Posts

Vax passports - theory and practice 2021-10-03T22:35:11.396Z
Louisiana Gets Vaccine Passports Right 2021-05-12T01:23:26.615Z
About Me: Background and Biases 2021-04-04T14:19:31.220Z

Comments

Comment by tkpwaeub (gabriel-holmes) on Covid 1/20/22: Peak Omicron · 2022-01-21T12:30:53.902Z · LW · GW

I wonder when those of us who are lucky enough never to have gotten Covid (as far as we know) are going to be in such a vanishingly small minority once it's endemic...that any collective political will to keep us from getting it is going to shrivel away? ("The rest of us got it, we lived, and we don't care if you get it because we all have hybrid immunity, suck it up")

Is that the reality we're headed for?

Comment by tkpwaeub (gabriel-holmes) on The IHME Report · 2022-01-11T11:32:32.627Z · LW · GW

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

Comment by tkpwaeub (gabriel-holmes) on Omicron Post #13: Outlook · 2022-01-11T11:25:18.623Z · LW · GW

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)?

Comment by tkpwaeub (gabriel-holmes) on Omicron Post #12 · 2022-01-07T07:11:18.731Z · LW · GW

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

Comment by tkpwaeub (gabriel-holmes) on Covid 1/6/22: The Blip · 2022-01-07T06:59:17.124Z · LW · GW

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.

Comment by tkpwaeub (gabriel-holmes) on Omicron Post #9 · 2021-12-24T15:55:15.439Z · LW · GW

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.

Comment by tkpwaeub (gabriel-holmes) on Omicron Post #8 · 2021-12-22T17:32:47.479Z · LW · GW

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

Comment by tkpwaeub (gabriel-holmes) on Omicron Post #8 · 2021-12-21T13:50:30.949Z · LW · GW

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

Comment by tkpwaeub (gabriel-holmes) on Omicron Post #8 · 2021-12-21T07:24:03.589Z · LW · GW

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

Comment by tkpwaeub (gabriel-holmes) on Omicron Post #7 · 2021-12-21T06:48:42.976Z · LW · GW

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

Comment by tkpwaeub (gabriel-holmes) on Law of No Evidence · 2021-12-20T23:44:20.051Z · LW · GW

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.

Comment by tkpwaeub (gabriel-holmes) on Omicron Post #7 · 2021-12-20T22:03:06.935Z · LW · GW

Gears! I love it!

Comment by tkpwaeub (gabriel-holmes) on Covid 12/16: On Your Marks · 2021-12-20T22:02:04.455Z · LW · GW

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

Comment by tkpwaeub (gabriel-holmes) on Omicron Post #6 · 2021-12-20T17:47:04.434Z · LW · GW

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

Comment by tkpwaeub (gabriel-holmes) on Omicron Post #7 · 2021-12-20T17:40:36.039Z · LW · GW

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?

Comment by tkpwaeub (gabriel-holmes) on Covid 12/16: On Your Marks · 2021-12-20T12:23:40.571Z · LW · GW

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.

Comment by tkpwaeub (gabriel-holmes) on Omicron Post #7 · 2021-12-19T18:20:07.998Z · LW · GW

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 act as a shield. If the virus moves too close to the surface of the aerosol, the mucins push them back in, so that they aren’t exposed to the deadly air.

“What we think is that it’s actually covering itself in these mucins, and that’s acting like a protective coating for it during flight,” Dr. Amaro said.

This discovery may help explain how the Delta variant became so widespread. Delta’s spike proteins have a more positive charge than those on earlier forms of the coronavirus. As a result, mucins huddle more closely around them. That attraction could potentially make the mucins a better shield.

Every now and then, one of the simulated coronaviruses flipped open a spike protein, surprising the scientists. “The Delta variant opens much more easily than the original strain that we had simulated,” Dr. Amaro said.

A simulation of the Delta variant’s spike protein suggests that it opens wider than the original coronavirus strain, which may help explain why Delta spreads more successfully.

Once a coronavirus enters someone’s nose or lungs, the Delta spike’s wide opening may make it better at infecting a cell. But Dr. Amaro suspects that it’s bad for a coronavirus to open a spike protein when it’s still inside an aerosol, perhaps hours away from infecting a new host. “If it opens too soon, it could just fall apart,” Dr. Amaro said.

Some of the molecules that are abundant inside aerosols may be able to lock the spike shut for the journey, she said. Certain lung surfactants can fit into a pocket on the surface of the spike protein, preventing it from swinging open.

