Chromosomes!

I can see my future now, for at least the next four months. I have committed myself to record all of my lectures so the students have asynchronous access to the course content to maximize flexibility in case pandemic catastrophe strikes, so what I’ve got to do is:

  • Every Monday and Wednesday, record my in-class lecture, then edit it and splice in the Keynote images I use. That means I put in my regular workday, and then when I get home that evening I get to play with Final Cut Pro. Two of those a week means I won’t be doing anything fancy, just dubbing the slides and uploading it.
  • Every weekend, I put together a video to describe the lab experiment for the week. The last one might be the longest of the bunch at about a half hour, once the students get into the routine it may not be too bad.
  • Every week I also assemble a clutch of problems for the students to solve. Those go on Canvas, our course management system.

There are always glitches. Last week, the audio recording of the lecture was unlistenable, so I had to re-record the whole thing. That was better (but far from perfect) today. Today, though, the in-class technology threw up a whole bunch of problems — nothing worked until I called in IT to fix it, so I lost over 10 minutes to annoying problems. I intensely dislike the way the university has configured the AV in our classrooms.

So anyway, here’s today’s lecture. It’s about chromosomes.

Genetics #1

Hooray for me! I got step #4 of my to-do list, and also step #3.

Tomorrow I’ll go back and get #2 (“Record a video summary of the fly culturing procedure”) done, and also #6 (“edit the fly culture video”), and then on to chromosomes, mitosis, and meiosis. I’m trying hard to build up slowly with a solid foundation before we get to the hard stuff.

The end is nigh! (not really)

There is a giant space rock hurtling towards Earth! It is predicted to miss, and usually I’d trust the math and physics, but given the Bayesian priors of our experiences the last few years, I would not be surprised if they forgot to carry the 3.

Anyway, the Virtual Telescope Project will be showing it live, in about an hour. You might want to watch it, just in case.

Unfortunately, the stupid asteroid scheduled its closest approach for when I’ll be in class. I guess I’ll have to watch it after the fact, I hope.

The Mystery of Silkhenge

If you have no idea what Silkhenge is, here’s a video:

It’s a curious ring of spider silk, with silk fenceposts, and then in the center, an egg sac with a silk spike coming off the top. It’s just weird, especially since it’s such an elaborate structure to house only a handful of spider eggs. It’s a lot of effort for a small reward. All we know is what the babies look like, no adults, and no observations of how it is constructed. Clearly, More Research is Needed.

The same people went back a few years later and found more examples, still no adults.

They’ve also been seen in Peru.

Do I need an excuse to visit Ecuador again? Will this do? (All exotic travel is pending the resolution of the pandemic, of course.)

What good is a lab without water?

That is my sad face. I went into the lab yesterday to get a bunch of things done, when I learned that the water to the whole building was shut off. Our science building is only about 20 years, but every year we have a battery of problems that shake out — rooms are too hot or too cold, the roof leaks, and come the winter, we often get pipes freezing and all the problems that causes. So no water for three days while the maintenance crew fixes everything.

This would have been catastrophic when I was working with fish, and it’s still awkward when working with spiders. On my list was the need to set up more flies so they’d have food in two weeks, washing spider poop out of their containers, and most tragic of all, I had set hundreds of vials soaking in soapy water the day before, and I was going to scrub ’em up and rinse them out and dry them yesterday.

Look! I even got a brand new bottle brush! I was so excited to be doing dishes, and then…crashing disappointment. I’ll have to wait until Thursday.

Sense/Anti-sense

First, I must remind everyone that billionaire Rupert Murdoch elbowed his way to the front of the queue to get the vaccine as soon as it was announced, and that all those blithering conservative on-air personalities on Fox News are required to be vaccinated, just to put this story on Fox News’ promotion of quacks in perspective. It lists ten of the COVID denialist and anti-vax and tepid apologists for inaction who have been featured on the network many hundreds of times. Names you should learn to recognize and scorn: Marc Siegel, Martin Makary, Nicole Saphier, Rand Paul, Brett Giroir, Janette Nesheiwat, Jayanta Bhattacharya, Harvey Risch, Scott Atlas, and Peter McCullough. They all have the title of “Dr”, but you should know that the majority of doctors disagree with these scam artists; Fox News has been carefully distilling the population of MDs to purify and isolate the most untrustworthy scum to selectively display on popular programs by even more reprehensible filth like Carlson and Ingraham and Kudlow. You don’t get a prime time opinion/bloviation slot on Fox if you hold a reasonable view of the science.

