12 ms·

I still remember how when the pandemic was breaking out, I and my colleagues in the lab were not taking this seriously because we were so confident we'd be able

I still remember how when the pandemic was breaking out, I and my colleagues in the lab were not taking this seriously because we were so confident we'd be able to get it under control. All we had to do was test rigorously, and, like c'mon. It's just qPCR. I remember overconfidently asserting that, like, the USA invented PCR - we know how to do it. laugh out loud. Hell, I had a plate in the machine as I was speaking! Colleagues agreed. After all, it only got so bad in china because they were covering it up, right? We just gotta run more tests, trace, and isolate. The stuff we were working on the lab was hard fundamental questions - the science needed to stop the pandemic was some PCR and quarantining people. And, the CDC was developing our own diagnostic instead of using the WHO's, but that makes sense, they're the CDC. What were the odds that they'd screw up so badly that the FDA would describe conditions as so bad they'd be reason enough to shut down the lab if they weren't the CDC? What were the odds that our friends in testing labs would find themselves describing the CDC as having "simply failed at molecular biology" [0]? Of course, I use the past tense when describing our feelings about our research since we're certainly not working on it now. It's all nonessential. We're not allowed to go to the lab now unless you really need to water the plants or feed the mice. Just to keep a sustaining gene pool of our model organisms alive, so we can breed back what we need when we get back. We really learned a lesson in humility. Part of miscalculating is having the wrong set of assumptions to derive calculations from. I don't think we were the only people who should have known better that were arrogant and overconfident. We're hearing from some local labs that they have enough reagents to run tests, they have the right primers, they have what they need. But they can't get the cotton swabs they shove all the way up your nose and the little plastic collection things they need to administer the test. Cotton swabs. And little plastic vials. We're talking about developing a vaccine, a cure, privacy-respecting contact tracing, fighting a once in a generation pandemic, keeping the hospital system from being overwhelmed. And we don't have the cheap disposable plastic and cotton things we need to run a test. Truly a lesson in humility. [0]https://www.nature.com/articles/d41586-020-01068-3 https://www.nature.com/articles/d41586-020-01068-3

