Remember when people were saying cases were going up but not deaths, so it's OK?

Yeah, back then it was "deaths are going down" vs. "there is a big time lag, just wait." So now we are starting to get through the 3-5 lag between infections being reported and deaths being reported. Here is what the big three (Arizona, Texas and Florida) look like as of a couple days ago:

So now it seems pretty clear that we are not out of the woods yet in terms of deaths. If we let cases increase dramatically we will also see increases in deaths. The only thing that has "gone right" in the past couple of months is that we know more about treatment. That is a definite plus in that it means fewer people with serious complications and fewer dying. But still way too many dying when we could have beaten this a few months ago and had it largely under control. Now it seems like the only way we will ever make this manageable is rapid testing. Even if we get great vaccines 50% of Americans say they won't take one, and the data on immunity seems to indicate it last for at best a bunch of months. So our only hope is to leverage some people getting the vaccine with testing and contact tracing. We will also have the problem of people not being willing to quarantine, but maybe by combining all of these measures we can eventually get a handle on this.

STRS and Private Prisons

This post is not about COVID-19. But the COVID-19 era has also become the (maybe) Black Lives (really do) Matter era. STRS, the Ohio teacher's retirement system, has fairly significant investments in two companies that operate for-profit prisons, GEOGroup and CoreCivic. For many educators, myself included, this is real moral problem. Our deferred compensation is supporting the school to prison pipeline. The school to prison pipeline is one of the key drivers of the inequity that BIPOC (and poor white) our students face. We want our support for that system stopped, just as the California teacher retirement system decided to do. 

I will write more later about the huge moral and actual operational problems involved with private prisons soon. That conditions are bad (for both inmates and staff), that it incentivizes the unequal sentencing that is the reason for its existence and that private prisons are terrible at rehabilitation. Which makes sense because they have a vested interest high recidivism rates. And we can talk about the whole problem of kids in cages. Right now I want to focus on the idea that they are probably not that great an investment. 

Private prisons were supposed to make things better by being cheaper than publicly operated prisons and increasing the quality of services by inducing competition. In the 1990s, when we were building prisons like mad, this seemed to some like a good idea. For the most part, neither of these "good" outcomes has has happened. The research is somewhat mixed but it is fairly clear that there are at least not any big savings. On the other hand, there is considerable pressure to stop using private prisons. While the Trump administration reversed an Obama administration decision to phase out the use of private prisons at the federal level, it seems likely that Joe Biden will be elected president in November and re-implement the policy. A Biden presidency would also likely see big changes in our use of private prison operators for detentions at our borders. In fact, just the Democratic control of the House of Representatives does this. Furthermore, there is growing support for decriminalizing marijuana and already a lot of moves being made to move to treatment over incarceration for opioid and other addictions. All of these factors could very quickly make the stock prices of private prison operators tumble, and tumble rapidly. The rosiest up side predictions are that they might produce modest growth if we don't see a change in administrations. The stock values simply do not provide anywhere near the level of potential returns to justify this level of risk. And certainly not enough to justify the moral issues with teachers using their deferred compensation to support the school to prison pipeline and children in cages at our borders.

To sign the petition to call on STRS to divest from private prisons, please go to: https://alleyesonstrsohio.com/

Meaningfully discussion what is safe or not safe requires correct information

Let me start by saying this by saying I am not an expert in epidemic modeling. I do have expertise in statistics, I do have graduate classwork and some professional experience with epidemic data analysis and modeling. And in spite of that I am NOT an expert. Which is why when I want to know what is most likely to happen next, I read and listen to the words of experts. What I can do is explain how a lot of the reasonable sounding, statistical sounding arguments floating around out there are either wrong, make unjustified assertions, or both. To illustrate I will use some words used to argue for five days per week in person school for everyone who wants it in the school district where I teach. My district is the Dublin City Schools, in Franklin County, Ohio. 

