Curse you, Reginald C. Punnett

Yesterday, I gave my first year students a teeny-tiny quiz over the current unit in basic genetics. No biggie, I’d been hearing some troubling concerns from the class tutor that some of the students were struggling, so this was more of an assessment of how well they were grasping the simplest concepts in Mendelian genetics. Here, I’ll even let you see the entirety of the quiz: 5 questions, 2 points each.

You have a true-breeding diploid organism with the phenotype AB, and a second true-breeding organism with the phenotype ab. A is dominant to a, and B is dominant to b.

  1. What are the genotypes of these two creatures?
  2. You cross these two and obtain a clutch of F1s. What are their genotypes and phenotypes?
  3. You cross two of the F1s with each other. Predict what the phenotypes and their proportions in the next generation should be, assuming that Mendel’s laws apply.
  4. You cross one of the F1s with another organism that has the phenotype ab. Predict what the phenotypes and their proportions in the next generation should be, assuming that Mendel’s laws apply.
  5. You actually do the experiment in #4, you get the following results:
    AB: 35%
    Ab: 15%
    aB: 15%
    ab: 35%
    Interpret this distribution.

See? If you were a student who’d just suffered through 3 weeks of an introduction to genetics, you’d probably have absolutely no problem with this. If you’ve been teaching genetics for a few decades, you could answer this quiz in seconds, in your sleep, while standing on your head. I think that might be part of the problem, because this is stuff I can totally take for granted.

I gave the students 20 minutes. Most of them used the entirety of that time. I scored the quiz that afternoon, and was aghast: mean score was 2.7/10, high score was 8. Yikes. How…? Where have I gone wrong? These are smart, hard-working students, and they missed everything. Then I saw the problem. The quizzes were covered with…

PUNNETT SQUARES. Jesus. They tried to solve every problem with a 4×4 Punnett square, which is insane. Punnett squares are a tool for graphically illustrating the outcome of a cross. They are not tools for calculating the results. They are a terrible, slow, clumsy tool for doing that. The textbook is full of ’em, I think because they’re easy to draw and give the illusion of a comprehensive answer. I’d shown a few in class, because I had to explain what the textbook was showing them, but I always told them that Punnett squares were terrible and useless, but this is what they knew, probably from high school, and then reinforced by the text, and then I made the mistake of trying to explain what the book figures were showing, and they came away with the impression that this is what geneticists do. It is not. Mendelian genetics are dead simple. You can just treat each locus independently (and they’re trivial, you can memorize all the possible results if you can hold 3 frequencies in your head), solve for A, solve for B, multiply to get the answer for A & B.

Christ, they’re trying to mechanically brute-force a solution with 4×4 Punnett squares, and it’s a disaster.

I can’t blame the students, though, it’s all on me. I remember being their age and taking Dr Sandler’s genetics course at the UW, and struggling for the first few weeks, until suddenly the light bulb flicked on in my head and I saw how easy Mendel was, and then when he started layering on the advanced stuff, like segregation distorters and epistatic interactions (seriously, try solving those kinds of problems with a Punnett square — you might be able to assemble some kind of nightmarish diagram, but it’s not efficient. You can’t even do linkage with a Punnett square.), it was all just an easy arithmetic modifier added on to the basic concept. But then, Sandler was a brilliant teacher, I’ve got some catching up to do.

So how to deal with this problem…next week, I’m going to rewind and go back to the basics, review these elementary problems without Punnett squares anywhere in sight, and actively tell the students that Reginald C. Punnett was of the devil, put on this Earth to confound generations of genetics students. Then, over Christmas break, I’m going to back over my stored presentations and notes and edit out every mention of the P word. Maybe I should print one out so I can put it on the floor the first day of class and piss all over it — nah, some administrator would probably complain.

Then, you out there — yeah, YOU, high school teachers and textbook publishers — stop poisoning students minds with these abominations. I’ve never liked them, but I keep using them because they are traditional, and because the books and students come with them preloaded. Just stop it. They’re pedagogically bad. I’ve got to explicitly unteach them now.

