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Flo Débarre Profile picture
@flodebarre
Oct 22, 2022 • 22 tweets • 9 min read • Read on X
Here is a curated collection of threads and tweets rebutting a preprint that made the rounds, illustrating the many ways in which the study is problematic. ▫️1/n Screenshot of tweets; big r...
Before we start:

- Disclaimer: I am a "dry-lab" evolutionary biologist. Part 3️⃣ is outside my strict domain of expertise.

- If you are unfamiliar with the names of the different restriction enzymes, here is how to pronounce them (sound on)▫️2/n

international.neb.com/products/restr…
1️⃣ Evolution

SARS-CoV-2's BsaI/BsmBI restriction sites are consistent with expectations from evolutionary theory. They do not look anomalous.

1a) 🧵 ▫️3/n

1b) 🧵▫️4/n

1c) a tweet complementing to the two previous threads with another close relative of SARS-CoV-2 that was omitted by the preprint authors ▫️5/n

2️⃣ Statistics

2a) The statistical analysis done in the preprint is an example of P-hacking*

*If you think they got the restriction enzymes right on their first try, see part 3 ▫️6/n

2b) The preprint authors are looking for even spaced fragments, but did their stats only on the length of the longest fragment. ▫️7/n

disq.us/p/2rj2xh2
3️⃣ Molecular biology

3a) The standard way of using the restriction enzymes picked in the preprint would not lead to SARS-CoV-2, because the restriction sites would be gone in the final product…▫️8/n

3b) … as exemplified by a reference (erroneously) chosen by the authors to back up their claim ▫️9/n

3c) Even the lengths of some fragments do not make sense▫️10/n

Screenshot of Fig 3A, showi...
4️⃣ People

So far we have only concentrated on the preprint’s arguments. But an exhaustive description should include a presentation of its authors. Have a look at their Twitter profiles to understand where these authors are talking from, ▫️11/n
… and to understand why researchers expressed frustration to have to spend time on the preprint, which got attention essentially because it was an extraordinary claim retweeted by big Twitter accounts, and not because it was sound work. ▫️12/n Screenshot of two tweets by...
To finish on a lighter note, here is the best joke I have read on this disaster ▫️13/n

(Explanation for non-biologists: "Bam" and "Eco" are parts of the names of other restriction enzymes
international.neb.com/products/r0101…
international.neb.com/products/r0136…)

Screenshot of the linked tweet
It seems that only a few people can see tweet 9, so here is a screenshot, and a link to the corresponding paper journals.plos.org/plospathogens/… (Figure S9)▫️14/+ screenshot of my tweet: &q...
A couple of useful definitions (#subtweet) ▫️15/+
help.twitter.com/en/resources/g… screenshots of the definiti...
1d) This thread details how one can change one's mind within just a few days after considering arguments put forward by others and analyzing data.▫️16/+
An interesting description of the preprint and its issues, and a discussion of whether the media should report on preprints, by @KelseyTuoc in @voxdotcom. Includes a noteworthy comment by @Ayjchan (thank you). ▫️17/+

vox.com/future-perfect… screenshot: "Even scie...
Official rebuttal, in the form of a detailed review, by the Uniklinikum Würzburg (the home institution of the preprint's first author)
h/t @_b_meyer▫️18/+

In German: ukw.de/aktuelle-meldu…

In English: idw-online.de/de/news803624
1e) 🔽 An even more detailed evolutionary analysis, addressing the "circularity" issue that some sceptics criticized. ▫️19/+

A noteworthy rebuttal (see the illustration of the first tweet of this thread). ▫️20/+

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More from @flodebarre

Flo Débarre Profile picture
Sep 21
Je ne suis pas la seule à avoir été choquée par l'accusation du Monde envers mes collègues, non justifiée (car infondée) et faite sans recherche de contradictoire. D'où vient-elle ? 1/8 Il demande une enquête en vue d’une possible rétractation de la nouvelle étude, et va jusqu’à évoquer des soupçons d’inconduite scientifique.
@hervenirom cite Richard Ebright, un spécialiste de bactéries qui n'a pas fait de recherche sur Covid-19, est un activiste de la fuite de labo, et qui passe ses journées à tweeter des insultes. 2/8
Comme raconté dans cet article dans la partie News de Science, le harcèlement et les insultes de Richard Ebright envers d'autres scientifiques ont fait l'objet de plaintes officielles. 3/8

