Big win for the University of Minnesota Morris

My colleagues here have earned a major award from HHMI.

The University of Minnesota Morris is one of 104 colleges and universities from throughout the U.S. that will receive a six-year grant through the Howard Hughes Medical Institute’s (HHMI) Inclusive Excellence (IE3) initiative.

This grant challenges US colleges and universities to substantially and sustainably build capacity for student belonging, especially for those who have been historically excluded from the sciences. The IE3 grants total more than $60 million over six years and are a part of HHMI’s national portfolio of experiments aimed at improving the introductory undergraduate science experience.

Associate Professor of Biology Heather Waye is leading the IE3 efforts at Morris, along with colleagues Rachel Johnson, Shaina Philpot, Barry McQuarrie, and Kerri Barnstuble.

“Our goal is to find the barriers that STEM students are facing and figure out how to tackle them,” Waye said. “This is an opportunity for us to change the system, not the student, so that the benefit of the grant will last beyond the scope of the grant.”

One of the first goals is to establish a Quantitative Learning Center (QLC) on campus, a dedicated space where students can build their quantitative skills with technologies used in their STEM classes. Waye stressed that student input is a key part of planning for this. In addition to providing practical help, the QLC would help students feel supported, valued and confident in their STEM abilities.

This is excellent news! All of my classes are heavy in the quantitative skills department, so having a campus initiative to get incoming students up to speed on math and stats will make my life easier, and I’m all about the easy life.

A patchwork dodo is not a dodo

Somebody has been watching too much Jurassic Park. They should read the original novel, which was a badly written Luddite pot-boiler with a bad take on genetic technology that emphasized the horrible ways technology would inevitably go wrong (that was a tiresome theme in practically all Michael Crichton novels), while the movies just highlighted the glorious resurrection of really cool animals. I guess the latest movie has hordes of perfectly healthy, vigorous dinosaurs swarming across the American West, as if that could happen.

In yet another George Church production, his company, Colossal Biosciences, proposes to resurrect the dodo, just as he said he was going to bring back the mammoth and thylacine. He hasn’t accomplished any of it. I’ll go out on a very thick limb and say he’s never going to succeed. The procedure, using CRISPR to incrementally patch dodo genes into an extant bird species, is fundamentally flawed.

To create a dodo from such genetic information, the company plans to try to modify the bird’s closest living relative, the brightly colored Nicobar pigeon, turning it step by step into a dodo and possibly “re-wilding” the animal in its native habitat.

Colossal has not yet created any kind of animal. It’s still working on developing the necessary processes. And making a dodo might not even be possible. That’s because it is hard to predict how many DNA changes will be needed to transform the Nicobar pigeon into a big-beaked, three-foot-tall dodo.

The dodo had a full, functioning, integrated genome that evolved gradually under a regime of continual selection — every intermediate was viable. Colossal’s approach is to splice a few dodo genes into a pigeon, raise it up, splice in a few more genes, etc. Those dodo genes evolved in a dodo genome. Gene A was in a cooperative relationship with gene B in the dodo, but you’ve just popped gene A into a genome that has a very different version of pigeon gene B. The gene you want to insert might be seriously deleterious in a pigeon context, and you don’t know what the relationship is. The dodo genes might also be optimized for a completely different environment, yet you’re trying to make them viable in lab-bred animals.

It’s insane. They’re going to plunk a few ancient genes into some poor pigeon and declare victory, but all they’re going to do is produce a sad fat flightless bird that is totally maladapted for everywhere, not a dodo at all, but a weirdly warped mutant pigeon. Good luck getting Chris Pratt to herd the flock around the landscape.

At least the dodo is only three feet tall…I can’t imagine what kind of botchwork monstrosity they’re going to build out of elephant stock. And they’re talking about “rewilding” these animals! The world they were adapted to no longer exists, these mutant freaks will not be able to thrive anywhere, and it’s pure fantasy to imagine they can let some loose in some environment that doesn’t want them, where the forces that drove the original extinction still exist, and get a supportable natural population. These are not serious ideas.

