Covid update (3)

It came through the house again. Several of Grandma's caregivers got it and I got it. But Grandma, and my wife and daughter were spared.

I spent my quarantine in the spare bedroom which is where my home office is set up in any case. Comfortable furnishings, a big picture window, and various internet equipped devices. About as good as sitting in one room for a week-and-a-half can be. Mild case. After all, I'd already had it and was vaccinated and boosted. I got a lot of work done and a little on my side projects, too.

My wife's long-covid persists. She'd been making good progress (and is at least burning through a lot less supplemental oxygen), but in the fall she got first her flu shot then her Covid booster and each one set her back a week or so on her exercise. Then my folks came, then her folks, and, and, and. She was just starting to get back up to speed on exercise when I got sick and she suddenly got a bunch of worked dropped on her. Sigh.

Covid update (2)

Not about the renewed threat from the delta variant. Not even about how depressingly unnecessary the renewed threat from delta is. More about the how Covid has affected us.

Both of my regular readers probably recall that the whole family got the thing in late November or early December. Well, we never had the child tested, but she had symptoms similar to, but less severe than her mother.

General update:

• Grandma was in the hospital for over a month. She was sent home in dreadful shape and still on a feeding tube. She rallied and transitioned to liquid, then chopped, then normal diet; but she remains on hospice and is still bed-bound (before Covid she needed increasing levels of assistance in walking and transfers but was decidedly not bed-bound). Her specialists say that Covid accelerated the progress of her underlying condition.
• My wife and I both experienced bouts of unexpected fatigue throughout January and February. One advantage of working from home is that if you have a irresistible need to take a ninety minute nap at 2:30pm the only disruption is the need to make up the lost time that evening.
• My wife seemed to recover well at first, but in March started to grow weaker. In April she was diagnosed with long Covid. One of the main features of the extended version of the disease is a swelling on the heat and lungs which puts pressure on them and reduces their efficiency. The treatment of choice at the moment is supplemental oxygen, avoiding any kind of intense exercise, and waiting for the swelling to go down. So we're lugging O2 bottle around when we go out, and she's been scheduled for consultations with half a dozen assorted specialists. Best guess is that we're in this boat for another six months, give or take.
• My on-going symptoms faded around the end of February. But my better half remains worried on my behalf to this day. So I asked about attending the long Covid clinic and got the expected answer (I'm not sick enough to justify any of their overbooked time), and have restricted my exercise regime to low intensity (walk, don't run; go steady, not hard on the rower; very modest levels of moderate resistance training). I began to feel something like my old self again around late May. Mind you, the gray that appeared in my hair hasn't gone away like it did the first few times it showed up (always during a particularly stressful period in the last ten years or so). I tell my self that a little salt-n-pepper at the temples is "distinguished". Sometimes I even believe it.

More on bureaucratic language

My wife and I got the Janssen (AKA Johnson&Johnson) vacinne today. No significant side effects at this point.

But I want to talk about the paperwork. The fact-sheet that I was required to acknowledge receipt of included language like

There is no U.S. Food and Drug Administration (FDA) approved vaccine to prevent COVID-19.

The Janssen COVID-19 Vaccine is an unapproved vaccine that may prevent COVID-19.

And several more variations on the same theme.

Now, on one hand the point is clear: the FDA has not completed its (lengthy) approval process and has just given permission to use these things because the pandemic represents an emergency situation.

But on the other hand the expectation is that hundreds of millions of Americans (not to mention billions of people in other parts of the world) will receive one or the other of these vaccines. So what is the difference between the current situation and approval? Nothing outside the structure of the bureaucracy's regulatory structure.

Not that I think there is anything malicious or even dishonest about this business. It's just that organizations create their own cognitive structure and then live in them even when they lose fidelity with the real world. In other cases that can be a problem.

Covid update

The bad news is that everyone in the family got it; the good news is that surprisingly only one of the six carers working with Grandma tested positive.¹ Alas the carer who did get it ended up giving it to her spouse and four kids, too.

