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Daniel Asarnow

@dabiophysicist.bsky.social
1.6K followers 1.5K following 1.7K posts

Postdoctoral scholar in Veesler Lab @ UWa. Former UCSF & SFSU & UCSC student & Exploratorium Explainer. He/him. I take tiny pictures, in 2 & 3 dimensions. github.com/asarnow

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Daniel Asarnow @dabiophysicist.bsky.social · 06/10/2026
I haven't read everything there is to read, but it seems Bernal had no confusion in 1958, either.
In this close collaboration between the Cambridge and London schools it is difficult to disentangle all the contributions of individuals, but what Miss Franklin had to give was the technique of preparing and taking X-ray photographs of the two hydrated forms of deoxyribonucleic acid and by applying the methods of Patterson function analysis to show that the structure was best accounted for by a double spiral of nucleotides, in which the phosphorus atoms lay on the outside.

from JD Bernal's July, 1958 obituary of Dr. Rosalind E. Franklin, in Nature
https://www.nature.com/articles/182154a0
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Daniel Asarnow @dabiophysicist.bsky.social · 03/10/2026
A friend sent me an interpretation of one of those just this morning, which I think is probably right.
Screenshot of a text message.

Friend:
https://arxiv.org/html/2609.16247v1

Doesn't this just mean that there exists a supported vector in English that makes everything sound bad? Idk stuff like this strains my ability to engage with the actual argument they're making because it seems to have such strange foundational notions

Paper:
"Summary of our findings.
We found a direction in the activation space that correlates with pain in all 25 models we tested. The signal is nearly orthogonal to fear and negative emotion and appears to be learned cheaply during pre-training. When injected into the residual stream, it produces the same ladder of distress in every model, regardless of size or training regime. This is evidence that models have coherent pain representations, as captured by our diverse sets of examples."

Friend:
English. English has a coherent pain representation
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Daniel Asarnow @dabiophysicist.bsky.social · 01/10/2026
I mean that imo "extrapolation" is more apt, fits both technical and English definitions (the post 20c examples in the OED are kinda fun)
https://www.oed.com/dictionary/extrapolation_n?tl=true

1903

    The necessity for having recourse to the risky expedient of ‘extrapolation’—that is, of applying unrestrictedly to the unknown, rules gathered from observation over a comparatively narrow area.

A. M. Clerke, Problems in Astrophysics 9
1922

    By extrapolation of the curve of our knowledge we can reconstruct within the range of conceivability, if not of probability, the course of process.

J. Y. Simpson, Man & Attainment of Immortality i. 16
1926

    Dr. Hubble strongly combats the contention that all non-galactic nebulae are spirals, which he characterizes as a ‘daring extrapolation’, ‘not justified by our present knowledge of nebular forms’.

H. C. Macpherson, Modern Astronomy 135
1965

    One of the chief concerns of all scientific theories..is to sanction extrapolation..and the expression of the distant and unknown in terms of what is familiar.

J. D. North, Measure of Universe xiv. 297
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Daniel Asarnow @dabiophysicist.bsky.social · 28/09/2026
I learned the EF2000 had some form of DVI a long time ago, from Wikipedia, but after LLMs brought true natural language interfaces into view I tried to dig into what pilots actually think about it. Great doc about natural language input in general imo.
...there had become a tendency for them to forget the details of commands to be given. This human deficiency was noticed mainly during flight demonstrations or during periods of high workload. 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 use recognisers with more intelligence that could interpret what the pilot meant.

From https://dn760101.eu.archive.org/0/items/DTIC_ADA230240/DTIC_ADA230240.pdf
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Daniel Asarnow @dabiophysicist.bsky.social · 25/09/2026
Part of an old cover for "The Drowned World," by J.G. Ballard. Aming the flooded ruins of London a next figure stands atop a submerged building beneath the cruel and unrelenting sun, while a giant iguana climbs from the water. In the foreground another figure is perched on floating detritus, and spearfishing.
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Daniel Asarnow @dabiophysicist.bsky.social · 25/09/2026
Then there's Janeway's version
Capt Janeway saying "over the years I've learned sometimes you just have to punch your way through," shortly before driving the ship through something
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Daniel Asarnow @dabiophysicist.bsky.social · 19/09/2026
Screenshot from the classic hacking game "Uplink" showing an illicit bank transfer
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Daniel Asarnow @dabiophysicist.bsky.social · 14/09/2026
If you add momentum vectors you may see the same difference between your stable and unstable eras, as in the mixed quadrupole dynamics.
"Einstein’s Unknown Insight and the Problem of Quantizing Chaos"
Douglas Stone, 2005

