All of tkpwaeub's Comments + Replies

The IHME Report

Holy smokes! 6 million per day is the same figure I was getting using this approach:

https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1009374

This paper is underappreciated

Omicron Post #13: Outlook

Is it accurate to say that Ct count is similar to the # of zero bits of the density of RNA in the sample (expressed in binary)?

Omicron Post #12

I've wondered about that too. And not just for Covid

Covid 1/6/22: The Blip

Speaking of risk factors - and I'll be mistaken for some weird variety of incel when I write this - why do we keep not taking sex into account when assessing risk for the purposes of prioritization of vaccines, medication, PPE, etc? We've known since the beginning that being male significantly increases the risk of mortality.

3CraigMichael11dThis is a good point. I don’t know if it’s changed with the variants, but believe that’s is unlikely as the mechanisms speculated were related to men having more ACE2 receptors.
Omicron Post #9

The fact that it may have or even probably did result from zoonosis from mice doesn't convince me that it had to have come from a lab. There are lots of humans, and lots of mice, and we pretty much live, eat, and poop together.

Omicron Post #8

Looks like you're gonna have to tweak your "Paxlovid still illegal" evergreen! It's legal for me because I'm fat

Omicron Post #8

I wonder if they're more independent when you alternate brands

Omicron Post #8

I think culling is more likely. If you have a pet snake, God help you

Omicron Post #7

So 3 hours was too low even for the original strain??? Jesus, no wonder so many cases are untraceable.

Law of No Evidence

In some cases it's evidence of cowardice, which could be seen as a form of bullshit. I'm thinking of situations where absence of evidence really is evidence of absence. If you do an exhaustive or near-exhaustive search for something, and you're unable to find it - that's pretty solid evidence of non-existence. And if you're stopping at "lack of evidence" you're implying something about the size of your "evidence space" and you owe it to people to explain why you think it's large relative to what's already been canvassed. So...still bullshit, no matter how you cut it.

1Kenny16dI picked that term up from Zvi but he himself links to this LW post for background/context: * Gears in understanding - LessWrong [https://www.lesswrong.com/posts/B7P97C27rvHPz3s9B/gears-in-understanding] It is a wonderfully useful term/idea to have in the back of your mind!
Covid 12/16: On Your Marks

I need to refine it a bit, I guess. But isn't picking your battles a principle in triage?

1Measure1moYep, you want to target your interventions where you'll see the greatest gains relative to no intervention. If you have a miracle cure, you'd focus on those with the lowest untreated odds. (In the specific case, however, you have to consider whether you're disincentivizing vaccination by giving better treatment to the unvaccinated.)
Omicron Post #6

I hope you're right about the effect size being small, I wish you'd given me a convincing argument that it's zero using some sort of brilliant sophistry, and I wish I was the only person speculating this. Sadly I'm not:

https://twitter.com/tomtom_m/status/1472561128240824324?t=PjtsZrO-mIrUWzdjTsF3Gw&s=19

Omicron Post #7

On the other hand, everyone seems to have given up on tracking full recoveries, so maybe the two things cancel one another out, so we end up just using the most naive approach possible?

Covid 12/16: On Your Marks

Regarding the moral quandary of who to give Paxlovid to: there are practical reasons to give it to the vaccinated person. Namely - it increases the probability that the treatment will be successful if the person you're giving it to already has good survival odds.

5Measure1moBy that logic, you'd rather give it to someone who isn't infected in the first place.
Omicron Post #7

This New York Times article seems to have an important clue about the increased transmissibility of Omicron (I boldfaced the key points):

 


The buzzing activity Dr. Amaro and her colleagues witnessed offered clues about how viruses survive inside aerosols. The mucins, for example, did not just wander idly around the aerosol. The negatively charged mucins were attracted to the positively charged spike proteins. Charged atoms such as calcium fly around the droplet, exerting powerful forces on molecules they encounter.

