Evidence supports claim that SARS-CoV-2 genes can integrate with human DNA
sciencemag.org
sciencemag.org
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.
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."
You're spot on on the comment about suppressing data, though.
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.
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.
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
"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. https://en.m.wikipedia.org/wiki/Plural_form_of_words_ending_...
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.
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.
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...
> 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.
[1] https://twitter.com/ArisKatzourakis/status/13904196191696732...
Coronaviruses 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.
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.
“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?