Figure 3. Billiards. In these particle trajectories, a yellow circle represents a neighborhood of the starting point, a red arrow represents an initial momentum, and green arrows represent momenta on return. (a) Generic trajectories in a circular billiard are quasiperiodic. The trajectory visits any neighborhood of the allowed region of motion an infinite number of times, but in only a finite number of momentum directions. The system is integrable because angular momentum and energy are conserved, and every generic trajectory exhibits Einstein's regular type (a) motion. (b) In the stadium billiard, a generic trajectory returns to any neighborhood of the allowed region in an infinite number of momentum directions. The system is nonintegrable, and generically exhibits only Einstein's chaotic type (b) motion. (c–d) In the quadrupole billiard, the behavior of the trajectory depends on initial conditions. Both regular (c) and chaotic (d) motions are possible. The quadrupole billiard, with its mixture of quasiperiodic and chaotic dynamics, manifests the generic behavior of Hamiltonian dynamical systems.
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Daniel Asarnow @dabiophysicist.bsky.social · 12/09/2026
Way ahead of you
Wikipedia
https://en.wikipedia.org/wiki/Giant_Powder_Company

The public outcry that ensued from these two accidents prompted the Giant Powder Company to move across the bay to a more remote site that today straddles the city limits of Berkeley and Albany, between Fleming Point and Cerrito de San Antonio (later renamed "Albany Hill").[4] The railroad station for the facility was named "Nobel".[5] The Judson Manufacturing Co., whose founder and CEO Egbert Judson[6] had acquired an interest in Giant when it was still located in San Francisco, established its chemical works adjacent to the Giant plant to supply it with the acids for manufacturing dynamite.[7]

On April 15, 1880, another accidental explosion occurred killing many workers and several visitors.[8] The company then instituted more stringent safety measures, including the planting of eucalyptus trees atop the adjacent hill to act as a buffer for surrounding communities. During the 1880s, Giant decided to start manufacturing its own acids, creating a rift with partner Judson who then left the company and formed his own in 1890, the Judson Explosives and Powder Company. He constructed his own facility nearby, on the northwest side of the Cerrito de San Antonio.

On July 9, 1892, an explosion occurred on the Giant property which killed nine workers and caused damage to the nearby Judson site. The blast was widely felt, shattering windows for miles around,
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Daniel Asarnow @dabiophysicist.bsky.social · 12/09/2026
How'd that work out last time?
Mrs. H.C. Hanscome, with revolver and baby, is shown in the act of holding up a wagon. 

San Francisco Call Bulletin, April 1908.
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Daniel Asarnow @dabiophysicist.bsky.social · 12/09/2026
Starting to show its age a little bit, but yes
The Albany, CA public library and community center, image from Google Street View.
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Daniel Asarnow @dabiophysicist.bsky.social · 23/08/2026
The rate of anosmia and ageusia did seem to decline post-omicron (BA.1 and BA.2, so early 2022). This study found ~40% prevalence falling to ~10% for example
Bar graph of symptom prevalence across several SARS-CoV-2 waves culminating in omicron BA.1 and BA.2. Anosmia shows a sharp decline from ~40% to ~10% after omicron emergence.

https://www.cell.com/heliyon/fulltext/S2405-8440(24)16144-0
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Daniel Asarnow @dabiophysicist.bsky.social · 20/08/2026
PROMPT_COMMAND="${PROMPT_COMMAND:+$PROMPT_COMMAND ; }"'echo $$ $USER "$(history 1)" >> ~/.bash_eternal_history'

