Maybe Santa will bring me some high end optical gear for Christmas this year

I admit, I drooled a little bit: HHMI has developed this cool gadget for imaging embryos. It’s got everything: a culture chamber for mouse embryos, the latest light-sheet imaging tech, and fancy digital processing so no matter how the embryo rolls or drifts, it realigns the image. It’s been built by Phillip Keller, who did some amazing work with visualizing zebrafish.

Until now, the best views of living embryos came from fish and flies. A decade ago, Keller and colleagues developed the first “digital embryo” of the zebrafish, a kind of see-through, striped minnow often studied by scientists.

Fish embryos have the advantage that they’re shaped more like a ribbon draped over a ball of yolk, which means you can almost ignore one dimension. Mice start out sort of 2-dimensional too, but are eventually shaped like little balls with all kinds of movement in 3 dimensions over time. I’m finding that spider embryos are similarly obnoxiously thick. But look at what this machine can do!

Also, amazingly, they’re giving it all away for free. The software is all downloadable, along with plans for building the scope (building one from scratch is still out of my budget, though), and they offer free access to the instrument out at Janelia Farm. Maybe someday — I’m still working on just getting reliable embryo production and am thinking about some basic genetics, and years from now when I’m ready to do some advanced digital imaging, maybe they’ll come in boxes of Cracker Jack.

Or better yet, some of my students will move on to do it for me.

Spider update (no photos)

We’re in a mundane phase of this project — I’ve got swarms of baby spiders, a handful of wild-caught adults, and I’m waiting for them to reach sexual maturity, so I can start breeding lab lines.

I’ve got a naming convention — the wild-caught adults (Generation 1) all get simple names like Cathy, Barney, Gwyneth, etc. I’ve had a few of them die off already, although I think it was actually murder. It seems that crickets above a certain size are actually able to turn the tables and eat the spider, or at least kill it, and they will definitely consume an egg sac if they stumble on it. I’m learning lessons as I go along — only small crickets. I’m considering trying mealworms as a safer alternative.

For the second generation, each clutch gets named by the first letter of their mother’s name, and the month their egg sac was made. As they reach sexual maturity, they’ll get a letter after the month to distinguish them as individuals. Third generation will get the initials of both parents, but we’re not up to that point yet. I am planning to keep track of the pedigrees of these spiders as I go, in case something unique and interesting crops up.

I do have a sad story. I’ve been particularly watching on individual, GIIXa, Gwyneth’s daughter by an unknown father, laid in August. I’d been calling her Igor, because she had a few deformities — her left foreleg was much longer than her right (it looked like a duplication of one limb segment), and her two hindlegs had limited mobility, so she crawled around dragging her hindlegs, and with her left foreleg raised high up in the air. She made it to near-adulthood, so clearly she was able to capture and eat flies, but today I found that she had died at last. I’d actually be interested in teratological defects, and that I’ve already seen one isn’t too surprising, given how prolific the spiders are.

I’m also pretty sure some of the second generation are reaching sexual maturity, which is about right, since some of them are almost two months old. I’ve got one, AIIXa (a son of Amanda), which already has the massive dark pedipalps that allowed me to recognize him as male — he’ll be losing his virginity soon. I don’t want to give him to one of the first generation females, since they’re so much bigger they might just eat him, but am waiting to be confident that one of the second generation females is ready.

I’m a little bit nervous about getting this next generation to maturity, because I’ve noticed that this species has become scarce as the weather is changing. We noticed that the best spots for finding them this past summer were our garage and sun room, places with lots of fresh air (and diverse prey, I presume) that were still sheltered by the proximity of a human habitat. We couldn’t find any indoors, but only in these attached spaces. Now we’re only finding Pholcidae out in the garage, as if there has been a seasonal shift in the spider populations. It’ll be interesting to see what spider species survive a Minnesota January. Maybe Steatoda/Parasteatoda are moving indoors? Maybe they die off and leave behind egg sacs to weather the winter and emerge in the spring? I’ve got my eye on a couple of egg sacs attached to my garage door, and I may bring them into the warm to see if they hatch out.

