reactivity values may be over-estimates.
    Bottom line: nowhere is reactivity in the general population over 3%, so “herd immunity” is a long, long way off.
    ETA testing was performed over the time period June 15 to August 23…

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  21. It looks like donna drumpf has been listening to Petrushka and Jock:

    WASHINGTON — President {idiot} argued this week that the death toll from the coronavirus was actually not so bad. All you had to do was not count states that voted for Democrats.

    “If you take the blue states out,” he said, “we’re at a level that I don’t think anybody in the world would be at. We’re really at a very low level.”

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  22. DNA_Jock: DNA_Jock on September 17, 2020 at 10:20 pm said:
    I think I need to follow Carl T Bergstrom religiously.

    You could do worse. Carl is, like me, trained in theoretical population genetics. He is at my university, and in one of the two departments with which I’m affiliated. I’ve served on Ph,D. thesis committees of a couple of his students. So I know him.

    He was the first person to publicize the slogan “flatten the curve” (in collaboration with graphic artist Esther Kim). This became a huge phenomenon. I wrote him and said, take it in, you just saved a lot of lives. Most of us can’t be sure we have saved even one life by the end of our careers. So you can retire now.

    But he has not retired, and has continued to do very good things, and I know he works very hard at it. It is gratifying to see him become one of the go-to people for comments in the media on breaking stories.

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  23. How will future generations ever be able to understand how an entire nation of people selected such a narcissistic windbag ignoramus as the so called leader to make policies and to promote the countries ideas and give direction.?

    That fucking piece of shit has never done a single thing his entire life to help anyone but his fat, piss stained self. And people actually chose him.

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  24. Joe Felsenstein: You could do worse.Carl is, like me, trained in theoretical population genetics.He is at my university, and in one of the two departments with which I’m affiliated.I’ve served on Ph,D. thesis committees of a couple of his students.So I know him.

    He was the first person to publicize the slogan “flatten the curve” (in collaboration with graphic artist Esther Kim).This became a huge phenomenon.I wrote him and said, take it in, you just saved a lot of lives.Most of us can’t be sure we have saved even one life by the end of our careers.So you can retire now.

    But he has not retired, and has continued to do very good things, and I know he works very hard at it.It is gratifying to see him become one of the go-to people for comments in the media on breaking stories.

    Fucking awesome

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  25. phoodoo: How will future generations ever be able to understand how an entire nation of people selected such a narcissistic windbag ignoramus as the so called leader to make policies and to promote the countries ideas and give direction.?

    Three million fewer voters selected Trump than Clinton. Not once in the last four years has Trump’s approval exceeded 50%. In the election in 2018, Trump lost the House. Only the numerically illiterate among future generations will be unable to understand that the entire nation did not select Trump.

    That fucking piece of shit has never done a single thing his entire life to help anyone but his fat, piss stained self. And people actually chose him.

    For the 42%, he got them three Supreme Court Justices. He kept Clinton out of the White House. He made them feel okay with their prejudices and insecurities. He was not and black man or woman. A little extra money in the paycheck. They seem pretty happy with the deal.

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  26. phoodoo:
    newton,

    The entire nation was allowed to vote. This is the bumbling psychopath they chose.

    But who is “they”? A bit less than 60% of eligible voters actually voted in 2016. About 27% of eligible voters went for trump, maybe 30% for Clinton. And even then, turnout for Democrats was weak, because (1) a lot of them despised Clinton; and (2) a lot of them were pissed at how the DNC stacked the deck against Bernie, and refused to vote for anyone.

    What we witnessed was the vast gulf between campaigning and governing. Someone with a lifetime of experience conning people (and that means banks, insurance companies, and contractors, as well as yokels), someone who can identify and appeal to bigotry, someone who would prefer to cheat even when it’s not necessary, some who plays a misleading character on reality TV, that’s your perfect candidate in a nutshell. Also your worst possible executive or administrator. Clinton was exactly the opposite, an unconvincing no-charisma candidate who had mastered the art of governing.

