Category Archives: Uncategorized

Crows, Zoey Ashe, and other Novels

I’ve been making friends with the crows at work. This week, one of them did the clicky rattle call at me. I think it might be a friendly sound? I think most of their communication is body language, but it’s cool when they vocalize at me.

I just finished the second in Jason “David Wong” Pargin’s Zoey Ashe series. I put off reading it because of the title, Zoey Punches the Future in the Dick. It’s embarrassing to even talk about the book thanks to the title. I’m just going to call it Zoey Ashe 2. I aksi made a video review about it. It’s my second Sci-Fi and Mixology video.

Something in Zoey Ashe 2 stood out to me: Zoey is serious about the responsibility that comes with wealth. She inherited a huge fortune in Book 1. At one point in Book 2, Zoey gets her people to fix a squeak in her air conditioning system. It costs twenty-six thousand dollars. She freaks out. She knows that, before she was rich, that much money would have changed her life. And she just spent it to fix a squeak. And the money didn’t come from reputable businesses, either. Twenty six thousand dollars represents a few percent profit on a lot of human misery. She is struggling to come up with something to do about it.

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Video, Photos, Links, Reading

Video and Photography:

I posted a new video last Monday about Air batteries. I had planned on exploring them more but left my lab in Idaho before I could get into it. It’s an interesting concept, even though it’s clearly very hard to make it work well. I’m very grateful to Dipak Koirala (co-author on several papers) who previewed it and caught a few mistakes.

This week I put one up about silicone earbuds. I’m starting to get back into the swing of it. I put it in my Beeminder, so I’m committed.

I’ve been taking more photos lately. The top photo was a strange thing. I was working in the lab when I looked out the window and saw this guy floating by in his balloon. It was a totally random rainy Thursday. Maybe he was trying out an unconventional commute.

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RNA, Protein design, and the Sunday Scaries

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Step aside CRISPR, RNA editing is taking off

Although gene editing is flashy, there are advantages to a more temporary solution. Gene editing needs to be done perfectly the first time or it causes bad permanent consequences. RNA editing can have a dose-dependent, time-limited effect. If bad things start to happen, doses can be removed and the effects reversed. Not so much for DNA editing. The downside is that the RNA to be edited needs to be present in the first place. If a gene is underexpressed or absent, RNA editing won’t help.

Incorporating an allosteric regulatory site in an antibody through backbone design

Protein design has come a long way. Here’s a paper that takes an antibody and redesigns the antibody gene to make it into a sensor for Zinc ions. Basically, nature made this antibody to be an always-on grabber for a molecule called fluorescein. These folks made it grab fluorescein only if there is a bunch of Zinc present. Designing that kind of function with accurate software was a dream 20 years ago.

Poorly Drawn Lines:

Modeling Peptide-Protein Structure and Binding Using Monte Carlo Sampling Approaches: Rosetta FlexPepDock and FlexPepBind.
Imagine you want to cure a viral infection. To do that, you could make a new molecule that binds to a virus coat protein and keeps it out of human cells. But all you have is the virus’s DNA sequence. How do you do it? First, you need to be able to predict what the virus’s coat protein looks like (you can use Rosetta, a computer program for protein structure prediction). Then you need to design a binding molecule (use Rosetta some more, see the paper above). There are other strategies, of course, but this is an interesting one. And I think it’s one that will get better and faster with time.

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Alternative to the Pyramid Scheme of “Aspirational content”

Youtube put out a caution about burnout. Penny arcade summed it up. “Creators: you’re feeling burned out because you are light bulbs. And there are always more light bulbs. You create young, energetic light bulbs with every video you make.”

Good educational content is distinct from aspirational content. As a chemistry professor, my primary job is to produce more chemists (and educate non-chemists who need the background). The point is not to generate a great many more chemistry professors. Complexly and the Scishow folks make great educational content. Aspirational content is the opposite: it endeavors to sell the idea that you too can become an aspirational content producer. Mostly by watching more aspirational content.

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