Poor Dimorphos

It’s just an innocent space rock, didn’t do anyone any harm, but NASA is getting ready to practice its marksmanship and shoot at it from a distance of 7 million miles. It’s getting hit tonight, so you can watch the livestream of the sniper shot right now.

Not the view you want to see through your windshield.

Frantically rewriting lectures

Aaargh, neglecting the blog again. My big distraction today: as always happens, I looked over last year’s notes and grumped at myself and said this will not do, this is totally inadequate, I need to rewrite the whole thing. The plan for tomorrow was to talk about the pentose phosphate pathway AKA the hexose monophosphate shunt AKA the phosphogluconate pathway because this stuff is important and, weirdly, our textbook doesn’t even mention it, so I can’t even punt and tell the students to go away, don’t bother me, just read Chapter X. As is common in cell bio, all we talk about is how we burn sugar to make ATP, and very little about essential anabolic reactions. And that bothers me.

The PPP is cool beans, too, so I rewrote the lecture from the ground up to cover more of the details, expanding what used to be a short aside into the whole dang talk, and I’m probably going to terrify them all with a peek into more advanced biochemistry (this is a class for 2nd year students, so it’s introductory level) and the way all of biochemistry is tangled and intertwined, but hey, they’re smart students. They can take it.

Unfortunately, it’s stuff that isn’t going to entertain a more general audience, unless you think filling in the details on this introductory slide would get you excited.

Man, I was so into biochemistry as an undergrad, and then I got distracted by neuroscience and development. I need to begin a second lifetime so I can catch up.

Now I have to finish grading, which is far less enthralling.

How to tell if the males of your species are assholes

Easy. Their harassing behavior affects the evolution of females. This isn’t sexual selection, it’s just that the juvenile females are disguising themselves with male plumage to escape harassment. These birds, white-necked jacobins, are typically sexually dimorphic, but juvenile females maintain a male-like coloration, because females with adult female coloration face more aggressive assaults from males. Adopting the male coloration allows them to feed uninterrupted, while putting on the sexy female green coat brings on a plague of annoying, obnoxious males.

Ornamentation is typically observed in sexually mature adults, is often dimorphic in expression, and is most apparent during breeding, supporting a role for sexual selection in its evolution. Yet, increasing evidence suggests that nonsexual social selection may also have a role in the evolution of ornamentation, especially in females. Distinguishing between these alternatives remains challenging because sexual and nonsexual factors may both play important and overlapping roles in trait evolution. Here, we show that female ornamentation in a dichromatic hummingbird, the white-necked jacobin (Florisuga mellivora), cannot be explained by sexual selection. Although all males are ornamented, nearly 30% of females have male-like plumage. Remarkably, all juveniles of both sexes express ornamented plumage similar to adult males (androchromatism), but 80% of females acquire non-ornamented plumage (heterochromatism) as they age. This unique ontogeny excludes competition for mates as an explanation for female ornamentation because non-reproductive juveniles are more likely to be ornamented than adults. Instead, avoidance of social harassment appears to underlie this female-limited polymorphism, as heterochrome taxidermy mounts received more aggressive and sexual attention than androchrome mounts from this and other hummingbird species. Monitoring electronically tagged birds at data-logging feeders showed that androchrome females accessed feeders more than heterochrome females, presumably because of reduced harassment. Our findings demonstrate that ornamentation can arise purely through nonsexual social selection, and this hypothesis must be considered in the evolution of not only female-limited polymorphism but also the spectacular ornamentation often assumed to result from sexual selection.

They’re evolving to be able to eat dinner in peace.

Boy birds should be ashamed of their behavior, is all I can say. They can’t even leave a taxidermy dummy alone!

Falk et al., 2021. Male-like ornamentation in female hummingbirds results from social harassment
rather than sexual selection. Current Biology 31, 4381–4387. https://doi.org/10.1016/j.cub.2021.07.043

Gen III, babieee!

Fantastic success, everyone! Two of the pairs of spiders featured in my spider porn video from last week have produced egg sacs! Stri7 & Stri4, and Stri2 & Stri5, to be precise. This is huge. It may be the start of, finally, a self-sustaining colony. I’ve been struggling with this for the past few years — I get a few thriving spiders, a few egg sacs, and then over the winter they die off and I need to replenish the stocks in the spring with wild-caught adults. This is no way to do genetics. Well, it is, but that’s a different kind of genetics than I want to do.

Now I can start making plans. It will be about a month before spiderlings emerge, and then another month or two (depending on how well my fortified fruit fly diet works) to reach adulthood, which means I could have a Gen IV by Hallowe’en, or Thanksgiving at the outside. Exciting! I could be doing crosses by spring term!