Anyway, that’s all I’m doing right now, the tedious business of spider breeding. I’ve ordered some of the reagents I’ll need to start poking around spider embryos, but those won’t arrive until next month, and I’m not doing experiments on babies until I have a stable colony anyway.

Bad genetics exposed

If you read Nathaniel Comfort’s scathing review of Robert Plomin’s book, Blueprint, you ain’t seen nothin’ yet. He was holding back, maintaining the decorum of the journal as best he could. He gives a more thorough criticism on his blog, Genotopia, and wow, it’s even more brutal. Sometimes a more thorough and nuanced analysis just leads to an even stronger condemnation.

…Plomin’s argument is socially dangerous. Sure, genes influence and shape complex behavior, but we have almost no idea how. At this point in time (late 2018), it’s the genetic contributions to complex behavior that are mostly random and unsystematic. Polygenic scores may suggest regions of the genome in which one might find causal genes, but we already know that the contribution of any one gene to complex behavior is minute. Thousands of genes are involved in personality traits and intelligence—and many of the same polymorphisms pop up in every polygenic study of complex behavior. Even if the polygenic scores were causal, it remains very much up in the air whether looking at the genes for complex behavior will ever really tell us very much about those behaviors.

In contrast—and contra Plomin—we have very good ideas about how environments shape behaviors. Taking educational attainment as an example (it’s a favorite of the PGS crowd—a proxy for IQ, whose reputation has become pretty tarnished in recent years), we know that kids do better in school when they have eaten breakfast. We know they do better if they aren’t abused. We know they do better when they have enriched environments, at home and in school.

We also know that DNA doesn’t act alone. Plomin neglects all post-transcriptional modification, epigenetics, microbiomics, and systems biology—sciences that show without a doubt that you can’t draw a straight line from genes to behavior. The more complex the trait in question, the more true that sentence becomes. And Plomin is talking about the most complex traits there are: human personality and intelligence.

Plomin’s argument is dangerous because it minimizes those absolutely robust findings. If you follow his advice, you go along with the Republicans and continue slowly strangling public education and vote for that euphemism for separate-but-equal education, “school choice.” You axe Head Start. You eliminate food stamps and school lunch programs. You go along with eliminating affirmative action programs, which are designed to remediate past social neglect; in other words, you vote to restore neglect of the under-privileged. Those kids with genetic gumption will rise out of their circumstances one way or another…like Clarence Thomas and Ben Carson or something, I guess. As for the rest, fuck ’em.

I can see how that wouldn’t get printed in Nature, but he’s exactly right on every single point. Plomin, no matter what his own political views, has written a garbage book that plays right into the hands of the right wing, from the title onwards. It’s shocking that Plomin is completely oblivious to how crude and wrong his understanding of modern genetics is…a lock of understanding that allowed him to write a whole book on his ignorance. It’s a bit like Nicholas Wade’s book, A Troublesome Inheritance — another instance of Dunning-Krueger fused with 19th century racism.

Hey, though, if you care about this stuff, and are interested in how good science can be communicated well, I have a treat for you: tomorrow, Tuesday, at 6:30 Eastern, you can tune in to an online discussion between Jennifer Raff and Carl Zimmer on Why You’re You: Explaining Heredity to a Confused Public.

Note that this is not a debate — it’s a conversation between two well-informed individuals on good science, and how to explain it. I’ll be checking in!

Spider party!

Just another mundane spider update. This batch of babies are now 18 days post-fertilization, and they’re just rockin’ out in their dish.

I also got some good news: I was awarded a small in-house grant to pick up a bunch of supplies for embryo imaging, so that’s in the works. I ordered a few necessities today.

And now everywhere I go on the internet, ads for halocarbon oil pop up everywhere. Or does everyone get those?

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