Contrast that with this genuinely excellent interview with Jonathan Eisen, a biologist at UC Davis. Eisen simply and plainly says what every biologist and informed citizen knows about SARS-CoV-2.

The Omicron variant is way more infectious [than Delta]. It’s horribly contagious. Even people who are boosted are still getting infected. [The vaccine] does not seem to provide a huge protection against getting infected. I think that’s part of why it’s spreading so fast—people who have been vaccinated and/or boosted have mistakenly thought they were not going to get infected, and so they were going maskless everywhere. But if you have five times as many people infected, that’s going to create havoc, and that’s what is happening in New York and the Northeast, where the hospitals are full. They’re already sending people away who have any other types of emergency or nonemergency health needs. I think we’re in for some tough times; that’s my prediction.

Exactly. This is what I’m expecting, too. It’s also what everyone who isn’t brainwashed by Fox News can figure out. So what should we do?

All the evidence right now shows that vaccines are incredibly effective in reducing the risk of severe illness and death from Covid. And this is true even for new variants such as Delta and Omicron, even though the vaccines were not specifically designed for them. One can reduce the risk of severe illness even more by getting a booster shot. This reduction in risk is very, very clear from all the data. The one issue with Omicron that is different than with other variants is that just getting the regular vaccine dose (e.g., two Pfizer shots) does not reduce the risk of severe illness as much as it did for other variants. In other words, to reduce the risk of severe illness or death, it seems that a booster is very important here.

This is what infuriates me. Everyone wants the quick fix, the easy treatment, the simplest, most painless way to prevent this disease, and science provides one: the vaccine. Go in to the clinic or pharmacy, poke, you’re done, death averted. And what happens? People who listen to Fox News whine, “I want an insta-fix, but not that one.” They’d rather dose themselves with hydroxychloroquine or ivermectin or bleach or betadine, treatments that don’t work, than take the medicine proven to work.

In a world with people who refuse the treatment that works, and other people who can’t, for other medical reasons, get the vaccine, what can we do to protect ourselves. That’s also easy. Wear a mask in public.

What I’m hoping is that people do a lot of behavioral intervention that can slow down the spread of the Omicron variant. It goes back to the whole “flattening the curve” thing from before, and there are many things we can do. If you’re in crowded indoor spaces, you can avoid doing things where you have to take off your mask—so, no eating. But even with your mask on, not all masks are created equal. There’s new guidance that has come out in the last few days that cloth masks just aren’t going to cut it against Omicron. They just do not, on their own, filter enough particles out to reduce your exposure when airspace is getting filled with virus. What you want is a KN95 or N95 mask.

Yes. Masks aren’t the imposition the whiny-ass-titty-babies of conservatism pretend they are. When I’m teaching, I wear them continuously all day long with no difficulty, other than that I’m generally soft-voiced and muffling me doesn’t help (I’m working on it by TALKING LOUDER with my teaching voice). I tried to order some N95 masks in time for spring classes, but right now they’re backlogged and horribly expensive, so I settled for N94…still expensive with slow delivery — I think they’re all coming from South Korea — but I’ll double-up with a cloth mask until N95s become more available, I hope. If they do.

Eisen mentions also that he avoids big indoor events, even restaurants, and won’t fly, although he thinks if everyone on the plane takes reasonable precautions it’s probably safe. It’s just that too many people have been infected with the Fox brain-rot. Just glance at YouTube fights over masks on airplanes — people are getting into brawls in the aisles because they refuse to wear a mask. It’s nuts.

I avoid going out because I live in a county where practically no one wears a mask, ever. Even when our governor imposed a mask mandate, briefly, a lot of people ignored it, and our local business wouldn’t enforce it — and even then, half the population was incapable of figuring out that the mask covers your mouth and nose. It was good news when my university reluctantly decided to require masks and vaccines for all of our incoming students, but we’re a tiny island of common sense in an ocean of conservative denialists of basic medical facts.

We also need to worry about the long-term consequences of infection. Idiots like those talking heads on Fox News want to pretend it’s just a kind of flu, you get over it and carry on, but COVID has complications you ignore at your own peril.

