Disappointed, and relieved

This was supposed to be a heavy research morning — we’ve started a new experiment in the lab and spiders need to be assayed, and we were going to do some scanning of egg sacs with our confocal, and I was figuring I’d be neck deep in spider work until at least noon. But then my student called in sick, which was exactly the right thing to do (COVID is going around the student body again), and I had to postpone everything until Monday. I wouldn’t want to deprive her of the fun part of science!

Instead, I did the drudgery part of science, feeding all the animals. They didn’t really need it, they had mealworms earlier this week, and look like little brown beach balls right now. I wouldn’t want them to wake up feeling peckish and discover the larder was empty this weekend.

I found two new egg sacs. Two others look very close to emergence, so I sorted those out into new small containers. The confinement makes it easier to remove newly scampering spiderlings.

Now I’m staring at a stack of lab reports and exams and senior thesis drafts that I’m going to have to get done this weekend. I also have to compose a genetics exam to mail out this evening. First, though, I have to deliver another lecture to my other class. There will be no joy in Morris today.

This was supposed to be my light semester.

Science apologizes

We all knew William Shockley was a disgusting racist, using bad biology to argue for bad goals, but he was the co-inventor of the transistor! He won a Nobel prize for his work in a field unrelated to biology! So while my friends and I were willingly calling him out as a fraud, a liar, and a racist while we were out for beers, all the major scientific publications were more mealy-mouthed and ingratiating, which was annoying. It was partly out of misplaced politeness, but also that a lot of the white male old guard were probably sympathetic to his ideas.

Maybe that’s changing. Science has published an editorial apologizing for their past indifference/support for Shockley, and promising to do better. They’re calling out the racists and phonies.

Shockley was part of a cadre of physicists who advanced ideas outside of their area of expertise to promote a right-wing agenda. He was a close friend of Frederick Seitz—president of both the National Academy of Sciences and Rockefeller University—who, following a career in physics, became a purveyor of misinformation on tobacco, nuclear weapons, and climate change. Like Shockley, Seitz carried out his nonphysics work through op-eds and conservative think tanks, not through the accepted mechanism of peer review that he used in doing physics. Seitz was not, at least publicly, as overtly in favor of eugenics as was Shockley, but he was a strong advocate for genetic determinism, even claiming at the behest of the cigarette industry that tobacco itself was not harmful because genetics determined whether smokers would ultimately contract lung cancer.

Sound familiar? There are many ‘scientists’ getting checks from right-wing think tanks right now, although most of them are now busy with careers in vaccine and climate change denialism. The words have changed but the song is much the same. Let’s see Science start calling out more of the living hucksters and propagandists for the far right. But for now, I’m reasonably happy with their apology for propping up a dead one.

Following Shockley’s death in 1989, Nature correctly called out his racism in an obituary, but then published a letter from Seitz defending Shockley and claiming that the reason Shockley became a eugenicist was because of physical trauma he experienced in a near-fatal car accident. When Science wrote about this dustup, it referred to Shockley’s ideas as merely “unpopular” and “extremely controversial.” It then ran a letter from an even more notorious eugenicist, J. Philippe Rushton, who argued that by merely covering the disagreement at Nature, Science was delivering an “ad hominem attack.” In addition to an ill-advised decision to publish Rushton’s letter, Science posted a response saying, “no criticism of Shockley was intended.” Yikes.
Looking back, it’s clear that what was intended as an attempt to make room for dissent and discussion only served to abet Shockley and his cohorts in their effort to build support for eugenics. Science gave them a platform and inadequate scorn. The lesson is that we at Science need to make more effort to think about everything that we do, not only from the standpoint of communicating science to the public, but also as an organization that above all, supports all of humanity. The process of science is one of continual revision, but it’s also one that must have a conscience.
It was only a few months ago, in a commentary on racism in science by Ebony Omotola McGee, that Shockley was described in our pages in the terms he deserved. But as recently as 2001, Science described him simply as a “transistor inventor and race theorist.” That won’t cut it anymore. As of today, a link to this editorial will appear along with any mention of Shockley in this journal.
Make no mistake. Shockley was a racist. Shockley was a eugenicist. That’s all.

That’s a pretty good apology: admitting the mistake, taking the blame for it, and planning an action to correct their error. Not that it will stop all the modern ‘race realists’ from relying on old boobs like Shockley and Rushton in their arguments.

Heed the octopuses’ warning!

Here’s a story that has sex, octopuses, population genetics, and climate change, all at once.

What should catch your eye, after the octopus sex, is the shift that enabled those populations to meet across the vast (currently) frozen mass of ice of the Antarctic: a 2°C increase in temperature relative to the modern day. Just 2°C will cause an ice sheet collapse, dramatic rises in sea level, and an increase in the frequency of extreme weather.

Earth scientists continually emphasize that humanity isn’t inescapably doomed by the coming, inevitable disruptions to the climate. It’s just the opposite. Society still has an extraordinary amount of influence in the matter: The more warming, the worse the impacts. But Earth’s inhabitants should be aware that a 2 C world has extreme effects. It’s all the more reason to avoid any warming above 2 C.

The Earth has been there before. It’s not a world we’d enjoy living on.

Stereotypical liberal college professor

Today I’m handing out the first exam of the semester in genetics, and some of the students are a bit anxious. I’ve been getting all these email questions about how to prepare for this exam, do I have to complete it in a set amount of time, am I allowed to talk to other people when I’m working on it, are there security things I have to do (man, high schools are warping students’ minds), etc., etc., etc. They seem discombobulated by the fact I don’t run the class like a drill sergeant, and that the exams are all open book, open notes, all this slackness you ought to expect from a liberal college professor.

So this morning I had to post a note to the class explaining that yes, it’s true, I have some rather loose and tolerant policies in my teaching. It’s OK if you work with other students on the exam, it’s not cheating, it’s called learning. What a weird thing to have to spell out!

[Read more…]

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.