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So to be clear, do you agree that almost all positive PCR tests for SARS-CoV-2 are true positives (i.e., that almost all patients testing positive are truly inf

So to be clear, do you agree that almost all positive PCR tests for SARS-CoV-2 are true positives (i.e., that almost all patients testing positive are truly infected)? If yes, then what do you think (or think Mullis thinks) is wrong with "the way that PCR is being used today"? The comment you replied to was speculating about "false positives where flu cases get labeled as Covid". Mullis's comments are not too coherent, but I read them as a claim that PCR tests will result in false positives, and I assumed that was why you thought they were relevant. At least one other user seems to have read them the same way, since user theclap responded with a link to a different article explicitly about PCR false positives. Do you read them as something else?

silicon2401 5y ago
I don't agree with anything; I don't have an opinion or stance, I've said that from the beginning. I'm looking for someone _else_ to give _their_ opinion or evidence. I don't know how many different ways I can rephrase the same point. Here's a quote from another reply to my original comment: > > Kary Mullis: I think misused PCR is not quite ... I don't think you can misuse PCR. No, the results, the interpretation of it. See if you can say, if they wanted, if they could find this virus in you at all, and with PCR if you do it well you can find almost anything in anybody. It starts making you believe in the, sort of buddhist notion, that everything is contained in everything else. Right, I mean because if you can amplify one single molecule up to to something that you can really measure which PCR can do, then there's just very few molecules that you don't have at least one single one of them in your body. Okay, so that could be thought of as a misuse of it just to claim that it's meaningful. It is, there's very little of what they call HIV and what's been brought out here by Phil ... the measurement for it is not exact at all, it's not it's not as good as our measurement for things like apples. An apple is an apple. You know, you can get something that's kind of like, if you've got enough things that look kind of like an apple you stick them all together you might think it as an apple. And HIV is like that. Those tests are all based on things that are invisible, and they are the results are inferred in a sense. PCR is separate from that, it's just a process that's used to make a whole lot of something out of something that's why it's not, it doesn't tell you that you're sick and it doesn't tell you that the thing you ended up with really was going to hurt you or anything like that. An example of what I'm looking for info on is this in particular: > PCR is separate from that, it's just a process that's used to make a whole lot of something out of something that's why it's not, it doesn't tell you that you're sick and it doesn't tell you that the thing you ended up with really was going to hurt you or anything like that. I don't have an opinion myself and I'm just looking for someone informed to comment on how today's use of PCR for diagnosing covid aligns with the inventor of PCR's comments that it isn't useful for diagnosing illness. Not whether or not today's covid tests are false or true positives
- tripletao 5y ago
  The PCR test is being used clinically in two major ways. First, people with a positive test are advised to isolate themselves, to avoid infecting others. As I noted in my very first reply, a positive PCR test doesn't necessarily mean that the patient is shedding viable virus (i.e., that the patient could infect others), and that's the kernel of truth behind Mullis's statements. I posted a link above to a paper that attempted to culture virus from PCR-positive samples: > It can be observed that at Ct = 25, up to 70% of patients remain positive in culture and that at Ct = 30 this value drops to 20%. At Ct = 35, the value we used to report a positive result for PCR, <3% of cultures are positive. https://academic.oup.com/cid/advance-article/doi/10.1093/cid/ciaa1491/5912603 https://academic.oup.com/cid/advance-article/doi/10.1093/cid... So it's absolutely true that some of the people who test positive by PCR would never have infected anyone else, and there was no need for them to isolate. But it's hard to distinguish who--the viral culture takes too much time to run for each patient, and no one really knows how sensitive that is anyways. So to be conservative, they just advise everyone to isolate. People have talked about advising isolation only if Ct is less than some lower cutoff, since there's a clear correlation between Ct and positivity in culture. But since a patient early in the infection might have high Ct now but lower Ct later, public health authorities haven't done so. The second way that PCR tests are being used is to diagnose the cause of illness--a patient comes in sick, and the doctor is trying to find the cause. At this point, we already know that the patient is sick, because they're coughing, complaining that they feel terrible, etc. The PCR test isn't what tells us that they're sick, but rather what tells us that the cause of their sickness is SARS-CoV-2. The alternative hypothesis is that people are dying of some different disease, and by coincidence the excess mortality due to that different disease correlates strongly with SARS-CoV-2 test positivity (which e.g. is why that's high in the USA, and low in Australia; you can also see the correlation within a single region if you look at the time series). That would be a pretty strange coincidence, and no one has proposed any mechanism for that. So do the above clinical uses seem reasonable to you? Or is there some other clinical use that seems unreasonable to you in light of Mullis's comments? Perhaps this confusion comes from the definition of "illness" or "sick". In a certain sense, if I don't feel sick, then no test can tell me otherwise. For example, was Typhoid Mary "sick"? Is an HIV patient with no symptoms? Kary Mullis says no: > A man with gray hair and a goatee raises his hand. He says he's been HIV-positive since 1984, that he took the anti-AIDS drug AZT for a couple years but stopped. Now, he says, his T-cell count -- the number of a kind of white blood cell that is killed by HIV -- has gone way down. > Mullis interrupts him: "Change doctors!" > The man continues. His T-cell count is down to 150, which is usually thought of as dangerously low. He asks Mullis for advice. > "I would say there is no evidence that I can find in the scientific literature that you should worry about HIV or your T-cell count," Mullis tells him. "If you'd stop worrying, maybe you'll be all right. You look pretty healthy to me." https://www.washingtonpost.com/archive/lifestyle/1998/11/03/nobel-chemist-kary-mullis-making-waves-as-a-mind-surfer/31e7e720-44e4-49ff-8458-a9822cdcb47e/ https://www.washingtonpost.com/archive/lifestyle/1998/11/03/... Do you think he gave that patient good advice?

