Zach Hensel
@zachhensel.bsky.social
single-molecule microbiology lab @ ITQB NOVA in Portugal
https://zach-hensel.github.io/
https://zach-hensel.github.io/
Pinned
Zach Hensel
@zachhensel.bsky.social
· Apr 5
A ghost draws near!
November 10, 2025 at 11:05 PM
A ghost draws near!
I added a short section to this preprint describing another simple and inexplicable error that Bruttel et al. have repeated for years.
![Misinterpretation of previous work
One criteria of the
“IVGA fingerprint” described by Bruttel et al. is
“Two unique recognition sites may flank regions
meant to be further manipulated.
” I did not consider this in the analysis above, because its inclusion in the
“fingerprint”
arises from misinterpretation of work described in a previous paper. Bruttel et al. write that this work
“
used two distinct endonucleases for genome assembly, with two sites of one enzyme [BsaI] flanking a region of
interest, enabling efficient manipulations of the flanking region without having to reassemble the entire viral
backbone for each variant.
” In fact, BsaI sites used for this assembly were not retained in the final construct (Hu et al.,
2017). Furthermore, infectious clones produced in that work did have BsaI sites in the backbone and in other
fragments that would make this procedure impossible without additional mutagenesis. In general, I could not find any
precedent in the literature on similar reverse genetics constructs for introducing type IIS restriction sites. Bruttel et al.
exclusively list examples of introducing BglI sites (not type IIS). There are some examples of removing sites to enable
one-pot assembly, but the fact that RecCA shares the SARS-CoV-2 BsaI/BsmBI restriction map strongly suggests that
there is no history of this for SARS-CoV-2 (Pekar et al., 2025).](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:x43yqs76dtuxqf7yzkqrlz4v/bafkreifstpgyyowj4m745ddrx5pbraua7j6aexqhoy4y4y5u7fgbr7hmpi@jpeg)
November 5, 2025 at 2:45 PM
I added a short section to this preprint describing another simple and inexplicable error that Bruttel et al. have repeated for years.
Reposted by Zach Hensel
Two weeks ago, a paper came out, claiming that the 2019 Brucella leak in Lanzhou, China, could have been detected months before it was publicly reported.
Problem: no proof was provided to support this extraordinary claim, as we explain in a letter to the editor.
Details follow ▫️1/6🧵
Problem: no proof was provided to support this extraordinary claim, as we explain in a letter to the editor.
Details follow ▫️1/6🧵
Correspondence regarding “Geospatial analysis of open-source intelligence data to early detect laboratory-acquired infections, using the 2019 brucellosis laboratory leak in China as a case study” - In...
Infection -
link.springer.com
November 3, 2025 at 8:30 PM
Two weeks ago, a paper came out, claiming that the 2019 Brucella leak in Lanzhou, China, could have been detected months before it was publicly reported.
Problem: no proof was provided to support this extraordinary claim, as we explain in a letter to the editor.
Details follow ▫️1/6🧵
Problem: no proof was provided to support this extraordinary claim, as we explain in a letter to the editor.
Details follow ▫️1/6🧵
🧵 Co-author Tony VanDongen has responded on X, arguing that recombination can't explain what they found.
His argument: If SARS-CoV-2 acquired one of its BsaI sites from RmBANAL247, it would have acquired the two adjacent sites!
While not a good argument, it's worse argument in light of new data.
His argument: If SARS-CoV-2 acquired one of its BsaI sites from RmBANAL247, it would have acquired the two adjacent sites!
While not a good argument, it's worse argument in light of new data.
October 31, 2025 at 1:22 PM
🧵 Co-author Tony VanDongen has responded on X, arguing that recombination can't explain what they found.
His argument: If SARS-CoV-2 acquired one of its BsaI sites from RmBANAL247, it would have acquired the two adjacent sites!
While not a good argument, it's worse argument in light of new data.
His argument: If SARS-CoV-2 acquired one of its BsaI sites from RmBANAL247, it would have acquired the two adjacent sites!
