Last 3 weeks!

The end is in sight! I’ve laid out all my lectures for this final part of my cell biology course.

  • This week: cell signaling.
  • Next week: multicellularity and cell motility.
  • Final week: cell origins.

It may seem weird to end the semester trying to answer where cells come from, but I’ve found that they need to know a lot of basic stuff about chemistry and metabolism before it all makes sense.

Now that I’ve got complete plans for the remainder of the course content, I can focus on just grading, my least favorite part of teaching, which means that now on top of sky-high stress levels I get to add nonstop tedium and misery. At least class itself should be fine! Maybe I should just stop handing out assignments so the work doesn’t pile up.

Next, though, a take-home exam comes due tomorrow, and I have vowed to get it completely graded by Friday. The nightmare continues.

Wow, Quantum Eraser was even worse than I imagined

Time for another Bad Science Sunday, and this time I followed up on the threat of a video by some gomer calling himself Quantum Eraser. I “watched” it. It was unwatchable. It’s basically a braying ass shouting “logical error” at every statement about scientific evidence, without following through and stating what the error was, or even addressing the evidence in any way. So I made a video, and along the way I bomb you with my opinions about science communication, because this guy was basically the antithesis of good teaching.

Oh, yeah, I also sorta kinda included a partial script, below the fold.

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Well, that was strange

I was in the lab, feeding the baby spiders, when I discovered something peculiar. I popped to tops on the spider vials, and they were fine, all placid and polite and saying “please” and “thank you” and just being all around delightful boys and girls, like always.

Then I gathered up a bunch of flies, and they were freaked out and hyper. Usually I can rely on them to scurry to the edge of the container, where I flick them one by one to the spiders. Not today! They were rushing about, charging the opening, and leaping to their doom by themselves, which was bad, because flies are stupid, and without my assist they often miss the open vials. It also made it difficult to control how many flies went to each spider, so some are feasting well, others got their usual fare, and more flies than usual ended up running off to feed the feral spiders living in my lab.

It was as if they’d heard that their Lord had become a crappy one term president, and they’d all decided to run in circles, scream and shout. They all still ended up juice in the guts of a spider, and eventually multicolored poop spots on the floor of a cage.

Which reminds me, I’ve got a major lab cleanup ahead of me, which I’m not going to have time to do until the semester is over. I hope the flies settle down and resign themselves to their fate by then.

Behold! Light box Mk II!

Last week, Ade & I “built” (I use the word loosely) a space cocoon out of aluminum foil to control the illumination of our experimental spiders. It worked, clumsily, and it looked hideous.


Today, we took a Great Leap Forward and advanced the cause of Spider Containment and Illumination technology by building Light Box Mk II. It is beautiful and elegant.

We constructed it with frame of Space Age™ PVC pipe, covered with sheets of Cutting Edge™ Black FoamCore, the edges sealed with Advanced Technology™ adhesive backed metallic fabric…in other words, cardboard and duct tape. It looks damned fine, though. We’ve got a spider in a cage beneath a NoIR camera in there, and Ade is caught in the act of activating our time-lapse software on the Raspberry Pi so we can quantify it’s behavior night and day. Our sole obstacle to doing Great Science is now the spider: our Mk I may have been clumsy, but it did work, and unfortunately this particular spider cowered out of sight* almost the whole time the computer eye in the sky was staring down at her. We’re doing another trial run now.

Another bonus is that we made the box fairly roomy, and we could eventually put 3 or 4 spiders in separate cages in there. We only have the one camera right now, though, so that will have to wait.

*Of course, a spider refusing to behave is still data in a behavioral observation, so that was fine.

Spiders!

It kills me that every time I see a splendid spider photo, I can’t share it here — too many people are freaked out by arachnophobia. I wish I could cure it by constantly rubbing more spiders in your faces, but I know that doesn’t work, so I’ll just gently point you in the direction of a couple of collections of gorgeous spiders, and you can choose to go look, if you want.

The Great Fox Spider has been rediscovered in Britain! These are related to wolf spiders, so you probably know what they look like, but it has the most wonderful mottled markings. I know some people are fans of the more garishly colorful spiders, like peacock jumpers, but I’ve come to appreciate the subtlety of the more variable and muted markings, like the ones I see on Parasteatoda. If you must do something bold, go for something simple and clean, like the distinctive swoosh on Steatoda borealis.

You want more variety? Check out Science Friday’s collection of spider photos. My favorite there is the Pirate Spider — there’s something about a gracile spider with delicate line art on its body and long bristling spikes on its legs that I find appealing. But if you’re into big bearish brute mygalomorphs, get an eyeful of that black purse-web spider with its massive chelicerae.

