"To avoid losing power with multiple comparisons, we focus our analysis on the BsaI/BsmBI sites in SARS-CoV-2 and compare the BsaI/BsmBI map in SARS-CoV-2 to all other restriction maps of all other CoVs used in our analysis." It's important to know whether or not the authors picked BsaI & BmBI blind, before looking at the genome. If they picked BsaI & BmBI with knowledge of the SARS-CoV-2 genome, that doesn't dodge t…
I realized why this being based on simulation bothered me: this is a machine learning classifier that classifies viral genomes as synthetic or natural. The training set n = 72 (all negative, which is justifiable if you're ok with null hypothesis significance testing) the validation set n = 6 (only synthetic examples, which is less fine), and there's no test set. No effort was made to estimate true positive rate, fals…
Endonuclease fingerprint indicates a synthetic origin of SARS-CoV-2?
231–240 of 250 posts
Re: Endonuclease fingerprint indicates a synthetic origin of SARS-CoV-2?
#232I've seen several papers with the opposite conclusion. Why do we only see the lab leak hypothesis front paged on HN?
To my mind, there are a few reasons: 1) It makes the pandemic deterministic (bad lab security means an outbreak) instead of stochastic (wildlife spillover). That is, to be frank, even as an epidemiologist who is very skeptical of the lab leak hypothesis, a comforting thought. 2) It's a popular topic in the Substack/Medium set, because it moves the pandemic back into their wheelhouse of expertise, international relati…
As if epidemiologists are the only profession studying stochastic phenomena. What does deterministic vs stochastic have to do with it? Every phenomena has stochastic effects.
Bad lab security is stochastic too: consider experimental security protocols; imagine them being set in year X, no protocol results in 100% security, we can only make attempts to drive down probability. Say a certain step requires tubes to be UVC sterilized with a certain fluence dose per cm^2. This was deemed suitable in year X during which experiments happened at rate R_x. This implicitly corresponds to some unknown rate of lab leaks world wide (perhaps once in a century for example). As education and automation progresses, such experiments are occurring at higher and higher rates. A possible lesson from a conclusion that it was a lab leak, and that people again underestimated the exponential curve of scientific growth could be that that security protocols be formulated in terms of the global rate of research. If theres 100x the rate of experiments compared to 20 years ago, perhaps the protocols should be tighter so that the scurity lapse rate decreases 100x as well, in order to maintain the constant tolerable global rate of lab leaks. The electrons in a flip flop may individually behave stochastically, but collectively very deterministically. The misconception -that it is safe enough if lab security protocols meet a constant per single execution safety bar- will deterministically be violated with constant growth of rate of experiments. (EDIT/ADDITION: In a world that includes the global rate of experiments, a current researcher, reading the securiy protocols of the past will find the current protocols unfairly absurd, when he realizes they are 100x more stringent, but thats because there was perhaps 10x fewer researchers in the past and 10x higher troughput of experiments; similarily a researcher at the end of his career will find the security measures to be say 100x more stringent compared to the start of his career)
> 2) It's a popular topic in the Substack/Medium set, because it moves the pandemic back into their wheelhouse of expertise, international relations, policy, etc. It becomes a human problem with human solutions.
Why does humanity like to install lightning rods? because it moves the 'act of god' lighting phenomena (and resulting fires etc.) back into their wheelhouse of expertise, policy, etc. It becomes a human problem with human solutions.
> 3) It appeals to the contrarian mindset.
There exists no such thing as the contrarian mindset. That's an epidemic idea used to silence criticism.
> 4) All of the lab leak papers at least attempt to show definitive proof. In contrast, actually finding the source of spillover events is the work of decades (and isn't always or even often successful). "Science is slow and uncertain" is a less compelling narrative.
For the average cold coronavirus (not sars cov), its very easy to detect and trace the path of a virus, its just that nobody bothers.
When a new potential epidemic is detected (just a few death and a few sick people, as the likelihood punctures the noise-floor), it was quickly traced to the cooling towers nearby the city where I live. Turns out there was negligence which allowed a microbe to prosper and infect people. Initially there was doubt about which cooling tower of which company caused the infections, but by genetic sequencing it was quickly identified which tower caused the issues. It didn't take decades, just weeks.
Re: Endonuclease fingerprint indicates a synthetic origin of SARS-CoV-2?
#233Earlier quoted context omitted.
> My opinion is we are not capable of developing in a lab a virus that is so transmissible and survivable in human species only. I think the complexity of the virus machinery and its interactions inside of our bodies and immune system is beyond astronomical in complexity. It's laughable to suggest that we are so intelligent as to invent a better version of the machinery that is hypothesized as the very machinery resp…
Sorry it does not. Was that virus more deadly, effective, or in any other measure better than the original polio? Or was it "polio" with a spike protein glued to it's head?
Re: Endonuclease fingerprint indicates a synthetic origin of SARS-CoV-2?
#234Wasn't this a conspiracy theory at the start if this? I'm sure this kind of talk might have been squashed, suppressed, and some people might even people got banned for saying such things?