throwaway894345 7y ago
Adding to the list of CDC failures was their utter failure to procure masks. You know, those things that would be absolutely vital for just about any epidemic or pandemic (never mind the respiratory variety that we knew would be the most likely). It’s not like preparing for an epidemic is the raisin d’etre for the CDC or anything. I’m normally not this snarky, but I too thought the CDC was the one functioning agency but it turns out that it’s closer to the opposite. And not only that, but their utter incompetence killed tens of thousands.
- Consultant32452 7y ago
  The CDC, US Surgeon General, and WHO have all claimed with a straight face that masks don't protect you from getting the virus. I guess that's why they didn't see any value in stockpiling them. /s
  - ashtonkem 7y ago
    I too assume that surgeons wear those masks for funsies. Of course the “masks don’t work” was pure, transparent, bullshit from the very beginning. It didn’t even pass the smell test. Now if the argument was “please save masks for healthcare workers first, they’re higher risk” that would be fine. But “they don’t work”? Fuck off. Edit: I’m referring to the CDC here, not you personally, dear HN commenter.
    - WrtCdEvrydy 7y ago
      If you tell people to save masks for healthcare workers... then the hoarding would have been worse. At least by telling people masks don't work... peer pressure would keep them from buying them?
      - ashtonkem 7y ago
        It doesn’t look like anyone bought it, masks still sold out quickly and health care providers are still reusing N95 masks. And in exchange the CDC spent a large amount of their credibility; a real lose lose.
        PopePompus 7y ago
        That's because the lies were so transparent. In the US we were told (by our wonderful Surgeon General) that citizens who wore masks were actually more apt to get covid than persons without masks.
        hsitz 7y ago
        I'm curious, was the official word always that even N95 masks didn't protect the wearer? Or just that "masks" in general (i.e., lesser masks) would not protect wearers?
anitil 7y ago
I have a couple of questions that I hope you would have insight in to. * Why did the CDC decide to develop their own diagnostic? Was there some issue with the WHO test that they were trying to avoid? Or just internal politics * What was the core issue with the CDC's tests? (It's possible that I'm not equipped to understand this, but an ELI5 would be great) (Edit - I have tried to research this, but for #1 it seemed kind of murky and #2 looks like either poor quality control or poor design - https://www.vice.com/en_us/article/y3mkpx/how-the-cdc-botched-basic-science-in-its-attempt-to-make-a-coronavirus-test https://www.vice.com/en_us/article/y3mkpx/how-the-cdc-botche.... I'm hoping for some clarity on these)
- vikramkr 7y ago
  1) No idea 2) You found the article I was about to link actually. Basically, for a PCR test, what you're doing is making a lot of a particular sequence of DNA if it's present. You set up the reaction conditions so that if a particular sequence of DNA is present in your test tube (actually a plate but same difference), that sequence of DNA will make a lot more of itself. If there isn't that sequence of DNA, nothing will happen. You don't get to pick the entire sequence youa re looking for. You basically hae to pick a start region and and end region for the piece of DNA you want to amplify. So if the nucleotide sequence for a coronavirus gene was atcgctatagc, and you are using 3 letter long end regions (in reality you use longer length sequences and regions), you might pick your targets as atc and agc from each end. Therefore, any sequence of dna in your sample with atg and agc will get amplified and you will get a signal telling you that a dna sequence that starts with that first target sequence and ends with that second target sequence is there. If you don't get a signal, that means no coronavirus. When picking that sequence (known as a primer sequences since it primes the replication reaction), you have to be careful. Lets say that in your body you have a gene that goes gtcatcagctga or something. Inside of that sequence, your primer sequences are present. If you run a test for your desired sequence, you're going to get signal from non-coronavirus DNA. In order to make sure there are no overlaps in your primers, you, well, this is the part that's hard to believe. You type in your sequences in to a website and hit a button. Hence the following excerpt from the article you found: “I just put the primers as input into this program and within seconds it tells you there’s problems with it,” Altman said. “It’s freely available. It’s not hard to use at all. It’s one of those things you’d do as a basic quality control check. It seems like they hand-designed these primers and it seems like they didn’t use computer tools to check it.” So, yeah. Everyone's still having a hard time wrapping their head around it. All it boils down to is that you want to find sequences of dna that are present in coronavirus but not in humans (and also maybe the reverse for some types of controls). It's, I mean. I don't have words for it. Designing primers is like the first thing an undergrad who joins a lab for a research project or internship is taught. And I had it rough when I was designing primers like 3 years ago. In those ancient times, I had to design the primer by opening a whole new tab and going to a whole new website! (The site is https://www.ncbi.nlm.nih.gov/tools/primer-blast/ https://www.ncbi.nlm.nih.gov/tools/primer-blast/). So much work. Thankfully the lab I was working in implemented an electronic lab notebook (I think it was benchling?) that had the feature built in. Now i don't have to open another tab. I'm being flippant but also, common, this is the CDC. The WHO had no problem doing it. Private labs had no problem doing it. It's not something weird about this virus. It's just, i don't know. There must have been deeper issues.
LiquidSky 7y ago
>Truly a lesson in humility. Not at all. You are making a fundamental, erroneous assumption: that the actions taken were made in good faith. This is a political failure. Trump and his administration chose again and again to put politics above public health. Over and over, given a choice, he chose to pander to his base and attack his perceived enemies rather than helping the country. These weren't miscalculations. The miscalculations happened at the state and local levels, but at the federal level there was very much a knowing purpose.
loopz 7y ago
Try demo-trading for more lessons.
rabboRubble 7y ago
For want of a nail the shoe was lost...

throwaway894345 7y ago

Adding to the list of CDC failures was their utter failure to procure masks. You know, those things that would be absolutely vital for just about any epidemic or pandemic (never mind the respiratory variety that we knew would be the most likely). It’s not like preparing for an epidemic is the raisin d’etre for the CDC or anything. I’m normally not this snarky, but I too thought the CDC was the one functioning agency but it turns out that it’s closer to the opposite. And not only that, but their utter incompetence killed tens of thousands.

Consultant32452 7y ago
The CDC, US Surgeon General, and WHO have all claimed with a straight face that masks don't protect you from getting the virus. I guess that's why they didn't see any value in stockpiling them. /s
- ashtonkem 7y ago
  I too assume that surgeons wear those masks for funsies. Of course the “masks don’t work” was pure, transparent, bullshit from the very beginning. It didn’t even pass the smell test. Now if the argument was “please save masks for healthcare workers first, they’re higher risk” that would be fine. But “they don’t work”? Fuck off. Edit: I’m referring to the CDC here, not you personally, dear HN commenter.
  - WrtCdEvrydy 7y ago
    If you tell people to save masks for healthcare workers... then the hoarding would have been worse. At least by telling people masks don't work... peer pressure would keep them from buying them?
    - ashtonkem 7y ago
      It doesn’t look like anyone bought it, masks still sold out quickly and health care providers are still reusing N95 masks. And in exchange the CDC spent a large amount of their credibility; a real lose lose.
      - PopePompus 7y ago
        That's because the lies were so transparent. In the US we were told (by our wonderful Surgeon General) that citizens who wore masks were actually more apt to get covid than persons without masks.
      - hsitz 7y ago
        I'm curious, was the official word always that even N95 masks didn't protect the wearer? Or just that "masks" in general (i.e., lesser masks) would not protect wearers?