But they’ve got serious money.

The two-year-old startup also said today that it had raised a further $150 million in funding (bringing the total it’s raised to $225 million)—some of which will go to a new effort around bird genomics.

How do they do that? Easy. It’s all hype. They’re building on the flashy, fictional pseudoscience plotted by Jurassic Park, with an audience of stupid rich people who are impressed by CGI and confuse it with reality. Hey, if you can sell Bitcoin, you can sell fantasy animals that don’t exist to people with too much money. They even admit it.

Colossal’s investors include the billionaire Thomas Tull, the CIA’s venture capital arm, and the prominent biotech venture capitalist Robert Nelsen. Nelsen invested in the company because de-extinction “is just really cool,” he said in an email. “Mammoths and direwolves are cool.”

Oh god. Billionaires are so fucking stupid. All this money, pouring into an absurd project, and what are they going to do with it? It’s all about profit in the minds of the people throwing cash at it.

Because there isn’t much money to be made in conservation, how Colossal will ever turn a profit is another evolving question. One Colossal executive told MIT Technology Review that the company could sell tickets to see its animals, and Lamm believes the technologies needed to create the mammoth or the dodo will have other commercial uses.

Conservation isn’t profitable, but you know what is? A $225 million freak show, with dismal mutant animals in cages. Pleistocene Park! Yeah, that’s the ticket! The concept made money in that movie and book written by a guy who hated science, so let’s try that!

I knew that venture capitalists were evil and stupid, but it’s disappointing that so many highly trained molecular biologists are being sucked into this futile endeavor by all the hypetrain money flowing into it. And George Church — he used to be a well-regarded Smart Guy, but now his reputation is going to be as an ethically-challenged PT Barnum.

I am prepared!

Genetics class begins this week, and I am ready for the first week. Syllabus: done. This week’s lectures: done. This week’s lab: done. I can sit back and relax and maybe go for a walk today, that bit of stress is gone.

Now the lab for the second week…that’s another story. That week the students are supposed to start breeding flies, and I got my fly stocks all set up in December, and I was supposed to be at the stage of expanding the colony to have a surplus in time to hand them out. Some of the lines have been duds. Wild type flies are doing fine, the scarlet mutants are proliferating like gangbusters, but the white miniature forked mutants are barely getting by, and I’m down to a handful of brown flies, because they keep dying off. Fresh stocks have been ordered, but I’m going to be cutting it close — every step in these crosses has to be carefully timed in order to get results that don’t conflict with those stupid interruptions in our schedule, like spring break.

So I’m fine this week except that I’m going to be panicking about next week. There’s always something to elevate my anxiety.

The things we don’t do in lab

I’ve told the story of Leeuwenhoek’s prudishiness to my students in the past — it’s amusing that the father of microbiology, who had horrified the public with the discovery of ‘animalcules’ living in drinking water, was himself disgusted by what came out of his own body, and was horrified that semen contained squiggly squirmy little creatures. He even wrote to the Royal Society to say he wouldn’t mind if his discovery was suppressed.

“If your Lordship should consider that these observations may disgust or scandalise the learned, I earnestly beg your Lordship to regard them as private and to publish or destroy them as your Lordship sees fit.”

Then there was the bit where he was practically falling all over himself to assure everyone that his sample came from proper conjugal relations, not from the sin of onanism or by any other less than blessed mechanism. It was weird, man.

“Without being snotty, Leeuwenhoek (the ‘van’ is an affectation he adopted later on) was not trained as an experimental thinker,” explained Matthew Cobb, a British zoologist and author of the book “Generation: The Seventeeth Century Scientists Who Unraveled the Secrets of Sex, Life and Growth.” Cobb recalled by email that when Royal Society Secretary Henry Oldenburg asked Leeuwenhoek to look at semen, the Dutch draper initially did not reply “because he felt it was ‘unseemly.'” Even though he eventually overcame his reservations, Leeuwenhoek added so many caveats to his semen research that it is clear he remained somewhat uncomfortable.

