iiinova — where your digital self keeps evolving

Daniel Asarnow @dabiophysicist.bsky.social · 29/09/2026

Broken Earth flashback, very spooky indeed

Reposted by Daniel Asarnow

Stuart Turville @turville.bsky.social · 25/09/2026

SARS-CoV-2 phenotypic trajectory and the Omicron Paradox. Discussion of the following pre-print and the complex intertwined pathways that have dictated phenotypic outcomes for SARS-CoV-2. This can be otherwise termed the pandemic to endemic trajectory: www.biorxiv.org/content/10.6...

biorxiv.org

Proteolytic control of the SARS-CoV-2 furin cleavage site defines the phenotypic evolution from the pandemic to endemic state

The successive emergence of SARS-CoV-2 variants with altered tissue tropism has progressively decoupled transmissibility from lower respiratory tract pathogenicity. Omicron lineages transmit exception...

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Reposted by Daniel Asarnow

Daniel Asarnow @dabiophysicist.bsky.social · 19/08/2026

I think the "direct to Whiskey India Tango" problem captures a lot of the difficulty with natural language input

On one occasion a pilot asked the author over the aircraft intercom, "What do I have to say to Go Direct to Whiskey India Tango?" The author replied, "Why don't you say, Go Direct Whiskey India Tango?" Even the pilot's question had not reminded him of what was required. In the short term, this problem can be addressed to 3ome extent by automatic prompting. A longer term solution would be to us- recognisers with more intelligence that could interpret what the pilot meant.

N. Cooke, "RAE Bedford's Experience of Using Direct Voice Input (DVI) in the Cockpit", 1990. https://dn760101.eu.archive.org/0/items/DTIC_ADA230240/DTIC_ADA230240.pdf

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Reposted by Daniel Asarnow

henrietteautzen.bsky.social @henrietteautzen.bsky.social · 12/08/2026

Happy to see our NHE6 story published today in @natcomms.nature.com! Led by @lukasfeilen.bsky.social we reveal the #cryoEM structure, ion selectivity and regulation of the endosomal Na+/H+ exchanger NHE6, providing a framework for understanding Christianson syndrome. www.nature.com/articles/s41...

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Jase Gehring @skyjase.bsky.social · 07/08/2026

Yes, it’s very weird! and incorrect. the ANN is granted agency, purpose, and equivalence with unrelated ANNs. And it’s quite rude to the humans as this was a very large project.

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Reposted by Daniel Asarnow

Dan Kaszeta FRHistS @dankaszeta.bsky.social · 03/08/2026

Penicillin was not, in fact, the first antibiotic.

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Daniel Asarnow @dabiophysicist.bsky.social · 03/07/2026

If you've lost a chicken in Northeast Seattle, she's safe with a neighbor (DM with breed and description) 🐓🐔🐣 #chickens #chickencoop #chickenkeeping #backyardchickens

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Reposted by Daniel Asarnow

Roland Dunbrack 🏳️‍🌈 @rolanddunbrack.bsky.social · 07/06/2026

STOP using ipTM for #AlphaFold PPI screens. * Artificially LOW when both full-length proteins have irrelevant, non-binding IDRs/domains. * If one protein is folded & other contains irrelevant IDRs or domains, the score is too HIGH bc of d0. * Use ipSAE or LIS. www.biorxiv.org/content/10.1...

ipSAE vs ipTM for sorting true interactors from non-interactors. ipSAE is better at separating them.

Post from "AF Cache: Efficient Pipeline for Running AlphaFold for High-Throughput Protein-Protein Interaction Prediction". Various scores on p53/mdm2 interaction.

AlphaFOld ipTM score goes up when extra disorder is added to ONE proten. It goes way down when added to both proteins. Example of KRAS with RAF1 RBD.

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Daniel Asarnow @dabiophysicist.bsky.social · 01/06/2026

Hello/goodbye C-17 low-level over Keechelus Lake, WA, seen from I-90

Underbelly of a C-17 Globemaster entering stage right

Tail of the C-17 receding into the distance at ~30° right bank, as it follows the lake valley North

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Daniel Asarnow @dabiophysicist.bsky.social · 14/05/2026

It's a common misconception that Reed College (in Portland, Oregon) has the only nuclear reactor operated by undergraduate students. In fact, though, the Idaho State and UNM reactors are also student-run

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Daniel Asarnow @dabiophysicist.bsky.social · 08/05/2026

Good opportunity to adopt a quarter system!

