Ralph Baric SARS-like cluster Paper Revised

[BurninBeard]

I noticed that this study https://www.nature.com/articles/nm.3985

(SARS-like cluster of circulating bat coronaviruses shows potential for human emergence)

has been altered from the original paper published in 2015. It is missing 6 references that appeared in the original paper published.

Here is the archived paper: https://archive.is/hY83J#selection-2449.0-3661.1

Is there any reason why these references would be removed from a paper?

There is no disclaimer on the paper that is currently up saying that there was an alteration from the original paper except for the funding notice.

[CharonY]

If you look at the title you will note that there are changes there too. IOW these are manuscripts at different level of editing. Moreover, the articles in PMC are generally the pre-edit author copies (many journals including Nature do not allow the author to upload the edited full-texts). Between formal acceptance after peer-review there can be final edits (e.g. reviewers may request certain changes but they are minor enough that they do not want to see it again, which might include cleaning up or changing references or adhering to rules set out by the journal) as well as the final proofs. Nature is also one of the journals which actually make quite some efforts to improve the final manuscript so they could also be lost there.

In short, it is the difference between an earlier author version and the final edit. The latter is generally considered to be the "real" published version. 

[BurninBeard]

Doesn't the removal of 6 references and the addition of 2 more seem strange? Is it normal for a journal to make that many changes to a paper?

Also removed was the Biosafety and biosecurity section. That section makes reference to this paper https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4801244/ as well as a link to the PDF detailing US Govt Dual Use & Gain Of Function Pause.

It seems highly odd that Nature would make this many changes to a paper. Also, all six of the removed references plus the link to the study above all concerned Gain Of Function experiments. The two added were both vaccine related.

 

Edited May 6, 2020 by BurninBeard

[Strange]

Why do you assume it is the journal that made the changes, rather than the authors?

[BurninBeard]

Was that question to me Strange? If so I am making no assumptions.

 

[CharonY]

7 hours ago, BurninBeard said:

Doesn't the removal of 6 references and the addition of 2 more seem strange? Is it normal for a journal to make that many changes to a paper?

Also removed was the Biosafety and biosecurity section. That section makes reference to this paper https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4801244/ as well as a link to the PDF detailing US Govt Dual Use & Gain Of Function Pause.

It seems highly odd that Nature would make this many changes to a paper. Also, all six of the removed references plus the link to the study above all concerned Gain Of Function experiments. The two added were both vaccine related.

 

No that is not how it generally works. Reviewers may make suggestions, or the co-authors may decide to drop it because they feel references or sections are too weak or speculative. Sometimes new data arises during review which also may lead to further editing. Nature articles tend to be more polished. However, all the edits have to be made and approved by the authors.

[Strange]

2 hours ago, BurninBeard said:

Was that question to me Strange? If so I am making no assumptions.

 

Ok. It was just that you said:

9 hours ago, BurninBeard said:

It seems highly odd that Nature would make this many changes to a paper.

I would assume the authors made the changes.

I don't think journals even edit papers for style; it is up to the authors to follow the journal's style guide.

[CharonY]

2 minutes ago, Strange said:

I don't think journals even edit papers for style; it is up to the authors to follow the journal's style guide.

The journals do not straight up edit, but they can make suggestions during the proof stage. Many journals do little than the bare minimum (e.g. if they spot typos or inconsistencies in numbering or such), Nature has copy editors doing quite more. But the author has to sign off every suggested change. 

[BurninBeard]

I think this paper was edited for a reason. It has nothing to do with style or typos or the strength or weakness of the references. It is to hide the amount of gain of function research that is ongoing. The experiments at UNC (Baric's Lab) that this paper describes are dual use - gain of function experiments as defined by Professor Francis Boyle the author of the Biological Weapons Convention. The references removed were gain of function studies. The section removed from the body of the paper contained a gain of function study. The study in question should have been halted by the moratorium yet it was allowed to move forward. https://www.the-scientist.com/news-opinion/lab-made-coronavirus-triggers-debate-34502 Why?

Why did Fauci and Collins offshore these experiments to Wuhan and The Lugar Center in Tblisi, Georgia http://armswatch.com/project-g-2101-pentagon-biolab-discovered-mers-and-sars-like-coronaviruses-in-bats/

I am not sure how you can in all honesty make the claim that this is how papers are normally published in peer review.

This whole thing stinks of guano.

[CharonY]

Well, I have been publishing papers for quite a while and as an author you sign off to all changes being made. What you are offering are conspiracy theories. Also quite funny is the following under the published paper:

Quote

Editors’ note, March 2020: We are aware that this article is being used as the basis for unverified theories that the novel coronavirus causing COVID-19 was engineered. There is no evidence that this is true; scientists believe that an animal is the most likely source of the coronavirus.

Feel free to contact the authors to ask them why they left things off, but please do not offer wild speculations as facts. Also in the paper version you linked (I have not read either of them fully so cannot comment on it as a whole) the authors did declare that they have initiated the study before the moratorium.