We are not in level 4, we are in level 3 and they removed the star last week that warned we might go up to 4. Franklin County is increasing in cases, but has had a downward trend in deaths for 8 weeks, and hospitalizations for 7 weeks. 

OK, let's address the "big claim" here, that cases are up but deaths are down. Here are the graphs of the seven day rolling averages for cases and deaths. 

So on it's face this looks kind of like a true claim. It is true that we have learned a lot about treating this disease so it has become somewhat less deadly. The problem is the same one we are having right now with people arguing that the death rate is dropping dramatically nationwide. When they say "death rate" they mean case fatality rate. And the reason the case fatality rate is dropping dramatically right now is not that fewer people are dying but that the number of cases is rising quickly. On the other average deaths are taking almost 2-4 weeks to occur after positive tests, with another week or more until the deaths are actually reported as COVID-19 deaths. So there is a 3-5 lag between the case numbers and the death numbers. If we put a line in the cases graph we get:

Noting that the death numbers are small compared to the case numbers so the graph won't be a smooth, look again at the deaths graph above, compare that the part of the cases graph to the left of the line, then think about it a bit and tell me what seems likely to happen to deaths over the next month? 

If you look at the percentage increase in how many more tests they have done, the pattern of increase in cases follows the testing increase almost exactly. We don't have more cases, they are just testing more and detecting the asymptomatic cases that have always been there.

OK, first off we don't know the test positivity rate, so this just can't justify this claim. We do have an estimated R-nought value of 1.11 for Franklin County, meaning the problem is growing not shrinking. Overall in Ohio the test positivity rate has gone from 4.3% to 6.3% in the past month, which argues very strongly that this is not a case of just having increased testing rooting out asymptomatic cases that have been there all along. And the increases in all of Ohio outstrip the increases in testing. In fact about 1/3 of all the cases in Ohio have been identified in the past three weeks but nowhere near 1/3 of all the testing occurred in the corresponding time frame. 

Also, the Dublin area has had very low numbers all along, with only a few hundred cases total. Only about 0.4% of the population in Dublin has even had this. 

The number of cases is growing in Dublin, just like in the rest of Franklin County. This is an attempt to throw in numbers that sound like they might support the "this is not a serious problem" idea but they don't. Also, a large part of the Dublin City Schools is in the City of Columbus. So you really need to look at the number of cases in all the parts of DCS. Like Dublin, the cases in Columbus are going up rapidly.

The common flu also is transmitted asymptomatically, and is much more dangerous to children than coronavirus, yet we don't test everyone for the flu each year. 

and

Yes, vulnerable populations need to be protected, but shutting down businesses and schools and destroying our country is not the answer to this virus. I am glad the schools are giving an option for people who are vulnerable or are scared, but I really hope those of us that aren't are given an option for our kids to return to school full time.

The flu is not much more dangerous to kids than COVID-19, we do a ton of flu testing every year, we aren't testing anywhere near everyone for SAR-COV-2 (that's part of the problem), and kids are not the only people we are worried about. We are also worried about kids spreading the virus. We don't yet know whether COVID-19 is more deadly than common influenza's than kids. We are nowhere near being able to argue that. When we closed schools we isolated kids from infection. It does appear that younger kids (under 10) are much less likely to contract it than older kids and adults. So it might turn out to be less deadly. But so far so many fewer kids have contracted it that we just don't know. We do know that there are other serious health risks with COVID-19 that are far more common than in influenza. So the evidence right not points to COVID-19 not being less dangerous for kids than influenza, and certainly does not support a claim that is less dangerous. W

e do lots and lots of flu tests every year. including this year. We also have flu vaccines which allow us to mitigate risk and spread. Initial flu tests take tens of minutes, so they are done right in a doctor's office. If we had similar testing for COVID-19 we might have controlled it. 