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Reposted by Daniel Asarnow

Edward Nirenberg @enirenberg.bsky.social · 07/05/2026

I cannot believe this is a real thing. If you are in Laurelhurst and are bothered by the helicopter noise from Seattle Children's Hospital to the degree that you think signing this petition is in anything other than unconscionable, move. You can afford it.

thestranger.com

Laurelhurst Community Council Isn’t Sure Helicopters Need to Land Sick Kids at the Hospital - The Stranger

This, the affluent North Seattle neighborhood will tell helicopters are quite the nuisance. Such a nuisance that a neighborhood group wanted to make sure the hospital wasn't landing flights on the hel...

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Reposted by Daniel Asarnow

Dimitry Tegunov @dtegunov.bsky.social · 03/05/2026

We're super excited to share MissAlignment: a new ML-based approach to reference-free tilt series alignment, spearheaded by @martenchaillet.bsky.social. We think it's going to make your cryo-ET life a lot better. Preprint: www.biorxiv.org/content/10.6... Code: github.com/warpem/miss-... 🧶 Thread:

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Reposted by Daniel Asarnow

Veesler lab @veeslerlab.bsky.social · 29/04/2026

Can we use #proteindesign to develop countermeasures before viruses cause pandemics? We describe the computational design of an ultrapotent and broadly neutralizing deltacoronavirus miniprotein in our latest work led by Nathan Avery @hhmi-science.bsky.social 1/12 www.pnas.org/doi/10.1073/...

pnas.org

PNAS

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...

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Reposted by Daniel Asarnow

Oli Clarke @olibclarke.bsky.social · 13/04/2026

Yay proportional editing is now available in the Coot 1 API (in the daily)! This alters the sphere of influence of dragged refinement, which helps a lot when making large adjustments - register shifts of helices, domain movements, etc. I've added in a little widget to set it in coot1-trimmings.

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Daniel Asarnow @dabiophysicist.bsky.social · 11/04/2026

"Something about the air hits different today" - student getting off the bus (1st year?) It's Springtime in Seattle, welcome to the other side! 🌇

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Daniel Asarnow @dabiophysicist.bsky.social · 05/04/2026

NASA solution: superparamagnetic resin dice (zero residual magnetism), electromagnetic game table activates when photodiodes occluded by dice CCCP solution: dice cup

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Daniel Asarnow @dabiophysicist.bsky.social · 05/04/2026

Fresh (after resting), Javanese anaerobic fermentation

Coffee beans in my sunlit palm, half green, half roasted just to second crack, still brown with a slight gloss.

Java Sunda Anaerobic Honey Puncak Sirna
from Sweet Maria.

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Reposted by Daniel Asarnow

Diego del Alamo @delalamo.xyz · 25/03/2026

The proteina-complexa paper is the 2nd this month suggesting that high K+E content, a staple of ProteinMPNN designs, is predictive of poor expression (the bits in bio benchmark paper showed a few weeks ago). In their case, they measure poor sequence recovery in phage display

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Reposted by Daniel Asarnow

Jeff Lewis @lewislab.bsky.social · 19/02/2026

"Submitting the AAM to PMC does not require payment to the publisher or publishing open access. Federal agencies have, by law, certain rights to products resulting from federal funding under the “Government Use License”... 1/2

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Daniel Asarnow @dabiophysicist.bsky.social · 06/03/2026

I'm waiting for the bus, bunch of kids just drove through campus in an open top Model A, bumping music, no headlights (Actual Model A, a really fly restoration, all blue, historical plates)

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Daniel Asarnow @dabiophysicist.bsky.social · 06/03/2026

There are right and left handed tubes in this bag and it's mildly disturbing 😨

Two Axygen MCT-150-C-S 1.5 mL tubes from the same lot. The graduations and fogged label box are bizarrely on opposite sides of either five, causing them to naturally rest either on the hinge or bill of the cap.

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Reposted by Daniel Asarnow

Artologica aka Michele Banks @artologica.net · 02/03/2026

Wave Interference, Ink on Yupo, 2026

two sets of concentric circles overlapping in blue and black

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Daniel Asarnow @dabiophysicist.bsky.social · 26/02/2026

Good to see the PhD lab is still following the rules

A whiteboard in an academic lab, with a years-old message left by a former student.

Computer Lab Rules:
NO OVERFITTING!