Dr. Amaro speculated that the mucins a

... (read more)
9gwillen1moThis is tangential, but it's been fascinating to me to watch the spread of that "three hours" factoid. I believe it originally comes from this paper: https://www.medrxiv.org/content/10.1101/2020.03.09.20033217v1.full.pdf [https://www.medrxiv.org/content/10.1101/2020.03.09.20033217v1.full.pdf] (Note that "HCoV-19" was referring to what is now designated "SARS-CoV-2", i.e. COVID-19.) I very gently criticized it at the time for having a quite misleading abstract, regarding the "three hours" figure: https://twitter.com/gwillen/status/1237854407007457280 [https://twitter.com/gwillen/status/1237854407007457280] https://twitter.com/DrNeeltje/status/1237895661967642626 [https://twitter.com/DrNeeltje/status/1237895661967642626] https://twitter.com/gwillen/status/1237896626355593221 [https://twitter.com/gwillen/status/1237896626355593221] This abstract, as far as I can tell, is where the "three hours" factoid originated, which has now become gospel that appears on public health pages like your link above. In reality, the abstract said they detected the virus in aerosols for "up to three hours" because that was the duration of the experiment. It's obvious from graphs, as well as their computed half-life figure -- which is coincidentally pretty close to three hours -- that if they had continued the experiment, they would have kept detecting viable virus for a multiple of that time. (Of course, this figure is also kind of meaningless anyway, since the initial quantity of virus they're experimenting on was arbitrary! Only the half-life is really meaningful, but that doesn't make good headlines.) It feels very weird to me to have "been there at the beginning" for this. I have no specific qualifications for interpreting this paper, beyond being smart and careful. It's a little depressing (but that's the COVID story.) (I would love for someone to correct my story here, and find some other explanation for where this factoid came from, or argue that I'm wrong about it being misl
4Kenny1moThanks for some possible details about the relevant 'gears'!
Omicron Post #7

That's what I did. I'll let you know how it works out. See you on the other side.

Omicron Post #6

I would actually rate the probability of a "pancoronavirus vaccine sometime in 2022" at 60%, which is why I doubt there's going to be an Omicron specific vaccine. Evusheld will probably be updated for Omicron, however.

Omicron Post #6

Does anyone have any leads on the idea that attrition could be making Omicron appear milder? Are the least "Covid-hardy" humans being picked off?

4Zvi1moEffect size here should be quite small, but not zero.
Omicron Post #6

R0 will go down a bit as more people become immune to Omicron, but...sure.

Omicron Post #6

On the matter of Paxlovid not having been approved yet, I'm considering writing to the CDER Ombudsman:

https://www.fda.gov/about-fda/cder-contact-information/cder-ombudsman

And cc'ing my elective reps. As a hedge, and so as not to be accused of foul play if I decide to jump into any of the prediction markets, I might bet against my preferred outcome (rapid approval)

Covid 12/9: Counting Down the Days

Full approval of Evusheld by the FDA looks to be a real game changer for folks who are immunocompromised.

Omicron Post #5

It will be interesting to see how Evusheld fits into the vaccine mandate "ecosystem" especially in Europe where they make allowance for natural immunity despite having broader mandates.

Omicron Post #5

I forgot how priceless that SNL skit was. Thanks for the excuse to re-watch it. I love when they break character - it just works.

"Are you OK, Kate?"..."Obviously I'm not"

2JenniferRM1moThanks for the suggestion to seach! The first one was charming [https://www.youtube.com/watch?v=2kQxVwYwrME] and the second was still ok [https://www.youtube.com/watch?v=vHdT73SbS2M].
Omicron Post #4

I wonder if there's a subset of the population for whom Evusheld might eventually either

  1. Count as vaccination
  2. Be mandatory in order to be considered immune
Omicron Post #4

Because there aren't enough hospital beds/nurses etc

Omicron Post #4

This lends credence to my theory about last week's exposure. Six negative rapid antigen tests and two negative PCR tests over the course of the seven days following the possible exposure, but I felt like hell about three days after.

