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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

#41

Post by data_acquired »

wosk wrote: post #23
data_acquired wrote: post #19

Earlier quoted context omitted.

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/124838739520184729…

Wow, didn't know about this case.

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

#42

Post by failwhaleshark »

dayofthedaleks wrote: post #18
failwhaleshark wrote: post #15

Earlier quoted context omitted.

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

Don't let the bastards drag you down, man. https://en.m.wikipedia.org/wiki/Illegitimi_non_carborundum

:D

I had actual Latin on a license plate frame on a sports car that roughly translated to "eat my dust/shit/detritus." I can't remember the exact tenses of the words, but it took me a while to get it right.

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

#43

Post by failwhaleshark »

theon144 wrote: post #22
failwhaleshark wrote: post #15

Earlier quoted context omitted.

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"?

Tangents and secants are how we learn.

And if we don't stop to smell the roses, how will we remember how good roses smell?

So let's not defenestrate curiosity wherever it leads with the culture of "no," because you're not a moderator. So don't pretend to be the king who decides what is permitted and forbidden to be discussed; that's contrary to an open and free society.

There's nothing wrong with "viruses" or "octopuses." Please read and understand that "faux Latin" means these tweaked "smarty" words aren't even Latin half of the time.

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

#44

Post by COGlory »

Y_Y wrote: post #38
COGlory wrote: post #29

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 thei…

I think a good compromise here is to publish your results (the truth must out), but to be really clear upfront what this means (in this case nothing) in the context of any hot topics of the day that might want to jump on your research and misuse it.

I would agree with this compromise.

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

#45

Post by vibrio »

data_acquired wrote: post #40
vibrio wrote: post #28

Earlier quoted context omitted.

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

Lovable HN snarkiness here. I didn't say that every virus does it. Geez.

Pardon the snark- it was not intended to be aggressive. I'm a microbiologist and have spent much of my life thinking about virus biology and pathogenesis. My perspective is skewed from general public but over the last year, the frequent casual comparisons between influenza, coronavirues, and other dramatically different viruses has heightened my sensitivity.

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

#46

Post by data_acquired »

vibrio wrote: post #45
data_acquired wrote: post #40

Earlier quoted context omitted.

Lovable HN snarkiness here. I didn't say that every virus does it. Geez.

Pardon the snark- it was not intended to be aggressive. I'm a microbiologist and have spent much of my life thinking about virus biology and pathogenesis. My perspective is skewed from general public but over the last year, the frequent casual comparisons between influenza, coronavirues, and other dramatically different viruses has heightened my sensitivity.

I guessed that you're a biologist (or have some kind of bio fascination) given your account handle ;) I'm a molecular biologist myself (more on the comp. side) for the last decade. HIV is certainly a special case given it codes its own RT enzyme.

I get the sensitivity and the frustration --- the most minor, off-hand comment (such as the one I made) can potentially fuel all manner of conspiracy theory. I spent much of my morning dealing with a group of people on a shared group suddenly re-discovering the Plandemic documentary.

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

#47

Post by acqq »

COGlory wrote: post #29

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 thei…

No, in the context in which Marie-Louise Hammarskjöld wrote her statement the "experiment" you mention was totally not scientifically "legitimate" and only for one not knowing the context can the impression remain that "it appears to be".

That is exactly why Marie-Louise Hammarskjöld wrote that.

The context is, it was about the preprint on bioRxiv, and the said preprint was totally worthless scientifically, because the authors didn't understand what they write about. Specifically, they aren't the specialists in the field about which they wrote, and they failed to understand that what they believed they did was a totally normal effect of the process they used, that is, a "noise" and not a "signal."

To compare with the computer related topics, in that preprint the proof was like when somebody would claim that the nature consists of 8x8 pixel blocks and as a proof claim that they "made photos" and "when made bigger the 8x8 blocks were obvious." All while not mentioning that they actually made JPEG which reduces every image to 8x8 blocks and not knowing that these are just the artifacts of the process used.

That is why the real experts criticized the existence of the paper -- exactly because they knew almost every journalist and anybody else will quote the text and use it for scaring people even if all was an obvious nonsense.

Unfortunately these "details" weren't stated so clearly in the OP too. Covering the science is not easy.

Additionally, the current paper, actually published, was "Contributed by" its author, which allows him to avoid the proper peer review, as explained in wosk's comment here.

The author of the article we discuss writes that the published paper contains some additional work, compared to the preprint, but the title of the article is unfortunately certainly too clickbaity, again, in the whole context. "Evidence" gives an impression that the "support" is strong, whereas, again, in the complete context of the preprint and the "contribution" mechanism, it would be surprising if it's that good.

That's why one should give much more weight to the Harmit Malik's statement that he "remains unconvinced that the explanation is integrated virus."

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

#48

Post by vMPQonVtAjLWmr »

jbaber wrote: post #33
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.

Whoa, whoa, whoa. "vira"? In Latin, virus is a mass noun (like applesauce), so you can pluralize however you want in English because using it in the singular only works in English anyway. https://en.m.wikipedia.org/wiki/Plural_form_of_words_ending_...

What makes you think you can pluralize it in English however you want? Yeah, I mean you can do whatever and ignore grammar I guess. It's not illegal.

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

#49

Post by vibrio »

COGlory wrote: post #29

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 thei…

Part of the concern around this work is that the PNAS publication route suggests that teh work didn't survive traditional peer-review. Should all peer review be abolished as data suppression, and we just go the bioRxiv route for all information distribution?
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