Taxacom: Science fraud - Nature

[Michael A. Ivie]

John,

Perhaps you need to look up the definition of fraud, as it is a word 
worthy of civil suit for slander:

"**intentional perversion of truth in order to induce another to part 
with something of value or to surrender a legal right"

Fraud is to get something of value, it is not the same as suppression.

perhaps you mean dispute or suppression.

Mike.

On 8/24/2023 2:16 PM, John Grehan via Taxacom wrote:
> **External Sender**
>
> 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%7Cfa4e3d5502a14a1a9f9108dba4e19df5%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638285061165978082%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=Mx0m5eFpaV21VZ92srHLhbrx8qllD%2F%2Bvk%2FjyP68EPNE%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%7Cfa4e3d5502a14a1a9f9108dba4e19df5%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638285061166134356%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=PiOw7yOgPl2Z0x8jmOscRMgK6nAL1tLpZG4hjVIyd34%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%7Cfa4e3d5502a14a1a9f9108dba4e19df5%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638285061166134356%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=RwfPvdqc3ms3UiZbe6ZRfKFcPKUwsu2c4y3Kz4YopuQ%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%7Cfa4e3d5502a14a1a9f9108dba4e19df5%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638285061166134356%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=RwfPvdqc3ms3UiZbe6ZRfKFcPKUwsu2c4y3Kz4YopuQ%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%7Cfa4e3d5502a14a1a9f9108dba4e19df5%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638285061166134356%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=qu1pEfmgpYbj5HsyFiSA7Tk7TzkvBbpJPefXc8xoGbI%3D&reserved=0  (use the 'visit archived web
>>>>>>>>> site'
>>>>>>>>> link, then the 'Ghost Moth Research page' link.
>>>>>>>>> _______________________________________________
>>>>>>>>> Taxacom Mailing List
>>>>>>>>>
>>>>>>>>> Send Taxacom mailing list submissions to:taxacom at lists.ku.edu
>>>>>>>>> For list information; to subscribe or unsubscribe, visit:
>>>>>>>>> https://lists.ku.edu/listinfo/taxacom
>>>>>>>>> You can reach the person managing the list at:
>>>>>>>>> taxacom-owner at lists.ku.edu
>>>>>>>>> The Taxacom email archive back to 1992 can be searched at:
>>>>>>>>> https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Ftaxacom.markmail.org%2F&data=05%7C01%7Ctaxacom%40lists.ku.edu%7Cfa4e3d5502a14a1a9f9108dba4e19df5%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638285061166134356%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=pEP0NKxVI%2FCYAyzp5ZUAc1NyOQD8%2FTFBvQSNL5deEI4%3D&reserved=0
>>>>>>>>>
>>>>>>>>> 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%7Cfa4e3d5502a14a1a9f9108dba4e19df5%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638285061166134356%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=qu1pEfmgpYbj5HsyFiSA7Tk7TzkvBbpJPefXc8xoGbI%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%7Cfa4e3d5502a14a1a9f9108dba4e19df5%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638285061166134356%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=qu1pEfmgpYbj5HsyFiSA7Tk7TzkvBbpJPefXc8xoGbI%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%7Cfa4e3d5502a14a1a9f9108dba4e19df5%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638285061166134356%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=qu1pEfmgpYbj5HsyFiSA7Tk7TzkvBbpJPefXc8xoGbI%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%7Cfa4e3d5502a14a1a9f9108dba4e19df5%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638285061166134356%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=qu1pEfmgpYbj5HsyFiSA7Tk7TzkvBbpJPefXc8xoGbI%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%7Cfa4e3d5502a14a1a9f9108dba4e19df5%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638285061166134356%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=qu1pEfmgpYbj5HsyFiSA7Tk7TzkvBbpJPefXc8xoGbI%3D&reserved=0  (use the 'visit archived web site'
> link, then the 'Ghost Moth Research page' link.
> _______________________________________________
> Taxacom Mailing List
>
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>
> Nurturing nuance while assailing ambiguity and admiring alliteration for about 36 years, 1987-2023.

-- 
__________________________________________________

Michael A. Ivie, Ph.D., F.R.E.S.

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