Finally, the biggest worry is that kids will spread COVID-19 to school staff and to the their families and neighbors. Even if we knew no kid would get seriously ill, if we went back and did school as normal we would have a lot of teachers, bus drivers, custodians and cafeteria workers die in Dublin. Because almost all of the adults would get it. We would also have a really high percentage of the parents of our students get COVID-19, and some of the them would die. And even more of the adults would suffer long term health impairment. 

Some Links Used:

https://github.com/nytimes/covid-19-data

https://www.wsj.com/articles/how-deadly-is-covid-19-researchers-are-getting-closer-to-an-answer-11595323801?mod=e2fb

https://coronavirus.ohio.gov/wps/portal/gov/covid-19/dashboards/overview

https://covidactnow.org/us/oh/county/franklin_county/?s=748128

https://drive.google.com/file/d/1wNl36_DQAowjZ6MzvkhjZsMphOny3mYr/view

https://www.cincinnati.com/story/news/2020/07/13/about-one-third-covid-19-cases-ohio-past-three-weeks/5429686002/

Can masks really help?

One of the big problems in looking at math in a situation like the pandemic, is that people, even people who are generally good at math, tend to be really bad at getting an intuitive feel for probability. Particularly in cases where there are a lot of probabilistic outcomes to factor in. To help my students understand this, I created a simple simulation to model contagion spread. It is based on the ZooSimulation that I do in my AP Computer Science and IB Computer Science classes every year. Basically you create autonomous agents that are placed in a simulated environment and interact. 

For my contagion simulation I ran simulations of 300 people moving about an environment randomly. For a baseline, I ran the simulation assuming everyone moves at every step of the simulation and that if an infectious person (infected are red) gets next to someone who is not infected and not immune (these people are blue) they will infect that person. In this stage of the simulation I also gave each infected person a 5% chance of "getting over" the infection at each step in the simulation. If they get over the infection they turn purple. These people cannot infect anyone else and are immune forever in the simulation. (Yes, I know that we now realize that immunity likely only last for a period of months, but this simulation was created to demonstrate how the math works. I will probably update it so that after some number of steps the purple people can turn blue again.) Here is a typical run for the baseline:

So the next thing I simulated was to add in social distancing. To do this, I simply made the people move less frequently. That would reduce their interactions with others. For this round, I made everyone in the simulation have the same chance of moving at each stage of the simulation. This was for simplicities sake. One of the more advanced versions a few of my students worked on this spring allows for a range of movement likelihoods in order to figure what percentage of population needs to socially distance in order to really inhibit spread. It does turn out that the average chance of moving is what really matters. So in this next run I had everyone move only 1/3 of the time.

You can see that this does tend to inhibit spread. But we decided that this was too optimistic to be realistic. So for the run after that we used everyone moves 2/3 of the time. 

This still was a lot better than everyone moving all of the time. Next we considered masks. For this first run we had masks be 25% effective at preventing infection. Note that this does not necessarily mean that everyone is wearing 25% effective masks. If a mask reduces the chance to you give an infection to someone by 40% and the chance you get an infection by 10% (both of those are lower that current estimates for cloth masks) and everyone is wearing masks then there is only a 54% chance of the infection passing from the infected to the non infected person. (0.6 x 0.9) In other words, that makes the masks 46% effective if everyone is wearing masks. 

The situation is a little more complicated if not everyone wears a mask. Using the above masks (and remember those are considerable less effective than current estimates), with 2/3 of the population wearing masks, you get  (4/9)*.54 + (1/9)*1 + (2/9)*.6 + (2/9)*.9 = 0.6844 or masks being net 32% effective in stopping infections. A little more on this math later. Now here is a simulation run with masks being 25% effective and people moving 2/3 normal. So not super effective masking or distancing, but something. 

Now we the infection spreading much more slowly. This is important not just for bending the curve purposes, but also because it makes contact tracing and isolation much easier to do and much more effective. I have some later models that estimate how likely it is a person gets tested and assumes that 90% of those who test positive will isolate themselves. If you can slow down spread this allows you to prevent outbreaks from ever growing out of control.

