5 ms·

Another thing that the blog post appears to be unaware of is that the absence of samples showing the step-by-step evolution towards omicron doesn't mean that th

by ufo 5y ago

Another thing that the blog post appears to be unaware of is that the absence of samples showing the step-by-step evolution towards omicron doesn't mean that this didn't happen. A lot of places in the world don't have the resources to do covid testing and genomic surveillance.

deleted 5y ago
[deleted]
mikeyouse 5y ago
And even if they did do genomic analysis - it's entirely plausible the results are sitting in a hospital database somewhere instead of uploaded to the international gene surveillance repository.
- Sevaris 5y ago
  Plausible, yes. If the data exists, it should be made public. The article still mostly just makes a hypothesis and makes the argument that this is something that should be seriously investigated, not that the author has determined without a doubt that this is a lab leak.
  - mikeyouse 5y ago
    Sure - but what are the chances that whichever hospitals did the sequencing even know they're in possession of the intermediate data? The OPs' method of "just asking questions" is really bad science and feels a whole lot like the God of the Gaps argument style that Creationists are so fond of using.
    - blix 5y ago
      I'm not sure the best way to judge the quality of a scientific argument is whether it 'feels like good science.' While the author is obviously only scratching the surface in an article targetted at non-scientists, the several PhDs he cites make decent arguments that are based on a little more than feelings. It would probably be more in line with the ideal of 'good science' to actually investigate the possibilities presented than dismiss them from emotional associations. It is a worrying trend that the way science feels is increasingly more important than the actual evidence (or lack thereof). One could even describe the current attitude towards science outside of scientitific institutions as religious.
rob_c 5y ago
And the reason not all of these spread fast is obviously that one mutation (or combination) impacts the spread rate more than the 30+other mutations in isolation... Although after enough conversations I've found this too needs spelling out in plain English...
dljones 5y ago
Absence of evidence is not evidence of absence, yes. But take another look at the phylogenetic tree. Those are huge gaps. See also this article describing how good South Africa is at spotting and sequencing variants."The reality is that southern Africa is a top international powerhouse of COVID-19 surveillance." https://www.businessinsider.com/how-southern-africa-detected-omicron-variant-so-quickly-2021-11?op=1 https://www.businessinsider.com/how-southern-africa-detected...
- ufo 5y ago
  The hypothesis is that it could have originated in a different country and was only identified after it arrived in South Africa.
klipt 5y ago
> absence of samples showing the step-by-step evolution Sounds much like the "missing link" gotcha that creationists loved to deploy.
TeeMassive 5y ago
Yeah but since spring 2020? This variant slept without getting replaced by other more contagious variants? That doesn't seem likely.
- tehjoker 5y ago
  The entire world has been blanketed in Coronavirus and as far as I know Africa has seen a mix of action that has been different from how Western countries have experienced it. The rates of infection are different, the rates of vaccination are different. Two VOCs have come out of South Africa, but who's to say that an earlier version from 2020 wasn't bumping around the continent and returned to South Africa? Everyone likes to posit human intervention when we have very little information, especially people highly motivated to declare COVID-19 a lab leak for geopolitical reasons. Give the science time and we might start to fill in the gaps.
  - TeeMassive 5y ago
    > The entire world has been blanketed in Coronavirus and as far as I know Africa has seen a mix of action that has been different from how Western countries have experienced it. The rates of infection are different, the rates of vaccination are different. Two VOCs have come out of South Africa, but who's to say that an earlier version from 2020 wasn't bumping around the continent and returned to South Africa? You're pointing out distinctions that do not make any relevant or substantial differences to the argument. > Everyone likes to posit human intervention when we have very little information, especially people highly motivated to declare COVID-19 a lab leak for geopolitical reasons. Give the science time and we might start to fill in the gaps. With lack of information, ideas that have the less assumptions and concepts tend to be true than their counterparts who require many possible sub-hypotheses and concepts. GoF happen and lab leaks happen and the genetic histogram and the genes makes make this hypothesis the more likely one. The opposite require many hypothetical actors (mouses, immunosuppressed patients, back and forth between geographically distant places and all the combinations thereof) to account for it "hiding" since spring 2020. > especially people highly motivated to declare COVID-19 a lab leak for geopolitical reasons. Nobody blamed nobody here. GoF research happens everywhere. > Give the science time and we might start to fill in the gaps. Science is not beholden to your worldview. Filling the gaps is part of the scientific method, by the way.
medimikka 5y ago
Yes, this is true. But it's also somewhat narrow. Consider this: days after the successful sequencing of Omicron, similar cases were reported in dozens of countries, having arrived there just before or just after the announcement. We know, that it's "just before," because references are being kept and re-analyzed in those cases, and none of the countries with the resources for genomic surveillance has any data on earlier strains in the phylogenic tree. It is simply very unlikely (not impossible, but if you're in London and hear hoof beats, it's probably a horse, not a zebra), that Omicron could have developed over 33 N and a superset of S mutations without ever popping up in any surveillance. South Africa, especially, is a key surveillance player. They're often much more granular than even European key players like the UK, Germany, or France. A strain with this level of infectivity doesn't linger in one hospital. From the looks of the genome, that part (infectivity) would have developed before immune evasion. Having a highly infective strain evolve would ring alarm bells in labs the world around. I guess it's pretty non debatable that Omicron started its World Dominance Tour in October or November 2021. To get there, it had to undergo a massive sequence of events making it as far removed from α.7 as it is. So we can state, with some certainty, that it evolved in isolation and broke free shortly before being discovered. If we now consider the possible origins, wild zoonotic, single origin immune compromised, or accidental leak from research, the latter doesn't sound so improbable anymore. Again, horse, not zebra.
- kurthr 5y ago
  But, the point is it was growling so fast you wouldn't expect it to show up in other places until the "knee" of the exponential showed up there as well. SA being just a couple of weeks ahead is a lifetime for Omicron.
  - medimikka 5y ago
    100% agreed. Again, this is a possibility, not a certainty. But I'd be loath to dismiss it, just as I am not willing to dismiss a reservoir origin. In the end, the author does make a good point: we need mandatory disclosures of GoF research and a general ban on GoF financing of labs who aren't working in full disclosure mode. Ideally, we should not have this discussion because the GoF leak is impossible. Sadly, as secretive as this research is, as much money as we funnel into labs in China and Russia, and as reluctant as oversight authorities (such as the WHO) are to even consider leaks, the best response would be a general ban on GoF and GoF financing.