[BurninBeard]

2 hours ago, CharonY said:

Also in the paper version you linked (I have not read either of them fully so cannot comment on it as a whole) the authors did declare that they have initiated the study before the moratorium.

Keep reading...

"Baric’s study on the SHC014-chimeric coronavirus began before the moratorium was announced, and the NIH allowed it to proceed during a review process, which eventually led to the conclusion that the work did not fall under the new restrictions, Baric told Nature. But some researchers, like Wain-Hobson, disagree with that decision.

The debate comes down to how informative the results are. “The only impact of this work is the creation, in a lab, of a new, non-natural risk,” Richard Ebright, a molecular biologist and biodefence expert at Rutgers University, told Nature.

But I guess Richard Ebright and Simon Wain-Hobson are just conspiracy theorists.The canned response is tired.

The reason the editors note was placed on this paper was because in multiple interviews this paper along with 2 others were presented by Professor Francis Boyle, Professor of International Law at University of Illinois College of Law, author of U.S. implementing legislation for 1972 Biological Weapons Convention, the Biological Weapons Anti-Terrorism Act of 1989 as proving dual use/gain of function bioweapon research. Those are his words not mine. You should read his book Biowarfare and Terrorism and after you are done with that you should read Seymour Hersh's 1968 classic Chemical and Biological Warfare they are illuminating.

You can try this one on for size too https://www.nature.com/news/engineered-bat-virus-stirs-debate-over-risky-research-1.18787

Its easy to name call but maybe instead of throwing out the tired "conspiracy theory" pejorative you should actually step back and think about this with an open scientific mind. I remember when calling a Nobel Prize winner a conspiracy theorist was risky business but I guess Luc Montagnier doesn't get any respect.

Do you even know the origin of the term "conspiracy theory"?

You act as if this GOF research isn't happening. In case you didn't know there was a lot, a lot, a lot of opposition to this type research. Much of it stemming from the H5N1 and H7N9 research of Ron Fouchier was doing using ferrets to create receptor affinity https://www.sciencemag.org/news/2011/11/scientists-brace-media-storm-around-controversial-flu-studies and https://www.nature.com/articles/500150a

Take for example a case from 1977 https://mbio.asm.org/content/6/4/e01013-15   Professor Osterholm confirmed on video that the 1977 outbreak came from a lab release.

I could hand you stacks of studies showing GOF research.

Did you actually read "The proximal origin of SARS-CoV-2" paper. The evidence for zoonotic jump is just not there.

– When a virus manages to infect a new species of host it’s known as a zoonotic jump, a process that generally takes months or even years to complete. The first stage is when a virus infects one individual in a new host species, which is typically a dead-end the first time it happens since there’s no way for the virus to be adapted to a different species’ biology. The second stage of a zoonotic jump is when the virus manages to move from the first new host into more hosts of the new species, which results in some temporary transmission in a localized area – these are known as endemics and generally fizzle out the first few times they happen as the virus adapts to its new host species, and mutations win or lose the survival battle. The final stage, the only time a zoonotic jump is considered complete, is when there’s sustained host-to-host transmission in the new species. These zoonotic jumps have some predictable characteristics, the primary one is that adapting to a new host inevitably requires mutations that weren’t optimal in the old host. And so the virus gets weakened as its initially attempting to jump into a new host species, which is why the above sequence of steps – one new host, a few new hosts that pass it among themselves temporarily, and then finally sustained transmission – takes at least several months if not years to play out, since a good bit of time is required for all three steps to occur. Viral trial-and-error is required for the virus to find the right mutations that will allow it to prosper in a new host species, it’s never been known to just happen magically all at once.

– And so assuming that COVID-19 emerged naturally in a matter of weeks in the middle of a massive urban metropolis the size of New York City, when the host population of bats was hibernating anyways, requires completely ignoring everything we know about how viruses transfer between species. Not only was Wuhan’s population not interacting with bats since they hardly interact with humans in urban situations to begin with, but any possible host bats were sleeping in their caves anyways. And not only would the circumstances of this transfer require rewriting the textbooks on zoonotic jumps if it occurred at all, but beyond that: supposedly not only did a zoonotic jump happen instantly without the necessary steps, but when it hit humans it was extraordinarily virulent from the start, something that’s supposed to take an extensive amount of time to ever happen as mutations go through selective trial-and-error. This trial-and-error takes time and is why viruses have never made a zoonotic jump and been instantly virulent in a new host species like COVID-19 has been in humans. And in 2018, a study looking for past infections by bat coronaviruses in Wuhan found no evidence whatsoever that anyone there had ever been infected by one at all, making the idea that these viruses have been circulating there entirely absurd. Nothing we know about how viruses naturally make zoonotic jumps point to that happening here.

Edited May 8, 2020 by BurninBeard

[Strange]

!

Moderator Note

Closed pending moderator discussion