Sends every command issued to the eternal history file.
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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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Daniel Asarnow @dabiophysicist.bsky.social · 24/07/2026
There must be some difference from the 4D and multichannel 4D OME examples. Here's the identify and tiffcomment output
identify output for OME 4D tif exampletiffcomment dump of imagej fields from OME 4D tif example
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Daniel Asarnow @dabiophysicist.bsky.social · 24/07/2026
Here's where the documentation says 3D tiff stacks should work, and 4D-series.ome.tif (docs.openmicroscopy.org/ome-model/5....) opens as a veries. The key seems to be ImageJ metadata, try bfconvert in.tif out.tif.
vseries  true | false
When multiple maps with the same grid dimensions are opened in a single command (multiple files specified with wild cards or globbing, or a single multi-map file), this option can be used to enforce loading them as a volume series for playback with the vseries command or the associated slider (if true), or as independent models (if false). If the option is not used, 3D TIFF images and Chimera map files containing five or more same-sized maps are automatically interpreted as series, if possible. When multiple maps are opened in a single command (multiple files specified with wild cards or globbing), time ordering is automatically discerned from the filenames, if possible: for example, a file will be identified as time point 12 if its name contains either of the following:

    _stack0012_
    _0012stack_ 

(and 0012 could be any integer).
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Daniel Asarnow @dabiophysicist.bsky.social · 17/07/2026
Found original 😎🔬
Cryo-ET slice at the cell periphery, centered on a microtubule extending into a budding exvagination of the plasma membrane. A motor protein pile-up can be seen at the tip, which is depolymerizing like a textbook cartoon, and membrane proteins, actin filaments, and ribosomes are visible all around the dense cellular milieu.
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Daniel Asarnow @dabiophysicist.bsky.social · 20/06/2026
This is all we get, but it sounds like (what is now) "conventional" software engineering
Di Mino used Claude Code to build a suite of Python scripts that query, cross-reference, and organize the digitized Linear A corpus (drawn from the GORILA and SigLA databases), enabling systematic hypothesis testing at a scale that would have been impractical to do manually.
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Daniel Asarnow @dabiophysicist.bsky.social · 14/06/2026
Suspension nothing! (These are from before, illustrative tests from the chat app)
On release, Fable 5 is asked to review the molecular mechanisms of translation inhibitors and is blocked by the safety filter.On release, Fable 5 is asked a high-school level question about the Central Dogma and is blocked by the safety filter.
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Daniel Asarnow @dabiophysicist.bsky.social · 08/06/2026
"I don't allow myself to be defined by others. I am an ACTOR, full stop." -Soccer the dog
Wishbone the dog as Ariel in The Tempest (by William Shakespeare). He's a small Jack Russell terrier (real name Soccer, 1988-2001) in a frilled pink tutu with a red, purple, and black feathered headdress and masque.Wishbone the dog as Le Chevalier Auguste Dupin, from Poe's The Purloined Letter. He's wearing the regalia of a minor 19th century French noble, sitting at a distinguished desk behind a golden ink stand with a white quill pen, with a sealed letter under his left paw.
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Daniel Asarnow @dabiophysicist.bsky.social · 08/06/2026
It seems other federal agencies were actually so annoyed by SA that they sparked the development of DGPS, first used to undermine SA "fuzzing" and later to boost practical accuracy en.wikipedia.org/wiki/Differe...
Wikipedia:

Throughout the early to mid 1980s, a number of [US Federal] agencies worked to develop a solution to the SA "problem".[dubious – discuss] Since the SA signal was changed slowly, the effect of its offset on positioning was relatively fixed – that is, if the offset was "100 meters to the east", that offset would be true over a relatively wide area. This suggested that broadcasting this offset to local GPS receivers could eliminate the effects of SA, resulting in measurements closer to GPS's theoretical performance, around 15 metres (49 ft). Additionally, another major source of errors in a GPS fix is due to transmission delays in the ionosphere, which could also be measured and corrected for in the broadcast. This offered an improvement to about 5 metres (16 ft) accuracy, more than enough for most civilian needs.