So that gives us a total of ten patients in "our" outbreak. Only one person (Grandma) had to be hospitalized. The rest of our family had "mild" symptoms; the carer and her kids are in a similar boat, but her husband seems to have gotten hit a bit harder (though not badly enough to need admitting). Still that's nine out of ten recovering without heavy intervention. ²

Grandma had a harder time. After about nine days in the hospital she developed a pneumonia and had to be transfered to the ICU and intubated. Eight days later they were able to extubate her and this evening she was transfered out of the ICU. She's still pretty foggy and, of course, is deeply deconditioned. She's looking at weeks of rehab before we can have her back. In the mean time we get a few minutes a day of video chat as the hospital is fully locked down: no visitors for any reason.

---

¹ Part of our last upgrade of procedured was asking the carers to wear masks full time on shift (and we provided KN-95s for those who wanted them); my wife and I also wore them whenever we went downstairs (that is into the space shared with Grandma and the carers). However, neither Grandma nor the toddler could be convinced to keep them on. None-the-less the policy seems to have made a difference.

² Recovery is not a simple thing, however. I've been "over" this for two weeks now and I'm still suffering unusual mental and physical fatigue. Just six or seven hours of work (i.e. programming and reports) is leaving me inattentive and slow for the rest of the day. Just walking two-and-a-half miles on an improved trail in forty-five minutes leaves me feeling like the day included a marathon martial arts workout. My wife has similar complaints.

Covid in the house

Well, at least two of us have it.

My better half got a test late last week and while she she doesn't have the results yet a contact tracer called. At the same time honorary grandma's cold sent her to the hostpital where it turned out to be covid, too. In addition I had some kind of gunk last weekend and the toddler may have had something durning the week. A couple of Grandma's carers have gotten negative tests in the last few days, but we're still waiting to hear how the others are doing.

So far everyone seems to have a mild case, but we're all holding our breaths (and thankful that this is still an option).

Covid getting close

Despite the notable success of my part of the country during the early months of the pandemic we're in the thick of it now. Some combination of luck running out and people getting careless through exhaustion with the continuous state of low level emergency, I guess.

My training as a physical scientists left me with an irresitable urge to put things into perspective in a particular numeric manner. I note that at this point the numbers in the news correspond to approximately 3% of the US population having been diagnosed with Covid19 at some point this year and a little less than one-tenth of a percent having died from it.

So it is very easy to not know anyone who has died from this thing and not particularly hard to not know anyone who has gotten it. Especially if you live in an area that had not been hard hit until recently.

On the other hand this means we can expect Covid19 to be the third largest cause of death among Americans in 2020, outstipping all causes of violent death.

Anyway, with the virus surging in our community we've been affected in two ways this week. First, my daughter's preschool (which had re-opened in mid summer) has closed again after two cases in a month (but apparently no transmission in the building). They won't be re-opening until after the new year. Secondly two members of the team who care for our honorary Grandma are quaratining after a relative of theirs was diagnosed with the virus. The contact tracers have not called us so *we* may be in the clear, but there are three adults and four kids who are in our immediate circle at risk. Scary times.

We're trying to tighen up our practices again, and we had also started wearing masks in the common areas of the house last week (though neither thte toddler nor Grandma pay much mind to that). The medicos have learned a lot about how to treat this thing in the last eight months, but our hospitals are running just about at capacity right now which is not promising.

Duty and painting oneself into a rhetorical corner

Duty is a debt you owe to yourself to fulfill obligations you have assumed voluntarily. Paying that debt can entail anything from years of patient work to instant willingness to die. Difficult it may be, but the reward is self-respect

Robert Heinlein

"Duty" in the sense of an obligation is a politically contentious idea. I am personaly a fan of Heinlein's definition, but it suffers for some people's purposes from not being something that you can dictate as in "Doing [this thing I'm interested in] is your duty". The best you can do is explain to them why you think their self-respect should depend on doing it.

As a legal reality a few "duties" are required and you can be punished if you don't comply. If you are summoned for jury duty and neither provide an excuse the court finds acceptable nor show up you can be held in contempt and subjected to fines or jail time. If you are a young but adult male in the US and don't register with the selective service you can get in trouble. In the same vein, many people were punsihed during the Veitnam war era for draft dodging, which brings us to the culture wars.¹

The political right in the country largely partakes of a long standing view that military service is and should be required of men "in times of war" (which really means at the discretion of the political leadership). Some who don't go quite that far feel that there simply shouldn't be a way for a "real man" to not want to join the fight which is a slightly different take. In either case the point is that the community needs defense at times, and the costs should be widely borne.