While not a good argument, it's worse argument in light of new data.
First author Valentin Bruttel has responded over at X. Here's my quick take:
a) Mutation rates are irrelevant; I show there aren't any mutations at all, so this part of Bruttel et al, which is also nonsense, is irrelevant.
b–e) Four things that are irrelevant to analysis in his paper.
a) Mutation rates are irrelevant; I show there aren't any mutations at all, so this part of Bruttel et al, which is also nonsense, is irrelevant.
b–e) Four things that are irrelevant to analysis in his paper.
October 29, 2025 at 3:14 PM
First author Valentin Bruttel has responded over at X. Here's my quick take:
a) Mutation rates are irrelevant; I show there aren't any mutations at all, so this part of Bruttel et al, which is also nonsense, is irrelevant.
b–e) Four things that are irrelevant to analysis in his paper.
a) Mutation rates are irrelevant; I show there aren't any mutations at all, so this part of Bruttel et al, which is also nonsense, is irrelevant.
b–e) Four things that are irrelevant to analysis in his paper.
🧵Remember the preprint claiming SARS-CoV-2 has a "synthetic fingerprint"?
It said a restriction map was "extremely unlikely to have arisen by random evolution.”
I took its claims seriously.
The "synthetic fingerprint" hypothesis collapses. My new preprint explains why.
arxiv.org/abs/2510.23833
It said a restriction map was "extremely unlikely to have arisen by random evolution.”
I took its claims seriously.
The "synthetic fingerprint" hypothesis collapses. My new preprint explains why.
arxiv.org/abs/2510.23833
October 29, 2025 at 7:32 AM
🧵Remember the preprint claiming SARS-CoV-2 has a "synthetic fingerprint"?
It said a restriction map was "extremely unlikely to have arisen by random evolution.”
I took its claims seriously.
The "synthetic fingerprint" hypothesis collapses. My new preprint explains why.
arxiv.org/abs/2510.23833
It said a restriction map was "extremely unlikely to have arisen by random evolution.”
I took its claims seriously.
The "synthetic fingerprint" hypothesis collapses. My new preprint explains why.
arxiv.org/abs/2510.23833
Really valuable and very normal feedback from Dr. Ebright the last two months.
October 26, 2025 at 10:44 AM
Really valuable and very normal feedback from Dr. Ebright the last two months.
Response from @philippmarkolin.bsky.social www.statnews.com/2025/10/25/s...
I was in high school in Kansas when this happened!
Rumsfeld said: there are known knowns, known unknowns, and unknown unknowns. He oddly excluded unknown knowns which are important to consider for complex topics.
I was in high school in Kansas when this happened!
Rumsfeld said: there are known knowns, known unknowns, and unknown unknowns. He oddly excluded unknown knowns which are important to consider for complex topics.
October 25, 2025 at 1:16 PM
Response from @philippmarkolin.bsky.social www.statnews.com/2025/10/25/s...
I was in high school in Kansas when this happened!
Rumsfeld said: there are known knowns, known unknowns, and unknown unknowns. He oddly excluded unknown knowns which are important to consider for complex topics.
I was in high school in Kansas when this happened!
Rumsfeld said: there are known knowns, known unknowns, and unknown unknowns. He oddly excluded unknown knowns which are important to consider for complex topics.
The FBI report concluding a "lab leak" origin is out by FOIA, mostly redacted. What's not redacted is a silly conspiracy theory in place of actual evidence.
First picture is the FBI report. Second picture is the DoS cable it's likely referencing here.
First picture is the FBI report. Second picture is the DoS cable it's likely referencing here.