The US Coast Guard was one of the more aggressive proponents of the DGPS, experimenting with the system on an ever-wider basis throughout the late 1980s and early 1990s. These signals are broadcast on marine longwave frequencies, which could be received on existing radiotelephones[further explanation needed] and fed into suitably equipped GPS receivers. Almost all major GPS vendors offered units with DGPS inputs, not only for the USCG signals, but also aviation units on either VHF or commercial AM radio bands.
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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 rightThe C-17 passes by at ~45° left bank 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 · 19/05/2026
Same contract fyi
Current 4811 GSR salary table
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Daniel Asarnow @dabiophysicist.bsky.social · 29/04/2026
I was given a refurbished 5GB 1st gen, I think it's the second thing I ever installed Linux on (pic is from Wikipedia, I don't have it anymore)
Picture of the 1st gen iPod from Wikipedia. 1.8" 5GB HDD, all mechanical buttons and scroll wheel. Encased in clear resin for some reason. Runs Linux.
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Daniel Asarnow @dabiophysicist.bsky.social · 05/04/2026
It was actually two of them cobbled together, it could do a whole pound very nicely but you had to watch it. Definitely outside! But now I use a Gene Café and a drier exhaust duct to direct the smoke away
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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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Daniel Asarnow @dabiophysicist.bsky.social · 23/03/2026
For sure something special about just reaching in...and taking a little peek
In situ cryo-ET slice featuring a mysterious ring (diameter ~48 nm) assembling around an organelle
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Daniel Asarnow @dabiophysicist.bsky.social · 21/03/2026
Does the UK not have education content standards? California's closely reflect what we had 30 years ago, still the foundation of my general knowledge. www.cde.ca.gov/be/st/ss/doc...
California History/Social Science content standard 6.1-6.3 (6th grade, age ~11)California History/Social Science content standard 6.5-6.7California History/Social Science content standard 7.1-7.3 (7th grade, age ~12)California History/Social Science content standard 7.7-7.9
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Daniel Asarnow @dabiophysicist.bsky.social · 17/03/2026
I <3 you too King County Metro
A tiny paper crane rests gracefully in a button crimp of a seat on a King County Metro bus, route 75 to Sand Point. Its wing and body reveal the paper is studded with hearts.
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Daniel Asarnow @dabiophysicist.bsky.social · 17/03/2026
Let's not forget the jelly bean mosaic of Ronald Reagan (and the thousands of teaching moments it must have made over the years)
That old devil rendered in jelly bean pointillism

(it's the mosaic from the Reagan shrine at the Jelly Belly factory).

https://www.atlasobscura.com/articles/jelly-belly-ronald-reagan
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Daniel Asarnow @dabiophysicist.bsky.social · 14/03/2026
Definitely...though I miss the light sticks, and the weird floor (pure asphalt?) that liquified under vibrating exhibits
The Light Sticks used persistence of vision to generate 2D images from vertical 1D displays as the viewer moved their head or eyes. 

Visitors could select a number of different programs with different pictures and messages. A favorite was Alfred Einstein saying "auf wiedersehen." The exhibit was controlled by an Apple II or original Mac (don't remember), likely contributing to its retirement.
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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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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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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 · 23/02/2026
I try to collect new ones when I'm home.
Another illustrated poster on the brick wall of the BART station. This one depicts Mt. Diablo, revered by the Ohlone as the center of creation, therefore slandered by missionaries. Also featured are several large, native avian predators.A third artistic poster at BART. The Edwards wildlife refuge, with native fish, birds, insects, lizard and snake illustrated.
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Daniel Asarnow @dabiophysicist.bsky.social · 23/02/2026
I really like these
BART station poster depicting the city roughly as seen from the shipping channel, South of the bridge and West of Yerba Buena, with illustrations of several native animals (bat, egret, coyote, river otter, raptor).
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Daniel Asarnow @dabiophysicist.bsky.social · 21/02/2026
So cool, didn't see them myself until after the Nobel! These were made in the first year boot camp @thomaspv.bsky.social used to run, ca. 2018. We kept them inverted on a window sill in full sunlight, and bet on how many PhDs they would last.
Three 15 mL conical tubes containing different FPs, lying on a UV lightbox and glowing in the dark
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Daniel Asarnow @dabiophysicist.bsky.social · 19/02/2026
My god man what's happened to you
Probably AI generated diagram of different kinds of biosafety cabinets. A researcher is bizarrely fused to the floor of the hood, doomed forever to live and work within its lonely confines.
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Daniel Asarnow @dabiophysicist.bsky.social · 17/02/2026
Stentor even have personalities. Well, at least two (fearful and bold)
Two individuals of giant single-cell organism Stentor roselli in bright field. They're 200-300 microns in length.

Popular Science
https://www.popsci.com/story/science/single-cell-decision-cognition-stentor-roeseli/
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Daniel Asarnow @dabiophysicist.bsky.social · 14/02/2026
Things might turn out real strange there though! I was thinking of the one from the epilogue. (Spoiler saying what I mean in alt text)
A picture of Xan from The Expanse TV show. Spoilers below.