The political left, on the other hand, mostly feels that it is the right of every citizen to question the motives behind and necessity of military action and to demur from participating if they find them unsavory or unecessary. Some go so far as to consider it an obligation to make such judgements. Some have even held unwilling particpants in military misadventures responsible for the failing of the political and military leadership under which they served.

That is a stark divide, and has been the cause of much dislike and mistrust between people on opposing political teams for the whole of my lifetime.

Then comes Covid19 and the issues of wearing masks in public, social distancing, enforced closures of some kinds of business and so on...

Suddenly there talk from the left of a duty to protect others by respecting these rules and talk from the right about their right to judge the urgency of the threat, the effectiveness of the suggested measures, and the motives of the leaders.

Laugh or cry.

---

¹ There is, of course, some tension between this notion and that of religious liberty. Quackers, various Menomnites and other conciencious objectors have been a bone of contension on this matter since the beginning of the nation.

Spherical cows #1: Face masks edition

Let's talk a little about the effectiveness of face masks and the way levels of participation in waering them change the overall outlook of a epidemic. I want to go there because I hear some complaints hear and there that cloths masks don't do "much" and so there is no point in waering them, and I don't think that position is terribly well thought out.

This is the first of a couple of articles I intend to write applying simple models to look for insight into policy choices related to infectous disease in general and aimed at understnding a little about Covid19 in particular. Thought I won't try to make the models numerically faithful to Covid19.

Basic reproduction number

In the jargon of epidemiology the "basic reproduction number" (givern the symbol $R_0$) is the number of people, on average, who any given carrier gives the disease to. In simple models, if this number is larger than one then the disease spreads throughout the susceptible population, if it is lower than one the disease fades away. And we can (again in simple models) further break this number into a product of the avearge number of people a carrier interacts with ($N$) and the average chance that they will transmit the disease in their interactions with a single person ($F$).

For our purposes we can say that masks reduce the chance of tranmission¹ Which means that the effectiveness of using masks translates directly into a reduction in $R_0$.

Guessing at the effectiveness of a properly worn mask

Here we consider "non medical" cloths masks that you make yourself or buy at retail. Now a mask could help in two ways: it can reduce the amount of virus a carrier puts into the environment and it can reduce the fraction of environmental virus that a un-infected wearer takes in. For simplcity I'm going to model these as each generating a equal reduction in the chance of transmission modeled by a multiplicative factor $f$ that is less than one (so it models a reduction) and greater than zero (which would be perfect effectiveness.

So, if a carrier has a single "interaction" with a uninfected but susceptible person the probability of transmission is:

• $F$ if neither is wearing a mask
• $fF$ is one (either one) is wearing a mask
• $f^2F$ if both are wearing masks

But what should $f$ be? I don't really know, so I'm going to guess. To be conservative I'm going to guess that they are not terribly effective. I'm arbitrarily assigning $f = 0.8$. That is, a single mask reduces your chances of getting infected by only one fifth, and both parties being masked gets you down to 64 percent.

What about compliance

Not everybody wears masks. This may be due to a oversight such a failing to grab one on the way out the door, lack of access, or by choice. It dosen't matter to the model. But what does that mean for the overall effectivenes of a masking policy. Not all iteractions will be between two mask wearers. Some will involve one mask and others no masks at all.

Call the rate of mask wearing $r$. If everyone wears them $r$ is one, if only people who were burned by acid wear them $r$ is essentially zero.

Sticking with our "do everything on average figures" approachand assuming that everyone has the smae chance of meeting everyone else² we can compute the overall fraction $\Gamma$ in a simple way \begin{align} \Gamma(f,r) &= \left[ (1-r) + f r \right]^2 \\ &= (1-r)^2 + 2f (1-r) r + f^2 r^2 ] \end{align} And that's the whole basic calculation. It's quadradic in $r$ and concave up. Done and dusted.

Except that we might want to manipulate the math a little in search of further insight. So we continue \begin{align} \Gamma(f,r) &= (1 - 2r + r^2) + f(r - r^2) + f^2 r^2 \\ &= r^2 (1 - f + f^2) + 2 r(f - 1) + 1 \end{align} Also quadratic and concave up in $f$.