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Reposted by Daniel Asarnow

ChimeraX @chimerax.ucsf.edu · 24/02/2026

The new ChimeraX CubeNTube plugin allows erasing parts of maps using cube, cylinder, and custom shapes and has undo. Created by Tamino Cairoli. Available from ChimeraX menu Tools / More Tools....

ChimeraX screenshot showing CubeNTube plugin.

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Daniel Asarnow @dabiophysicist.bsky.social · 24/02/2026

Share a movie you incorrectly think no one else remembers 😇

The 35th anniversary poster for the animated sci-fi classic, La Planète Sauvage, aka Fantastic Planet.

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Daniel Asarnow @dabiophysicist.bsky.social · 22/02/2026

What speaks all languages, but has no voice? Would be silent, but has no choice? As old as the air, it spoke only when we did.

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Daniel Asarnow @dabiophysicist.bsky.social · 21/02/2026

Pacific chorus frogs aptly named 🐸

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Daniel Asarnow @dabiophysicist.bsky.social · 21/02/2026

The most important command IMO: help ChimeraX includes the online documentation in a built-in viewer. Guarantee you'll learn something useful if you read these three... help alias help functionkey help view

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Reposted by Daniel Asarnow

Pranav NM Shah @proteincapsid.bsky.social · 19/02/2026

priviliged to be witnessing these amazing cellular vistas! makes you wonder about all the unknownwhat biology is being captured here!

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Reposted by Daniel Asarnow

Roland Dunbrack 🏳️‍🌈 @rolanddunbrack.bsky.social · 17/02/2026

We posted a biorxiv preprint on structural bioinformatics, AlphaFold modeling & machine learning on predicting specificity of E3 ligase ring domains for different E2 enzymes. 1/4 Preprint: www.biorxiv.org/content/10.6... Models/data (UbiqCore website): dunbrack.fccc.edu/ubiqcore

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Reposted by Daniel Asarnow

Alex Merz 🇺🇸🇨🇦🇺🇦 @merz.bsky.social · 16/02/2026

🧵 After years out of the field, I and my lab are again working on bacterial type IV pili. We have just posted our first preprints, and I'm excited to share what we have discovered. This shows Neisseria gonorrheae bacteria infecting a human epithelical cell. Here, you can see the pili in red. 1/

Fluorescence micrograph. Emma Miller and Alex Merz, unpublished.

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Reposted by Daniel Asarnow

Dimitry Tegunov @dtegunov.bsky.social · 16/02/2026

I had Claude make this as a mini-game for Relay's disconnect screen (like Chrome's dinosaur), but then pivoted to stand-alone. In this game, you have to find Euler angles matching the target projection, i.e. cosplay RELION. It can be pretty hard. Works on mobile too! warpem.github.io/euler-hunt/

warpem.github.io

Euler Hunt

Can you find the Euler angles of a cryo-EM projection?

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Daniel Asarnow @dabiophysicist.bsky.social · 10/02/2026

The striped HSB Silverfish. Lives in the basement of UWMC on a diet of hematology journal backissues from the 1950s. Much faster than regular silverfish, and camouflaged to match the floor.

A weird striped silverfish I only see inside the UW Medical Center. They are extra fast!

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Reposted by Daniel Asarnow

Alex Merz 🇺🇸🇨🇦🇺🇦 @merz.bsky.social · 06/02/2026

As Fran was nice enough to highlight this, I thought I'd put up a brief thread. 3 in 10 proteins that our cells make are either embedded in membranes (ion channels, adhesion molecules, etc.) or secreted (insulin, antibodies). They move through the secretory pathway. 1/

simple diagram of the secretory pathway.

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Daniel Asarnow @dabiophysicist.bsky.social · 18/01/2026

The trainees when you're at the GRC:

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Daniel Asarnow @dabiophysicist.bsky.social · 16/01/2026

Great video (and voice over)! Missing sound effects though 😉

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Daniel Asarnow @dabiophysicist.bsky.social · 16/01/2026

Quote with a movie that's 10/10? Mitsuo Yanagimachi's "Who's Camus anyway?" (Kamyu nante shiranai) doesn't even have a Wiki entry, but is as close to filmically perfect as anything

Movie poster for "Who's Camus Anyway?" by Mitsuo Yanagimachi (2005). Film students are piled into the back of an old pickup with their gear.

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Daniel Asarnow @dabiophysicist.bsky.social · 15/01/2026

Very much so, but for every kind of lysate! Also start with most highly cited Abs (check citeab.com), more likely to work but if they don't at least you'll know which papers are affected...

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