Taxacom: Science fraud - Nature

Thu Aug 24 15:16:12 CDT 2023

Yep - although CODA stands for center of origin, dispersal, and
adaptation (adaptation as a means of dispersal, and dispersal as a
mechanism for differentiation). I see no problem bringing the matter up
here as many taxonomists have strong views about biogeography (haven't met
any that don't at least), and all the molecular taxonomists/systematists
practice CODA methods that don't do what they claim, or use non
empirically non-existent units of analysis.

On Thu, Aug 24, 2023 at 3:52 PM Tony Rees <tonyrees49 at gmail.com> wrote:

> Hi John, an 800 word (all right, 791) extended quotation disputing the
> origins of COVID hardly qualifies as "not wanting to go down the COVID
> hole", but I will let it pass...
>
> I must confess the acronym CODA as related to biogeography is unfamiliar
> to me, however a brief google search led me here: "Biotic assembly in
> evolutionary biogeography: a case for integrative pluralism" by Juan J.
> Morrone. published in 2020 in "Frontiers of Biogeography", which claims to
> "... discuss the differences between the dispersal-vicariance model and the
> center of origin-dispersal-vicariance (CODA) and vicariance models". My
> guess is that if you have a problem with claimed fraud in "CODA practice",
> you should take it up in a forum or publication route relevant to that
> topic. Sorry.
>
> Tony Rees, New South Wales, Australia
> https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fabout.me%2FTonyRees&data=05%7C01%7Ctaxacom%40lists.ku.edu%7Cfc4dd2bec74949eceb4708dba4df0de4%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638285050207440892%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=IIY6rahHlAWWjIm7i9psugzYGJ2Ks8j4a1dUg59eCpE%3D&reserved=0
>
>
> On Fri, 25 Aug 2023 at 05:31, John Grehan <calabar.john at gmail.com> wrote:
>
>> I would add that the examples given concern instances where the fraud
>> involved a minority but what happens when the fraud is committed by the
>> majority (as in CODA practice)?
>>
>> On Thu, Aug 24, 2023 at 3:26 PM John Grehan <calabar.john at gmail.com>
>> wrote:
>>
>>> Yeah  - not wanting to go down the COVID hole, or any other subject.
>>> Just happened to be example issues. Cheers, John
>>>
>>> On Thu, Aug 24, 2023 at 3:04 PM Tony Rees <tonyrees49 at gmail.com> wrote:
>>>
>>>> Hi John, you wrote:
>>>> >  If a climate paper was published in Nature or Science, which are not
>>>> climate journals, is this because the authors wished to avoid peer review?
>>>>
>>>> No, I think it is fair to say that these are special cases, that sit
>>>> somewhere above more discipline-specific journals, for articles deemed to
>>>> have high importance; and accordingly, would seek out the best (?) experts
>>>> in relevant fields for review of any particular article. That would be the
>>>> hope, anyway :)
>>>>
>>>> Not going to go down the rabbit hole of origins of Covid at this time,
>>>> however I note that the Rupert Murdoch-owned "Australian" was strongly
>>>> promoting views by a Sky News Journalist (who wrote a book on the same
>>>> subject last year) that everything is a cover-up and the virus escaped from
>>>> the Wuhan Lab. I fact checked her first 4 statements and they were all
>>>> incorrect, after which I lost faith in her analysis. For now I think the
>>>> best summary is probably at
>>>> https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fen.wikipedia.org%2Fwiki%2FOrigin_of_COVID-19&data=05%7C01%7Ctaxacom%40lists.ku.edu%7Cfc4dd2bec74949eceb4708dba4df0de4%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638285050207440892%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=Zm7iS9T3nqvzunFwfSvDta%2B9SIiaDSX%2B4R4NlQA%2BVgI%3D&reserved=0, which Taxacom
>>>> readers are welcome to consult for more detail, or even amend if they
>>>> disagree with it.
>>>>
>>>> Regards - Tony
>>>> Tony Rees, New South Wales, Australia
>>>> https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fabout.me%2FTonyRees&data=05%7C01%7Ctaxacom%40lists.ku.edu%7Cfc4dd2bec74949eceb4708dba4df0de4%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638285050207440892%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=IIY6rahHlAWWjIm7i9psugzYGJ2Ks8j4a1dUg59eCpE%3D&reserved=0
>>>>
>>>>
>>>> On Fri, 25 Aug 2023 at 04:43, John Grehan <calabar.john at gmail.com>
>>>> wrote:
>>>>
>>>>> That's an interesting quote about not publishing in a climate journal
>>>>> for a climate paper:  "This is a common avenue taken by 'climate skeptics'
>>>>> in order to avoid peer review by real experts in the field." But just
>>>>> because a climate paper is not published in a climate journal does not mean
>>>>> that it can avoid 'peer' review. It depends on the journal and the intent
>>>>> of the editor to ensure that proper peer review takes place. If a climate
>>>>> paper was published in Nature or Science, which are not climate journals,
>>>>> is this because the authors wished to avoid peer review?