This is a tragic setback, because what my plan for the course was saying is that I start next week on the developmental biology unit, my favorite stuff, and now it’s getting bounced back two weeks, and is going to get slammed up against the end of the term. I’m going to blame Punnett.

Problem solving!

Teaching is a whole new world nowadays. I faced three different problems today.

One of our sports teams has been exposed to COVID-19, and they’ve been quarantined and can’t come to class.
Solution: I’ll be recording my lectures for a while and passing them on to the affected students. Also, we’ve been working through some genetics problems, so I’m forwarding those for them to work on in their isolation chambers.

A student had a serious family crisis and had to miss the last exam, and is panicking over it.
Solution: For them, I’ll pretend that exam never happened, and their final grade will be based on the average of four exams, rather than five, like the rest of the class. The exams are cumulative so it’s not like they won’t be evaluated on part of the class.

One of my international students has been abruptly drafted into the military service for a certain Eurasian country, and is flying away from the US prematurely.
Wooo. I wouldn’t want to be in that situation. Solution: I am arranging to email them a take-home final exam so they can get credit for the course, and I hope come back to finish up their degree.

I’m thinking now that I actually have it pretty easy. My job is to make everything as smooth and doable for the students who don’t have it so easy.

All we have to do next is end the pandemic, all other health problems, and end war, and teaching will get easier.

I’ve been in grading hell all day

But I finally finished the exam for introductory biology. There were two huge problems.

  1. Never again will I give a take-home multiple choice exam. I thought I was being generous: 16 multiple choice questions, one multi-part essay question, and I even gave them a form to fill in. Somehow, many of them didn’t follow the instructions. A form with a space to put in A, B, C, or D for the answer? Nope. Many wrote out answers. What I thought would be an easy grading exercise turned into a nightmare. If I were to do it again, I’d be extremely obvious and specific in how to answer.
  2. Scores were abysmal, but that’s on me. I didn’t spend enough time going over the problems…so now I have to backtrack and cover the material again and give them some more exercises to try out.

Now I have to collapse in a soggy heap. Tomorrow it begins again with an exam from my second course.

Well, that was challenging

Today I tried to lead my students through some simple genetics problems over Zoom. In class, it would be easy: put up the problem, have the students pull out a piece of paper and try to solve it, while I wander the classroom seeing what they were doing, offering hints and suggestions as I go, and at the end I’d have an idea of where the individuals were struggling.

On Zoom, nope.

I’d present the problem, and then…no, I have no way to observe the process. I told them they could let me know their answer over the private chat, and if it looked good, I’d call on them and they could explain how they solved it.

First difficulty: these are smart students, and they quickly figured out the flaw in my plan. If they gave the answer, I’d call on them; simple solution: sit on the answer for as long as possible. The first problem I put up produced a deadly silence, with all those black rectangles not showing anything, and my chat window being totally blank. I’d try to nudge them along, but not knowing where they were in the problem meant I had no idea where they were stuck. Or if they even were stuck.

They started to warm up as the hour went on — probably as they realized these weren’t really that hard, and they were seeing how to reach the solution — but it was still agonizing. It took us the whole hour to do 3 problems. And I’ve promised/threatened to do it again on Thursday. As it stands, they’re getting an exam next week and I’ve had little opportunity to interact with them to work through even simple problems.

Stupid virus. Let me get back into a real classroom again.

Dread teaching

I’m caught up on a lot of grading, but today I now have to explain while they got so much wrong. The mean on the last exam was 75, which isn’t bad, but a lot of students are certain they deserve an A on everything, so I have to tell them today that the grade they got was the grade they deserve, and then explain how to solve the problems correctly. Many of the errors were due to invalid assumptions. For example, some people were confused by the term “wild type” — they had it in their heads, largely from their introductory population genetics course, that wild type was simply the most common phenotype in the cross, so for instance, whatever the phenotype of the heterozygotes was in a simple hybrid cross, that was “wild type”. Yikes. So now I also have to reset my brain and stop assuming they know all the basic conventions.

