The realistic perspective

My university has closed all face-to-face classes until 1 April, when, I presume, they’ll reassess what should be done. I hope no one thinks everything will be over then, because it won’t be. We’re just getting started. I expect April is when the pandemic in the US will be just roaring into action.

Some experts agree.

40-70% of the US population will be infected over the next 12-18 months. After that level you can start to get herd immunity. Unlike flu this is entirely novel to humans, so there is no latent immunity in the global population.
[We used their numbers to work out a guesstimate of deaths— indicating about 1.5 million Americans may die. The panelists did not disagree with our estimate. This compares to seasonal flu’s average of 50K Americans per year. Assume 50% of US population, that’s 160M people infected. With 1% mortality rate that’s 1.6M Americans die over the next 12-18 months.]
The fatality rate is in the range of 10X flu.
This assumes no drug is found effective and made available.
The death rate varies hugely by age. Over age 80 the mortality rate could be 10-15%.
Don’t know whether COVID-19 is seasonal but if is and subsides over the summer, it is likely to roar back in fall as the 1918 flu did

There is no guarantee that this will be a replay of the 1918 pandemic, but we should prepare as if it is. I’m teaching cell biology in the fall, I’m going to spend the summer getting organized for possibly having to teach it online.

I hope that’s all I have to do, and we’re not going to end up preparing by digging trenches for mass graves.

This next recommendation is personally bothersome. My wife flew to Colorado before the extent of the crisis became unavoidably obvious. She was supposed to fly back next week. Flying is out of the question anymore, so we’ve been trying to come up with alternative methods of getting her back home.

We would say “Anyone over 60 stay at home unless it’s critical”. CDC toyed with idea of saying anyone over 60 not travel on commercial airlines.

Right now we’re considering that instead maybe she should stay in Boulder with my daughter for some indefinite period of time. Safety apart is smarter than travel together that maximizes our chance of infection.

“Stop testing.”

They started testing for SARS-CoV-2 in Seattle, with one researcher, Helen Chu, leading the way. They started getting positive hits, and then the federal government stepped in, but not to anyone’s benefit.

The state laboratory, finally able to begin testing, confirmed the result the next morning. The teenager, who had recovered from his illness, was located and informed just after he entered his school building. He was sent home and the school was later closed as a precaution.

Later that day, the investigators and Seattle health officials gathered with representatives of the C.D.C. and the F.D.A. to discuss what happened. The message from the federal government was blunt. “What they said on that phone call very clearly was cease and desist to Helen Chu,” Dr. Lindquist remembered. “Stop testing.”

I found that shocking. Stop collecting information, stop responding to patient concerns, minimize the threat. This is not what I want the government to do.

On a phone call the day after the C.D.C. and F.D.A. had told Dr. Chu to stop, officials relented, but only partially, the researchers recalled. They would allow the study’s laboratories to test cases and report the results only in future samples. They would need to use a new consent form that explicitly mentioned that results of the coronavirus tests might be shared with the local health department.

They were not to test the thousands of samples that had already been collected.

While I sympathize with privacy concerns, this is a situation where public health ought to have priority. Being diagnosed with COVID-19 does not create a permanent stigma. It guides the appropriate response to the affected individual.

Especially since this is what’s happening:

In the days since the teenager’s test, the Seattle region has spun into crisis, with dozens of people testing positive and at least 22 dying — many of them infected in a nursing home that had unknowingly been suffering casualties since Feb. 19.

My mother lives in that area, she’s a few years older than I am (just a few), and she’s already had a few respiratory episodes that required temporary hospitalization. When I talked to her the other day, she’s self-quarantining and avoiding going out in public at all…but I feel like if there were a problem, she wouldn’t get the help she would need, but instead is going to be told to shut up.

Michigan State University suspends all face-to-face classes

Uh-oh. Given that move, I’m expecting dictates from on high at my university any day now.


Also Ohio.


Oh. And Minnesota.

“While the Duluth, Rochester and Twin Cities campuses are on Spring Break this week, and in anticipation of the Crookston and Morris campus breaks next week, we encourage our faculty to begin preparing to move classroom instruction online, especially for courses where this can be implemented immediately,” University of Minnesota-Twin Cities President Joan Gabel wrote in a letter to students, faculty, and staff Tuesday.

“Encourage” is different from “ordering”. I’m going to talk to my students in class about this today.


Add my alma mater, the University of Washington, to the list. Although I see that the Seattle Mariners are still dithering about their sporting events. Will it wipe out all the sportsball fans who go into crowded stadiums next?

What will I do if a virus closes my classes?

Yikes. I just read this comment about the coronavirus shut down in Poland — 22 cases in the whole country, so all university classes are suspended for the next month. That’s taking the issue seriously and taking major steps to slow the spread of the disease.

At my university, it’s only provosts and deans and chancellors and department heads talking about contingency plans, with no imminent threat of a shut down. But it could happen! With the number of cases doubling every week, I might come back from Spring Break to find my students have been ordered to stay away. I’ve scribbled up a quick contingency plan for my genetics course, just in case.