>>>>>
>>>>> On Thu, Aug 24, 2023 at 2:40 PM John Grehan <calabar.john at gmail.com>
>>>>> wrote:
>>>>>
>>>>>> Thanks for that clarification Tony. As for Nature "might have a
>>>>>> higher degree of scrutiny" - who knows. Saw this as yet unresolved issue
>>>>>> below, this time involving Nature. I don't keep regular track of such
>>>>>> questions, although perhaps I should, and write something on fraud in CODA
>>>>>> biogeography - but then who would publish such?
>>>>>>
>>>>>> A growing number of people, including prominent scientists, are
>>>>>> calling for a full retraction of a high-profile study published in the
>>>>>> journal Nature in March 2020 that explored the origins of SARS-CoV-2.
>>>>>> The paper, whose authors included immunology and microbiology
>>>>>> professor Kristian G. Andersen, declared that evidence clearly showed that
>>>>>> SARS-CoV-2 did not originate from a laboratory.
>>>>>> “Our analyses clearly show that SARS-CoV-2 is not a laboratory
>>>>>> construct or a purposefully manipulated virus,” the authors wrote in
>>>>>> February.
>>>>>> Yet a trove of recently published documents reveal that Andersen and
>>>>>> his co-authors believed that the lab leak scenario was not just possible,
>>>>>> but likely.
>>>>>> “[The] main thing still in my mind is that the lab escape version of
>>>>>> this is so friggin’ likely to have happened because they were already doing
>>>>>> this type of work and the molecular data is fully consistent with that
>>>>>> scenario,” Andersen said to his colleagues, according to a report from
>>>>>> Public, which published a series of Slack messages between the authors.
>>>>>> Anderson was not the only author who privately expressed doubts that
>>>>>> the virus had natural origins. Public cataloged dozens of statements from
>>>>>> Andersen and his co-authors—Andrew Rambaut, W. Ian Lipkin, Edward C.
>>>>>> Holmes, and Robert F. Garry—between the dates January 31 and February 28,
>>>>>> 2020 suggesting that SARS-CoV-2 may have been engineered.
>>>>>> ” …the fact that we are discussing this shows how plausible it is,”
>>>>>> Garry said of the lab-leak hypothesis.
>>>>>> “We unfortunately can’t refute the lab leak hypothesis,” Andersen
>>>>>> said on Feb. 20, several days after the authors published their pre-print.
>>>>>> To complicate matters further, new reporting from The Intercept
>>>>>> reveals that Anderson had an $8.9 million grant with NIH pending final
>>>>>> approval from Dr. Anthony Fauci when the Proximal Origin paper was
>>>>>> submitted.
>>>>>> ‘Fraud and Scientific Misconduct’?
>>>>>> The findings have led several prominent figures to accuse the authors
>>>>>> of outright deception.
>>>>>> Richard H. Ebright, the Board of Governors Professor of Chemistry and
>>>>>> Chemical Biology at Rutgers University, called the paper “scientific
>>>>>> fraud.”
>>>>>> “The 2020 ‘Proximal Origin’ paper falsely claimed science showed
>>>>>> COVID-19 did not have a lab origin,” tweeted Ebright. “Newly released
>>>>>> messages from the authors show they did not believe the conclusions of the
>>>>>> paper and show the paper is the product of scientific fraud and scientific
>>>>>> misconduct.”
>>>>>> Ebright and Silver are among those pushing a petition urging Nature
>>>>>> to retract the article in light of these findings.
>>>>>> Among those to sign the petition was Neil Harrison, a professor of
>>>>>> anesthesiology and molecular pharmacology at Columbia University.
>>>>>> “Virologists and their allies have produced a number of papers that
>>>>>> purport to show that the virus was of natural origin and that the pandemic
>>>>>> began at the Huanan seafood market,” Harrison told The Telegraph. “In fact
>>>>>> there is no evidence for either of these conclusions, and the email and
>>>>>> Slack messages among the authors show that they knew at the time that this
>>>>>> was the case.”
>>>>>> Only ‘Expressing Opinions’?