Referring to the colony that invented the "safe" FTL drive above. I think they say there were ~30 of a few hundred colonies that survived?

Based on what happened with Amos on Earth over the next 1000 years, I think eventually everyone on Laconia is turned into a repair drone entity and they become a wacky immortal telepath community...
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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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Daniel Asarnow @dabiophysicist.bsky.social · 09/02/2026
I can see the lab from up here! 🔬 #cryoem
Bluesky Map screenshot showing my account within the cluster of cryo-EM practitioners, with CCPEM highlighted for reference. The cryo-EM cluster is a satellite of Molecular Biology.
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Daniel Asarnow @dabiophysicist.bsky.social · 03/02/2026
Mitch (I'm assuming it's from this recent Morning Consult) pro.morningconsult.com/trackers/sen...
Here are the senators with the highest disapproval ratings.

    Mitch McConnell (R-Ky.): 27% approval, 63% disapproval
    Susan Collins (R-Maine): 41% approval, 54% disapproval
    Dan Sullivan (R-Alaska): 39% approval, 47% disapproval
    Ron Johnson (R-Wis.): 41% approval, 47% disapproval
    Lisa Murkowski (R-Alaska): 37% approval, 46% disapproval
    Joni Ernst (R-Iowa): 41% approval, 46% disapproval
    Lindsey Graham (R-S.C.): 43% approval, 45% disapproval
    Pete Ricketts (R-Neb.): 44% approval, 43% disapproval
    Deb Fischer (R-Neb.): 40% approval, 43% disapproval
    Ted Cruz (R-Texas): 48% approval, 42% disapproval
    Tim Sheehy (R-Mont.): 50% approval, 42% disapproval.

https://www.nj.com/politics/2026/01/the-most-beloved-and-most-hated-senators-in-america-have-just-been-revealed-in-a-massive-new-poll.html
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Daniel Asarnow @dabiophysicist.bsky.social · 17/01/2026
I understand there are certain limits 😇
NOMPC ion channel is a war of the worlds alien walker, descending from the sky to alight in a crowded downtown street. It's been reconstituted into a gigantic lipid nanodisc and people are fleeing their vehicles in terror or gaping in awe.

Original art by @melodygcampbell.bsky.social (2017)
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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 · 12/01/2026
Tbh if I can't skip the video I use the JavaScript console to increase the playback speed
Screenshot from a cybersecurity training video. On the left is a scary red wireframe guy with AR glasses. On the right, two innocent CGI humans in front of an office building with a crosshairs over them (presumably from the AR glasses).
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Daniel Asarnow @dabiophysicist.bsky.social · 06/01/2026
Megabyte (from 90s CGI TV show ReBoot) smiling at the camera
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Daniel Asarnow @dabiophysicist.bsky.social · 05/01/2026
It does look pretty dangerous considering a "wrong way" lane could be on either side. A young woman disappeared there and was thought to be a potential murder victim until her car was found in the water. Site linked below says 4 deaths total, way less than Bundy
Black and white aerial photograph of the old I-90 bridge facing Mercer Island from the Seattle sideGrainy color photograph showing first-person view of cars careening through the bulge created by the moveable section of the old I-90 bridge from Seattle to Mercer Island
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Daniel Asarnow @dabiophysicist.bsky.social · 04/01/2026
In 2022, Trump told the journalists Peter Baker and Susan Glasser: “I love maps. And I always said: ‘Look at the size of [Greenland]. It’s massive. That should be part of the United States.’”

https://www.politico.com/news/2025/05/10/trump-maps-obsession-history-geopolitics-00339935
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Daniel Asarnow @dabiophysicist.bsky.social · 30/12/2025
My old Sherpa/Free Radical had been sitting around for a few years until my 2nd oldest friend and I tracked down possibly the last surviving kid-carrier hardware (thanks @xtracycle.bsky.social!) and now he's *safely* taking his kids everywhere with it 🤩 (1st oldest is his wife btw)
Xtracycle Free Radical (~2008) on a Dorado Sherpa (late 80's) with bar tassles and a big ol' New Belgium bell.The Sherpa Free Radical converted to a safe kid-carrier, on the way back from a grocery run. Did I mention the tassles and the bell??
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