Sticking some numbers in

Just looking around me I think it's little optimistic to expect more than 90% mask compliance, so a optimistic number of the overall effect would be $$ \Gamma(0.8,0.9) = 0.672 \;, $$ or a little better than a 30% reduction. That's not great but it is significant. If $R_0$ was as small as 1.45 that alone would be enought to squeeze off the epidemic.³

A more pesimistic value of compliance might be around 60%, leading to $$ \Gamma(0.8,0.6) = 0.774 \,. $$ which is to say less than a 25% reduction in the tranmition proability. For that to be enough we'd need to have started with $R_0$ less than 1.3.

---

¹ We could also say that stay-at-home orders and the like reduce the number of interactions. Social distancing could be modeled as a little of each. I'll say more about this in the next post.

² I'd guess that this is the worst assumption in this calculation, but making it better requires a huge increase in the complexity of the problem and probably necessitates a Monte Carlo (randomized simulation) approach. I'm doing a back-of-the-envelope calculation, so this is what we get.

³ I haven't seen a number recently but early reports suggested something larger than 2.0, and I suspect it might be a little higher than that simple because early on there wasn't much awareness of how many people get it but remain asymptomatic.

Your messaging isn't reaching the virus

I talked a bit in a previous post about how nerds mostly don't rule the world. One of the big issues is that we think that we live in a world of facts, but most of humanity lives in a world of opinions masquerading as facts. And if enough people believe them then for political purposes they are facts. Politicians get their way in large messure by controlling the way people understand things; spin doctoring works at least some of the time. Which is why message control looms large in the minds of politicians.

But there are some things you can't message your way out of.

When you hear politicians complaining that too much testing is the problem you know they're locked in a mindset where messaging is more important to them than reality. They aren't making any progress in asserting their view of things because of the relentless drumbeat of daily figures, so rather than addressing the hard problem they try to just get rid of the reporting. Rather like the Ravenous Bugblatter Beast of Trall; which is to say "Daft as a bush".

---

Consdier, if you will, what we could do with enough data.

If we could test everyone all at once, we would have a very powerful tool for isolating the virus. Given that we can't do that, if we could at least test everyone who had been in contact with known carriers we would have nearly as good a grip, which is the point of contact tracing (note how quickly South Korea contained their initial outbreak as an example).

What we can actually accomplish is a lot less powerful, and without some help from the population at large it may not be enough to choke off the transmission, but asking for less data is the best way to guarantee that we don't stop this thing.

"Rights"

I've been thinking about 'rights' as in "constiutional rights" in the context of mask orders.

Leaving aside the reasonableness of mask orders and the long history of the courts upholding public health measures, I've been wondering in particular about why people might¹ claim there is (or should be) a 'Right' to not wear a mask in a retail establishment.

And I think we should see it, at least in part, as pedictable fallout of a long-running campain from the political left.

I'll explain.

Originalism

It is a common argument on the political right (or at least the political right as it was in my younger days) that 'rights' are something that the people have against the government. That's basically the content of the Bill of Rights, after all: things the government may not do to "the people" or to individual people.² In that view restraints may be imposed on people vis a vis other people by way of laws, but those are different from and limited by 'rights'.

Plenty of newfangled models

But here's the thing. For more than my entire lifetime there have been 'rights' that control how a person may interact with another person.³ A business may not discriminate against a person on the basis of a moderately long list of things, right? Nor is this limited to corporate entities (which recieve privileges from the state), but also applies to a person who is simply doing business with their own money. Similarly a business (i.e. even a person) generally may not discriminate in hiring against a person with a recognized disability nor in most cases forbid some service animals.

Now, I think a pedantic examination would suggest that these aren't 'rights', but rather requirements of the Civil Rights Act in the former case and the American's With Disabilities act in the latter (and various pieces of legislation that have followed) and as such are "laws".⁴ But the narrative I see in the popular press uses 'rights' or 'right' on a regular basis. To the extent that the descriptivists have won the argument over the meaning of words, that's a change in the understanding of what a 'Right' is from the beginning of the republic.