>>>>>> Dr. Joao Monteiro, chief editor of Nature, has rebuffed calls for a
>>>>>> retraction, The Telegraph notes, saying the authors were merely “expressing
>>>>>> opinions.”
>>>>>> This claim is dubious at best. From the beginning, the Proximal
>>>>>> Origin study was presented as authoritative and scientific. Jeremy Farrar,
>>>>>> a British medical researcher and now the chief scientist at the World
>>>>>> Health Organization (WHO), told USA Today that Proximal Origin was the
>>>>>> “most important research on the genomic epidemiology of the origins of this
>>>>>> virus to date.”
>>>>>> Dr. Anthony Fauci, speaking from the White House podium in April
>>>>>> 2020, cited the study as evidence that the mutations of the virus were
>>>>>> “totally consistent with a jump from a species of an animal to a human.”
>>>>>> Fact-check organizations were soon citing the study as proof that COVID-19
>>>>>> “could not have been manipulated.”
>>>>>> Far from being presented as a handful of scientists “expressing
>>>>>> opinions,” the Proximal Origin study was treated as gospel, a dogma that
>>>>>> could not even be questioned. This allowed social media companies (working
>>>>>> hand-in-hand with government agencies) to censor people who publicly stated
>>>>>> what Andersen and his colleagues were saying privately—that it seemed
>>>>>> plausible that SARS-CoV-2 came from the laboratory in Wuhan that
>>>>>> experimented on coronaviruses and had a checkered safety record.
>>>>>> Indeed, even as media and government officials used the Proximal
>>>>>> Origin study to smear people as conspiracy theorists for speculating that
>>>>>> COVID-19 might have emerged from the Wuhan lab, a Defense Intelligence
>>>>>> Agency study commissioned by the government questioned the study’s
>>>>>> scientific rigor.
>>>>>> “The arguments that Andersen et al. use to support a natural-origin
>>>>>> scenario for SARS CoV-2 are based not on scientific analysis, but on
>>>>>> unwarranted assumptions,” the now-declassified paper concluded. “In fact,
>>>>>> the features of SARS-CoV-2 noted by Andersen et al. are consistent with
>>>>>> another scenario: that SARS-CoV-2 was developed in a laboratory…”
>>>>>>
>>>>>> On Thu, Aug 24, 2023 at 2:22 PM Tony Rees <tonyrees49 at gmail.com>
>>>>>> wrote:
>>>>>>
>>>>>>> Hi John,
>>>>>>>
>>>>>>> I took a look at the paper which is online and open access. I must
>>>>>>> say when I saw it at the time of original publication I thought its main
>>>>>>> conclusions very odd and at variance with almost all other research on the
>>>>>>> topic.
>>>>>>>
>>>>>>> Just to be clear per your thread title - the paper does not appear
>>>>>>> in "Nature" (which I imagine might have a higher degree of scrutiny), but
>>>>>>> in "The European Physical Journal Plus" which is a different outlet, albeit
>>>>>>> from the same publisher.
>>>>>>>
>>>>>>> Best - Tony
>>>>>>> Tony Rees, New South Wales, Australia
>>>>>>> https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fabout.me%2FTonyRees&data=05%7C01%7Ctaxacom%40lists.ku.edu%7Cfc4dd2bec74949eceb4708dba4df0de4%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638285050207440892%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=IIY6rahHlAWWjIm7i9psugzYGJ2Ks8j4a1dUg59eCpE%3D&reserved=0
>>>>>>>
>>>>>>>
>>>>>>> On Fri, 25 Aug 2023 at 03:59, John Grehan via Taxacom <
>>>>>>> taxacom at lists.ku.edu> wrote:
>>>>>>>
>>>>>>>> Recently when I noted about ZooNova as a publication option, a
>>>>>>>> Taxacom
>>>>>>>> colleague implied (oof list) that the journal was dubious because he
>>>>>>>> considered one (or more) papers to be dubious (in that person's
>>>>>>>> judgement).
>>>>>>>> Here is a classic case of a 'Top' journal retracting a paper,
>>>>>>>> showing that
>>>>>>>> the supposed 'prestige' of a journal has nothing necessarily to do
>>>>>>>> with its
>>>>>>>> content. In this case it was picked up on because the paper in
>>>>>>>> question
>>>>>>>> appears to have run afoul of a sufficient number of prominent or
>>>>>>>> influential researchers. In biogeography this does not happen, as
>>>>>>>> the
>>>>>>>> prominent (powerful and influential) players all play to the fraud
>>>>>>>> (that
>>>>>>>> being the misrepresentation of what CODA methods can or cannot do or
>>>>>>>> support). Power is everything in science.