by ufo 5y ago

deleted 5y ago

[deleted]

mikeyouse 5y ago

And even if they did do genomic analysis - it's entirely plausible the results are sitting in a hospital database somewhere instead of uploaded to the international gene surveillance repository.

Sevaris 5y ago
Plausible, yes. If the data exists, it should be made public. The article still mostly just makes a hypothesis and makes the argument that this is something that should be seriously investigated, not that the author has determined without a doubt that this is a lab leak.
- mikeyouse 5y ago
  Sure - but what are the chances that whichever hospitals did the sequencing even know they're in possession of the intermediate data? The OPs' method of "just asking questions" is really bad science and feels a whole lot like the God of the Gaps argument style that Creationists are so fond of using.
  - blix 5y ago
    I'm not sure the best way to judge the quality of a scientific argument is whether it 'feels like good science.' While the author is obviously only scratching the surface in an article targetted at non-scientists, the several PhDs he cites make decent arguments that are based on a little more than feelings. It would probably be more in line with the ideal of 'good science' to actually investigate the possibilities presented than dismiss them from emotional associations. It is a worrying trend that the way science feels is increasingly more important than the actual evidence (or lack thereof). One could even describe the current attitude towards science outside of scientitific institutions as religious.

rob_c 5y ago

And the reason not all of these spread fast is obviously that one mutation (or combination) impacts the spread rate more than the 30+other mutations in isolation... Although after enough conversations I've found this too needs spelling out in plain English...

dljones 5y ago

Absence of evidence is not evidence of absence, yes. But take another look at the phylogenetic tree. Those are huge gaps. See also this article describing how good South Africa is at spotting and sequencing variants."The reality is that southern Africa is a top international powerhouse of COVID-19 surveillance." https://www.businessinsider.com/how-southern-africa-detected-omicron-variant-so-quickly-2021-11?op=1 https://www.businessinsider.com/how-southern-africa-detected...

ufo 5y ago
The hypothesis is that it could have originated in a different country and was only identified after it arrived in South Africa.

klipt 5y ago

> absence of samples showing the step-by-step evolution Sounds much like the "missing link" gotcha that creationists loved to deploy.

