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.

First day back, and I survived!

I got through the first lecture, and even had an easy time prompting students to speak up and ask questions, so I’m doing OK so far. Also, I gave them my background and told them I work on spiders, and nobody passed out…in fact, after class they asked to see the colony, and about half the class was crammed into my lab. That’s a good sign, that they’re not all arachnophobes (it’s OK if they are). I also plugged all the other research going on here, in case they weren’t aware of the opportunities.

So now I get to go home and celebrate with a nice dinner. Involving tomatoes. We have so many tomatoes, and I have to cook down another batch tonight. We’ve got marinara sauce dribbling out of our ears, we had fried tomatoes yesterday, I’m going to have to come up with a lot of different ways to make tomatoes delicious. I think Mary needs to plant slightly fewer tomatoes next year. That has nothing to do with my class, it’s just that I’m drowning in tomatoes.

She also planted zucchini. I’m doomed.

I’m skipping class for a few days…what will my poor students do?

I’m flying away to give a talk on Moscow, Idaho this week, and early next week I’m going to be a consultant on an NSF grant awarded to the Science Museum of Minnesota, so I’m missing a few class days soon. Oh, the wailings and lamentations of my students! They howled with grief at missing out on my sparkling presence for any length of time! Or I might have imagined that, but it was pretty vivid.

Fortunately, I found a babysitter. I’m having them attend the 2017 Evolution conference in Portland last June. That’s something technology lets you do nowadays — the Society for the Study of Evolution recorded all the session talks and uploaded them to YouTube, so you can attend, too, sans the hallway schmoozing and the arguments at the bar (we can only hope technology progresses to that point someday). I’m telling them to watch with a critical eye and report back when I get home about which of the subset of talks they enjoyed, and why, and to summarize the questions that were asked and methods that were used.

I remember getting the opportunity to attend Western Nerve Net and Friday Harbor Development meetings when I was a senior in college, and they impressed me greatly…but I was just lucky, getting to tag along with advisors at these events. We couldn’t bring along a whole class to a 3-day meeting back then, but now I can do it virtually, which is pretty cool.

Done but for all the grading

Scattered throughout this semester, I’ve been discussing my EcoDevo course, Biol 4182, Ecological Development. It’s done now, so I’m just going to make note of a few things that I’d do differently next time around.

  • Fix the squishiness. I envisioned this as more like a graduate level course — a 15 week conversation on ecological development, with a textbook that kept us centered. Assessment was largely subjective, based on students demonstrating their understanding in discussion. I had an oral exam, for instance, where we just talked one on one. I think that went well, but in the end, I’ve only got a few specific metrics to use to assign a grade, and much of it will be built around how well they engaged with the material.

    I don’t mind that, but students are a bit bewildered by the absence of hard grades throughout the term. I’ll have to incorporate more detailed assignments next time around, something where they go home with a number that they can work on improving, artificial as all that is.

  • Personally, I greatly enjoyed the student presentations, and I want to do more to have students bring their interests to the course. I might include a student poster session next time — a different medium, and if in a public place, bringing in new perspectives.

    The oral exam was also valuable in getting to know where their interests were. I think I’d schedule it earlier in the term, when I do it again.

  • No way will I ever offer this course at 8am again. It was stuff that required interaction and attentiveness, and somedays it was tough to wake everyone up. These were really smart students, too, so the fault isn’t in them, but in timing.

    Maybe I’d do it at 8am if the college provided a big pot of coffee with donuts every day for the students in compensation. Hah, right.

  • One of the most dramatic effects on student participation was making it mandatory that they ask at least one question a day. Late in the course I added that requirement, and it worked surprisingly well — I could tell they were paying attention to try and find something to pursue further. They also asked good questions, so it wasn’t just pro forma noise. I’ll do that from day one in the future.

    It would be nice if that provided one of those non-squishy metrics I need to add, but it worked too well — they all met that minimal requirement easily. Guess I’ll just have to give them all As.