![Unredacted text from 2021 FBI "lab leak" investigation report reading: "A November 2020 Italian serological study claimed there was evidence of SARS-CoV-2 circulating in Italy pre-global pandemic; this was published in an obscure Italian medical journal and the research institute was the recipient of Chinese funding, per the DoS [Department of State].](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:x43yqs76dtuxqf7yzkqrlz4v/bafkreidix2c57vmx2nq4fofj43auoonphxcwnjandbkcpv52amlnwyixye@jpeg)
![Excerpt from State Department cable from 23 Nov 2020 released by FOIA. Text:
The Possible Source
4. (U) In an interview with Italy's Corriere della Sera on November 17, one of the principal authors of the study tried to defend his results and said the group had tried to publish in Nature, the New England Journal of Medicine, or another more well-known journal but it was not accepted. He admitted to the interviewer that he had been in contact with both the WHO and Chinese authorities about the results. The story generated considerable enthusiasm among China-based social media users. PRC state media also seized on the story. Notably, the Chinese Communist Party's People's Daily first covered the study on November 16, and T-House (part of China Global Television Network) interviewed one of the study's authors on November 18. And on November 23, PRC media company Xinhua published an article titled "Why COVID-19's origin story is still a mystery" that relied heavily on the Italian study's findings.
5. (SBU) NCI is a governmental institution overseen by the Lombardy regional government and funded by both the region and the ministries for health and research. NCI's website contains a July 2020 research cooperation agreement (attached) with the Italian Chinese Institute (ICI; Istituto Italo Cinese), an organization with no publicly known funding sources and whose principal work is establishing exchange agreements between Italian and Chinese entities. The agreement specifies further research cooperation with Chinese doctors, including the eventual presence of Chinese doctors and researchers at NCI. The NCI-ICI agreement outlines future agreements with the Chinese Ministry of Health to advance cooperation with Chinese researchers, institutions, and hospitals. ICI's scientific committee includes a researcher from NCI, and the ICI committee traveled to China in 2018 to explore further possibilities for cooperation.
Italian Funding Issues [truncated...]](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:x43yqs76dtuxqf7yzkqrlz4v/bafkreigbdkv6qnfjswkxd7h6nxkxua4mhukavibe4rpoo7lro3xetevdou@jpeg)
October 22, 2025 at 9:45 AM
The FBI report concluding a "lab leak" origin is out by FOIA, mostly redacted. What's not redacted is a silly conspiracy theory in place of actual evidence.
First picture is the FBI report. Second picture is the DoS cable it's likely referencing here.
First picture is the FBI report. Second picture is the DoS cable it's likely referencing here.
Reposted by Zach Hensel
AF-CALVADOS: AlphaFold-guided simulations of multi-domain proteins at the proteome level https://www.biorxiv.org/content/10.1101/2025.10.19.683306v1
October 20, 2025 at 1:47 AM
AF-CALVADOS: AlphaFold-guided simulations of multi-domain proteins at the proteome level https://www.biorxiv.org/content/10.1101/2025.10.19.683306v1
CBS News finally has a story on it... I fact checked a few state capitols in states with Republican governors. Four out of the first four alphabetically was enough to know you'd blow by any definition of "several".
October 19, 2025 at 9:19 AM
CBS News finally has a story on it... I fact checked a few state capitols in states with Republican governors. Four out of the first four alphabetically was enough to know you'd blow by any definition of "several".
Reposted by Zach Hensel
Lancet: Offline: Those one should not forgive (Makary and Bhattacharya)
by Richard Horton
bit.ly/3IPC0PD
by Richard Horton
bit.ly/3IPC0PD
October 3, 2025 at 2:25 AM
Lancet: Offline: Those one should not forgive (Makary and Bhattacharya)
by Richard Horton
bit.ly/3IPC0PD
by Richard Horton
bit.ly/3IPC0PD
Sigrid Bratlie posted a response. It doesn't dispute anything that I wrote.
October 1, 2025 at 6:28 PM
Sigrid Bratlie posted a response. It doesn't dispute anything that I wrote.
HUD with a pop up ON top of a giant red banner.
Interesting to see NIH, FDA, DOD (all I checked) admins not agreeing to do something illegal.
Interesting to see NIH, FDA, DOD (all I checked) admins not agreeing to do something illegal.
October 1, 2025 at 5:03 PM
HUD with a pop up ON top of a giant red banner.
