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.

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.

Can we not pick the “safe” one who always seems to lose?

I pretty much agree with everything this guy says, except for the clumsy Batman analogy, but I fear it might be too late. I don’t have much hope that today’s primaries will change the trajectory of the electorate towards the moderate centrist. Ick.

But sure, vote for whoever wins the nomination. You know, the Democrats had a low bar to hurdle this time around, it’s rather depressing that they picked the guy that barely clears it.

Quick, email me some energy

I have to go teach in 15 minutes, and I’m barely conscious. I’m chugging coffee, but it isn’t doing the trick, and I’m afraid I might fall asleep in my own lecture. I have a seminar after that, a lab this afternoon, and another seminar at 5, and it’s going to be tough getting through this day.

I hate Tuesdays. They’re worse than Mondays.

OK, I made it through the first class of the day — the magical lightning bolts from hither and yon helped a lot. Sorry, trolls, I know you think you’re zapping me with hatred, but it’s all fuel for the machine. I managed to do a lightning-quick summary of both mitosis and meiosis for the first year students — next I’ve got to give them a bunch of homework to make sure it sticks.

I have a short break before the senior seminar on NKX-2.5, homeobox proteins involved in cardiac devalopment always keep me awake. Before that, though, it’s time to tend to my spiders for a bit.

I made it through the whole day! Fortunately, the student seminars were both very good, and the lab was painless. I still need a nap.

A golden opportunity for quacks

The threat of a pandemic creates so many ways for parasites to prosper. Take Stefanie Kelley Haines, of Eastern Oregon, who is, surprisingly, the director of clinical services for Harney District Hospital.

Stefanie Haines is director of clinical services for Harney District Hospital in Burns. Like many rural health care workers, she plays more than one role in the region’s isolated health care system. Haines owns the only fitness center in a town, which isn’t just a gym. It’s also an affiliate of The Wellness Way, a chiropractic company selling pricey lab tests to diagnose all kinds of ailments. The program also markets treatment plans like the “vaccine detox.”

On her personal Facebook page, Haines advances conspiracy theories about the debunked dangers of vaccinations, while promoting services available through the fitness center. Through memes, articles and her own words, Haines has vilified immunizations that protect millions of people from communicable diseases like measles, influenza and polio.

Before people in the U.S. started dying from the new COVID-19 disease, for which there is no vaccine, Haines told friends and followers, “the flu shot increases susceptibility to Coronavirus.”

Don’t worry about Ms Haines, though. The hospital is distancing itself from her views, but isn’t doing anything about their employee spreading misinformation.

Great. There is always a line of frauds ready to take advantage of people’s fears.

A simple genetics problem I could never put on an exam

My genetics students are learning a bit about sex linkage and modes of inheritance, so I’ve got them thinking about an entirely hypothetic problem outside of class. I’ll be interested to hear their explanations, but this is the kind of problem that would drive me nuts to try and grade. Let’s see how you all do with it.

In Guardians of the Galaxy, the assassin Gamora is bright green. Her sister Nebula is blue. 


a. Invent a genetics of skin color in her species, the Zehoberei, that explains their differences in color, using an autosomal gene and modeling it after human patterns of inheritance, and use it to predict the skin color of their parents. (Note: Thanos is purple, but he’s a different species and is their adoptive father.)


b. Now assume the trait is X-linked. Does it change your prediction for their parents? What color(s) would a hypothetical brother be?


c. A new twist: in Zehobereians, females are the heterogametic sex. What does this do to your model?

The fun part is (a), which could have all kinds of possible explanations (that’s why I couldn’t put it on an exam, the range of possibilities is huge), with the one constraint being that it has to be autosomal. I want to see some dueling discussions about how it would work, brought down to earth by the need to make a prediction about the parents.

Then (b) changes the assumptions, and forces their model to change, and (c) flips it around some more. I don’t want to grade this kind of question, I just want to see how their brains logic their way around it. It should be fun. I hope.

I also had some ideas about the inheritance of color in Minecraft sheep, but decided that was just too weird. Blending inheritance + acquired characters? Heretical. Not very instructive about Earthly rules of genetics.

Of course, it may all be moot because attendance in all of my classes is declining this semester — only half the students showed up today! I don’t know if it’s pandemic fears (no diagnosed cases in Morris), the imminence of Spring Break, or that I’m just horribly boring.

Max von Sydow is dead

He’s gone. He had some impressive roles, he had some cheesy roles, but one thing he always had was presence.

One thing that always struck me about him is that he reminded me of my great grandfather: that slight accent, the pitch of his voice, and that he was tall and physically similar (I think my great grandfather was tall, but I was also very small when I knew him). I kind of hoped I’d grow old to be like Great-Grandpa Westad, or like Max von Sydow, but I think I got too many Myers genes.