To test that idea and explore others, Dr. Amaro and her colleagues are stretching out the time frame of their simulation a hundred times, from ten billionths of a second to a millionth of a second. They’ll also investigate how the acidity inside an aerosol and the humidity of the air around it may change the virus.

Dr. Amaro and her colleagues are making plans to build an Omicron variant next and observe how it behaves in an aerosol. They want to wait for structural biologists to work out the three-dimensional shape of its spike proteins before getting started. But just looking at the early findings about Omicron, Dr. Amaro already sees one important feature: “It is even more positively charged,” she said.

Because Omicron’s spike proteins are even more positively charged than Delta’s, it may build a better mucin shield in aerosols. And that may help make it even more transmissible.

 

In other words, Delta lasts longer in the air than the original strain (which itself could last in the air for as long as three hours) and Omicron is even hardier.  This seems to track pretty well with increased spread in households and across hotel corridors. In the latter example, the prevailing theory seems to be that it passed from one occupant to the other when they were getting their meals. I find it much easier to imagine the increased transmission resulting from a build-up of Omicron in the air, which then seeped through a gap in the door, rather than Omicron having developed sentience and seeking out new hosts during fleeting encounters. Doors to hotel rooms aren't exactly airtight.  Together with the aforementioned 70-fold replication speed in the bronchus, that would tie up the transmissibility question quite nicely - infected people are spewing a lot more virus, which lasts longer in the air. We are all super-spreaders now.
 

The "air hardiness" also makes the jump from wild mice that much more plausible. With a virus that survives such a long time in the air, it's a lot easier to imagine zoonosis and reverse zoonosis occurring, without having to get terribly close to an infected animal. 
 

Another corollary of all this would be that you should assume that you're going to get infected if you live in a multi-family residence with any shared indoor spaces whatsoever. Or consider getting an indoor air purifier, even if you live alone. Scratch that; if you haven't already gotten an air purifier it's probably too late. 

God help us.

Comment by tkpwaeub (gabriel-holmes) on Omicron Post #7 · 2021-12-19T14:54:48.536Z · LW · GW

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

Comment by tkpwaeub (gabriel-holmes) on Omicron Post #6 · 2021-12-16T09:58:06.039Z · LW · GW

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.

Comment by tkpwaeub (gabriel-holmes) on Omicron Post #6 · 2021-12-15T21:07:30.736Z · LW · GW

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?

Comment by tkpwaeub (gabriel-holmes) on Omicron Post #6 · 2021-12-14T10:14:03.863Z · LW · GW

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

Comment by tkpwaeub (gabriel-holmes) on Omicron Post #6 · 2021-12-14T10:10:53.339Z · LW · GW

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)

Comment by tkpwaeub (gabriel-holmes) on Covid 12/9: Counting Down the Days · 2021-12-12T00:43:08.073Z · LW · GW

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

Comment by tkpwaeub (gabriel-holmes) on Omicron Post #5 · 2021-12-10T16:02:17.794Z · LW · GW

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.

Comment by tkpwaeub (gabriel-holmes) on Omicron Post #5 · 2021-12-10T16:00:31.997Z · LW · GW

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"

Comment by tkpwaeub (gabriel-holmes) on Omicron Post #4 · 2021-12-09T20:14:32.652Z · LW · GW

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
Comment by tkpwaeub (gabriel-holmes) on Omicron Post #4 · 2021-12-09T08:22:39.598Z · LW · GW

Because there aren't enough hospital beds/nurses etc

Comment by tkpwaeub (gabriel-holmes) on Omicron Post #4 · 2021-12-09T08:19:51.827Z · LW · GW

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.

Comment by tkpwaeub (gabriel-holmes) on Omicron Post #4 · 2021-12-08T09:47:06.867Z · LW · GW

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

Comment by tkpwaeub (gabriel-holmes) on Omicron Post #4 · 2021-12-07T10:36:27.804Z · LW · GW

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.

Comment by tkpwaeub (gabriel-holmes) on Omicron Post #4 · 2021-12-07T10:29:11.031Z · LW · GW

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 attempt to contain it is an exercise in futility?

Comment by tkpwaeub (gabriel-holmes) on Omicron Post #4 · 2021-12-07T02:43:45.256Z · LW · GW

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

Comment by tkpwaeub (gabriel-holmes) on Omicron Post #4 · 2021-12-07T01:23:19.228Z · LW · GW

Chance we are broadly looking at a future crisis situation with widely overwhelmed American hospitals, new large American lockdowns and things like that: 12% → 17% (EDIT: Should have been at least 25%).