So let's think about mask effectiveness for a little bit. The masks above were only 40% effective in reducing the chance you infect someone else and 10% effective in preventing you from getting infected. If everyone wore them we could cut the infection chance by 46%. If only 2/3 of people wore the masks we could cut infection rates by almost 1/3 (32%). Here is a run with 50% social distancing and 33% effective masks.

That is starting to look like something actually controllable. Actual cloth mask effectiveness is difficult to measure, because so many factors like regular washing, wearing it correctly, tightness of fit and other things intrude. Meta-analysis is heading toward about a 70% reduction in the chance you spread the virus on the average and about a 20% chance to protect you from getting infected. If everyone worse masks that would mean masks would stop 75% of infections. 

There is more research showing the effect of masks all the time now. I have read three new articles in the past week. Think of a mask this way, effectively it amplifies the distance between you and someone else and decreases the time you are near each other. A mask traps some particles, and reduces the velocity of others. So infected droplets spread out more slowly over less distance. Effectively doing the same thing that spending less time in contact and being further apart do.

Masks are not magic. Only complete isolation can guarantee you won't get infected. And that isn't practical. But masks coupled with distancing efforts could actually make this pandemic something that we could navigate much more safely. We would be able to shut down just areas where infections were spiking, and shut down for far less time. We would be able to contact trace because the speed of infections would slow so that for a lot of places there would be no need to go on full lockdowns. 

To Wear or not Wear (a mask)

When this pandemic started, the general consensus was that wearing masks in public was not helpful. As is often the case with an evolving crisis like this, as more data becomes available scientists, medical professionals, public health professionals, statisticians and policy makers looked at the data and decided the initial recommendations were wrong. The more evidence that comes in, the more compelling the case for wearing masks in public is, and the harder it is to understand the resistance. Please folks, if you have been resisting or mocking masks, take a little while and read. Peruse some of the links. This is not a conspiracy. I promise I am not trying to take away your freedom. I am trying to get more people to wear masks so that there is less spread of this virus. If you read the news, things are not looking good right now on the virus front. 

Initially, I wanted to make a short explanation of why masks in public are important, but instead I decided to write answers to some of the most common counter-assertions or questions. I am NOT a mask expert. But I have spent the last three months working on mask design, mask testing and mask production. So I have worked with a lot of experts. I also know some other folks who are experts. I am relatively expert in statistics and I actually do have formal experience working with pandemic models, that includes classes and paid work. So I do understand infection models quite well. Most of the actual experts on masks are too busy dealing with the actual crisis, so I am going to try to do my best to fill in for them. I am also going to try to keep updating this, and the links at the end, as more information comes in.

1. "I heard that cloth masks let through 97% of virus sized objects so they are useless."  OK, the first part of is sort of true. (The type and thickness of cloth and design of the mask play a big role.)  And if we were spewing just viruses the masks would not be that useful. Not useless, but not very useful. But that isn't the case. Most of the viruses we exhale (when we breath, talk, sing, cough and sneeze, in order of ascending velocity) they are almost all in droplets of liquid. From smaller to larger in size. Larger droplets if they stay in the air will become smaller as the liquid evaporates. But even a simple cotton cloth mask can stop 30-70% of droplets, and it will reduce the speed of others. It also changes the geometry of the spread, making more of the virus come to rest on you and less on other people and surfaces. It is that if you are talking as protection for the wearer in any extended exposure setting, their effectiveness rapidly drops below 20%. Not nothing, but not much. 

[Hint: Ask yourself why in surgery most of the operating team are typically wearing surgical masks, which are basically more effective cloth masks, and not n95s. Because in surgery the principal danger masks are there to avert is infecting the patient from the medical personnel.