That is one of my biggest concerns with this attitude of not worrying about Omicron too much because it might cause less severe symptoms. We know that long Covid is a problem for the other variants. It’s a big problem that is poorly understood medically, but is very clearly a real thing. These are real medical problems that people are having for months to now years after infection. Some people are saying everybody is going to eventually get Omicron, and that’s just the wrong attitude. We can make it so that not everybody gets it, and therefore reduce the risk of long Covid in too many people. We can’t just let it spread to everyone on the globe, because that’s going to be a medical catastrophe. Now is not the time to do nothing and hope for the best. It is the time to take measures while at the same time trying not to damage people’s lifestyles and lives and the economy.

Eisen’s is the kind of sensible voice we ought to have been hearing all along in our news media, providing accurate, honest information. I guess Rupert Murdoch knows that that doesn’t sell, unfortunately. And that’s why we’re screwed right now.

My new vicarious pleasure

I have discovered a subreddit called Abandoned Porn. This is very much my kind of porn : photos of old, crumbling, abandoned buildings. Very romantic. So tempting. I made a kind of Homer gurgle when I stumbled across it.

Imagine the spiders in there! I want to go exploring…this summer, I hope. I have to get over this annoying tendinitis (I can walk without pain now, I’m just at the stage of having to be very careful not to worsen anything), and then start casing a few joints in the region. Then, new spider survey! In empty buildings where a pandemic can’t bring everything to a screeching halt! I’m going to have to put this in my to-do list:

  • Get strong.

  • Wait for the snow to melt.

  • Rummage through the wreckage of ancient days.

I’ve got a couple of hardhats with helmet lights, and a collection of bright portable LED lights. I should probably get some nice steel-toed boots with good ankle support.

I should also stake out some sites that aren’t abandoned ruins for comparison.

Behold my mountain of digital papers!

All the final exams have been turned in, so now it’s time to sit my butt down and read them all. I’ve got two classes with about 25 students each, so here’s what I am to complete this weekend. These were all due on Friday, yesterday.

Comprehensive Final Exam for Fundamentals of Genetics, Evolution, and Development. This is the monster, 7 pages of questions in different formats that cover the topics in the title of the course and also a bit of the history and philosophy of science. FunGenEvoDevo is a first year overview course that doesn’t dig too deeply, but prepares them with the general background (there is also another intro course, Evolution of Biodiversity, that hits them with evolution again and also basics of ecology and systematics). I started on this one yesterday, and am a bit more than halfway through; I plan to finish it by this afternoon.

Lab Final for Cell Biology. Another longish exam, this one emphasizes basic quantitative skills they should have learned in the lab. So lots of questions about unit conversions, calculating concentrations, interpreting data, etc. For instance, they get some measurements of reaction rates, and they then have to calculate enzymatic Km and Vmax. There are a lot of parts to this one, too, but most of the answers are short, specific, and numeric, which are relatively easy to grade.

Required Final Essay for Cell Biology. Oh boy, this will be challenging. I gave them a paper to read (“How energy flow shapes cell evolution” by Nick Lane) and asked them to summarize it and relate it all to the content of the course. On this one, I demand high writing standards and coherence in addressing the subject, so we’ll see how that goes.

Optional Final Exam for Cell Biology. Another big ol’ comprehensive exam, but this one is optional for the students: whatever score they get on the final will replace their lowest midterm score. Everyone has a bad day, so this is their opportunity to vindicate themselves. It’s a long exam, but grading it might not be too bad — only about a third of the class has opted to do it.

So that’s my weekend! This is all I’m doing for a few days. I hope to get it all done by Sunday evening and get all those grades submitted to the registrar early.

Then on Monday I have one more class to grade, Biological Communications II, in which students spend the semester writing a 10+ page review paper under my tutelage, so I already have a good idea of what they’ve done — I just have to go over what is supposed to be the final polished draft of the paper. And then I’m ALL DONE!

I guess I better buckle down and get to work now.

10:45 Saturday: FunGenEvoDevo done! Grades submitted! Students mostly did OK, but a few of them may have learned that skipping an exam or two is a good way to fail a course.

3:45 Saturday: Lab final done! Starting on the required final essay.

1pm Sunday: Required lab final done! Now to polish off the optional final.