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Scientists claim to find HIV virus-like insertions in the 2019-nCov [pdf]

biorxiv.org

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Re: Scientists claim to find HIV virus-like insertions in the 2019-nCov [pdf]

#121

Post by dang »

yters wrote: post #112
dang wrote: post #49

Earlier quoted context omitted.

Please don't feed egregious comments by replying. This is in the site guidelines: https://news.ycombinator.com/newsguidelines.html . A religious flamewar on top of whatever else we've got here is the last thing this thread needs!

How is this religious?

"Intelligent design" is an argument for the existence of God, which is a religious topic.

The issue from an HN moderation point of view isn't religion; it's religious flamewar, which is what internet arguments about religion—at least in large public forums—inevitably degrade into. Therefore we don't go there.

Re: Scientists claim to find HIV virus-like insertions in the 2019-nCov [pdf]

#122

Post by folli »

jszymborski wrote: post #28

I think the important things to know here are: 1. A group of scientist have submitted a manuscript for review with a number of exceptionally (and uncharacteristically) bold claims. 2. A huge amount of scrutiny and additional reproducibility will necessarily need to be conducted before conclusions of this nature can be drawn. 3. This manuscript hasn't even passed the normal muster... a biorxiv post isn't much differen…

#2: replicating their BLAST search is easy: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=398N4CS... and it shows that the matches of these short inserts are completely by chance and don't constitute any statistically significant relationship.

Re: Scientists claim to find HIV virus-like insertions in the 2019-nCov [pdf]

#123

Post by Palptine »

folli wrote: post #119

Sorry, but it's very easy to verify that these claims are crap by replicating their study, i.e. doing a simple blast search of the insert sequence against the virus database. Here's the result of the first insert: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=398N4CS... Although, there are some hits against HIV, there are also equally matching hits against bacteriophages; viruses that only target bacterias, th…

What's the chance of hitting all 4 of them though? This is a good step in verification but you are awfully too quick to reject their claim.

Re: Scientists claim to find HIV virus-like insertions in the 2019-nCov [pdf]

#124

Post by im3w1l »

cs702 wrote: post #103
jszymborski wrote: post #28

I think the important things to know here are: 1. A group of scientist have submitted a manuscript for review with a number of exceptionally (and uncharacteristically) bold claims. 2. A huge amount of scrutiny and additional reproducibility will necessarily need to be conducted before conclusions of this nature can be drawn. 3. This manuscript hasn't even passed the normal muster... a biorxiv post isn't much differen…

As regards #3, I agree: the more eyes who see this unconfirmed claim, the better. That's the main reason I upvoted the OP. A great outcome would be if reputable scientists see this on HN or Twitter or learn about it through colleagues, and subsequently refute it or dismiss it as bad science.

> the more eyes who see this unconfirmed claim, the better.

Isn't it a waste of those eyes' time if it turns out to be false? When there are plenty of confirmed things they could be reading?

Re: Scientists claim to find HIV virus-like insertions in the 2019-nCov [pdf]

#125

Post by nextos »

folli wrote: post #119

Sorry, but it's very easy to verify that these claims are crap by replicating their study, i.e. doing a simple blast search of the insert sequence against the virus database. Here's the result of the first insert: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=398N4CS... Although, there are some hits against HIV, there are also equally matching hits against bacteriophages; viruses that only target bacterias, th…

Large (but And the fact that there's no known CoV with any of these inserts is quite intriguing.

Re: Scientists claim to find HIV virus-like insertions in the 2019-nCov [pdf]

#126

Post by folli »

Palptine wrote: post #123
folli wrote: post #119

Sorry, but it's very easy to verify that these claims are crap by replicating their study, i.e. doing a simple blast search of the insert sequence against the virus database. Here's the result of the first insert: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=398N4CS... Although, there are some hits against HIV, there are also equally matching hits against bacteriophages; viruses that only target bacterias, th…

What's the chance of hitting all 4 of them though? This is a good step in verification but you are awfully too quick to reject their claim.

Read the paper, they actually only match 2 inserts, the other two inserts are modified by the authors in such a way that they are made to match (Table 1).

Both inserts 1 and 2 also match to Streptococcus phage, but a bacteriophage would of course not be such a bold claim as HIV matches are.

Also, be aware that because of the scientific interest in HIV, there are hundreds of HIV strains sequenced, a virus known for its mutation rate (especially in these two proteins gp120 and gag, as they are under pressure to mutate in order to evade the immunesystem). So in such a large library of protein sequences one is bound to find a match of a short 6 letter (amino acid) sequence. That's why E values exist to make a statement about the statistical significance.

Re: Scientists claim to find HIV virus-like insertions in the 2019-nCov [pdf]

#127

Post by xvector »

fapjacks wrote: post #93
xvector wrote: post #63

Earlier quoted context omitted.

It would be a pretty lame bioweapon given how few people it’s killed.

Be advised that there are many posts on Chinese social media claiming the crematoriums are backlogged with people whose listed cause of death is "viral pneumonia" (or just "pneumonia") because hospitals are turning away so many and diagnostics are not catching up. Do not take statistical reporting for granted: The numbers are a best case scenario of definitive knowns. Also, bioweapons have as diverse a variety of use…

While I think China is hiding the number of infected, it'd be pretty hard to hide the proportion of dead to infected as the virus has already escaped Wuhan.

Re: Scientists claim to find HIV virus-like insertions in the 2019-nCov [pdf]

#128

Post by folli »

nextos wrote: post #125
folli wrote: post #119

Sorry, but it's very easy to verify that these claims are crap by replicating their study, i.e. doing a simple blast search of the insert sequence against the virus database. Here's the result of the first insert: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=398N4CS... Although, there are some hits against HIV, there are also equally matching hits against bacteriophages; viruses that only target bacterias, th…

Large (but And the fact that there's no known CoV with any of these inserts is quite intriguing.

The last two (look at table 1) are interesting in such a way that its almost scientific misconduct akin to photoshopping a picture in a scientific paper. They blasted the inserts, but apparently couldn't find any matches to HIV, so they just changed them until they found something.

Re: Scientists claim to find HIV virus-like insertions in the 2019-nCov [pdf]

#129

Post by folli »

folli wrote: post #126
Palptine wrote: post #123

Earlier quoted context omitted.

What's the chance of hitting all 4 of them though? This is a good step in verification but you are awfully too quick to reject their claim.

Read the paper, they actually only match 2 inserts, the other two inserts are modified by the authors in such a way that they are made to match (Table 1). Both inserts 1 and 2 also match to Streptococcus phage, but a bacteriophage would of course not be such a bold claim as HIV matches are. Also, be aware that because of the scientific interest in HIV, there are hundreds of HIV strains sequenced, a virus known for it…

For posteriority, here's the link to the Blast results for the second insert: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=39ACRKV...

Re: Scientists claim to find HIV virus-like insertions in the 2019-nCov [pdf]

#130

Post by 45ure »

folli wrote: post #119

Sorry, but it's very easy to verify that these claims are crap by replicating their study, i.e. doing a simple blast search of the insert sequence against the virus database. Here's the result of the first insert: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=398N4CS... Although, there are some hits against HIV, there are also equally matching hits against bacteriophages; viruses that only target bacterias, th…

>These guys that published such a paper are either completely clueless or nefarious in trying to stir up conspiracy theories.

In your opinion, do you think this kind of subterfuge could have been picked up by Dr. Eric Feigl-Ding or someone with a similar calibre, before broadcasting this preprint for wider consumption? Thanks.

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