Omicron Post #4

Aw, thanks for answering despite the point not being clear! Guilty as charged! Respect for answering them anyway!

"We choose to go to the Moon in this decade and do the other things, not because they are easy, but because they are hard" - JFK

Omicron Post #4

I may have experienced this last week, after having a mild sub-detectable exposure. It felt a lot like after shots 2, 3 and 4. But I still haven't tested positive.

Omicron Post #4

Some insight into the transmissibility - Omicron made its way from one hotel room to another. The occupants had no contact.

https://www.bloomberg.com/news/articles/2021-12-05/omicron-s-spread-across-hotel-hall-highlights-transmission-worry

It still doesn't quite answer the question of what the exact physical characteristics are that allow it to be this transmissible (smaller? Stickier? More likely to linger in the air or fill up a space uniformly?)

Which makes me suggest another "side bet" - what's the probability that Omicron is so transmissible that any att... (read more)

Omicron Post #4

Oof, yeah, that sounds like playing to an inside straight.  You're braver than I.

Omicron Post #4

Do you distinguish between "encouraging with an incentive" and simply encouraging? Similarly, where would "scolding or shaming" fit in?

And is it possible to disguise a mandate as an incentive? For instance, if we gave a million dollars to everyone who gets vaccinated and boosted, wouldn't that start to have a material impact on the CPI, forcing people to get vaccinated just to stay afloat?

1cistrane1moHow would this policy affect the price of the vaccines?
7Pattern1moWhere do I start. 1. Example of "Encouraging": curfew for everyone not vaccinated (unless they have medical reasons to not). Something as vague as 'encouraging' is rather unclear. 2. A massive impact on the Consumer Price Index, in the outcome you outline. It's possible. (The scenario you outlined seems unlikely - 1 million dollars?) The point of your questions isn't entirely clear, which makes answering them difficult. Yes, one could argue that an incentive that large is...kind of equivalent to a mandate in that few who are not at health risk would refuse, even many who would be at risk might take a gamble with their lives for that much. (Also, while many ideas around the vaccine being risky are ridiculous - microchips etc, such a surprising approach might prompt a re-evaluation. It also might hit supply, at least temporarily, as that could cause a large increase in demand.) At the same time I haven't looked at CPI to see what it does and doesn't include. The economic effects would be large, though I'm not sure how exactly things would change.
Covid 12/2: But Aside From That

Not necessarily. In many ways variants seem to evolve much more deterministically than one might think, and there's good reason to hope that we might ultimately exhaust the repertoire of viable combinations of mutations.

2Gurkenglas1moThat doesn't sound like less then 20 percent probability! Just in case, we could close all borders just ahead of the billions-of-infections peak for a month to check whether the omnicronomicon opens; then at least each country might only get swept by its own variant.
Covid Prediction Markets at Polymarket

I'm inclined to bet against my preferred outcome, for peace of mind.

Omicron Variant Post #2

So, overdispersion is as valid now as it's ever been, I guess?

Omicron Variant Post #1: We’re F***ed, It’s Never Over

"Another possibility, still speculative but discussed by many scientists in recent days, is that omicron evolved over many months within an immunocompromised patient with a protracted infection. In a patient treated with therapeutics such as monoclonal antibodies or convalescent sera, a viral strain that can survive the assault can potentially amass a host of mutations. Such cases have been documented, but they are not known to have led to outbreaks in the general population."

Source:

https://www.washingtonpost.com/health/2021/11/29/how-bad-is-omicron-varian... (read more)

Omicron Variant Post #1: We’re F***ed, It’s Never Over

This doesn't directly answer your question but it appears that people who received mRNA vaccines produced fewer antibodies for one of the four endemic coronaviruses than those who were naturally infected. If that's true, it's very encouraging news as far as adapting vaccines is concerned:

https://www.medrxiv.org/content/10.1101/2021.09.30.21264363v1

Omicron Variant Post #1: We’re F***ed, It’s Never Over

It seems that Omicron may have mutated over time within a single immunocompromised host, so it's not clear to me how natural selection applies.