>>>>>>>>
>>>>>>>> Top science publisher Springer Nature said it has withdrawn a study
>>>>>>>> that
>>>>>>>> presented misleading conclusions on climate change impacts after an
>>>>>>>> investigation prompted by an AFP inquiry.
>>>>>>>> AFP reported in September 2022 on concerns over the peer-reviewed
>>>>>>>> study by
>>>>>>>> four Italian scientists that appeared earlier that year in the
>>>>>>>> European
>>>>>>>> Physical Journal Plus, published by Springer Nature.
>>>>>>>> The study had drawn positive attention from climate-sceptic media.
>>>>>>>> The paper, titled "A critical assessment of extreme events trends
>>>>>>>> in times
>>>>>>>> of global warming", purported to review data on possible changes in
>>>>>>>> the
>>>>>>>> frequency or intensity of rainfall, cyclones, tornadoes, droughts
>>>>>>>> and other
>>>>>>>> extreme weather events.
>>>>>>>> Several climate scientists contacted by AFP said the study
>>>>>>>> manipulated
>>>>>>>> data, cherry picked facts and ignored others that would contradict
>>>>>>>> their
>>>>>>>> assertions, prompting the publisher to launch an internal review.
>>>>>>>> "The Editors and publishers concluded that they no longer had
>>>>>>>> confidence in
>>>>>>>> the results and conclusions of the article," Springer Nature told
>>>>>>>> AFP in an
>>>>>>>> email late Wednesday.
>>>>>>>> The journal's editors published an online note stating that the
>>>>>>>> paper was
>>>>>>>> retracted due to concerns over "the selection of the data, the
>>>>>>>> analysis and
>>>>>>>> the resulting conclusions".
>>>>>>>> --
>>>>>>>> https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fhepialidsoftheworld.com.au%2F&data=05%7C01%7Ctaxacom%40lists.ku.edu%7Cfc4dd2bec74949eceb4708dba4df0de4%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638285050207440892%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=f%2F66rjDUeG6a2IsMMKLu0ezgerWrRsMsQ55feGYFR0s%3D&reserved=0 (use the 'visit archived web
>>>>>>>> site'
>>>>>>>> link, then the 'Ghost Moth Research page' link.
>>>>>>>> _______________________________________________
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>>>>>>>>
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>>>>>>>> For list information; to subscribe or unsubscribe, visit:
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>>>>>>>> The Taxacom email archive back to 1992 can be searched at:
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>>>>>>>>
>>>>>>>> Nurturing nuance while assailing ambiguity and admiring
>>>>>>>> alliteration for about 36 years, 1987-2023.
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>> --
>>>>>> https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fhepialidsoftheworld.com.au%2F&data=05%7C01%7Ctaxacom%40lists.ku.edu%7Cfc4dd2bec74949eceb4708dba4df0de4%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638285050207440892%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=f%2F66rjDUeG6a2IsMMKLu0ezgerWrRsMsQ55feGYFR0s%3D&reserved=0 (use the 'visit archived web
>>>>>> site' link, then the 'Ghost Moth Research page' link.
>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fhepialidsoftheworld.com.au%2F&data=05%7C01%7Ctaxacom%40lists.ku.edu%7Cfc4dd2bec74949eceb4708dba4df0de4%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638285050207597118%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=8do1%2BovqY%2FImRyW6rDhYassVfPPf3BTu0zlMmXwOZjM%3D&reserved=0 (use the 'visit archived web
>>>>> site' link, then the 'Ghost Moth Research page' link.
>>>>>
>>>>
>>>
>>> --
>>> https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fhepialidsoftheworld.com.au%2F&data=05%7C01%7Ctaxacom%40lists.ku.edu%7Cfc4dd2bec74949eceb4708dba4df0de4%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638285050207597118%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=8do1%2BovqY%2FImRyW6rDhYassVfPPf3BTu0zlMmXwOZjM%3D&reserved=0 (use the 'visit archived web site'
>>> link, then the 'Ghost Moth Research page' link.
>>>
>>
>>
>> --
>> https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fhepialidsoftheworld.com.au%2F&data=05%7C01%7Ctaxacom%40lists.ku.edu%7Cfc4dd2bec74949eceb4708dba4df0de4%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638285050207597118%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=8do1%2BovqY%2FImRyW6rDhYassVfPPf3BTu0zlMmXwOZjM%3D&reserved=0 (use the 'visit archived web site'
>> link, then the 'Ghost Moth Research page' link.
>>
>

-- 
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link, then the 'Ghost Moth Research page' link.