TeeMassive 5y ago

Yeah but since spring 2020? This variant slept without getting replaced by other more contagious variants? That doesn't seem likely.

tehjoker 5y ago
The entire world has been blanketed in Coronavirus and as far as I know Africa has seen a mix of action that has been different from how Western countries have experienced it. The rates of infection are different, the rates of vaccination are different. Two VOCs have come out of South Africa, but who's to say that an earlier version from 2020 wasn't bumping around the continent and returned to South Africa? Everyone likes to posit human intervention when we have very little information, especially people highly motivated to declare COVID-19 a lab leak for geopolitical reasons. Give the science time and we might start to fill in the gaps.
- TeeMassive 5y ago
  > The entire world has been blanketed in Coronavirus and as far as I know Africa has seen a mix of action that has been different from how Western countries have experienced it. The rates of infection are different, the rates of vaccination are different. Two VOCs have come out of South Africa, but who's to say that an earlier version from 2020 wasn't bumping around the continent and returned to South Africa? You're pointing out distinctions that do not make any relevant or substantial differences to the argument. > Everyone likes to posit human intervention when we have very little information, especially people highly motivated to declare COVID-19 a lab leak for geopolitical reasons. Give the science time and we might start to fill in the gaps. With lack of information, ideas that have the less assumptions and concepts tend to be true than their counterparts who require many possible sub-hypotheses and concepts. GoF happen and lab leaks happen and the genetic histogram and the genes makes make this hypothesis the more likely one. The opposite require many hypothetical actors (mouses, immunosuppressed patients, back and forth between geographically distant places and all the combinations thereof) to account for it "hiding" since spring 2020. > especially people highly motivated to declare COVID-19 a lab leak for geopolitical reasons. Nobody blamed nobody here. GoF research happens everywhere. > Give the science time and we might start to fill in the gaps. Science is not beholden to your worldview. Filling the gaps is part of the scientific method, by the way.

medimikka 5y ago

Yes, this is true. But it's also somewhat narrow. Consider this: days after the successful sequencing of Omicron, similar cases were reported in dozens of countries, having arrived there just before or just after the announcement. We know, that it's "just before," because references are being kept and re-analyzed in those cases, and none of the countries with the resources for genomic surveillance has any data on earlier strains in the phylogenic tree. It is simply very unlikely (not impossible, but if you're in London and hear hoof beats, it's probably a horse, not a zebra), that Omicron could have developed over 33 N and a superset of S mutations without ever popping up in any surveillance. South Africa, especially, is a key surveillance player. They're often much more granular than even European key players like the UK, Germany, or France. A strain with this level of infectivity doesn't linger in one hospital. From the looks of the genome, that part (infectivity) would have developed before immune evasion. Having a highly infective strain evolve would ring alarm bells in labs the world around. I guess it's pretty non debatable that Omicron started its World Dominance Tour in October or November 2021. To get there, it had to undergo a massive sequence of events making it as far removed from α.7 as it is. So we can state, with some certainty, that it evolved in isolation and broke free shortly before being discovered. If we now consider the possible origins, wild zoonotic, single origin immune compromised, or accidental leak from research, the latter doesn't sound so improbable anymore. Again, horse, not zebra.

kurthr 5y ago
But, the point is it was growling so fast you wouldn't expect it to show up in other places until the "knee" of the exponential showed up there as well. SA being just a couple of weeks ahead is a lifetime for Omicron.
- medimikka 5y ago
  100% agreed. Again, this is a possibility, not a certainty. But I'd be loath to dismiss it, just as I am not willing to dismiss a reservoir origin. In the end, the author does make a good point: we need mandatory disclosures of GoF research and a general ban on GoF financing of labs who aren't working in full disclosure mode. Ideally, we should not have this discussion because the GoF leak is impossible. Sadly, as secretive as this research is, as much money as we funnel into labs in China and Russia, and as reluctant as oversight authorities (such as the WHO) are to even consider leaks, the best response would be a general ban on GoF and GoF financing.