3Rudi C2moSources?
Omicron Variant Post #1: We’re F***ed, It’s Never Over

I dunno, it's pronounced "Kai" (rhymes with "guy") but you might be right

[This comment is no longer endorsed by its author]Reply
7jimv2moNo, the letter between nu and omicron is pronounced something like 'ksai'. https://en.m.wikipedia.org/wiki/Xi_(letter) [https://en.m.wikipedia.org/wiki/Xi_(letter)] The one you're probably thinking of is later in the Greek alphabet. https://en.m.wikipedia.org/wiki/Chi_(letter) [https://en.m.wikipedia.org/wiki/Chi_(letter)]
Omicron Variant Post #1: We’re F***ed, It’s Never Over

Is original antigenic sin widely accepted? It's not clear to me that there's a strong consensus based on your link. 

EDIT:

I did a bit of (not very thorough) googling on original antigenic sin, and managed to convince myself that, yes, it's a thing. But then to help myself sleep I looked up "overcoming original antigenic sin" and came across this:

https://news.emory.edu/stories/2012/08/flu_vaccines_original_sin/campus.html

Adjuvants! I really have no idea what they are, but I seem to remember that these are added to all the covid vaccine?

5Liam Donovan2moMy uninformed impression is that an "adjuvant" is just something that stimulates increased immune response, which has historically been an additional chemical ( [https://theconversation.com/adjuvants-the-unsung-heroes-of-vaccines-156548]such as an aluminum salt) added to vaccines. The mRNA vaccines do not contain these chemicals [https://en.adioscorona.org/questions-reponses/2021-02-17-adjuvants-vaccins-arn-covid.html] , but some people confusingly refer to the lipid nanoparticles that surround and protect the mRNA as adjuvants (because they also help increase immune response). I haven't seen any evidence that these lipid nanoparticles are the kind of adjuvants that might mitigate OAS, but that doesn't mean much because I'm a total nonexpert.
Covid 11/25: Another Thanksgiving

I'm guessing that the facial hair ban for unvaccinated people has to do with the fact that it compromises the effectiveness of face masks, particularly N95's that are meant to protect the wearer from others.

Paxlovid Remains Illegal: 11/24 Update

Just read about that. I think we need more information before updating our overall assessments?

Covid 11/18: Paxlovid Remains Illegal

On the other hand, it could be handy to use your more stringent definition of non-scarcity whenever I need a reason not to do something. If you feel like scribbling some calculations to back I that up, I'll be forever in your debt

Covid 11/18: Paxlovid Remains Illegal

So I guess my task is to adjust my definition of non-scarcity "for me"? I don't want set the bar too high for myself!

Alternatively this could be more of a Potter Stewart situation - I'll know it when I see it.

1rossry2moI think I was unclear. I meant that if you did correctly estimate the number of cases, you'd need mamy times that many courses of medicine "in the system" to make sure that no one worried about running out in their part of the system, so that no one started hoarding where they were. I estimated that about ten times as many cases as you natively needed would about do it. If our standard is non-scarcity for prophylactic prescription for close contacts, then 10x the expected number of close contacts in your "part of the system"... (To be clear, this is just a statement about hoarding/availability dynamics, not about when "things should go back to normal".)
Covid 11/18: Paxlovid Remains Illegal

Aw man, that sucks. I really don't think loss of smell is being taken as seriously as it should be as a public safety matter, but it really should be. Gas leaks, house fires, and food poisoning are all heightened risks for those who are "hard of smelling."

Covid 11/18: Paxlovid Remains Illegal

How about number of cases times average household size?

1rossry2moI would guess that having that many courses of Paxlovid "in the system" would be about an order of magnitude too low for true non-scarcity. (See: how many vaccine doses needed to be in the system before you could assume that there was going to be adequate supply anywhere you might try to look?)
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