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, there are several types of viruses that purposely insert things into DNA. In fact, a significant part (more than half?) of our DNA comes from viruses (but is inactive).
Coronaviruses are not known to do this, so I'd bet on a lab error for now. But it is conceivable.
Not sure where you all get your numbers from, when it is even explicitly mentioned in the posted article:
> The enzyme, reverse transcriptase, is encoded by LINE-1 elements, sequences that litter 17% of the human genome and represent artifacts of ancient infections by retroviruses.
It happens frequently with retroviruses. In fact 5-8% of the human genome is from (ancient) retrovirii. Coronavirus however is a completely different class of virus which makes it interesting, at least to me.
> The enzyme, reverse transcriptase, is encoded by LINE-1 elements, sequences that litter 17% of the human genome and represent artifacts of ancient infections by retroviruses.
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.
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.
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"?
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.
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.
Apparently this seems to be an ongoing and contentious internet debate lol. There's even a wiki article on the subject.[1] The main three arguments appear to be that virii 1) is grammatically incorrect Latin, 2) virus has historically never had a latin plural "as it is a mass noun" and 3) it's a neologistic folk etymology.
While I may agree with the grammatical merits [1)] I'm not convinced (yet). The second argument [2)] that it's never had a historical plural doesn't hold up. The field of virology is much more recent so the need for a plural 'virus' didn't exist at the time.
And 3) is literally how words are formed. If a term used frequently enough it eventually becomes a word regardless of the original grammatical correctness. The term even has 175 years of precedent.[2] As cactus has the plural cacti it's non-obvious why the same doesn't hold true for virus.
According to this thread from another virus expert [1], you can integrate pretty much every class of viruses in the system the authors of this paper used.
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.
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.
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.
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 (an important step for such a journal). When you are in this position, finding reviewers that will not reject you is really easy: academia is a small world with a few really powerful individuals.
I think the reason for this is that NAS members performs a lot of editorial works for the Academy, and they are very good scientist hence their contribution should be valued, and fast.
This has been the source of a lot of outrage (I was maintaining a list but I can't find it). Some NAS members used this process to rapidly publish when timing was important (such as covid-19 research), scooping the work of researchers that don't have such a convenient outlet. It is especially problematic when a professor is a member of the NAS for his work in some field, but uses "contributed" papers to push mediocre or naive work in another field (s)he doesn't know at all (such as physicist in epidemiological modeling). A lot of very bad quality work ended up in the news because it was in PNAS.
To mitigate these issues, I think it's now limited to two papers per year. Moreover, the paper mentions "contributed by" and the name of the reviewers. But if you go and check some google scholar page, some people made a career out of it. For any idea, you get an audience and tons of credibility for free.
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 X number of papers to graduate. More often than not, good ideas do get held up in other journals for all kinds of non-scientific reasons. I've certainly not seen too many examples of overly-erroneous science in this track either, at least in genomics.
I do thoroughly understand your concerns and distaste here that this allows prominent academics to push their (possibly incorrect) views/results on something far outside their expertise. I would love if PNAS publishes the peer reviews for papers such as these that pertain to ongoing health crises (eLife makes peer reviews public, but keeps the reviewers' identity anonymous).
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.
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.
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.
“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?
> 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
Which is why I have trouble trusting any policy related to COVID mitigation. It has firmly become another orthodoxy - especially given it's politicization, and the association of skepticism with being "anti mask" or "anti vax". The bulk of related science will be heavily biased - certain research avenues are simply unlikely to be pursued.
There is at least one other preprint floating around now [0] which suggests that the spike protein itself is a general inflammatory agent, and another preprint (having trouble finding it) indicating that the spike protein is possibly responsible for the clotting/vascular nature of COVID. Now as I understand the mRNA vaccines induce cells to produce spike proteins.
So if the reports in these preprints are confirmed, then there is a likelihood that the mRNA vaccine will cause chronic inflammation in some proportion of recipients. And given the new orthodoxy, and the political momentum behind a successful vaccine, I expect that confirmation and acknowledgement of such findings to be a long uphill battle. Particularly given the ambiguous nature of chronic inflammatory conditions. Note that a retroviral tendency of the COVID virus could explain positive tests post symptomatic infection as well as so called long COVID.
Yes, but I also feel like you have to empathize with said histrionics when there's a pretty short causal chain from (a) things anti-vaxxers and other conspiracists can use for propaganda to (b) people actually dying.
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.