silicon2401 5y ago

I don't agree with anything; I don't have an opinion or stance, I've said that from the beginning. I'm looking for someone _else_ to give _their_ opinion or evidence. I don't know how many different ways I can rephrase the same point. Here's a quote from another reply to my original comment: > > Kary Mullis: I think misused PCR is not quite ... I don't think you can misuse PCR. No, the results, the interpretation of it. See if you can say, if they wanted, if they could find this virus in you at all, and with PCR if you do it well you can find almost anything in anybody. It starts making you believe in the, sort of buddhist notion, that everything is contained in everything else. Right, I mean because if you can amplify one single molecule up to to something that you can really measure which PCR can do, then there's just very few molecules that you don't have at least one single one of them in your body. Okay, so that could be thought of as a misuse of it just to claim that it's meaningful. It is, there's very little of what they call HIV and what's been brought out here by Phil ... the measurement for it is not exact at all, it's not it's not as good as our measurement for things like apples. An apple is an apple. You know, you can get something that's kind of like, if you've got enough things that look kind of like an apple you stick them all together you might think it as an apple. And HIV is like that. Those tests are all based on things that are invisible, and they are the results are inferred in a sense. PCR is separate from that, it's just a process that's used to make a whole lot of something out of something that's why it's not, it doesn't tell you that you're sick and it doesn't tell you that the thing you ended up with really was going to hurt you or anything like that. An example of what I'm looking for info on is this in particular: > PCR is separate from that, it's just a process that's used to make a whole lot of something out of something that's why it's not, it doesn't tell you that you're sick and it doesn't tell you that the thing you ended up with really was going to hurt you or anything like that. I don't have an opinion myself and I'm just looking for someone informed to comment on how today's use of PCR for diagnosing covid aligns with the inventor of PCR's comments that it isn't useful for diagnosing illness. Not whether or not today's covid tests are false or true positives

tripletao 5y ago
The PCR test is being used clinically in two major ways. First, people with a positive test are advised to isolate themselves, to avoid infecting others. As I noted in my very first reply, a positive PCR test doesn't necessarily mean that the patient is shedding viable virus (i.e., that the patient could infect others), and that's the kernel of truth behind Mullis's statements. I posted a link above to a paper that attempted to culture virus from PCR-positive samples: > It can be observed that at Ct = 25, up to 70% of patients remain positive in culture and that at Ct = 30 this value drops to 20%. At Ct = 35, the value we used to report a positive result for PCR, <3% of cultures are positive. https://academic.oup.com/cid/advance-article/doi/10.1093/cid/ciaa1491/5912603 https://academic.oup.com/cid/advance-article/doi/10.1093/cid... So it's absolutely true that some of the people who test positive by PCR would never have infected anyone else, and there was no need for them to isolate. But it's hard to distinguish who--the viral culture takes too much time to run for each patient, and no one really knows how sensitive that is anyways. So to be conservative, they just advise everyone to isolate. People have talked about advising isolation only if Ct is less than some lower cutoff, since there's a clear correlation between Ct and positivity in culture. But since a patient early in the infection might have high Ct now but lower Ct later, public health authorities haven't done so. The second way that PCR tests are being used is to diagnose the cause of illness--a patient comes in sick, and the doctor is trying to find the cause. At this point, we already know that the patient is sick, because they're coughing, complaining that they feel terrible, etc. The PCR test isn't what tells us that they're sick, but rather what tells us that the cause of their sickness is SARS-CoV-2. The alternative hypothesis is that people are dying of some different disease, and by coincidence the excess mortality due to that different disease correlates strongly with SARS-CoV-2 test positivity (which e.g. is why that's high in the USA, and low in Australia; you can also see the correlation within a single region if you look at the time series). That would be a pretty strange coincidence, and no one has proposed any mechanism for that. So do the above clinical uses seem reasonable to you? Or is there some other clinical use that seems unreasonable to you in light of Mullis's comments? Perhaps this confusion comes from the definition of "illness" or "sick". In a certain sense, if I don't feel sick, then no test can tell me otherwise. For example, was Typhoid Mary "sick"? Is an HIV patient with no symptoms? Kary Mullis says no: > A man with gray hair and a goatee raises his hand. He says he's been HIV-positive since 1984, that he took the anti-AIDS drug AZT for a couple years but stopped. Now, he says, his T-cell count -- the number of a kind of white blood cell that is killed by HIV -- has gone way down. > Mullis interrupts him: "Change doctors!" > The man continues. His T-cell count is down to 150, which is usually thought of as dangerously low. He asks Mullis for advice. > "I would say there is no evidence that I can find in the scientific literature that you should worry about HIV or your T-cell count," Mullis tells him. "If you'd stop worrying, maybe you'll be all right. You look pretty healthy to me." https://www.washingtonpost.com/archive/lifestyle/1998/11/03/nobel-chemist-kary-mullis-making-waves-as-a-mind-surfer/31e7e720-44e4-49ff-8458-a9822cdcb47e/ https://www.washingtonpost.com/archive/lifestyle/1998/11/03/... Do you think he gave that patient good advice?