How are we supposed to teach in the Plague Years?

Yesterday, I got all my grades turned in, meaning Fall semester is all done…oh, wait, I had to write a bunch of student recommendations and get those sent off. OK, that done, now the semester is behind me, I’m care-free and can go dancing in the streets, or whatever I want for a little while. So what do I do? I opened up my calendar and started planning my schedule for next semester, sketching in lab protocols and exam dates, assembling the information that’ll go into my syllabus. I had some ideas for revising the content/pedagogy of the course, and I wanted to map them out.

It was kind of pointless.

Universities elsewhere (not the University of Minnesota, which will drag its heels to the last moment) are noticing this Omicron variant, and how quickly it may potentially spread, and are scrambling to adjust their schedules, just in case. Four California universities are switching to online only instruction for the first few weeks of the spring term; the University of Washington is going online only for the first week. This is bad news. If you’ve paid any attention at all to university management for the last few years, you’d know that they are always reluctant to adjust to reality, and are never pro-active. If this is what the UW and UC are doing, the situation has to be far worse than anyone is telling.

UM is doing nothing new. Not even a whisper of concern. You’d think, given the fact that our governor and his family just tested positive for COVID-19, that maybe there’d be an alarm bell ringing faintly in some neglected corner of the administration building. For that matter, you’d think Governor Walz might wake up and realize that his lackadaisical, half-assed approach of doing the bare minimum to contain the pandemic wasn’t working, but I don’t expect that to happen, either.

I realized then that next term might be more challenging than I expected, especially since I’m now required to teach all of my classes in-person. Brilliant. Maybe that will change, but I think the faculty and students are now sacrificial lambs laid out on the altar of an optimistic sense of normalcy. It’s all on the shoulders of the faculty to figure out how to flexibly cope with the changing situation.

I made a decision as I was drafting my syllabus. I am required by my employers to be there in Sci 1020, the genetics classroom, but I don’t have to demand that students be there. I’m making attendance optional. I’ll record all my lectures and post them online. Exams will all be take-home. I’ll hold office hours on campus (you better be vaccinated & wearing a mask if you show up in person) and held simultaneously on Zoom.

The lab is a problem. Actually doing the data collection and analysis of independently acquired data is kind of the core purpose of doing a lab, and it’s going to require using on-campus facilities. I have a plan for that, too. The first week of lab will be online: it’s all preparation in basic probability and statistics to get ready for the actual work, and I have exercises in coin-flipping and die-rolling they can do at home. That one is manageable.

Subsequent labs are all about working with flies, and most people would rather not breed thousands of fruit flies in their kitchen. Once again, I am required to teach in-person, so I’ll go in, record myself doing the procedures and showing the students who show up how to do them, and make that available online. Then I’m throwing the lab schedule out the window: the genetics lab will be open from 9am onwards, students will come in when they’ve got available time to do the work on our incubators and microscopes, and I’ll be on call to help out from 9-whenever. That should help spread out attendance. If the university shuts down (I hope the severity of the pandemic isn’t so great that that is necessary), I’ll do the experiments alone, supplemented with class data from previous years, so the students will at least have numbers and phenotypic data to analyze.

It’s going to be a lot of extra work, but I’ll do it. The university administration better be prepared, too: so help me Dog if any of my students die of COVID-19 because of the mandated university environment, I’ll be preparing my letter of resignation and will take my retirement right now, thank you very much. I am so damn tired of irresponsible, incompetent responses to the pandemic, not just from my university, but from every level of government.


  1. planter says

    I hear you on the burnout. I took a 6 month sabbatical covering the fall term so I would not have to teach my 120 seat intro ecology course online. I figured I would be safe to deliver my 15 seat advanced course in the winter term – this course is a joy to teach in person but just does not work well online – but who knows now. At least our admin here closed the “get tested weekly” loophole in our vaccine mandate; as of Jan 4th you have to be two-dose vaccinated to set foot on campus.

    To put the cherry on the cake, a planned Christmas trip to BC so my elderly parents can see their grandkids is now off, because the kids have only gotten their first dose.

    Amid the burnout, I am reminded occasionally why I (normally) rather like my job. I had a rare trip into the office to meet in person with a MSc. student and post-doc who have been working on some rather interesting data. After a great discussion they disappeared; an hour later I ran into the grad student in the hall excited to show me some new results. Glimmers of hope that life will continue post-plague.

  2. raven says

    I’ll put this here as a PSA.
    For vaccines available in the UK, effectiveness against symptomatic Omicron infection ranged from 0% to 20% after two doses, and from 55% to 80% following a booster dose.
    The current 2 dose vaccines don’t work very well against Omicron. 0%? They can’t easily work less than 0%.
    The good news is that the booster doses work well. 55% to 80%.

    Get your booster shots ASAP and be careful until you do and until they start working, say 2 weeks.

    We also now know that it is more transmissable than Delta and a serious partial immune escape variant.
    The pathogenicity is still unknown.
    Some studies say it is equal to Delta, some say milder.

    Dec 20 (Reuters) – The following is a summary of some recent studies on COVID-19. They include research that warrants further study to corroborate the findings and that has yet to be certified by peer review.

    Omicron infections no less severe based on early UK data.
    Infections caused by the Omicron variant of the coronavirus do not appear to be less severe than infections from Delta, according to early data from the UK.

