They’re trying to snatch all of my joy away!

We’ve been sent a letter from our university president. As of Wednesday, 18 March, everything is shutdown. How’s this for a thorough expulsion?

As I communicated this weekend, I expect all employees to work from home by no later than Wednesday, March 18. This is not optional for faculty and staff at all levels of the organization systemwide, and I expect supervisors to honor this decision.

Not optional. This isn’t a choice for a lot of faculty who maintain live animal labs. Or the greenhouse. Or anything that requires regular maintenance.

A little further, it links to more details for us slaves to other organisms.

Each lab should develop a list of essential operations to continue ongoing experiments and research that would suffer a major impact if temporarily discontinued, such as loss of years of effort, data, or loss of a major investment. Work that maintains essential equipment and safe standby mode in labs or maintains essential samples and animal populations also meets the criteria for essential operations.

Other laboratory research is to be discontinued. The only expansion of research that is allowable during this time is research related to the COVID-19 virus.

Examples of essential operations for projects unrelated to COVID-19 include (but are not limited to): 1) maintaining liquid nitrogen levels in storage tanks, 2) maintaining ongoing animal experiments where stopping the experiment would compromise the project, 3) feeding and caring for animals, 4) maintaining critical cell cultures, and 5) processing specimens for those clinical trials that will remain open during this period.

So I’m supposed to continue all research? If I go in to throw flies at spiders, I can’t even spend an hour or two on the microscope? I really work solo most of the school year, and have a few students — if I’m lucky — in the summer.

So right now I have no family, no students, I have to do all my teaching through a computer screen, and everything is frozen outside so I can’t go spider hunting, and now they tell me I can’t even work alone in my lab? I’m just to be trapped inside my big empty house with an evil cat all day, every day? I might snap. Mary will eventually come home to a gibbering madman. Well, more gibbering and more mad than usual.

Hmm. I could bring the spider cages home, and an incubator, and at least my dissecting scope. Then Mary could come home to less gibbering, but a house full of spiders and lab gear instead.

Sacrifices. We all must make sacrifices.

Aww, heck. If Idris Elba has been diagnosed and is staying home, I have to buck up and hang on here, too.

I haven’t been tested, and can’t be — we still have too few testing kits.

On the other hand, does Idris Elba have a colony of spiders he has to take care of? I think not.

In other dismal news…

I just learned in their newsletter that the American Arachnology Society meetings are cancelled this year. Aw, darn — I was looking forward to that. The thing is, too, that they were scheduled to take place in early July, at UC Davis, so this is right now the most proactive cancellation I’ve encountered yet. Meanwhile, my university is pretending we’ll be back in business in 2½ weeks, which is rather absurdly optimistic. The other con I regularly attend in the summer is Convergence, around the end of August. There aren’t any whispers about cancelling that, at least not yet.

The AAS newsletter also has a nice article on teaching kids to be comfortable with spiders, so that’s a plus.

I think I’ll be spending the whole summer right here in Stevens County.

No plan survives contact with the enemy (or students)

When I first heard that we were going to switch to online classes, my first thought was that this will be a lot of work, but it’ll be easy, mindless work: I’ll just lift everything I do in class and plop it down on the intertubes, and I’ll send stuff home with the students so they can do their lab work there. Straightforward. A nuisance, but no, I don’t need to change my approach at all.

That lasted about 24 hours, and then I took the radical step of talking to my students. First casualty: nope, no way am I going to raise flies in my house.

Then I learned that some of my students get online routinely…but through their phone or campus computer labs. I’m sitting here in my home office with two big monitors and a fast internet connection, they might be only getting online intermittently and peering at it through a tiny screen. Whoops, no big productions of my hour-long lectures. No required online sessions.

So, today, I rethink and refocus. I’m going back to the syllabus and figuring out exactly what concepts I have to get across to the students to prepare them for the next course in the curriculum (for introductory biology) or grad school/professional life/existence as an informed citizen (for genetics). I have to deliver those concepts to the student who has minimal internet access.

That means — oh no — I have to rely much, much more on the textbook. I have to be the guide, rather than the source, of the information. I can’t expect the students to absorb knowledge on a schedule, but instead, have to point them to information and tell them what my expectations are, and give them the freedom to meet them on a flexible schedule.

It’s a lot of compromises and not entirely satisfactory, and I look forward to someday returning to the normal world where students and I actually see and interact with each other in person. Until then, though, I have to make sure the goals of my courses are reached, somehow.

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.

This is my life for a while, isn’t it?

I just got out of class, which was part explaining science, and part negotiating how we’re going to continue from here to the end of the semester. The students had questions, I have questions, and we have relatively few answers.

Next up, I’m coordinating a biology faculty meeting which may get eaten up with addressing the multiple questions we’re going to have about how to suddenly switch to teaching online. We’ll have questions, I hope we have some answers.

Then I’m teaching a lab, which will be very short, because I’m just going to abort the experiment we were about to start and tell them we’re going to switch to me doing online demos and getting results, which they’ll have to analyze and interpret.

Finally, I’m just going to lie down. I didn’t get much sleep last night, trying to figure out how I’m going to have to revamp everything in both my classes. I expect I’ll be spending spring break trying to cope with this headache.

“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.