I’m going back up on this based on a higher certainty that Omicron is the real deal, and the higher chance it’s a very fast version of the real deal that is likely to peak quite high and overwhelm the hospitals temporarily. If that happens, there’s going to be a lot of pressure for extreme measures. What’s keeping this from rising more is the possibility the cases will remain mild. 

 

As a benchmark, 17% edges out 16.67% - the odds associated with Russian roulette. 

Comment by tkpwaeub (gabriel-holmes) on Omicron Post #4 · 2021-12-06T23:14:43.150Z · LW · GW

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?

Comment by tkpwaeub (gabriel-holmes) on Covid 12/2: But Aside From That · 2021-12-03T19:32:37.424Z · LW · GW

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.

Comment by tkpwaeub (gabriel-holmes) on Covid Prediction Markets at Polymarket · 2021-12-02T13:42:30.422Z · LW · GW

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

Comment by tkpwaeub (gabriel-holmes) on Omicron Variant Post #2 · 2021-12-01T20:47:37.834Z · LW · GW

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

Comment by tkpwaeub (gabriel-holmes) on Omicron Variant Post #1: We’re F***ed, It’s Never Over · 2021-11-30T16:46:35.555Z · LW · GW

"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-variant/

This does seem to be a recurring theme - very slow mutation for the most part, and lots of new mutations occurring in immunocompromised "supermutators".

Comment by tkpwaeub (gabriel-holmes) on Omicron Variant Post #1: We’re F***ed, It’s Never Over · 2021-11-28T14:56:43.353Z · LW · GW

Good point - "boy who cried wolf" syndrome

Comment by tkpwaeub (gabriel-holmes) on Omicron Variant Post #1: We’re F***ed, It’s Never Over · 2021-11-28T12:34:24.537Z · LW · GW

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

Comment by tkpwaeub (gabriel-holmes) on Omicron Variant Post #1: We’re F***ed, It’s Never Over · 2021-11-28T12:29:57.006Z · LW · GW

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.

Comment by tkpwaeub (gabriel-holmes) on Omicron Variant Post #1: We’re F***ed, It’s Never Over · 2021-11-28T11:21:48.026Z · LW · GW

Looks like Australia just found cases of Omicron:

https://www.theguardian.com/australia-news/2021/nov/28/covid-update-nsw-chief-health-officer-says-omicron-may-already-be-here

Comment by tkpwaeub (gabriel-holmes) on Omicron Variant Post #1: We’re F***ed, It’s Never Over · 2021-11-27T07:33:08.249Z · LW · GW

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

Comment by tkpwaeub (gabriel-holmes) on Omicron Variant Post #1: We’re F***ed, It’s Never Over · 2021-11-27T02:03:17.879Z · LW · GW

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?

Comment by tkpwaeub (gabriel-holmes) on Covid 11/25: Another Thanksgiving · 2021-11-26T10:48:27.993Z · LW · GW

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.

Comment by tkpwaeub (gabriel-holmes) on Paxlovid Remains Illegal: 11/24 Update · 2021-11-26T10:39:12.817Z · LW · GW

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

Comment by tkpwaeub (gabriel-holmes) on Covid 11/18: Paxlovid Remains Illegal · 2021-11-23T01:54:40.321Z · LW · GW

It's weird to read this kind of fundamentally invalid argument on the anniversary of JFK's assassination. Stripped down to its bare bones, it's the watchmaker argument. Natural spillover doesn't explain why the outbreak occurred in Wuhan and nowhere else, or why the virus looks weird, because it doesn't have to. Many viruses don't jump between species, and the ones that do, every few decades, look weird.

Comment by tkpwaeub (gabriel-holmes) on Covid 11/18: Paxlovid Remains Illegal · 2021-11-22T20:11:39.012Z · LW · GW

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

Comment by tkpwaeub (gabriel-holmes) on Covid 11/18: Paxlovid Remains Illegal · 2021-11-22T20:08:36.408Z · LW · GW

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.

Comment by tkpwaeub (gabriel-holmes) on Covid 11/18: Paxlovid Remains Illegal · 2021-11-22T17:36:18.374Z · LW · GW

We could use this heuristic to estimate "true" prevalence:

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