4 ms·

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

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.

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dnautics 5y ago
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.
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acqq 5y ago
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."
Y_Y 5y ago
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.
- COGlory 5y ago
  I would agree with this compromise.
boringg 5y ago
Suppression of real data is no good. 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!
vibrio 5y ago
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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dnautics 5y ago

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.

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acqq 5y ago

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."

Y_Y 5y ago

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.

COGlory 5y ago
I would agree with this compromise.

boringg 5y ago

Suppression of real data is no good. 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!

vibrio 5y ago

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?