Contingency plan for Genetics (Biol 4312)

Genetics is an unusual lab course in that it already doesn’t fit the mold of the weekly intensive lab session. We’re working with Drosophila, and are at the mercy of their 9 day reproductive cycle, so we have to be more flexible. Typically, we meet for a half hour to an hour at the scheduled lab time, during which I explain the steps that the students need to take that week. The students need to come in frequently during the course of that week to maintain their flies, set up crosses when they’re ready, and count phenotypes. Some weeks this is a light load, coming once or twice on their own time to check on flies; other weeks they may have to come in 3 or 4 times a day to collect flies for a cross; and on several occasions they have to come in for long sessions of fly screening. The variability and flexibility suggest one fairly non-disruptive way to protect students.

Staggered, scheduled lab times. To minimize exposure, I could set up specific, individual lab times for each student. Right now, it’s a free-for-all with students doing their work whenever they can, but we could switch to exclusive lab sessions for each. So far this semester we have completed one whole experiment involving 3 different crosses, so students are familiar with the details of the methods, and they are experienced enough to not need direct instruction from me; I could manage with an explicit set of detailed instructions on Canvas for the steps in the next experiment.

They would still be using a shared lab facility, so we’d couple this scheduling with instructions on using sanitizers and sterilizing lab benches with alcohol between students.

In a worst case scenario, in which the university is shut down, another alternative is:

Drosophila genetics kits. I could assemble a kit with two fly stocks, a half dozen fly bottles, a small supply of medium, some anesthetic, and a hand lens for each student or pair of students. They could then carry out the whole experiment at home, again with detailed week-by-week instructions on Canvas. Data would be shared between students online.

Potential problems: Lack of an incubator would mean developmental rates might vary significantly. A hand lens is going to make it harder for students to score phenotypes. Currently, if one student’s cross fails, they can share specimens with other students and complete the experiment; in isolation, if one cross fails, they’ll be unable to finish. The final assays are somewhat labor intensive, alleviated by the fact that a group can share the load of counting thousands of flies.

Please note that these alternatives are only feasible because the students have completed an experiment with multiple crosses in the first half of the semester, with direct instruction and demonstration from me on how to set up a cross, how to maintain flies, and how to analyze phenotypes. The second half of the semester is repeating these same methods with a very different kind of cross and different mutant phenotypes. These stop-gap procedures would not be applicable to teaching a full semester lab course in fly genetics.

Setting up staggered lab times looks like wishful thinking now, if entire countries are locking out universities in the face of the threat. I might have to spend my spring break boxing up flies and media for distribution.

You are here

It’s amazing. This is the universal comic, it applies to everything right now.

Except spiders and cephalopods, that is. They’re looking better and better.

Aw, jeez. South Dakota has COVID-19?

It’s cutting close to home now. South Dakota has reported FIVE putative cases of COVID-19 with one death scattered across the state, among people who had no contact with each other.

It’s entirely possible that this is a case of paranoia and misdiagnosis, since adequate testing kits have not been available, despite the fact that Trump officials keep saying it is contained. We can’t know. That’s a big part of the problem, that when science denialists are running the government they interfere with getting good information and allowing us to manage a disease effectively.

Here’s Richard Lenski’s take on the situation.

The news just came out that South Dakota — South Dakota! — has 5 presumptive cases of SARS-CoV-2 infections, including 1 death. South Dakota has lovely people and places, but it’s not exactly the center of the universe, or even of the midwest. It has ~885,000 people in total … roughly 0.3% of the US population. So a simple extrapolation to ~330 million people would imply something like 1,800 infections over the entire USA.

There’s good news and bad news. Good news: there weren’t 5 cases reported in North Dakota, which has an even lower proportion of the US population.

All the rest is bad news. We’re assuming all potential infections have been tested and discovered. We’re also looking in the rear-view mirror, time-wise. In most cases, it takes a few weeks for an infection to lead to death (when it does, which fortunately is not usually the case). Maybe a week or so to develop symptoms that would lead to someone being tested. So let’s call it a week. Well, this virus typically doubles in a week or so. So 1,800 infections a week ago (ones that have become symptomatic today) implies ~3,600 infections at present in the USA as a whole.

It’s personally worrisome, because Morris, where I live, is way out on the western edge of Minnesota, physically closer to South Dakota than we are to Minneapolis. Isolated rural communities aren’t supposed to be hotspots for pandemics, don’t you know — we leave that to the big city folks. Yet here we are, where we might have to deal with this at home.

We’ve received some concerned messages from the university administration, too. We’re supposed to develop a plan for how we’d complete lab courses if we go on lockdown, which isn’t exactly reassuring. I’ve been thinking about it, and have some less-than-satisfactory ideas about how I could wrap up the genetics course, and we’re supposed to have a meeting to discuss biology’s response tomorrow.