Not that am I terribly worked up about it. I'm strongly in favor of treating people decently whatever their color, gender, religion, etc and even ::shudder:: poltical beliefs or favorite college football team.⁵ And I recognize that a coordinated campaign of "individual" intolerance by the majority is completely asymmetric and every bit as oppresive as legal inequality,⁶ so allowing people to freely discrimiante in their public lives would be little if any movement toward equality. Nor do I think it is reasonable to say to the members of an oppresed minority "Well, I think you're right about this, but you really need to suffer for another couple of generation so that we can have a smoother transition with less friction", which seems to be the alternative.

But it sets the rhetorical stage for the idea that people can have 'rights' to deploy against other people

Right 'Rights' right back

The political right has been getting beat up using this language for roughly sixty years, so it shuoldn't come as a surprise to find that they have decided to retailiate in kind. In this the left have won the cultual wars: the rhetorical weapons of choice have become those the left selected way back before I was born.

---

¹ I say "might" because I am just guessing.

² And we'll just not talk about how incredibly wonky it is to have a system that on one hand holds up these shining ideals that people are in many ways more important than governments and on the other lets people be held as property. Denial is not just a big river in Egypt, after all, and even people who try to be rational and principled can suffer from it in startlingly large ways.

³ Here I'm attributing existance to positions held up by the courts and by the Supreme Court in particular. You're welcome to believe (as I do) that some of these are in error, but they are the things that will be enforced for good or for ill.

⁴ Generally the rulings are that the governement may in fact make such a requirement in law.

⁵ "I don't have anything against Buckeyes, but would you want your sibling to marry one?"

⁶ Even if we posit a lack of organized and legally unaddressed violence and intimidation ala Jim Crow (and even if you can belive it starts that way how long do you think it would last in the face of any resistance?).

When did that happen?

Of course babies and toddlers grow fast. You know that from constantly having to retire clothes and shoes and bring new, bigger ones home amung other little hints. But you don't really notice the gradual change unless something focusses your attention.

There is a local store we go to occassionaly. My daughter loves the place. Partly becuase there is lots of room to run around but also because they have a giant gumball machine with a spiral ramp for the treats to roll down.¹ The store was fully closed down for a couple of months, what with the plague abroad on the land, but they are open again (short hours and low occupancy limits, but doing business).

It's been four or five months since we'd been there, but we went yesterday.

Everytime we've gone before I had to help her insert the coin² because she couldn't see the slot (positioned above here eyes and sunken behind the handle). Yesterday, she had it in there before I even finished saying "Thank you" to the person who changed a dollar for me.

She must have put on nearly three inches since our last visit.

---

¹ Thankfully she doesn't know you're suppose to chew them, she just thinks they are balls to roll and throw. We cherish and encourage this understanding of the situation.

² Her economic philosophy right now seems to be "Coins are good because I can put them in machines". And she seems to understand that quarters are more useful that way than other coins.

Paradoxical success

Many parts of the US are starting to significantly relax public health restrictions related to the virus. To judge from the infection rate data one finds batted about the web some of them are being more responsible than others.

My particular corner of the world is in a weird place. The state has been largely successful in slowing the spread of the virus. Excepting one locality there haven't been any high-intensity outbreaks and the hospitals have not been overwhelmed.

Yeah! Go us! Whoo! Hoo!

But with something as contagious as this a large fraction of the population is going to get it eventually, so slowing the spread means it hangs around longer. Our hospitalization rate is actually still rising, and we're not ready for large scale relaxation of the restrictions. The Governor's existing order has been tweaked and extended.

My employer has established rules for returning work at the office (though they would be physically challenging at the actual facilities we have in this state) but we are allowed and encouraged to continue with full time telework.

Virial disruptions

As I noted before, my household went into a moderate social lock-down a few days before the Governor made the call for the whole state. And we've tightened up our practices a couple of time since then.

We're not completed locked down first because the government order allows for moving around is outdoor public space (yeah jogging!) as long as you keep your distance and secondly because one member of the household gets in-home healthcare.¹

We've started getting groceries by delivery and less perishable stuff from Amazon.²

Internet

We get out internet from our cable TV provider³ which means that we're on a shared segment. Of course these guys always advertise the maximum bandwidth you could possible get and you always actually get less because you are using a shared resource. Easy enough to understand and you can buy with that in mind.

