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.

Craftin’

Busy morning. They’re only going to get busier.

One of the things I got done today was to assemble of set of my Spider🕷 Studios™️, Mk II this time, with thinner papers and small tabs of tape. As you can see, once I’ve got spiders and their webs inside, I can use the helping hands to hold the hoops in any orientation I want.

I had to get them ready today because…see the small box? What’s in the box? Not Gwyneth Paltrow’s head, although it might fit. You might see a small mottled ball in the box — that’s a Steatoda triangulosa egg sac, and the mottling is caused by the embryos maturing enough to have black legs on their pale bodies. The legs are twitching (maybe they’re dreaming?) so their emergence is imminent, and I need to promptly set up the babies so I can document pigment changes over the next few weeks.

Really, it’s all just playing with office paper, a paper cutter, and time tape. It won’t be real science until I progress to duct tape, hot glue, and cardboard.

Do spiders dream of arthropod sheep?

You ever watch a sleeping cat or dog, and see their little paddy-paws twitching and their legs all curled up? Cute, isn’t it? You can just imagine they’re dreaming.

Spiders do it, too.

Jumping spiders are special because, unlike most arthropods which have fixed eye positions — they have to turn their heads to change their field of view — they have telescope eyes which can swivel, so you can actually see their eyes move while they are presumably sleeping. This has led some investigators to suggest they have a kind of REM sleep.

Sleep and sleep-like states are present across the animal kingdom, with recent studies convincingly demonstrating sleep-like states in arthropods, nematodes, and even cnidarians. However, the existence of different sleep phases across taxa is as yet unclear. In particular, the study of rapid eye movement (REM) sleep is still largely centered on terrestrial vertebrates, particularly mammals and birds. The most salient indicator of REM sleep is the movement of eyes during this phase. Movable eyes, however, have evolved only in a limited number of lineages—an adaptation notably absent in insects and most terrestrial arthropods—restricting cross-species comparisons. Jumping spiders, however, possess movable retinal tubes to redirect gaze, and in newly emerged spiderlings, these movements can be directly observed through their temporarily translucent exoskeleton. Here, we report evidence for an REM sleep–like state in a terrestrial invertebrate: periodic bouts of retinal movements coupled with limb twitching and stereotyped leg curling behaviors during nocturnal resting in a jumping spider. Observed retinal movement bouts were consistent, including regular durations and intervals, with both increasing over the course of the night. That these characteristic REM sleep–like behaviors exist in a highly visual, long-diverged lineage further challenges our understanding of this sleep state. Comparisons across such long-diverged lineages likely hold important questions and answers about the visual brain as well as the origin, evolution, and function of REM sleep.

If this were happening in a cat or a dog we’d easily assume the behaviors were a reflection of whatever they were dreaming about. It would be nice to imagine this was just as true of spiders, but I’m going to be slightly skeptical of the idea that the behavior is indicative of “dreaming” or even analogous to REM sleep. The authors are cautious, too.

The complex visual and cognitive behaviors of salticids and their relatively small nervous system facilitate experimental tests of the role of visual experience in REM sleep–like retinal movements. Eye movement patterns during REM sleep have been hypothesized to be directly linked to the visual scene experienced while dreaming—begging the deeper question of whether jumping spiders may be experiencing visual dreams. This raises a unique opportunity to test this “scanning hypothesis” in jumping spiders, where retinal movements can be observed. Since visual input can be controlled in jumping spiders early on (unlike in humans), retinal responses to repeated visual stimuli presented during the day might partially reappear during REM sleep–like states.

The problem I have is that we don’t know all that is going on in the brains of humans during dreaming or REM sleep — so how can we compare that to what spiders experience? A deeper analysis of the activity of the nervous system would be needed to do a good comparison, and this paper is only looking at behavior.

An alternative to “dreaming”: spiders go through waves of alertness during sleep. At some levels, they are awake enough to monitor their environment, so those eye movements aren’t a consequence of dreams — that’s the spider doing sentry duty, scanning what’s around it to search for prey or threats. The movements tell us nothing about the inner life of a spider, only that it wants to eat or avoid being eaten. You know they don’t have eyelids, right? They aren’t as blind as we are while sleeping.

That doesn’t mean the behavior lacks any homology with vertebrates. Maybe our REM sleep is also a consequence of the evolution of rising and falling levels of alertness, and dreaming is just a side effect of brains randomly invoking patterned activity on top of all that.