anitil 7y ago

I have a couple of questions that I hope you would have insight in to. * Why did the CDC decide to develop their own diagnostic? Was there some issue with the WHO test that they were trying to avoid? Or just internal politics * What was the core issue with the CDC's tests? (It's possible that I'm not equipped to understand this, but an ELI5 would be great) (Edit - I have tried to research this, but for #1 it seemed kind of murky and #2 looks like either poor quality control or poor design - https://www.vice.com/en_us/article/y3mkpx/how-the-cdc-botched-basic-science-in-its-attempt-to-make-a-coronavirus-test https://www.vice.com/en_us/article/y3mkpx/how-the-cdc-botche.... I'm hoping for some clarity on these)

vikramkr 7y ago
1) No idea 2) You found the article I was about to link actually. Basically, for a PCR test, what you're doing is making a lot of a particular sequence of DNA if it's present. You set up the reaction conditions so that if a particular sequence of DNA is present in your test tube (actually a plate but same difference), that sequence of DNA will make a lot more of itself. If there isn't that sequence of DNA, nothing will happen. You don't get to pick the entire sequence youa re looking for. You basically hae to pick a start region and and end region for the piece of DNA you want to amplify. So if the nucleotide sequence for a coronavirus gene was atcgctatagc, and you are using 3 letter long end regions (in reality you use longer length sequences and regions), you might pick your targets as atc and agc from each end. Therefore, any sequence of dna in your sample with atg and agc will get amplified and you will get a signal telling you that a dna sequence that starts with that first target sequence and ends with that second target sequence is there. If you don't get a signal, that means no coronavirus. When picking that sequence (known as a primer sequences since it primes the replication reaction), you have to be careful. Lets say that in your body you have a gene that goes gtcatcagctga or something. Inside of that sequence, your primer sequences are present. If you run a test for your desired sequence, you're going to get signal from non-coronavirus DNA. In order to make sure there are no overlaps in your primers, you, well, this is the part that's hard to believe. You type in your sequences in to a website and hit a button. Hence the following excerpt from the article you found: “I just put the primers as input into this program and within seconds it tells you there’s problems with it,” Altman said. “It’s freely available. It’s not hard to use at all. It’s one of those things you’d do as a basic quality control check. It seems like they hand-designed these primers and it seems like they didn’t use computer tools to check it.” So, yeah. Everyone's still having a hard time wrapping their head around it. All it boils down to is that you want to find sequences of dna that are present in coronavirus but not in humans (and also maybe the reverse for some types of controls). It's, I mean. I don't have words for it. Designing primers is like the first thing an undergrad who joins a lab for a research project or internship is taught. And I had it rough when I was designing primers like 3 years ago. In those ancient times, I had to design the primer by opening a whole new tab and going to a whole new website! (The site is https://www.ncbi.nlm.nih.gov/tools/primer-blast/ https://www.ncbi.nlm.nih.gov/tools/primer-blast/). So much work. Thankfully the lab I was working in implemented an electronic lab notebook (I think it was benchling?) that had the feature built in. Now i don't have to open another tab. I'm being flippant but also, common, this is the CDC. The WHO had no problem doing it. Private labs had no problem doing it. It's not something weird about this virus. It's just, i don't know. There must have been deeper issues.

LiquidSky 7y ago

>Truly a lesson in humility. Not at all. You are making a fundamental, erroneous assumption: that the actions taken were made in good faith. This is a political failure. Trump and his administration chose again and again to put politics above public health. Over and over, given a choice, he chose to pander to his base and attack his perceived enemies rather than helping the country. These weren't miscalculations. The miscalculations happened at the state and local levels, but at the federal level there was very much a knowing purpose.

loopz 7y ago

Try demo-trading for more lessons.

rabboRubble 7y ago

For want of a nail the shoe was lost...