    Anyone who put in the effort to dig into Trump’s past knew what he was, but few did so. NOW, however, we’ve had years of incompetence and dishonesty shoved down the national throat, even Fox News watchers know he’s a liar and a cheat, and this time it boils down to just how bigoted the public is. This time, we deserve the candidate we get, and we go into it with our eyes open and our fears and hatreds front and center.

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  27. phoodoo: The entire nation was allowed to vote. This is the bumbling psychopath they chose.

    It is clear that the system you are an apologist for, where nobody is allowed to vote, is far superior.

    Whatever the ills of the USA are at least we are able to hear about them. The horrors that are happening next door to you you will never know. And, somehow, that’s just fine with you.

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  28. phoodoo:
    newton,

    The entire nation was allowed to vote. This is the bumbling psychopath they chose.

    True, more or less. Republicans are masters at repressing the vote. Those who voted against Trump did not select him to be President. In fact they have impeached him for abusing the office to remove him. They actively seek to replace him through the electoral process.

    What those voters did select was to respect the Democratic process. Despite evidence than their opponents did not. If future generations wish to judge those of us living through the Trump Presidency harshly, that is their right.

    I do understand the confusion from those have no choice in the selection. The entire nation by default chooses who is selected .Though that hardly seems a praiseworthy alternative to Trump.

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  29. Flint,

    You think people didn’t know what they were voting for? They didn’t realize he was this thin skinned, vindictive, unimaginative, uneducated, self serving, lying bigot? You think that only came to light AFTER he was elected??

    He has the soullessness of a dick cheney and the brain of a frog that lacks any curiosity. It’s quite a stretch to say that wasn’t obvious before the election.

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  30. I mean, isn’t this what your so called free press guarantees? That you know the idiot you are choosing.

    What a blessing.

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  31. phoodoo: You think people didn’t know what they were voting for?

    What I’m concerned about is that a large chunk of the US electorate will vote for him again.

    And that a new Trump appointee on the Supreme Court will ensure a close result gets called in Trump’s favour.

    I hope everyone who can vote gets registered and votes.

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  32. phoodoo: I mean, isn’t this what your so called free press guarantees? That you know the idiot you are choosing.

    What a blessing.

    Far better to have that choice made for you, right?

    It’s amazing how deeply you have drunk from the authoritarian well.

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  33. phoodoo:
    newton,

    The entire nation was allowed to vote. This is the bumbling psychopath they chose.

    Not all US citizens are allowed to vote, but yes, voter turn-out was depressingly bad. There are lots of reasons for this, but one of which is that Election Day is not a national holiday (unlike in more functioning democracies), so people need to vote before work or after — if they have time at all. There’s also a good deal of active voter suppression in Black majority counties throughout much of the GOP controlled states, since Black voter turnout is bad for them.

    That said, I am genuinely concerned that lots of people will vote for Trump in 2020 because they either don’t know that he’s a bumbling psychopath (despite many decades of evidence) or know but don’t care.

    I suspect that White evangelicals, who might have at least been on the fence, will come out in droves for Trump — because by the time of the election he will have nominated a replacement for Ginsburg who will promise to vote to overturn Roe vs Wade.

    My guess is that his ideal nominee will also think that police should be encouraged to use tear gas and rubber bullets against unarmed protestors, and align nicely with Barr’s views about antifa.

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  34. Alan Fox: What I’m concerned about is that a large chunk of the US electorate will vote for him again.

    Yes. And he doesn’t need a popular vote majority to win the Electoral College. He won the 2016 GOP primary with 16% of the vote (because it was a crowded field) and the general with 27% of the vote.

    And that a new Trump appointee on the Supreme Court will ensure a close result gets called in Trump’s favour.

    Count on it.

    I hope everyone who can vote gets registered and votes.

    That’s an awful lot of faith to have in a broken system.

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  35. Kantian Naturalist,

    There is also the possibility that some of those evangelicals who say they don’t want abortion, don’t really mean it, because they know it could be one of their girlfriends or daughters who might end up needing one.

    If they think it is a real possibility that they could actually be banned, they just might start to be careful what they are wishing for.

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