Next bit of fun: we’re wrapping up a standard complementation assay in the lab, so I have to talk to them about writing up a lab report, which means that, while I’ve finished a painful backlog of grading, I’m about to tell them to create a lot more work for me.

Somehow, in all that, I also have to teach them about deletions, duplications, and translocations this week, and then next week we plunge into the happy world of recombination and gene mapping, and more math. Sometimes I wonder how I can keep going, since I’m pretty sure that by the end of the semester all of my students hate me.

The lesson for the day is…

Sex. Today I have to lecture my genetics students about sex. On Monday I explained to them how simple Mendelian inheritance isn’t the whole of genetics, that it’s much more complicated than you can possibly imagine, and now I have to explain to them that everything they know about sex is a gross oversimplification. I’m hoping everyone comes out of this course confused and uncertain, since that’s the proper state of mind for learning.

Also, I’m giving them a take-home exam. Am I the most evil college professor in the universe or what?

For further confusion, I pharyngulated myself and put up a poll on YouTube. I’ll look at it later this afternoon and heed the voice of the people.

Fly Time was a bust

That was agonizing. My students have projects ongoing, so I leave the lab open so they can get in and work with their flies. I go in early in the morning specifically to unlock it.

Someone locked it back up again after I left!

Students were backed up, trying to get in, and were frantically phoning and messaging me!

While I was trying to teach my other class!

It was agonizing: non-stop ringing and beeping while I’m trying to deliver a lecture, and it wasn’t so much that the noise bothered me, but that I couldn’t just ditch one class to help another, and so I couldn’t answer or do anything about it. I finally broke down and ran into the other room to ask my long-suffering wife to take my keys and unlock it for them. I’ve now posted prominent signs telling people not to lock it during class hours.

I guess I should be grateful for diligent staff who maintain our security, and for eager, ambitious students, but wow was that a stressful class hour.

(For that matter, this pandemic has already pushed my stress levels off the charts.)

We’re on fly time now, boys and girls

My new regime begins today, and it’s one of the awkwardnesses of teaching a fly genetics lab. Mere human schedules don’t work; I informed the students from the very beginning that we’re going to be at the mercy of the flies’ schedule, and they have a roughly 9 day generation time, which doesn’t align well with our 7 day class cycle.

So what do we do? The class becomes more of an exercise in independent study. We have the regularly scheduled lab time, which I use to explain where we should be at and what to do in the next week, and then I open up the lab early every morning so they can come in whenever they want. I’m also posting my personal cell phone number on the door so they can call me at any time to come over (it’s not at all far, fortunately) — I’ll be requesting no calls after midnight, though. So starting now, I am on Fly Time and Student Time.

Which means I have to zip over to the lab right now.

Man, it would be handy to have one of those Time Tacos.

Flies have pretty eyes

I made a quick trip to the lab this morning (it’s -25°C! I walked quickly!) to take some fly photos for this week’s genetics lab. The students are doing a simple complementation assay with fly eye colors — can you tell which one is scarlet (st) and which one is brown (bw)? Every year it’s a struggle to get them to recognize even obvious mutations like these, but it’s not the students’ fault. This is their first time working with flies, and it’s easy to get overwhelmed with the alienness of Drosophila.

Me, I’m always impressed with how beautiful their eyelashes are.

Of course, immediately after their glamorous photo shoot, these flies were sacrificed on the altar of the spider gods.

Oh joy, first exam

This week, I gave my first exam of the semester — a take-home, with ten multi-part questions requiring lots of calculations and and statistical tests, and I required that all answers by typed and in a specific format. It was due last night at midnight.

Nobody took the hint. I got 100% on-time submissions, so this morning I’m looking at a big stack of pages of numbers and formulas and explanations and hard work that I have to get evaluated this weekend.

Why didn’t you guys tell me to make it all multiple choice and true/false? I’m blaming you all. You need to come to my house and grade them for me.