However, with everyone home (and presumably doing a lot more gaming and streaming than usual) our segment appears to be close to saturated and the realized bandwidth is mush lower than I'm used to (and often with higher latency as well). At a time when I'm working from home.

What fun.

Time to call them and upgrade our plan, but it's not clear how much good that will do ... can they actually give me more just now?

It's not exactly cabin fever, but ...

I'm an introvert and not particular social, so staying at home for days at a time is perfectly normal for me. But I'm not completely asocial so staying at home for weeks at a time is not. Oftentimes, taking my books and papers or computer to some coffee shop and sitting quietly working by myself in a setting with some action and conversational buzz would be enough to get my fix, but I need something beyond work even in normal times.⁴

My wife is a bit less introverted and a bit more social than I am. She used to get out more, so it's hitting her harder. She frets. The more so because she's the one who manages the logistics of the household, which has settled down to just enough work everyday to keep her thinking about it but not enough to keep her busy.

We've gotten to the point where going to the pharmacy drive-through is an exciting family outing. Our toddler really likes the local drive-through car wash.

---

¹ And, yeah. That's a nice balancing act.

² Tip these people. Seriously. Folks working these jobs generally need the money in the first place, and they are doing a huge service for the public good by letting many of us huddle down and minimize contact, while running more risk than the rest of us in the process.

³ The only other option is a heavily over-subscribed municipal-scale WiFi network operated by a commercial outfit. They must have good marketing because a lot of communities around here contracted with them. Alas, they seem either unwilling or unable to provide enough bandwidth to meet the promises they've made.

⁴ Being a programmer in a small shop is not a highly social activity, but you do get out from behind the keyboard to talk to your colleagues several times a day if your are doing it right. Teams need to coordinate, managers need to be kept up to date, and communication with the customer has to be kept up.

Why I don't like telework

With the arrival in my patch of this year’s scary new disease,¹ my manager has both drawn a line in the sand for when we go on mandatory telework and given us broad approval to make that call on our own.

Our mandatory conditions have not quite been met, but my household includes a person who easily qualifies for a compromised immune system and two more who are more vulnerable than average, so we’ve declared it time to button up.

Whee!

I’m a programmer these days and a team leader at that, so I’m a ideal candidate for telework, but I spent the early part of the afternoon getting a useful workspace set up² because I haven’t asked my employer for any work-from-home time until now. I’ve done it before and I don’t actually care for it much.

Boundaries

There aren’t any natural boundaries when you work from home, which leads to two kinds of trouble.

• To make it work you need the cooperation of anyone else present, they have to treat you as “at work” when you are working or your productivity will be nibbled to death by ducks.
  
• The flip side is, of course, that you have to be off work the rest of the time, and that’s not necessarily easy either. Especially when you get one of the flashes of insight that will take “just a few minutes” to get into code and test. Write a note, drop it on the keyboard and come away.
  

I need a dedicated space with a door I can close. When I’m in there with the door closed I’m at work. When I’m not at work I don’t go in there. This worked pretty well the last time I did it, but that was when it was just me and my better half in the place. The toddler does not care for the idea that Daddy can be home and not available to her.

On the up side—maybe…

I’m planning on using my commute time to get a little less out-of-shape. At least as long as they don’t order a full time curfew.
And I’m going to grumble quite a lot if they do because my trotting down the sidewalks (which are habitually empty in this little piece of suburban wasteland) is a decidedly not an issue.

---

¹ And it is more than a little scary and even more disruptive, but to my mind the run-in-circles-scream-and-shout responses on display tell you more about the level of either ignorance or willful denial that most people live with than it does about covid19. We’ve been lucky the last few times out the gate, but you should have felt put on notice, people. It’s not like you weren’t given any hints.


But then maybe we should excuse the person on the street. After all, we’ve seen more than a little of both in high places, too. Haven’t we?

² And once I got that done I order a couple of upgraded bits and pieces. My work computer is an unreasonably beefy (six fast i7 cores and 32 GB of ram) and trim (less than 2 kg) laptop. Alas, while its keyboard and trackpad are functional, I don’t want to be stuck with them for long.

Written with StackEdit.