Interesting to see NIH, FDA, DOD (all I checked) admins not agreeing to do something illegal.
Interesting to see NIH, FDA, DOD (all I checked) admins not agreeing to do something illegal.
Who says LLM is such a problem? Thanks, Gemini, for the very unearned compliment.
October 1, 2025 at 4:44 PM
Who says LLM is such a problem? Thanks, Gemini, for the very unearned compliment.
Here’s an op-ed I wrote arguing to get back to a focus on the relevant facts when it comes to pandemic origins.
I wrote it in response to a debate that’s played out over the last year in Norwegian media that rarely slows down to check what’s true and false.
I wrote it in response to a debate that’s played out over the last year in Norwegian media that rarely slows down to check what’s true and false.
October 1, 2025 at 9:14 AM
Here’s an op-ed I wrote arguing to get back to a focus on the relevant facts when it comes to pandemic origins.
I wrote it in response to a debate that’s played out over the last year in Norwegian media that rarely slows down to check what’s true and false.
I wrote it in response to a debate that’s played out over the last year in Norwegian media that rarely slows down to check what’s true and false.
The *original* standard?
September 30, 2025 at 2:39 PM
The *original* standard?
Reposted by Zach Hensel
Excellent paper on the origins of SARS-CoV-2!
pubmed.ncbi.nlm.nih.gov/40905595/
pubmed.ncbi.nlm.nih.gov/40905595/
September 26, 2025 at 11:52 AM
Excellent paper on the origins of SARS-CoV-2!
pubmed.ncbi.nlm.nih.gov/40905595/
pubmed.ncbi.nlm.nih.gov/40905595/
I guess it’ll be some time before the DOGE guys making the tax avoidance card website get an AI video generation model that doesn’t hallucinate how birds blink.
September 21, 2025 at 1:43 PM
I guess it’ll be some time before the DOGE guys making the tax avoidance card website get an AI video generation model that doesn’t hallucinate how birds blink.
Reposted by Zach Hensel
Any rich dems want to fund an independent science news and commentary outlet, hmu
(climate, vaccines, energy, public health, biomedical research, assults on science writ large, etc)
(climate, vaccines, energy, public health, biomedical research, assults on science writ large, etc)
September 19, 2025 at 7:58 PM
Any rich dems want to fund an independent science news and commentary outlet, hmu
(climate, vaccines, energy, public health, biomedical research, assults on science writ large, etc)
(climate, vaccines, energy, public health, biomedical research, assults on science writ large, etc)
I guess I'm a day too late, but here's what I sent in as a comment on the NIH policy for publication fees.
TL;DR Why is the guy from the Hoover Institution running the NIH selecting from a menu of price controls?
TL;DR Why is the guy from the Hoover Institution running the NIH selecting from a menu of price controls?
September 16, 2025 at 6:40 PM
I guess I'm a day too late, but here's what I sent in as a comment on the NIH policy for publication fees.
TL;DR Why is the guy from the Hoover Institution running the NIH selecting from a menu of price controls?
TL;DR Why is the guy from the Hoover Institution running the NIH selecting from a menu of price controls?
Regarding the call to reform publication with a paternalistic policy to save scientists from themselves by banning resources going to some publishers, now is not the time in my opinion.
Commissioner Gomez's dissent to the FCC approval is worth a read: docs.fcc.gov/public/attac...
Scientists frustrated with inefficiency of journals who see a silver lining in exploiting this assault on the first amendment e.g. to ban paying publication fees from grants could take a step back.
Scientists frustrated with inefficiency of journals who see a silver lining in exploiting this assault on the first amendment e.g. to ban paying publication fees from grants could take a step back.
September 15, 2025 at 2:52 PM
Regarding the call to reform publication with a paternalistic policy to save scientists from themselves by banning resources going to some publishers, now is not the time in my opinion.
Asher salivating at finally breaking into US media from Australian conspiracy docs.
September 9, 2025 at 9:56 PM
Asher salivating at finally breaking into US media from Australian conspiracy docs.