3 ms·

Damn this is the first comment contrarian to the article that acually addresses the main argument : Silent vs non-silent mutations ratio. The article pretty mu

Damn this is the first comment contrarian to the article that acually addresses the main argument : Silent vs non-silent mutations ratio. The article pretty much convinced me and I am not sure I am really unconvinced yet but I have to thank you.

civilized 5y ago
The S:NS ratio cited in the blog post also appears to be simply incorrect: https://twitter.com/eigenrobot/status/1471336024827568130?s=20 https://twitter.com/eigenrobot/status/1471336024827568130?s=...
- dljones 5y ago
  So, you take on faith that the s/ns ratio as described by "Eigenrobot" who is quoting "Brett" (who are they?) is correct, and the s/ns ratio described by many microbiologists and genome experts, identifiable on their Twitter accounts, is wrong? I mean, we can find anyone on Twitter saying anything. I could create an account right now that says I'm an expert on time travel and tweet about it. And of course now that omicron is circulating widely in humans, its pattern and ratio of mutations is occurring as one would expect. I wonder why something we know is a natural occurrence (mutation as it infects humans worldwide) looks natural. It makes me wonder why the original omicron looked so weird. To me this is not a conversation about whether a lab leak occurred. It's a conversation about why the experts are not ruling out hypotheses that explain the information so they can (if necessary) move on to other hypotheses. Just dismissing hypotheses that explain the existing information is not very scientific, unless the hypotheses are untestable or are truly off the wall. This hypothesis is not truly off the wall.
toufka 5y ago
It's also much more complicated to define "silent" in the context of a virus. In a larger-genomed organism there is a relatively clear (though still not completely clear) function of a coding region, where the change of a nucleic acid will have no effect on the protein made - but still might (subtly) effect regulation in some way. In a virus, most nucleic acids have multiple, layered, and unknown functions - it's much much harder to assign any given nucleic acid as "silent", and be confident that that is the case from an evolutionary perspective. As another posted, it's a good hypothesis that's straightforward to test statistically against all of the other variants. But on its own, it's not necessarily convincing here that the S/NS ratio is particularly concerning (and as above, doesn't speak to how directed evolution works either).

civilized 5y ago

The S:NS ratio cited in the blog post also appears to be simply incorrect: https://twitter.com/eigenrobot/status/1471336024827568130?s=20 https://twitter.com/eigenrobot/status/1471336024827568130?s=...

dljones 5y ago
So, you take on faith that the s/ns ratio as described by "Eigenrobot" who is quoting "Brett" (who are they?) is correct, and the s/ns ratio described by many microbiologists and genome experts, identifiable on their Twitter accounts, is wrong? I mean, we can find anyone on Twitter saying anything. I could create an account right now that says I'm an expert on time travel and tweet about it. And of course now that omicron is circulating widely in humans, its pattern and ratio of mutations is occurring as one would expect. I wonder why something we know is a natural occurrence (mutation as it infects humans worldwide) looks natural. It makes me wonder why the original omicron looked so weird. To me this is not a conversation about whether a lab leak occurred. It's a conversation about why the experts are not ruling out hypotheses that explain the information so they can (if necessary) move on to other hypotheses. Just dismissing hypotheses that explain the existing information is not very scientific, unless the hypotheses are untestable or are truly off the wall. This hypothesis is not truly off the wall.

toufka 5y ago

It's also much more complicated to define "silent" in the context of a virus. In a larger-genomed organism there is a relatively clear (though still not completely clear) function of a coding region, where the change of a nucleic acid will have no effect on the protein made - but still might (subtly) effect regulation in some way. In a virus, most nucleic acids have multiple, layered, and unknown functions - it's much much harder to assign any given nucleic acid as "silent", and be confident that that is the case from an evolutionary perspective. As another posted, it's a good hypothesis that's straightforward to test statistically against all of the other variants. But on its own, it's not necessarily convincing here that the S/NS ratio is particularly concerning (and as above, doesn't speak to how directed evolution works either).