Another perk for my Patreon patrons

For patrons only, I’m going to post the YouTube videos I’m doing for my courses during this period of isolation. Note that these are rough, I’m not doing any fancy editing at all, and abbreviated. I’m aiming too keep them under 15 minutes, and then they are supplemented by discussion sessions on Zoom…and by the textbook, of course.

I have to whip out a couple of these every week so when I say rough, I mean rough — they’re just recordings of Keynote presentations. Normally I’d hope to be interacting with students and handling questions and throwing out problems to solve, and these 10-15 minute summaries would expand out to an hour, but we gotta do what we gotta do during this pandemic.

I may have made a small mistake

In my struggle to get my classes back on track as quickly as possible after spring break, I wanted to get everyone thinking and focused again, so…

  • In my intro class, I assigned a set of homework problems, due on 30 March.
  • In my intro class, I gave a take-home exam on Friday, due on 30 March.
  • In my genetics class, I assigned a set of homework problems, due on 30 March.
  • In my genetics class, I gave a take-home exam on Friday, due on 30 March.

They were supposed to send them to me by email.

Today, you may notice, is 30 March.

I opened my inbox this morning, and recoiled in horror. So many of my students were industrious and on the ball and possibly bored out of their minds, so they got everything done early. There are others who are still working on them, so I expect even more to trickle in during the course of the day.

The next exams are staggered a bit, at least, but I should have done that this time. The shock of the sudden isolation event just put everything in sync.

All plans fail

But usually not this spectacularly. I’m teaching two courses this term, and had to throw out the syllabus and juggle everything around, so I’m going to be feeding them lectures on YouTube, adjusting the grading, etc., and have just now finished posting summaries to the students online.

Fundamentals of Genetics, Evolution, and Development:


Those two videos lay out pretty much the same thing. The major difference is that genetics has a lab, and no, you can’t come in and do experiments. Even I have been told I can’t! So instead, I’m pulling up old data from previous years, and I’m presenting that to them as an exercise in analysis and summarizing an experiment.

This is no fun, but at least I’m getting a grip on how to carry on.

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.

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.

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.

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.

It’s going to be a long semester

Tuesdays I have a morning class and an afternoon lab; sandwiched in between was a discipline meeting. I think I’m plum wore out today.

Just to make it more awful, the first genetics assignment is due tomorrow, and I made an awful hash of it, trying to juggle multiple textbook editions, so the students are all confused. So I made an announcement that the assignment is basically cancelled, ignore everything I said, and I’ll come in tomorrow with a whole new problem set that we’ll work on together. What a mess. I’m exhausted just thinking of sorting it all out.

Dramatic wars begin with a grievous setback that makes everyone desperate to fight back, right?

I isolated myself in a coffee shop, buckled down, and pounded straight through my grading. I got it done! Early even! The students…well, umm, there were some rough spots. The mean was about 65%, brought down by one specific page where they had to do some math, and it was a massacre. I was imagining that page soaked in blood, with more pouring out of my wicked pen, and was getting a little uneasy. I know what we’re going to be going over in the next class!

Now, though, I get to go home, where my wife has some chore involving the picket fence I’m supposed to do, but once that’s over, I’ve got to honor the completion of one onerous task (if not the outcome).

I’m thinking I’ll sit back and read the new Joe Abercrombie, A Little Hatred. It seems appropriate, very grim-dark, with lots of close-fought bloody battles. For that 65%, you know, which is barely passing and means half the class is getting Ds or worse so far.

(The title does not reflect my feelings towards the students, who are my brave compatriots in the struggle to master cell biology.)

Chemistry and triangulosa

Work is heating up as it always does in the first few weeks of classes. Today and Friday I’m blitzing through a basic chemistry review in cell biology, because…biology is all chemistry. A very narrow and specific domain of chemistry, sure, but if you don’t understand how electrons flow you’re getting nowhere in cell biology. Yesterday was spent re-reading a lot of introductory chemistry stuff to remind me of how this all works, today I lay it all out for the students, who might be bored, but still a bunch of them will mess up on the easy chemistry questions in the first exam.

It always shocks incoming students who think biology is all frog dissections and memorizing organs. Nope, all chemistry, and in order to get the chemistry, you need to know the math. So all you high school kids thinking it would be neat to major in biology and play with spiders, buckle down and learn your basic algebra and pre-calc, at the least, and work through chemistry and physics.

Then I have some lab stuff to do. Today I’m going to focus on our Steatoda triangulosa. We’ve got a few young second generation juveniles coming up that I need to sort into larger quarters, and another egg sac that is full of baby spiders. The cool thing about S. triangulosa, besides the pretty pigment patterns, is that their egg sacs are fluffy, loosely woven silk and are semi-transparent, so you can see the eggs right through them, and right now I peek in and it’s a mass of writhing spider legs, so they’re about to emerge, I’m sure. The less cool thing about them is that they seem to be slower to develop, and for at least the one mama I’ve got in the lab, lay a smaller number of eggs. I might have to go hunt down some more adults so I have a larger sample before the frost hits.

Anyway, I’ll take pictures! I think I’ll post a purely S. triangulosa article later today.

But first, chemistry! That’s my day sorted.