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.

The devils on Mars

When I was a boy, we lived for a time at the edge of farmland — acres and acres of lettuce and corn. My brother and I would often wander those fields, looking for entertainment. We’d scan for anything, whether it was a chance to skip stones across a pond, or climb a tree, or poke a stick at a skeletonized dead animal, or find an opportunity for a dirt clod fight, or just whatever. One of the things we would do when the season was right was dust devil chasing. The right season was late spring before the planting or the fall after the heads had been plucked and the corn reduced to stubble, after at least a week of dryth, so there was dust, and then we’d see the dust devils skirling about. What else would a couple of 12 year olds do but try to run and catch them? We rarely succeeded, and when we did it accomplished little more than tousle our hair and get grit in our eyes.

I thought of this because there was a strategy we didn’t try, which was to stop and wait for one to spawn nearby and fortuitously run over us. That’s never an option for 12 year old boys, but that’s what NASA’s Perseverance rover on Mars did. They just waited for a Martian dust devil to happen on them, and recorded it.

Murdoch said the team’s success in capturing a dust devil’s sound reflects both luck and preparation. The rover’s microphone takes recordings lasting a little under three minutes, and it does that only eight times a month. But the recordings are timed for when dust devils are most likely to occur, and the rover cameras are pointed in the direction where they are most likely to be seen.

“Then we have to just cross our fingers,” she said.

That clearly did the trick, because Perseverance managed to capture the dust devil through multiple instruments, registering the drop in air pressure, changes in temperature, the sound of grains making impact, all topped off with images that show the size and shape of the vortex.

And now we can hear it!

That’s the sound of lonely ghosts on a dead planet.

An ugly science spat

About a year ago, there was some sensational science news: the approximate time of year that the big dinosaur killing cataclysm occurred was determined. It was in the Northern hemisphere spring. That’s kind of cool.

Paleontologist Robert DePalma speaks about the fossil evidence discovered which support the impact event believed to have wiped out most of the dinosaurs almost 66 million years ago at the Goddard Space Flight Center in Bldg 28.

Now a small scandal has sprung up, one that doesn’t change the conclusion at all, but does highlight the fact that some scientists can be colossal jerks. It seems that one paleontologist, Melanie During, came up with the evidence to support that conclusion, and talked about it with a colleague, Robert DePalma, who quickly threw together a sloppy paper to scoop her.

In June 2021, paleontologist Melanie During submitted a manuscript to Nature that she suspected might create a minor scientific sensation. Based on the chemical isotope signatures and bone growth patterns found in fossilized fish collected at Tanis, a renowned fossil site in North Dakota, During had concluded the asteroid that ended the dinosaur era 65 million years ago struck Earth when it was spring in the Northern Hemisphere.

But During, a Ph.D. candidate at Uppsala University (UU), received a shock of her own in December 2021, while her paper was still under review. Her former collaborator Robert DePalma, whom she had listed as second author on the study, published a paper of his own in Scientific Reports reaching essentially the same conclusion, based on an entirely separate data set. During, whose paper was accepted by Nature shortly afterward and published in February, suspects that DePalma, eager to claim credit for the finding, wanted to scoop her—and made up the data to stake his claim.

Well, yuck…but on the bright side, independent corroboration of the conclusion is a good thing, right? Not so fast.

After trying to discuss the matter with editors at Scientific Reports for nearly a year, During recently decided to make her suspicions public. She and her supervisor, UU paleontologist Per Ahlberg, have shared their concerns with Science, and on 3 December, During posted a statement on the journal feedback website PubPeer claiming, “we are compelled to ask whether the data [in the DePalma et al. paper] may be fabricated, created to fit an already known conclusion.” (She also posted the statement on the OSF Preprints server today.)

The plotted line graphs and figures in DePalma’s paper contain numerous irregularities, During and Ahlberg claim—including missing and duplicated data points and nonsensical error bars—suggesting they were manually constructed, rather than produced by data analysis software. DePalma has not made public the raw, machine-produced data underlying his analyses. During and Ahlberg, a member of the Royal Swedish Academy of Sciences, question whether they exist.

DePalma refuses to release the raw data, which is a big red flag. Also another big problem: DePalma literally owns the site with all the fossil data!

DePalma holds the lease to the Tanis site, which sits on private land, and controls access to it.

I find that disturbing. He bought up the lease and controls who has access to the specimens and data? I can’t be the only one who finds that troubling. Maybe he’s a hero who snatched it up to protect it, and lets anyone who asks do research there, but then…uh-oh, another ugly revelation. Someone who knew him well for many years has come out to say that he’s a creep.

DePalma has a different perspective on the whole affair, but the timing of publication and the fact that the paper has many errors and that the raw data is hidden away leaves me suspicious. Also that he is trying to turn the tables and claim that During stole his ideas.

DePalma characterizes their interactions differently. He says his team came up with the idea of using fossils’ isotopic signals to hunt for evidence of the asteroid impact’s season long ago, and During adopted it after learning about it during her Tanis visit—a notion During rejects. After his team learned about During’s plan to submit a paper, DePalma says, one of his colleagues “strongly advised” During that the paper must “at minimum” acknowledge the team’s earlier work and include DePalma’s name as a co-author. DePalma says his team also invited During’s team to join DePalma’s ongoing study. “During the long process of discussing these options … they decided to submit their paper,” he says.

Collaboration and open communication are an essential part of the scientific process. This whole conflict would go away if the data, and the field site, were shared openly, but someone seems to be hoarding all that. It’s a shame, too, that such interesting work and such a spectacular fossil site are being tainted by this ugly possessiveness and grubbing for priority.