2. Until recently the WHO and CDC and others were telling people they didn't need to wear masks unless they were in a high risk group, so no one really knows what the truth is. For this one, it is true that the guidance has changed. It has changed for simple, straightforward reasons. The first was concern that people would hoard N95 masks needed by medical professionals. The second is that when they thought that you were contagious mostly while symptomatic, they were recommending against wearing masks in order to keep people from engaging in risky behavior like "I am sick, but if I wear a mask I can still go out." Once it became clear that people can be contagious for a week or two before symptoms show, or maybe even longer, wearing masks in public spaces became the prudent thing to do.

3. Masks will harm my immune system or somehow else make us sicker. I really want to just say no. Because the research just isn't there to support this. No any. It was literally invented out of whole cloth. But... ok, there is research that says if you wear the same simple cloth mask all day, every day, then you might be increasing your risk level because it might make you act as though the mask will prevent you from getting infected. Since the recommendations for lay people is to wear a mask only when you are out in public in relatively close quarters where you are likely to infect others if you are infectious, and to take off and hopefully clean the mask at home, this is a non-issue. Again, it does not harm your immune system. But IF a mask makes you engage in risky behavior it could be bad. But if you are saying I am still going out, but I am not wearing a mask, then you are already engaging in the risky behavior but you are penalizing other people.

4. Masks will cause CO2 poisoning. OK, I honestly scratch my head at this one. Doctors and nurses wear cloth surgical masks for hours without CO2 poisoning. But seriously, the same people who argue that it so impermeable that it can't stop any viruses also think that it will keep CO2 from escaping? It is a perfect example of "throw stuff at the wall to see what sticks" mentality for promoting misinformation. 

5. What about people with damaged lungs. It is actually true that for people with significant lung damage, for example who have lost a lung, or who have survived something like COVID-19 or lung cancer but with significant damage, that a mask can make it too hard to breath properly. Bringing them up in this context as an argument for everyone not wearing masks is pretty lame, however. Those are exactly the people most in need of the protection provided by you wearing a mask in their presence. (And by the way, they make special masks that actively provide air for such folks, because they need the protection.)

6. Shouldn't this be a personal choice? OK, this one is not as clear cut to refute. But to me, it is like saying shouldn't I be able to drive as fast as I want on the roads? Your freedoms are always bounded when they endanger other people. It is particularly galling to me to have people argue against businesses requiring masks. Because those same people generally are vociferously against anti-discrimination laws being enforced for businesses. They are also the type of people who would call police on neighbors playing loud music. And, statistics show, tend to be very supportive of infringements on the rights of the *right* other people. But before I get myself completely worked up, what the are really saying is that *they personally* should be free to do what they want and other people, even the owners of businesses they wish to patronize, should not be able to tell them what to do. Basically, this comes down to wearing masks protects other people. There are a few people for whom masks are legitimately problematic, but for most people who object it is simply that they prioritize their desire to do what they want over other people's health. 

https://www.washingtonpost.com/health/2020/06/13/spate-new-research-supports-wearing-masks-control-coronavirus-spread/

https://www.theatlantic.com/health/archive/2020/04/dont-wear-mask-yourself/610336/

https://rs-delve.github.io/reports/2020/05/04/face-masks-for-the-general-public.html

https://www.vanityfair.com/news/2020/05/masks-covid-19-infections-would-plummet-new-study-says/amp?fbclid=IwAR3Er1N8GEUSCPxuD_ET2eF87D-qSuUK7IeMqLpqeJ4HNMfNWweU4Y-OEM0

https://www.mayoclinic.org/diseases-conditions/coronavirus/in-depth/coronavirus-mask/art-20485449

https://www.cdc.gov/coronavirus/2019-ncov/prevent-getting-sick/diy-cloth-face-coverings.html

https://health.clevelandclinic.org/heres-how-wearing-a-cloth-mask-helps-fight-the-spread-of-coronavirus/

https://www.yalemedicine.org/stories/wear-covid-mask/

https://www.cnn.com/2020/06/14/health/us-surgeon-general-coronavirus-masks/index.html