    Researchers at Imperial College London compared 11,329 people with confirmed or likely Omicron infections with nearly 200,000 people infected with other variants. So far, according to a report issued ahead of peer review and updated on Monday, they see “no evidence of Omicron having lower severity than Delta, judged by either the proportion of people testing positive who report symptoms, or by the proportion of cases seeking hospital care after infection.”

    For vaccines available in the UK, effectiveness against symptomatic Omicron infection ranged from 0% to 20% after two doses, and from 55% to 80% following a booster dose.

  3. raven says

    Omicron is projected to have entirely taken over the USA by the end of the month, which is 8 days away. It’s spread as fast in 3 weeks as Delta did in 3 months.
    The estimates are that it is twice as transmissable as Delta, which was already one of the most transmissable viruses we know of.
    In a lot of the USA, the health care systems are already way overloaded with antivaxxed Covid-19 virus patients and the quality of care has gone way down. In several places, they’ve already called out the army and National Guard to help.

    It is going to be a long, dark winter.

    Omicron is now the dominant strain of coronavirus in the US, according to the CDC
    By Travis Caldwell and Claire Colbert, CNN Updated 4:59 AM ET, Tue December 21, 2021

    (CNN)The Omicron Covid-19 variant is now the most dominant strain in the US, accounting for over 73% of new coronavirus cases less than three weeks after the first was reported, according to estimates posted Monday by the US Centers for Disease Control and Prevention.

    It’s been just 20 days since the US detected its first case of Omicron.
    For the week ending December 18, Omicron accounted for 73.2% of cases, with Delta making up an additional 26.6%. The week prior, ending December 11, Omicron was estimated at just 12.6% of circulating virus, and in the first week of December, Omicron accounted for about 1% of new cases.
    Omicron is even more prevalent in certain parts of the country — making up over 95% of circulating virus in parts of the Northwest and Southeast, the data shows.

  4. Erp says

    Stanford University will also do the first couple of weeks online (announced Dec 16, school restarts Jan. 3). Students will be required to document a booster shot by Jan 31 (barring exemption or not yet eligible). Testing will continue to be weekly (twice weekly for those with exemptions) and two tests for those in the first week for those who have left the area and arrive back.

  5. chuckj says

    Professor in the State University System of Florida here. Our governor has been very busy banning mask mandates and mandatory vaccinations, and we’re due back in class Jan 6, in person. Moreover, our provost has informed us that if we (the faculty member) tests positive, we cannot switch to online instruction; instead, we must take sick leave and arrange for another professor to cover our classes in person. It sounds like they are really going out of their way to make sure this this gets very bad very quickly. Like “planter” above, i love my job and want to get back to working closely with my graduate students, but its getting harder and harder to deal with the stupidity…

  6. says

    You remind me that it could be worse. I could be working in Florida rather than Minnesota…which is an odd thing to say in December.

  7. hemidactylus says

    @5 raven
    Your assessment seems off:
    “For vaccines available in the UK, effectiveness against symptomatic Omicron infection ranged from 0% to 20% after two doses, and from 55% to 80% following a booster dose.

    The current 2 dose vaccines don’t work very well against Omicron. 0%? They can’t easily work less than 0%.
    The good news is that the booster doses work well. 55% to 80%.”

    0% effectiveness is against any symptoms? You might be setting too high a bar, especially in the long term. Mild symptoms could still mean immune memory from previous vaccination will quickly kick in as B cells (perhaps undergoing mutations against Omicron) proliferate and produce antibodies, remaining pre-exposure antibodies perform non-neutralizing functions, and T-cells (which parse knowledge of antigens differently) help B cells undergo affinity maturation toward Omicron or tell infected cells to commit seppuku [helper versus killer Ts].

    Sure being boosted is preferable, but something of a immune response may make non-boosted people better off than the unvaxxed. I was boosted almost two months ago so wonder when my window of protective antibodies will start closing…yet hope remains. The spike antigen experienced immunocytes are still going to be there to some degree.

    I had B&T immunocytes geared against SARS-CoV-2 well before the pandemic, just not many. They resulted from a process of gene shuffling specific to immunocyte development. After vaccination they proliferated and the B cells underwent mutation and selection to better match the ancestral Wuhan spike look and maybe have some play in their breadth if not overly inbred to the vaccine antigens.

    At some point this coronavirus is going to have a normalized presence as we develop broader immunity based on more specific vaccinations per variant and get exposed to the virus and develop immunity that way. Not sure where the fatality rate will wind up though. Hopefully way down.

  8. birgerjohansson says

    Raven @ 6
    One reason this variant spreads faster may be the succession of symptoms.
    Earlier variants generally started with fever, then coughing.
    For omricon, coughing is usually first. So you start with the symptom that is guaranteed to infect people nearby.
    They have identified the gene that changed but I forgot the designation.

  9. birgerjohansson says

    Anticipated new rule for Florida and Texas. True patriots will cough their friends in the face. Only wimps cover jo the mouth. Feel free to drink bleach.

  10. birgerjohansson says

    You need nurses with a lot of extra training to handle patients that need ventilators. The anti-vaxxers will overload the capacity of the staff, no matter how many ventilators the factories churn out.