“He reassured the Royal Society that he had not obtained the sample by any ‘sinful contrivance’ but by ‘the excess which Nature provided me in my conjugal relations,'” Cobb explained. “He wrote that a mere ‘six heartbeats’ after ejaculation, he found ‘a vast number of living animalcules.” A few months later, he wrote the aforementioned letter saying that he would not at all mind if his discovery was suppressed. After all, in addition to being grossed out, Leeuwenhoek was not under the impression that he had found anything special.

Unfortunately, after laughing at such Puritanism in lecture, I once went to lab and discovered that a student had made a quick trip to the lavatory and made his own slide, which he proudly showed off in class. I had to be the modern prude and explain that we discouraged the collection of human fluids in lab because they are a source of infection and contamination, and handed him a bottle of 70% alcohol and told him to sterilize all the gear he was using and dispose of his sample in the biological waste container.

The Science Fair experience

Today, I have witnessed abominations of science. So many experiments shoe-horned into the model of “The Effect of X on Y,” which is fine, but then you discover that they didn’t actually change X, or that nothing happened to Y, so they looked at Z instead. So many exercises in the obvious. Trivial phenomena measured, no thought to the underlying mechanisms considered. Experiments whipped together in a day. Tables of data with no assessment of variation, where you were lucky to see a mean reported.

I gave them all “A”s.

What else can you do when you ask a kid why they even did this experiment, and their answer is, “I don’t know, I like to do X, and I wanted to see what happened.” Gold star, kiddo, you understand science. That was exactly the right answer. Keep doing that!

Also gratifying: the kid who tested different kinds of stain removers, and hypothesized that the one he saw advertised the most would be most effective. They were all the same! Another gold star for concluding that maybe advertisers lied.

Big ups to the kid who had me baffled with his experiment — why would wheel size matter for his mousetrap car, when they are all propelled by exactly the same amount of force? He clearly explained that the design meant the axle would make the same number of rotations no matter the wheel size, therefore…oh, now I get it. Well done.

All of the students were well-prepared and gave solid summaries of their experiments, and I think I have to give a round of applause to the 7th & 9th grade science teachers at Morris Area High School, who really know their stuff.

That was fun! I should do it again next year.

Oh no! Classes begin one week from today!

Also, candidate visits for our chemistry position start in one week.

My genetics class is fairly well organized except for one thing: the stocks of brown (bw) eyed flies have almost completely crapped out. That’s always been a sickly line, but this year they’ve been pathetic. I’m desperately trying to nurse a handful of flies into vigor, and if they don’t get it together real soon now, I’m going to flush them all and order fresh flies. I’ve got a backup plan to do a different cross to keep the students busy for 6 weeks or so, but it’s also more difficult experiment, and I prefer to do the bw x st cross as a warmup.

We also have the board of regents visiting in March, and they’re being invited to sit in on the lab. Our students aren’t very happy with the regents as it is, and if they use it as an opportunity to ask pointed questions, I’m going to allow it. I’ll probably encourage it.

Today and tomorrow are the local high school science fair. I’m one of the judges. That should be interesting, around here we get a mix of brilliant kids with creative ideas and kids who like an excuse to shoot things.

I’m feeling mildly distracted right now — and this stupid cold, while gradually abating, isn’t helping much.

Turning point in the war against my personal virus

I have been cold-free for the last couple of years, which is a desirable condition to be in. Then, almost a week and a half ago, my granddaughter showed up at my doorstep with a face full of snot. We let her in. We knew the price we would pay.

I’ve been miserably clogged up ever since. I was waking up 3 or 4 times a night, struggling to breathe. I was horking up thick, slimy mucus all the time, feeling exhausted and disgusting.

Last night, though was a welcome turning point. I slept a continuous 8 hours! I woke up still able to breathe! I’m still messily congested, but it’s clearly at the mop-up phase where I send macrophages armed with flamethrowers into the caves and tunnels of my face to torch the invaders. Yay! I might be back to normal in time for back-to-school.