It is a conspiracy theory until you have good data and rigorous analysis. If you cannot see that people resisting jumping on an emotionally appealing bandwagon with racist undertones before careful evidence is collected on it, then I honestly don't know what to do for you.
At any rate, this particular conspiracy theory was obviously very likely to be true right from the moment it was first proposed. The analysis and data was always rigorous. This new genetic evidence is good, but the extraordinarily tiny probability of a very unusual new virus emerging right next to one of the only labs in the world doing research on that exact type of thing, already rendered it irrational to adopt the natural origin theory right from day one. You don't even need to study the RNA at all to know that SARS-CoV-2 is a very unusual event, having CoV virus labs in a city is also very unusual, that lab leaks are common, that public databases being pulled offline due to "hacking" right before such a virus emerges is very unusual, and that these things intersecting followed by suspiciously immediate and vehement denial on the back of no evidence at all is also very unusual. Estimate those probabilities and then multiply them together. The number you get is astronomically low.
Re: Endonuclease fingerprint indicates a synthetic origin of SARS-CoV-2?
#235Earlier quoted context omitted.
Again, bayesian priors. If there are only 4 labs worldwide messing with exactly these viruses, the combinatorics of this happening 20km from one of those 4 is infitesimal.
I'm bored of this debate that happens every time one of these charlatans releases a paper that grabs a bunch of headlines and is disproven two days later (as already has happened with the original in this thread). But "This happening" needs to be defined for Bayes to be of any use. State clearly what you think happened and it can be judged, because as has been proven over and over again, the virus is of natural origi…
Re: Endonuclease fingerprint indicates a synthetic origin of SARS-CoV-2?
#236Earlier quoted context omitted.
Studied and then escaped from a lab does not equal synthetic. Exactly nothing in your post supports a synthetic origin over a sample from nature that got studied in a lab. Jumping to these kinds of one sided conclusions should be a red flag.
It could also be studied and altered in a lab, and then escape.
Of course. But saying "It was studied in a lab, therefore it must be synthetic" is just idiotic and pretty much derails the entire conversation.
It derails the conversation because it conflates a number of issues that have to be assessed seperately: lab safety, mucking about with deadly deseases, and the intent to set deadly deseases free.
If you start conflating any one of these, it becomes more easy to deride the entire conversation as tinfoil hattery. If just one of those components is an easy target for derision or is seen as unlikely, everyone who dares to pick up any of the other points gets painted in the same colour in the public eye. There doesn't even need to be any evil intent behind it. It's just how people are.
And this is precisely what happened when people started pointing out the existence of a lab next to ground zero. A lot of scientists retracted their speculation on this because they were immediately put into the same category as the crowd shouting "tHe cHiNeSe made iT!!".
Re: Endonuclease fingerprint indicates a synthetic origin of SARS-CoV-2?
#237Earlier quoted context omitted.
I'm bored of this debate that happens every time one of these charlatans releases a paper that grabs a bunch of headlines and is disproven two days later (as already has happened with the original in this thread). But "This happening" needs to be defined for Bayes to be of any use. State clearly what you think happened and it can be judged, because as has been proven over and over again, the virus is of natural origi…
See how your wording is super biased? "Charlatans"
What if they’d done that multiple times?
“Bias” isn’t relevant when it comes to calling out bad actors.
Re: Endonuclease fingerprint indicates a synthetic origin of SARS-CoV-2?
#238Earlier quoted context omitted.
It could also be studied and altered in a lab, and then escape.
> It could also be studied and altered in a lab, and then escape. Of course. But saying "It was studied in a lab, therefore it must be synthetic" is just idiotic and pretty much derails the entire conversation. It derails the conversation because it conflates a number of issues that have to be assessed seperately: lab safety, mucking about with deadly deseases, and the intent to set deadly deseases free. If you start…
Re: Endonuclease fingerprint indicates a synthetic origin of SARS-CoV-2?
#239The opening line: "To prevent future pandemics, it is important that we understand whether SARS-CoV-2 spilled over directly from animals to people, or indirectly in a laboratory accident." Is that true? I mean I understand why people would be curious, but does it really matter, in terms of what we need to do? We know that viruses _can_ spillover from animals to people, and we know that viruses in a laboratory setting…
Re: Endonuclease fingerprint indicates a synthetic origin of SARS-CoV-2?
#240The opening line: "To prevent future pandemics, it is important that we understand whether SARS-CoV-2 spilled over directly from animals to people, or indirectly in a laboratory accident." Is that true? I mean I understand why people would be curious, but does it really matter, in terms of what we need to do? We know that viruses _can_ spillover from animals to people, and we know that viruses in a laboratory setting…
Yes, this is true. If we knew that this pandemic came from a lab, that would have massive implications for how tightly we control this type of lab research - both in terms of whether we do the gof research, and also in how we run and regulate the labs. Surely you can imagine the reaction if, hypothetically, the world knew that this coronavirus was made in a lab and then escaped? I'm amazed that you think otherwise -…