science.org/content/articl…
Read 9 tweets
Flo Débarre Profile picture
Sep 20
The quote attributed to @Ayjchan in Le Monde was so dumb that I thought she was misquoted, but she posted something even more stupid on Twitter.
No, Alina Chan, this is not what the papers claim!!
And I know it because I co-led the new study... 1/ The latest analysis by Proximal Origin authors and colleagues directly refutes their own 2022 claims in Science. Their new Cell paper argues that the pandemic most likely started with Lineage A (but the early market cases were all Lineage B) & likely only in early Dec 2019. 7:31 PM · Sep 19, 2024
Two figures having similar layouts does not mean that they show the same things!!!
What is even weirder is that @Ayjchan is posting the legend, and it's clear the percentages are about totally separate points 🤦‍♀️ 2/ screenshot of Chan's tweets of the figures
We did not do the type of simulations of Alina Chan's top figure in our recent work. When @Ayjchan is quoted in Le Monde as saying the modeling results differ, it's absurd: we repeated the value from the previous study. 🤷‍♀️3/
[Translation in ALT text] But she questions the proposed models, which have varied over time, ending up in Cell with a handful of cases on the market at the beginning of December 2019. “And suddenly all these countries are affected at the same time? That doesn’t make sense,” she believes.
Read 10 tweets
Flo Débarre Profile picture
Aug 28
Let's now talk a bit about some science:
In his 2021 article, Jesse Bloom over-emphasized the significance of the "recovered" sequences.
They contain only limited information, because they are partial, and key positions are not covered: ▫️1/🧵

J Bloom's paper contained two figures with phylogenetic trees, one without the "recovered" sequences, one with them. The three trees correspond to his three proposed progenitors: A+C18060T, A+C29095T, A+T3171C.
In the recovered sequences, only 29095 is covered. ▫️2/ slide showing the two figures with three trees each
J Bloom not only added the "recovered" sequences, but also re-colored existing sequences. Visually, you'd think there is a lot of new information. In fact, in the middle node, there is only one "recovered" sequence. And we can't even know if it is actually like the progenitor▫️3/ slide showing the middle progenitor node, with annotations
Read 7 tweets
Flo Débarre Profile picture
Aug 23
It is time to share our findings about a study by @jbloom_lab that had a lot of echo in 2021.
TL;DR: The sequences that J Bloom recovered were not from the earliest cases, but from late January 2020. He had the information, deleted it during his analysis, then ignored it.▫️1/8 composite image showing our preprint, Bloom's paper title ("Recovery of Deleted Deep Sequencing Data Sheds More Light on the Early Wuahn SARS-CoV-2 Epidemic"), and with arrows describing findings. Main finding: The “recovered” sequences were not that early: they were collected on 30 January 2020. The information was present in the datasets used by Jesse Bloom, but he deleted it, and never mentioned it.
In June 2021, Jesse Bloom announced in a Twitter thread and in a preprint having recovered sequences from early in the epidemic. His description and the media coverage (including his press release) led people to think that some sequences were from the earliest cases. ▫️2/8 Slide showing screenshots of media articles, with the term "earliest" cases / patients / samples underlined
Yet, via a press conference in July 2021, the Chinese authors, Wang et al., specified that the sequences were not that early: they had been collected on 30 Jan 2020. J Bloom noted it in his article, but presented it as a contradiction. ▫️3/8 screenshot of the video of the press conference, with subtitle "according to our knowledge, the earliest sample time was January 30th"
Read 30 tweets
Flo Débarre Profile picture
May 17
[A very niche thread]

There were live bats in Wuhan, both inside and outside of the Wuhan Institute of Virology, but neither seem relevant to the origin of the pandemic. ▫️1/10🧵 illustration: images of bats
Zeynep has been repeating the odd and false claim that Wuhan's only bats were in labs. There are bats in Wuhan! And if @zeynep had cared to just properly read what she cites (see QT), she'd have realized she was the one making up the claim. ▫️2/

screenshot of iNaturalist in Wuhan, showing bats
As shown in the previous tweet, bats within Wuhan are mostly Myotis and Pipistrellus, unlikely to carry sarbecoviruses. Rhinolophus bats are occasionally found within Wuhan (h/t @mikeydoubled), but also nearby and then with sarbecoviruses ▫️3/ slide with images from two studies, one having sampled Rhinolophus bats in Wuhan, the other nearby
Read 10 tweets
Flo Débarre Profile picture
Apr 20
Proponents of a lab origin of the Covid-19 pandemic often claim that circumstantial evidence is in favor of their hypothesis... while ignoring key circumstantial evidence *against* it.

Some examples in this thread: ▫️1/🧵

1⃣ We now know that SARS-CoV-2 was already spreading in Wuhan in December 2019. Some lab leakers claim that WIV scientists were infected and hospitalized in November 2019. This should have caused alarm. And yet, Shi Zhengli was at a meeting in Singapore in December 2019. ▫️2/ photo of Shi Zhengli and colleagues at a Nipah meeting in Singapore in Dec 2019
Some could argue that they did not know yet that the virus was spreading in Wuhan, as the first cases were detected later in the month.
Early in January 2020, Shi's group at WIV had sequenced SARS-CoV-2, and knew that there were human cases in hospitals in Wuhan. And yet... ▫️3/
Read 8 tweets

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