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Evidence supports claim that SARS-CoV-2 genes can integrate with human DNA

sciencemag.org

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Re: Evidence supports claim that SARS-CoV-2 genes can integrate with human DNA

#21

Post by macinjosh »

FTA:

“If there ever was a preprint that should be deleted, it is this one! It was irresponsible to even put it up as a preprint, considering the complete lack of relevant evidence. This is now being used by some to spread doubts about the new vaccines,” Marie-Louise Hammarskjöld, a microbiologist at the University of Virginia, posted in a comment on bioRxiv at the time.

While I understand the point I think this is unfair to publishing scientists. The public and news media picture science as this oracle of sorts that brings us truth where in fact it is just smart people feeling around in the dark for hard information to go on. That is a process that takes time, an open mind, and deep thought. Three things which are antithetical to social media, TV news, and politics. Limiting discussion and the pursuit of science because some people read too much into it, too quickly seems dangerous to me. Who is wagging the tail here? The reasonable or the unreasonable?

Re: Evidence supports claim that SARS-CoV-2 genes can integrate with human DNA

#22

Post by theon144 »

failwhaleshark wrote: post #15
vMPQonVtAjLWmr wrote: post #10

Earlier quoted context omitted.

Sorry for the nitpick but virii is neither in Latin nor English a plural of virus. The Latin would be vira the English viruses. There are a couple of common variants floating around that probably originate from misunderstanding Latin.

Faux Latin and "Latin" declension is annoying because it's often just plain wrong.

We're getting completely off track here but I agree; to me it seems to be kind of an extension to grammar pedantism, as it only serves to indicate little beyond "I know this word's origins". What's wrong with "viruses" or "octopuses"?

Re: Evidence supports claim that SARS-CoV-2 genes can integrate with human DNA

#23

Post by wosk »

data_acquired wrote: post #19
wosk wrote: post #17

Tangentially related, a glimpse into academia. The paper[1] was contributed in PNAS, the Proceedings of the National Academy of Sciences of the United States of America. PNAS is a very well regarded, and high impact journal. Members of National Academy of Science, usually proeminent professors, have the possibility to "contribute" their work. They can choose reviewers, and the paper will be accepted by the editors (a…

Yeah, this is a well-known controversial aspect of PNAS publishing. However, not all uses of this track of publication is necessarily nefarious. See this for instance -- https://www.nature.com/news/scientific-publishing-the-inside... . I was also told that use of this track is some times for very mundane reasons too --- like a professor trying to help a struggling grad student satisfy PhD requirements such as needing…

This came to my mind as a recent outrage in genomics[1].

Indeed there are some wonderful contributed papers and some members use it responsibly. I also concur with with everything you said, just adding that even in laudable cases (struggling grad, ...), there is some injustice and it'll always be misleading.

Thanks for the precisions and the mention of eLife.

[1] https://twitter.com/arambaut/status/1248387395201847296?s=19

Re: Evidence supports claim that SARS-CoV-2 genes can integrate with human DNA

#24

Post by jeegsy »

> Both Young and Jaenisch say they received more intense criticism for their preprint than any studies in their careers, in part because some researchers worried it played into the hands of vaccine skeptics spreading false claims about the newly authorized mRNA vaccines.

I understand that there are strongly desired policy outcomes to consider here but seriously, the histrionics that follow anything that even smells like a deviation from the conventional wisdom regarding this pandemic cannot possibly be helpful

Re: Evidence supports claim that SARS-CoV-2 genes can integrate with human DNA

#25

Post by krona »

brutos wrote: post #9

I implore everyone to read the full article and not only the headline. The paper that is being reported on was widely criticized in its scientific community for its weak evidence and should probably be seen (if you are very charitable) only as a starting point for other virus experts to jump into the discussion and do more experiments and not as something for general consumption.

Yes because poor science is never jumped on by the media for general consumption.

Re: Evidence supports claim that SARS-CoV-2 genes can integrate with human DNA

#26

Post by vibrio »

jdjkckfkrrn wrote: post #14

The scientists from This Week in Virology admitted when asked that in principle it's possible for both the virus and the mRNA vaccine to be integrated into the genome, if you have reverse transcriptase and integrase in a cell, which can happen if it's infected by another virus for example.