Our goal has to be to slow the spread of the disease to prevent medical services from being overwhelmed. Nobody is panicking — I’m already seeing conservatives mocking any response as panic — but taking necessary steps so that we don’t reach a situation that is unmanageable.

We already have examples we should be learning from, in China, in South Korea, in Italy. This rather cluttered infographic summarizes the lessons from Italy. It’s like a tsunami.

There’s a lot of medical jargon in that — I hope my local clinic is paying attention.

The dilemma: to fly or not to fly

My wife is currently in Longmont, Colorado. She is scheduled to fly back home in 10 days, which is the problem. Look at the ratfuckery our administration is up to with coronavirus recommendations. They just don’t care what the CDC says, and I trust the CDC far more than I do Trump/Pence.

The White House overruled health officials who wanted to recommend that elderly and physically fragile Americans be advised not to fly on commercial airlines because of the new coronavirus, a federal official told The Associated Press.

The Centers for Disease Control and Prevention submitted the plan as a way of trying to control the virus, but White House officials ordered the air travel recommendation be removed, said the official who had direct knowledge of the plan. Trump administration officials have since suggested certain people should consider not traveling, but have stopped short of the stronger guidance sought by the CDC.

So now Mary is considering not flying, and instead renting a car to drive back — it’s 800+ miles and 12 hours of driving. Yikes. I have concerns about that, too.

  • Maybe the CDC recommendations don’t apply to her. She’s a healthy, active 62 year old (yes, I’m a cradle-robber, and I’m not ashamed to admit it). Which also means she’s capable of the drive.
  • If she has to rent the car and return it to an airport, she’s still going to be exposed to all those diseased world travelers.
  • You may not have noticed, but this time of year has unpredictable weather. She could have to drive through a blizzard, an ice storm, or a flood.
  • She flew there, and could already be infected. She might turn into a zombie on the drive back.

I am not helped by the dithering of the incompetents in the White House. I am also not helped by the vague recommendations of the CDC; I don’t consider either of us to be elderly or physically fragile in our ability to respond to disease…although I mentioned that a high school acquaintance of ours just lost her husband to COVID-19, so maybe we are.

Indecision can have terrible consequences, and the Republicans have so thoroughly politicized what ought to be scientific decision-making that now I’m being indecisive.

Time to huddle alone in my man-cave

Now that COVID-19 cases have been reported in 28 states, I think we can say that efforts to confine it have failed. We have our first case here in Minnesota, a person returning from a trip on a cruise ship (Why do people do those cruises anymore, anyway? It’s like jumping into big bottle of culture medium and getting stirred around for a few weeks.) My university has sent out information to all faculty about what to do if cases arise — we’re referred to this Safe Campus website for updated info. Ironically, the email about this also says, “Our Emergency Management team—made up of individuals from across campus—is meeting weekly”. Well, that’s the problem, isn’t it? If someone on the team is infected, the whole damn lot of them will go down.

My wife is off in Colorado, and as it turns out went through the Denver airport at the same as an infected but asymptomatic traveler from Italy was walking among the oblivious herd. She’s coming back in about two weeks through the same mob of disease-ridden cattle. We old, frail people have been advised to avoid all social contact, which sounds like a fine idea to me — I’m a denizen of the internet, that’s where I do all my socializing — but I have a job that involves talking with lots of people all the time. Fortunately, I don’t touch students…but I do get piles of papers handed to me. Maybe this will motivate me to adopt all electronic submissions.

We’re also advised that, instead of crude handshakes, we should adopt the Vulcan greeting. I can do that. I’m all for it.

“Live long and prosper”

However, this recommendation rarely comes with the necessary warning: do not, I repeat, DO NOT ever greet someone with a Vulcan mind-meld. This is right out, even if it would be a great teaching technique.

“Do you actually…understand…epistatic interactions in genetics?”

I was planning on going out for a nice walk in town today, but I think I’ve just talked myself into sitting at home alone.

The bad news will keep on coming

A diagram putting the danger of infection with COVID-19 in perspective:

Not shown is the human cost. Deaths from the coronavirus in Washington state have crept up to 6. All of them were people over 70; the death rate for the afflicted over that age is 15%. The virus isn’t done yet, either.

“We expect the number of cases to increase in the coming days and weeks,” said Jeff Duchin, health officer for the public health agency, who stressed that most cases will be mild. “We are taking this situation extremely seriously.”

Uh-oh. My mother lives in King County, and she is over 70. I hope she’ll take this as an excuse to quarantine herself and stay home for a while.

When did you last wash your hands?

John Oliver has some sensible advice.

As for my handwashing…all day long. I work with students every day all day (who I avoid touching, obviously), so I tend to wash my hands thoroughly about once an hour, or before and after I go to class. Not just for coronavirus, but because they’re filthy animals and disease vectors for all kinds of crap…and I have the potential to transfer diseases to a diverse lot of people who wouldn’t normally hang out together but are forced into my classrooms for those sweet, sweet credits.

Spiders are far less infectious than other humans, you know.