  • I was bad. I got summoned to Washington DC for important grant-related meetings twice during the semester, which rather gutted two weeks out of 15. That was unavoidable, but while I managed to cover the material in my syllabus, my hope that we could go a bit further and get into the evolution and development side of the textbook was thwarted. But then I never get as deeply into the subjects of any of my courses as I’d like.

    Next time, if I have planned absences, I’ll try to bring in colleagues from ecology or environmental science to cover for me, and keep the momentum going. I was really reluctant to do that this term because…8 goddamn am. I wasn’t going to ask that of anyone.

What I really got out of the course was getting to go in twice a week, even at an ungodly hour, and getting to think about more than just basic, familiar stuff. The core courses I teach in cell biology and genetics are fine, but fairly routine — I know those subjects inside and out, and the challenge is in improving the pedagogy, not in getting exposed to new science. +1, would do again.

Also, one of the best things about small upper-level classes like this is that I can get to know the students a little better, and they reaffirm my faith in humanity because they actually are smart and thoughtful and likeable (I can say that now, I’m not sucking up, because they’ve already done the course evaluation and turned it into the office). Maybe I should just give everyone an A+, with gold stars and smiley face stickers.

Goodbye Spring Break, hello Spring

It’s officially the first day of Spring. I looked outside to see if flowers had suddenly erupted, but it’s too early and too dark to see.

It’s also the end of our Spring Break, and I have to get back to work, although it’s not as if I took it easy this last week. I’m actually prepared! This is my agenda for the week:

  • Genetics: We’ve been working through chromosomal changes, and I’ve been a little concerned about some of the students not quite understanding what’s going on, so we’re going to spend the first half of class with me leading them through some visualization exercises. I’m going to give them some word problems and have them draw the answers — it should also be a gentle warm-up to the class. Then it’s all sex and mapping for a while.

  • Genetics lab: Our mapping experiment is done, we just have to collate the results and do the calculations. Simultaneously, we’re starting a new experiment, a complementation assay.

  • Ecological Development: Endocrine disruptors! That’s always a fun way to start your week. Even more fun: an exam! An oral exam! The last half of this week and the first half of next week are going to be dedicated to meeting one-on-one with students to grill them on general concepts.

  • Biological Communications: I don’t think I’ve mentioned it before, but I’m also teaching a course in science writing — this semester it’s more of an independent study sort of thing, where they’re supposed to be putting together a substantial term paper on a subject of their choice. So far, it’s been little stuff — come up with a topic, do the preliminary research, give me short writing samples to demonstrate that you’re actually working on it — but their first full rough draft is due this week, so I’m getting stacks of papers to grade over the coming weekend.

  • We also have a guest seminar this week from an immunologist, Amy Weinmann, who is going to talk to us about epigenetics and development, which will fit in just fine with my eco-devo course.

I’m actually all planned out for the next two or three weeks. I just have to do the actual work. At least I think I know what I’m doing.

Juggling flies, fish, and students all week long

farsidevet

Time for another reflection on my mundane week of teaching. I know this is unexciting, but I’m trying to be self-aware about what I’m doing in the class.

I’ve already summarized some of what I did this week: we explored the meaning of “epigenetics”, and I made a big push to get them to think critically about the papers we’re reading. They’re supposed to be developing a topic they’ll explore independently, so I’ve had them doing library work to find a line of research they find interesting, and master the skill of extracting the key questions the work is trying to address. I’ve got a small stack of short papers that I’m going to read this weekend and we’ll see how well they can do that.

We also discussed symbiotic interactions in development, and next week the topic is other environmental effects. They are getting much, much better at opening up and talking at the miserable hour of 8am.

The other regular highlight of my week is FlyDay, when I have to scrub dead maggots and pupae out of fly bottles. I had to postpone FlyDay this week! Yesterday I was scheduled to meet with students and parents visiting the university to confirm their plans to attend, and I was all spiffed up in a nice suit, which isn’t the best thing to wear when one is flicking bits of chitin and gooey medium around. I went in early this morning to scrub bottles and get them cooking in the autoclave.