  "it's possible" means something very different to scientists than it does general public or popular media. Scientists rarely say impossible. The effect is of like "theory of evolution".  This  makes it hard for scientific-based discussion to address hype-filled conspiracy theories.
mRNA Integration is very very unlikely given the scenario described. Show me data to support otherwise, beyond the PNAS paper.

Re: Evidence supports claim that SARS-CoV-2 genes can integrate with human DNA

#27

Post by em500 »

wosk wrote: post #17

Tangentially related, a glimpse into academia. The paper[1] was contributed in PNAS, the Proceedings of the National Academy of Sciences of the United States of America. PNAS is a very well regarded, and high impact journal. Members of National Academy of Science, usually proeminent professors, have the possibility to "contribute" their work. They can choose reviewers, and the paper will be accepted by the editors (a…

I can't assess the quality of PNAS, but the one thing I remember about it is that Columbia statistics prof Andrew Gelman disses them all the time for peddling pseudo-science based mostly on junk statistics[1]. He paints it as basically a science oriented clickbait tabloid.

[1] https://statmodeling.stat.columbia.edu/?s=PNAS, https://statmodeling.stat.columbia.edu/2017/10/04/breaking-p...

Re: Evidence supports claim that SARS-CoV-2 genes can integrate with human DNA

#28

Post by vibrio »

data_acquired wrote: post #20
andy_ppp wrote: post #2

Does this happen with lots of viruses or just SARS-CoV-2? Seems like it’s pretty rare and would not be a whole copy of the virus or that many cells, surely it would just be a small percentage to the point where it doesn’t matter?

Yes, happens a lot. HIV is a notable instance.

Yes, and birds fly frequently, but elephants don't seem too. All viruses are not the same, they are extremely diverse.

Re: Evidence supports claim that SARS-CoV-2 genes can integrate with human DNA

#29

Post by COGlory »

Well this cost me some brain cells. Here is the summary:

A retrotransposon/RT (not sure the distinction), that may or may not be active in humans (mostly isn't active), when overexpressed, in the presence of SARS-CoV-2 RNA, will integrate it into the human genome in a preferred orientation.

That is the very definition of a laboratory artifact, and there is no biological significance. If the authors want to waste their time trying to prove some biological significance, be my guest, but short of finding it integrated into "wild-type" human cells, good luck.

Also, from the article:

>Both Young and Jaenisch say they received more intense criticism for their preprint than any studies in their careers, in part because some researchers worried it played into the hands of vaccine skeptics spreading false claims about the newly authorized mRNA vaccines. “If there ever was a preprint that should be deleted, it is this one! It was irresponsible to even put it up as a preprint, considering the complete lack of relevant evidence. This is now being used by some to spread doubts about the new vaccines,” Marie-Louise Hammarskjöld, a microbiologist at the University of Virginia, posted in a comment on bioRxiv at the time.

Shame on you, Marie-Louise Hammarskjöld for even suggesting that. If the experiment was legitimate (which it appears to be), you have no business calling yourself a scientist and then advocating for the suppression of real data. For any reason, whatsoever. It is completely antithetical to the scientific process, and I am now immediately skeptical of any published work you've ever created, and what data you omitted.

Re: Evidence supports claim that SARS-CoV-2 genes can integrate with human DNA

#30

Post by COGlory »

wosk wrote: post #17

Tangentially related, a glimpse into academia. The paper[1] was contributed in PNAS, the Proceedings of the National Academy of Sciences of the United States of America. PNAS is a very well regarded, and high impact journal. Members of National Academy of Science, usually proeminent professors, have the possibility to "contribute" their work. They can choose reviewers, and the paper will be accepted by the editors (a…

PNAS has garnered itself a nickname among my peers, for these exact reasons. The worst is the sponsored paper section. I have encountered some real garbage in PNAS papers.

However, I've also encountered real garbage in other respected journals, like Nucleic Acid Research. Journals are a business, and most of them go after what's catchy.

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