Also, right now I’ve got so many spiders and spiderlings I have exceeded my lab’s capacity. In another first, while in previous years I have raided my garage for new spiders, today I took a container of about 50 Steatoda triangulosa spiderlings and released them into my garage. Sorry, babies, I can’t take care of you all, so you’re going to have to forage for yourself in the hard cruel world. Winter is coming, grow up fast.

Take your time, no rush, I’m not going to see chestnut forests in my lifetime anyway

I should look up from the spiders now and then. I did not know what was happening to forests.

Global trade and climate change are poised to make the spread and severity of arboreal plagues and pestilence worse. The hills around Syracuse are silhouetted with pale ash trees slain by emerald-colored borers. Ancient bristlecone pines out West are succumbing to bark beetle outbreaks triggered by rising temperatures. As many as 1 in 6 trees native to the Lower 48 states are at risk of extinction.

I should know. We bought a house 20 years ago that had a yard full of impressive trees, which we’ve watched steadily decline. Every few years it seems the city splashes another one with neon paint and we’re told it has to come down. But there’s hope! Science rides to the rescue, maybe! The article is about the American Chestnut, and how it’s been wiped out by a fungus.

All it takes is one gene.

The fungus infecting chestnut trees thrives by secreting a chemical called oxalic acid, which kills cells and allows the pathogen to feast on the dead tissue. But many other plants, including bananas, strawberries and wheat, avoid that fate by producing an enzyme called oxalate oxidase that breaks down the toxin.

By 2014, Powell and Maynard successfully added the wheat gene to chestnuts and were growing infection-resistant trees. The pair dubbed one line Darling 58, in honor of Herb.

Many plants use oxalate oxidase as a defense mechanism. It catalyzes the oxidation of oxalic acid into CO2 and peroxides — reactive oxygen species. Is that going to have a side effect? I don’t know. Barley makes multiple forms of oxalate oxidase, and it doesn’t seem to harm beer production.

“Making a transgenic tree — I hate to say it like this, but it isn’t that hard,” Newhouse said. The most difficult hurdle for Darling 58, he said, is winning regulatory approval.

Well. This is sort of true. Making transgenic organisms is relatively easy nowadays, EXCEPT…the difficult part is figuring out what gene to use, and since most traits have complex origins, and since the expression of the gene is going to have multiple effects on the organism, it’s difficult to predict all of the consequences. There are good reasons regulatory approval is tough to get.

But in this case, they seem to have found a relatively simple way to confer fungus resistance on a tree, and it’s been tried experimentally, and they have successfully produced healthy, blight resistant chestnut trees. However, I think uncertainty about possible outcomes is a good reason to go slow, and regulatory agencies are doing the right thing by putting the brakes on the process.

There are also bad reasons for resisting the transgenic trees, and there seem to be a lot of people blocking it. Their primary argument is this weird idea that “natural” mechanisms like breeding hybrid trees are somehow “better” than transgenic methods — this is the same reasoning that has led to GMO labeling in our grocery stores, as if somehow the fact that an agricultural scientist has intentionally tweaked a plant is bad, while wholesale, random interbreeding of varieties is more pure. I don’t get it. Don’t people realize that all of the crop plants producing your food have been extensively modified by centuries or millennia of intentional manipulation of their genomes? Everything in the supermarket is a mutant, GMO or non-GMO. I’d argue that the genetically modified plants have undergone less drastic changes than those produced the old-fashioned way.

…Powell countered that crossbreeding transfers far more genes between species. “Genetic engineering is actually a less-risky procedure than a lot of things that we’ve done in the past,” he said. “We are very precise. We’re only moving one, two — just a small number of genes into the tree.”

That the changes are small are not a reason to dismiss regulatory oversight, of course. The reason they can use only one or two genes is that they have specifically selected target genes of very large effect.

Of course, re-creating vast chestnut forests would also be a huge effect.

A good analysis, even with the Wittgenstein

LonerBox addresses the “What is a woman?” question, and I pretty much agree with him — it’s a bad question, asked in bad faith, and the answer is more complex than a conservative would be willing to accept. Of particular interest is the section starting at about 19:45, where he talks about what “an increasing number of biologists” advocate, that sex is biological, but expressed at different levels, and that brain sex is just as, or more, important than gonad sex or hormonal sex or chromosomal sex or all those other important biological aspects.

I can at least say that this biologist agrees with him, although I can think of a few others that are a bit batty on the subject.

I think we’ve figured out who Tucker Carlson’s role model is

So that’s where the weird speech patterns come from: Tucker Carlson is Jiminy Glick, fictional comedic character.

It’s uncanny.

The big difference is that Glick didn’t lie as much as Carlson. Science magazine went through the full transcript of one of Carlson’s recent tirades, and almost everything Tucker Carlson said about Anthony Fauci this week was misleading or false. I never watch Carlson’s show, so I had no idea how unhinged and divorced from reality his opinions have become. A taste:

Carlson asserted Fauci had committed very serious crimes and said he apparently engineered the single most devastating event in modern American history. Carlson, infamous for assailing people’s looks, also called Fauci a an even tinier version of the Dalai Lama and a Stalinist midget.