One more photo I wish I had: yesterday, Mary spotted a tiny juvenile cellar spider descending on a strand of silk, and she brought it to me (I’m desperate to see more live spiders, it’s gotten too cold for them). I tried to catch it by snaring its thread, but it got away fast before I could get my camera ready. We think it landed on my pants. So while I didn’t get a picture, I’ve got that going for me, that maybe a baby spider has taken up residency in my clothing. It’s too bad I’m not going to be able to do laundry, ever.

Man, it’d be easier to be a popular blogger if I had an obsession with cats.

Did native Americans have more equality 9000 years ago than we do now?

A pretty picture of a Peruvian hunter from 9000 years ago, bringing down vicuna with her atlatl and spear:

The image is based on the remains of the dead hunter, and an analysis of grave goods.

At Wilamaya Patjxa, an archaeological site in southern Peru, archaeologists unearthed the skeleton of a young woman whose people buried her with a hunters’ toolkit, including projectile points. The find prompted University of California Davis archaeologist Randall Haas and his colleagues to take a closer look at other Pleistocene and early Holocene hunters from around the Americas.

Their results may suggest that female hunters weren’t as rare as we thought. And that, in turn, reminds us that gender roles haven’t always been the same in every culture.

“The objects that accompany [people] in death tend to be those that accompanied them in life,” Haas and his colleagues wrote. And when one young woman died 9,000 years ago in what is now southern Peru, her people buried her with at least six stone spear tips of a type used in hunting large prey like deer and vicuña (a relative of the alpaca). The points seem to have been bundled along with a stone knife, sharp stone flakes, scraping tools, and ocher for tanning hides.

I also learned a new genetics fact! The bones were fragmentary, and the bits that you use for a morphological assessment of sex had crumbled to dust. But you can sex a skeleton by looking at the proteins that make up tooth enamel.

Tooth enamel contains proteins called amelogenins, which play a role in forming the enamel in the first place. The genes that produce these proteins are located on the X and Y chromosomes, and each version is slightly different. As a result, people who are genetically female have slightly different amelogenins than people who are genetically male. The proteins in the ancient hunter’s tooth enamel had a distinctly female signature, with no trace of the Y chromosome version.

The hunter from Wilamaya Patjxa is a young woman with the tools of an activity usually associated with men. If the objects people are buried with are the objects they used in life, then that raises some questions.

Maybe she was some weird outlier, I hear you ask. So they surveyed what was found at other grave sites, and it looks like a significant fraction of ancient hunters in the Western hemisphere happened to be women.

The hunter from Wilamaya Patjxa raises a similar question: was she the exception that proved the rule, or does her burial suggest that (in at least some ancient cultures) women were sometimes hunters? To help answer that question, Haas and his colleagues looked for other ancient people who had been buried with hunting tools. In published papers from archaeological sites across the Americas, they found 27 people at 18 different sites: 16 men and 11 women.

…the fact that so many apparent women turned up on that list is surprising. “Female participation in early big-game hunting was likely nontrivial,” wrote Haas and his colleagues. They suggest that as many as a third to half of women across the ancient Americas may have been actively involved in hunting.

The final line in this article is perfect.

Based on animal bones at Wilamaya Patjxa, large game like vicuña and taruca (a relative of deer) were extremely important to the community’s survival. In that case, hunting may have been an all-hands-on-deck activity. Haas and his colleagues also suggest that letting other members of a community keep an eye on the kids while the parents hunted might have freed more women up to bring home the bacon—or venison, in this case.

In other words, whether women hunted or fought probably depended on social factors, not biological ones.

I thought I ought to let David Futrelle know about this, since it makes the title of his blog even more ironic, but he beat me to it and has already posted about how She Hunted the Mammoth.

I thought enrollments were supposed to be down?

Yikes. It’s the first day of spring term registration, first thing in the morning, and my genetics class is already full…plus I’m giving a few students permission to take it beyond capacity (I’m splitting all the labs to meet pandemic requirements).

Spring: all the anxiety and overwork of the fall, only with crappier weather. They better cure this pandemic soon, or I may keel over from the stress.

Oh, wait. Pandemics don’t happen anymore.

Well, if a Harvard Professor says so, it must be true.

Pumpkin science

If you’ve ever wondered how giant pumpkins can get so big, Bethany Brookshire has the answer.

Giant pumpkins need a lot of water and sugar, and they need it fast. A typical giant pumpkin grows from seed to huge orange squash in only 120 to 160 days. At peak growth, it’s putting on 15 kilograms (33 pounds) every day. That’s like daily adding a two-year-old child to its mass. And all of that mass must move through the stem, Savage notes. Most of the time, the stem is so narrow that you can still easily get your hands around it.