By the way, at that student meeting I was the official biology representative, and although biology is currently the largest major on campus, almost no one stopped by to talk to me. It might have been my terrifying glare, or my sciencey reek, but no: it was because there was a separate table for the pre-professional programs (pre-med, pre-vet, pre-dental, etc.). This is a minor peeve of mine: this is not 19th century England. You do not graduate from your public school education and go straight into medical school — no, here in 21st century America you get a broad-based undergraduate education first, and then you apply to med school. You should be thinking about your liberal arts education first, and in a couple of years we’ll start coaching you on how to get into those professional programs.

Oh, well. They ignore me now, but I know that I’ll get my claws on most of them soon — they’ll want all those bio classes to prep them for the MCATs.

I should mention that I am teaching another course beyond ecological development — I’m teaching a lab course on transmission genetics. They’ve been doing crosses with flies all semester long, and we’re getting to an interesting point.

The first half semester we’re doing a mapping cross, using recombination to estimate the distances between a couple of genes on the X chromosome. We’re using flies that are mutant for eye color (white, w), wing length (miniature, m), and bristle morphology (forked, f), and I’ve also got a few groups mapping body color (yellow, y), wing veins (crossveinless, cv) and forked, f; the latter are doing a pilot test to see if I want to add that cross to our regular repertoire.

The way this works is that they are given wild type and triple mutant flies. I first have them raise a new generation of the purebred stock, simply to get a little practice in sexing flies and basic skills in growing them. So they first do these crosses:

♀w– m– f–/w– m– f– x ♂w– m– f–/Y

which produces bottles full of homozygous white-eyed, miniature-winged, forked-bristled flies, and

♀w+ m+ f+/w+ m+ f+ x ♂w+ m+ f+/Y

which produces bottles full of homozygous wild type flies.

Then I have them do a reciprocal cross of flies from the two bottles. These are X-linked traits, so it matters which strain is the mother and which the father, and I want them to see that. That is, they cross wild type females to triple mutant males, like so:

♀w+ m+ f+/w+ m+ f+ x ♂w– m– f–/Y,

which produces progeny that are all wild type, both male and female (they all inherit the dominant wild type allele at all loci from their mothers). After they’ve scored the flies from this cross, we dispose of them all and don’t think any further about them.

They also cross mutant females to wild type males, like this:

♀w– m– f–/w– m– f– x ♂w+ m+ f+/Y.

That has the useful result that all the sons inherit w– m– f– from their mother and a Y chromosome from their father, so they all express the mutant phenotype. The daughters, however, are all heterozygous, inheriting the mutant alleles from their mother and a wild type chromosome from their father, so their genotype is:

♀w– m– f–/w+ m+ f+

Now the fun begins. Meiotic recombination in those flies will rearrange the +’s and -‘s in those chromosomes with a frequency dependent on their distance from one another — you’ll get less recombination between genes that are close to one another.

This week, they completed the reciprocal cross and got their heterozygous females and mutant males. Yay! That worked. They are now setting up a test cross to assess recombination frequencies.

I just want to say that I think I planned everything perfectly. That test cross will be ready to score next week, which is the week before spring break, which means we’ll have the data for all the calculations before they leave, and when they get back, I’ll be able to lead them through all the theory. It also means I’ll be able to purge a lot of fly bottles and get them scrubbed up over the break (you can tell already that I have glamorous plans for my short vacation). Trust me, though, this is good — there have been semesters where, due to student error, the flies haven’t been ready, and then my spring break is spent maintaining 120 bottles of student flies.

It also means we can launch into the next experiment as soon as they get back: we’re going to do a complementation cross between two eye color mutants, brown eye (bw) and scarlet eye (st). If I’ve got this one all timed out correctly, we’ll be getting F2 results of crosses between heterozygotes for both loci a week before the end of classes.

Now you know. I choreograph fly sex for my convenience.

Next up, I have to choreograph my schedule. It turns out I have been summoned to Howard Hughes headquarters on 8 March and 18 April, which punch big holes in my planned lessons, and which I hadn’t accounted for in my syllabi. I’m going to have to juggle lectures and exams and rearrange the order of various things in a big way this coming week.