Carlson seems to relish criticisms of his comments, which inevitably draw more attention to him and his show. But at the risk of playing into his hand, Science fact-checked his criticisms of Fauci. The analysis shows Carlson took facts out of context and cited long-debunked studies or reports to attack Fauci. He also repeatedly blamed Fauci and other scientists for changing their minds based on new evidence—the bedrock of scientific progress. In Carlson’s calculus, such reversals equal lying.

Obviously, Fauci has committed no crimes, especially not serious ones, and did not engineer the COVID pandemic (which, I thought, Fox News belittled anyway — now it’s the single most devastating event in modern American history?) His ideas about Fauci’s appearance are his to hold, but I don’t think there’s anything Stalinist about him, and hey, what’s wrong with looking like a Tibetan or being a little person anyway?

The article goes through Carlson’s claims line by line and shows that they’re bogus. It’s astonishing that he’s the flagship commentator for a news organization. It’s almost as if Fox has nothing to do with “news”.

So beautiful…

Biden really is trying to make me vote for him in the next election.

This is big. Really big. Open up all that science, we paid for it! From the White House:

This research, which changes our lives and transforms our world, is made possible by American tax dollars. And yet, these advancements are behind a paywall and out of reach for too many Americans. In too many cases, discrimination and structural inequalities – such as funding disadvantages experienced by minority-serving colleges and institutions – prevent some communities from reaping the rewards of the scientific and technological advancements they have helped to fund. Factors including race, age, disability status, geography, economic background, and gender have historically and systemically excluded some Americans from the accessing the full benefits of scientific research.

To tackle this injustice, and building on the Biden-Harris Administration’s efforts to advance policy that benefits all of America, the White House Office of Science and Technology Policy (OSTP) released new policy guidance today to ensure more equitable access to federally funded research. All members of the American public should be able to take part in every part of the scientific enterprise—leading, participating in, accessing, and benefitting from taxpayer-funded scientific research. That is, all communities should be able to take part in America’s scientific possibilities.

What’s Crazy Joe going to do next? Legalize marijuana, create a Universal Basic Income, strip the broadcasting license from Fox News, free university, declare the Age of Aquarius? I like it.

Your scientists were so preoccupied with whether or not they could, they didn’t stop to think if they should

As usual, First Dog on the Moon scores.

Oh yeah. This again. Some molecular biologists with no training in population genetics or ethics think they can go into a lab and resurrect an extinct species.

Almost 100 years after its extinction, the Tasmanian tiger may live once again. Scientists want to resurrect the striped carnivorous marsupial, officially known as a thylacine, which used to roam the Australian bush.

The ambitious project will harness advances in genetics, ancient DNA retrieval and artificial reproduction to bring back the animal.

They won’t succeed. At best, they’ll assemble a maladapted hybrid something or other to be exhibited in some freak show of a zoo. It won’t be a thylacine, it’ll be a Frankenstein’s monster of an extant marsupial with no home environment and no prospects for the future and no population of conspecifics with which to live and no history. So much bugs me about this story.

They talk about “the thylacine genome”. There’s no such thing. A living population has many genomes. How many individuals are they sampling? How many individuals will they generate? Where will they live? These are carnivores — what will they feed on? Or are they just planning on conjuring up a technology demonstration that they’ll put in a cage and then move on to some other “project”?

They make a token nod towards the problem of extinctions, but aren’t very convincing.

“We would strongly advocate that first and foremost we need to protect our biodiversity from further extinctions, but unfortunately we are not seeing a slowing down in species loss,” said Andrew Pask, a professor at the University of Melbourne and head of its Thylacine Integrated Genetic Restoration Research Lab, who is leading the initiative.
“This technology offers a chance to correct this and could be applied in exceptional circumstances where cornerstone species have been lost,” he added.

No, it won’t accomplish any of that. The species is extinct because their habitat is destroyed and people killed them. That’s where you start, by rebuilding their environment, not with PCR machines and microinjection apparatus and flasks in incubators. It’s no surprise who is behind this: a guy with impressive credentials in molecular biology who thinks every problem is a lab exercise.

The project is a collaboration with Colossal Biosciences, founded by tech entrepreneur Ben Lamm and Harvard Medical School geneticist George Church, who are working on an equally ambitious, if not bolder, $15 million project to bring back the woolly mammoth in an altered form.

Yeah, right. He was claiming that he’d be bringing back the mammoth within two years…five years ago. He was also working on a dating app to eliminate genetic diseases (I guess he never heard of eugenics?).

Church has also speculated about resurrecting Neandertals. Nope. Not going to happen. If his thoughts on these matters were more than a millimeter deep, he wouldn’t be jumping onto high profile media to promote these sci-fi fantasies. It’s bad science.