To study how pumpkin stems transport so much food and water, she asked growers of giant pumpkins to donate small slivers of their competition fruits. She also got any pumpkins that burst before they could be judged. She even got small pumpkins that farmers had rejected before they plumped up. (To grow a massive pumpkin, farmers will only let one pumpkin on each plant reach full size.) She also grew a few of her own.

Savage took a close look at the stems, leaves and pumpkins and then compared them to those from other large squashes. Giant pumpkins don’t produce more sugars, she found. And their xylems and phloems don’t work differently. The titans just have more transport tissue. “It’s almost like there’s this mass growth of the vascular tissue in [the] stem,” she says. Extra xylem and phloem help the stem pump more food and water into the fruit, leaving less for the rest of the plant.

It’s a transport difference! We don’t appreciate the importance of transport in multicellular organisms enough.

Of course, what you really want to see are elephants smashing giant pumpkins.

Hey, I just realized that we didn’t carve a pumpkin for our house this year! I guess the nonexistent trick-or-treaters won’t have anything to kick around.

Spider science lurches fitfully forward!

Oh, hey, it’s the day before Halloween, and I only just now looked up from my work. This has been a busy day — it’s advising week, and all these students have been lining up at my virtual door to get me to validate their choices for spring term courses. We didn’t have this when I was an undergrad at the UW. Instead, we had a scavenger hunt every quarter: we’d puzzle out on our own what courses we needed, then we’d run around campus, tracking down professors and asking them for a precious computer punchcard, which they’d give us if we met their standards, and then we’d get in a long line and file in to the registrar, turn in our deck of cards which would go into a cardreader, and then 10 minutes (or so) later, we’d get a printout of the courses we were taking (unless there was a conflict or error, in which case we’d get our cards back and go on another scavenger hunt to find a card that fixed everything), and we’d turn around and walk a few meters to the conveniently located billing office to cough up our tuition on the spot.

So that ate up a good part of today. It might have been better in the good old days when the students had to do all the legwork.

We also reviewed our recent spider experiments, which were kind of disappointing. The spiders were mostly immobile in the time-lapse recordings, and we were wondering what we were doing wrong, and then we noticed…”say, how come the illumination in these videos never changes?”…so I checked the timer on our light source, and realized it was broken and it has permanently been 3pm all week long. No wonder I’m so tired! So I ordered new timers.

While we were waiting for that to arrive, we tried a wild-ass sloppy experiment, and just let the lights in the lab regulate the light level for a few days in our time-lapse rig. We discovered that lab lighting is temporal chaos, with custodians and security guards doing their thing, so that there is no such thing as a 14:10 light cycle. There’s supposed to be a pattern! The cage goes purplish pink when the IR camera is working, and shades of gray when we’ve got daylight, but no: they’ve been on an 8:2:3:1:7:3 cycle, I think, and who knows what’s going on. The spiders probably don’t.

We did notice that our reclusive spiders did go into overdrive in the brief periods of real darkness, though, so now we just have to get that functioning reliably.

So the new timers arrived today, and Ade built a Space Cocoon.

What that is is, on top, a clamp light with a natural daylight lamp on a functioning timer with a 14 hour on/10 hour off cycle. Below that is a Raspberry PI with a NoIR camera, and also an IR lamp that is permanently on. Below that is a cage with a spider in it, trapped in a kind of panopticon. And then, elegantly wrapped around the whole contraption, a couple of layers of aluminum foil so the only thing illuminating the spider’s living quarters is our controlled lighting. It ain’t pretty, but we’ll try to get some data and then fuss over making it fancy.

Then I fed the babies.

I’m getting pretty slick at that. Here’s the way I work it:

I put a few hundred fruit flies in the wide mouth plastic cup in the foreground, with a petri dish as a lid to prevent them from escaping. Then I remove the foam plugs from a row of spider vials, tap tap tap to knock all the flies to the bottom of the cup, remove the petri dish, and incline the cup so one side is almost horizontal over the vials. The flies (wingless, so they have to walk) rush to the lip of the cup, where I’m waiting with a paintbrush to flick, flick, flick flies into the hellmouths of the vials, where they are instantly trapped in the dense mat of silk therein. Cap the cup, restore the foam plugs, and repeat. I can do 300 baby spiders in 15 minutes now. 1200 spiders per hour. I could raise an army of about 10,000 spiders if I didn’t have to do that pesky teaching and committee work stuff. DOES NO ONE UNDERSTAND MY PRIORITIES?

That was my Friday.

You know, if I could kidnap the students I advise and put them to work in my spider farm, I’d be able to raise hundreds of thousands of spiders. I’d have to take over some adjacent labs to accomplish that, but if I must, I must. We demand Spinnenraum, it is our destiny!