I would not call it an artefact. An artefact is something that is the result of a lab condition (like the type of plastic you use). Overexpressing a retrotransposon is not an artefact, it's the applied factor, even if it's less likely to be biologically relevant.
You're spot on on the comment about suppressing data, though.
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.
Publication of a pre-print that appeals to the use of misinformation for the sole purpose of publicity is another thing. Certainly timing of this could have been better especially in this current covid world where we now use pre-print as an almost equivalent to peer-reviewed.
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."
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?
49 comments
[ 3.3 ms ] story [ 101 ms ] threadCoronaviruses are not known to do this, so I'd bet on a lab error for now. But it is conceivable.
> The enzyme, reverse transcriptase, is encoded by LINE-1 elements, sequences that litter 17% of the human genome and represent artifacts of ancient infections by retroviruses.
> The enzyme, reverse transcriptase, is encoded by LINE-1 elements, sequences that litter 17% of the human genome and represent artifacts of ancient infections by retroviruses.
https://en.m.wikipedia.org/wiki/Illegitimi_non_carborundum
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.
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.
https://en.m.wikipedia.org/wiki/Plural_form_of_words_ending_...
While I may agree with the grammatical merits [1)] I'm not convinced (yet). The second argument [2)] that it's never had a historical plural doesn't hold up. The field of virology is much more recent so the need for a plural 'virus' didn't exist at the time.
And 3) is literally how words are formed. If a term used frequently enough it eventually becomes a word regardless of the original grammatical correctness. The term even has 175 years of precedent.[2] As cactus has the plural cacti it's non-obvious why the same doesn't hold true for virus.
[1] https://en.wikipedia.org/wiki/Plural_form_of_words_ending_in... [2] https://archive.org/details/homopathictreati00test/page/48/m...
[1] https://twitter.com/ArisKatzourakis/status/13904196191696732...
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.
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 (an important step for such a journal). When you are in this position, finding reviewers that will not reject you is really easy: academia is a small world with a few really powerful individuals.
I think the reason for this is that NAS members performs a lot of editorial works for the Academy, and they are very good scientist hence their contribution should be valued, and fast.
This has been the source of a lot of outrage (I was maintaining a list but I can't find it). Some NAS members used this process to rapidly publish when timing was important (such as covid-19 research), scooping the work of researchers that don't have such a convenient outlet. It is especially problematic when a professor is a member of the NAS for his work in some field, but uses "contributed" papers to push mediocre or naive work in another field (s)he doesn't know at all (such as physicist in epidemiological modeling). A lot of very bad quality work ended up in the news because it was in PNAS.
To mitigate these issues, I think it's now limited to two papers per year. Moreover, the paper mentions "contributed by" and the name of the reviewers. But if you go and check some google scholar page, some people made a career out of it. For any idea, you get an audience and tons of credibility for free.
[1]: https://www.pnas.org/content/118/21/e2105968118
I do thoroughly understand your concerns and distaste here that this allows prominent academics to push their (possibly incorrect) views/results on something far outside their expertise. I would love if PNAS publishes the peer reviews for papers such as these that pertain to ongoing health crises (eLife makes peer reviews public, but keeps the reviewers' identity anonymous).
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
[1] https://statmodeling.stat.columbia.edu/?s=PNAS, https://statmodeling.stat.columbia.edu/2017/10/04/breaking-p...
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.
“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?
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
There is at least one other preprint floating around now [0] which suggests that the spike protein itself is a general inflammatory agent, and another preprint (having trouble finding it) indicating that the spike protein is possibly responsible for the clotting/vascular nature of COVID. Now as I understand the mRNA vaccines induce cells to produce spike proteins.
So if the reports in these preprints are confirmed, then there is a likelihood that the mRNA vaccine will cause chronic inflammation in some proportion of recipients. And given the new orthodoxy, and the political momentum behind a successful vaccine, I expect that confirmation and acknowledgement of such findings to be a long uphill battle. Particularly given the ambiguous nature of chronic inflammatory conditions. Note that a retroviral tendency of the COVID virus could explain positive tests post symptomatic infection as well as so called long COVID.
0. https://www.biorxiv.org/content/10.1101/2021.03.16.435700v1
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.
You're spot on on the comment about suppressing data, though.
Publication of a pre-print that appeals to the use of misinformation for the sole purpose of publicity is another thing. Certainly timing of this could have been better especially in this current covid world where we now use pre-print as an almost equivalent to peer-reviewed.
Also thanks OP for the summary!
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."