If spiders dream, though, I do wonder what bloodthirsty scenarios are playing out in their heads. That may also be similar to vertebrate dreaming — I don’t think my cat dreams of frolicking in fields of dandelions, but of ripping the heads off smaller mammals. But that’s my psycho cat.

It doesn’t work on spiders

Mary told me I should mention this app, Merlin Bird ID, in case you don’t already have it. You fire it up, click on a button, and it just listens and tells you what birds it hears. I got it a while back because the crazy early morning bird cacophony was bugging me — at least I ought to know who’s shrieking at me early in the morning. I can sit in my office and have it inform me what all the noise is about. This morning it was black-capped chickadees chattering away, blue jays and redwinged blackbirds making a ruckus, and an American robin fussing about. It’s not as bad as it was earlier this summer, because we also have a Cooper’s hawk hanging about in the neighborhood. When it squeaks, it gets quiet, briefly.

Hey, I’ve noticed fewer squirrels making pests of themselves lately. I wonder if I should play recordings of a Cooper’s hawk when they start climbing the bird feeder and scrabbling at my window. (Before you say squirrels are pretty clever and will just learn to ignore the noise, that’s part of the plan: they’ll become more vulnerable to hawks then.)

If you’re more of a visual person, I’ll also recommend Seek from iNaturalist. Put that on your phone, aim it at any organism, and it’ll use the iNaturalist database to let you know the scientific name of what you’re seeing. It’s very handy. It even works on spiders, unlike the Bird ID program.

Metabolism First! And the origin of life

Two and a half weeks until classes resume, so I’m shifting brain gears to get excited about cell biology again. One of the tools I use to get into the right mindset is reading more biochemistry, and lately that means reading more Nick Lane, who is one of those biochemists who is obsessed with evolution and does a marvelous job of integrating the finicky little details electrons and protons and small molecules and chemistry with the big picture of where all this comes from and how it has shaped life.

I’ve read and reread Lane’s latest book, Transformer: The Deep Chemistry of Life and Death, and recommend it highly. I’ve been struggling with how to explain it’s contents, and it’s not easy — in my class, I spend weeks just gradually building up the background needed to understand the chemistry of the cell, which makes it hard to dump on a blog or a single video as anything but a huge indigestible bolus. And of course it took Lane 400 pages in a densely packed book to cover it all.

I should have known I could just let Nick Lane do all the hard work.

“KREBS CYCLE” is not a phrase that usually gets students excited — I know from experience — but this is juicy stuff. The talk itself covers a huge amount of ground, giving the basics of metabolic cycles and going into the origins of life and the great leap forward provided by mitochondria in endosymbiosis, and the diverse ways various organisms have taken the basic toolkit of the Krebs cycle and used it in novel ways. That’s all good solid science, and I don’t understand how anyone can have any doubts about the general chemistry that leads to life (well, I sorta do — they don’t know any biochemistry. All the YouTube debates about the origin of life are a waste of time, given that creationists are disgracefully ignorant of even the most rudimentary understanding of biochemistry).

Near the end, he gets farther out into weeds with speculation about aging, cancer, and consciousness. It’s interesting and he could very well be right — he’s a smarter man than I am — but the ideas range from very likely (metabolic shifts as agents of senescence and cancer), to potentially revolutionary but still on the fringe (the role of calcium and membrane potentials in Alzheimers), to some that, well, sound like how a biochemist would view neuroscience, for instance claiming that consciousness is a product of the electrical potential across the membrane of a cell, which is rather too reductionist for me.

Watch the video, though. If there are bits that you find heavy slogging, or just too out there to grasp, let me know in the comments. That’s information I can use to present these ideas to a class of second year students. And if you find it really deeply enlightening, go out and read Transformer. It contains a lot of the ideas about cellular metabolism I’d like to get across to my students.

It would make my life a whole lot easier if I could just show a one hour video that explains everything, then say, “Well, that’s all done then. We spend the rest of the semester reading poetry and dancing and playing video games! Yay!” I suspect I should probably fill in a lot more background and talk about the details, but maybe the video would be a nice dessert for the end of the semester. I’ll have done my job if all the students can watch it and say they already knew all that, but that Lane did a fine job of tying it all together.