Unfortunately, there is a more worrisome virus waiting in the wings: XBB-1.5.

Three years after the novel coronavirus emerged, a new variant, XBB.1.5, is quickly becoming the dominant strain in parts of the United States because of a potent mix of mutations that makes it easier to spread broadly, including among those who have been previously infected or vaccinated.

XBB.1.5, pegged by the World Health Organization as “the most transmissible” descendant yet of the omicron variant, rose from barely 2 percent of U.S. cases at the start of December to more than 27 percent the first week of January, according to new estimates by the Centers for Disease Control and Prevention.

More than 70 percent of cases in the Northeast are believed to be XBB.1.5.

We must remain ever-vigilant. Mask up, everyone! I’m afraid my university administration, as well as the federal administration, are committed to downplaying all concerns. My university hasn’t changed their policies since last May, when they decided that nobody needed to wear a mask at all.

We’ve also got the usual idiots who understand neither evolution nor public health who have decided that new variants are caused by vaccination.

While there is no evidence so far that XBB.1.5 is more virulent than its predecessors, a recent swirl of misinformation linking the rise of new variants to vaccination has cast a spotlight on this latest strain and raised concern among some health experts that it could further limit booster uptake.

“XBB did not evolve because people were vaccinated,” said Vaughn Cooper, a professor of evolutionary biology at the University of Pittsburgh. “The way it evolved, let’s be straight, is because people were infected by multiple viruses at the same time.”

Since the omicron variant ignited an explosion of cases last winter, it spawned a host of descendants that are even more adept at slipping past antibodies and caused most infections in the United States. The XBB line emerged as a result of two other omicron subvariants swapping parts.

Isn’t that obvious? I mean, you’ve got the responsible people who take every measure to avoid the disease, and then you’ve got the people who go to football games and Walmart without taking precautions, who end up being little ambulatory cauldrons mixing up multiple variants simultaneously, and then some bozo decides the emergence of the explosion of new mix-and-match variants must be the fault of the guy who got the vaccines and stayed home in a safe little bubble.

You know that bozo is going to be featured almost every night on Fox News and Newsmax, and is going to have a popular Facebook page, because the media are fucked.

Student Evaluation of Teaching

For you non-academics unfamiliar with life at the university, yesterday was the day I got my evaluations. Yes, it’s true, the students get to turn everything around and grade the faculty on their performance. I can’t actually fail — tenure, you know — but these things do matter when it’s time to determine raises and that sort of thing (which will be roughly in mid-March). The department gets a tiny pot of money that the chair will dole out to the good little boys and girls, and she will use student evals as part of the determination, which also includes research and service.

So yesterday I cracked the virtual envelope to get the results, and they were fine. On a scale of 0 to 6, I got all 5s and 6s, which might translate into a raise of a few tens of dollars in a few months. It probably isn’t worth it, because I have to bust my ass for a year to get biology across to the students.

What’s more interesting is the comments students write, which I take far more seriously than numbers punched into a Likert scale, and are far more likely to get me to change things in the course. I got a few criticisms that made me happy.

Students said, “wasted too much time on creationism” and “I want to learn more biology, not creationism.” For context, I give ONE(1) lecture out of 30 that addresses religious objections to evolutionary theory. One. And this audience of smart millennials is just completely over it. That makes me so happy.

OK, have it your way. I’m cutting that lecture out of next year’s curriculum, and replacing it with more straight-up unvarnished biology, with no regrets. I hope this class is representative of their generation, because it’s about time we could ignore that nonsense.

Photoreceptor evolution

There was a fair amount of interest in my discussion of eye evolution last week, so let’s get a little more in-depth. This is a lecture on the level of what I tell my first year students in intro biology, so let’s see if I can put you to sleep, too.

Premieres at 2pm Central this afternoon. I’ll check in then to answer any questions, if any.

I’ve got a nasty cold, but I think my voice held up as well as could be expected — at least I held off the sneezing & coughing & vulgar snerks.